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testing_data_set.vcf
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##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="RMS Mapping Quality">
##FORMAT=<ID=VF,Number=1,Type=Float,Description="Variant Frequency, the ratio of the sum of the called variant depth to the total depth">
##INFO=<ID=TI,Number=.,Type=String,Description="Transcript ID">
##INFO=<ID=GI,Number=.,Type=String,Description="Gene ID">
##INFO=<ID=EXON,Number=0,Type=Flag,Description="Exon Region">
##INFO=<ID=FC,Number=.,Type=String,Description="Functional Consequence">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record">
##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y] , y <= max(x+3,(x*(1+0.3))). All printed site block sample values are the minimum observed in the region spanned by the block">
##FILTER=<ID=LowGQX,Description="Locus GQX is less than 10.0000 or not present">
##FILTER=<ID=LowVariantFreq,Description="Low variant frequency < 0.20">
##FILTER=<ID=LowGQ,Description="GQ below < 30.00">
##FILTER=<ID=R8,Description="IndelRepeatLength is greater than 8">
##FILTER=<ID=SB,Description="Strand bias (SB) is greater than than -10">
##FILTER=<ID=LowDP,Description="Depth (DP) is less than 20">
##FILTER=<ID=IndelConflict,Description="Locus is in region with conflicting indel calls.">
##FILTER=<ID=SiteConflict,Description="Site genotype conflicts with proximal indel call. This is typically a heterozygous SNV call made inside of a heterozygous deletion.">
##FILTER=<ID=LowMQ,Description="Site MQ is less than 0.0000">
##FILTER=<ID=LowQD,Description="Locus QD is less than 0.0000">
##annotator=MARS
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[\\169.254.89.108\data\MiSeqDx\RUO\160321_M02792_0168_000000000-AHJNP\Data\Intensities\BaseCalls\Alignment\I241_S4.bam] read_buffer_size=null phone_home=NO_ET gatk_key=null read_filter=[] intervals=[\\169.254.89.108\data\MiSeqDx\RUO\160321_M02792_0168_000000000-AHJNP\Data\Intensities\BaseCalls\Alignment\Segment_intervals_M1.0.picard] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=5000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=OFF log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=1.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false annotateNDA=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 max_alternate_alleles=3 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false includeGVCFData=true dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chrM,length=16571>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##reference=file://C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa
##gvcftools_version="0.12"
##gvcftools_cmdline="C:\Illumina\MiSeq Reporter\Workflows\EnrichmentWorker\gatk_to_gvcf.exe --no-default-filters --min-qd 0.0000 --min-gqx 10.0000 --min-mq 0.0000"
##source=GATK 1.6
##bcftools_mergeVersion=1.3.1+htslib-1.3.1
##bcftools_mergeCommand=merge -m all 1.vcf.gz 10.vcf.gz 11.vcf.gz 12.vcf.gz 2.vcf.gz 3.vcf.gz 4.vcf.gz 5.vcf.gz 6.vcf.gz 7.vcf.gz 8.vcf.gz 9.vcf.gz
##bcftools_normVersion=1.3.1+htslib-1.3.1
##bcftools_normCommand=norm -m-both -o MERGE_split.vcf MERGE.vcf.gz
##bcftools_normCommand=norm -f /Users/henri/Bioinfo/genome_ref/hg19.fa -o MERGE_split_normalized.vcf MERGE_split.vcf
##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele">
##INFO=<ID=Func.refGene,Number=.,Type=String,Description="Func.refGene annotation provided by ANNOVAR">
##INFO=<ID=Gene.refGene,Number=.,Type=String,Description="Gene.refGene annotation provided by ANNOVAR">
##INFO=<ID=GeneDetail.refGene,Number=.,Type=String,Description="GeneDetail.refGene annotation provided by ANNOVAR">
##INFO=<ID=ExonicFunc.refGene,Number=.,Type=String,Description="ExonicFunc.refGene annotation provided by ANNOVAR">
##INFO=<ID=AAChange.refGene,Number=.,Type=String,Description="AAChange.refGene annotation provided by ANNOVAR">
##INFO=<ID=Func.knownGene,Number=.,Type=String,Description="Func.knownGene annotation provided by ANNOVAR">
##INFO=<ID=Gene.knownGene,Number=.,Type=String,Description="Gene.knownGene annotation provided by ANNOVAR">
##INFO=<ID=GeneDetail.knownGene,Number=.,Type=String,Description="GeneDetail.knownGene annotation provided by ANNOVAR">
##INFO=<ID=ExonicFunc.knownGene,Number=.,Type=String,Description="ExonicFunc.knownGene annotation provided by ANNOVAR">
##INFO=<ID=AAChange.knownGene,Number=.,Type=String,Description="AAChange.knownGene annotation provided by ANNOVAR">
##INFO=<ID=Func.ccdsGene,Number=.,Type=String,Description="Func.ccdsGene annotation provided by ANNOVAR">
##INFO=<ID=Gene.ccdsGene,Number=.,Type=String,Description="Gene.ccdsGene annotation provided by ANNOVAR">
##INFO=<ID=GeneDetail.ccdsGene,Number=.,Type=String,Description="GeneDetail.ccdsGene annotation provided by ANNOVAR">
##INFO=<ID=ExonicFunc.ccdsGene,Number=.,Type=String,Description="ExonicFunc.ccdsGene annotation provided by ANNOVAR">
##INFO=<ID=AAChange.ccdsGene,Number=.,Type=String,Description="AAChange.ccdsGene annotation provided by ANNOVAR">
##INFO=<ID=cytoBand,Number=.,Type=String,Description="cytoBand annotation provided by ANNOVAR">
##INFO=<ID=CLINSIG,Number=.,Type=String,Description="CLINSIG annotation provided by ANNOVAR">
##INFO=<ID=CLNDBN,Number=.,Type=String,Description="CLNDBN annotation provided by ANNOVAR">
##INFO=<ID=CLNACC,Number=.,Type=String,Description="CLNACC annotation provided by ANNOVAR">
##INFO=<ID=CLNDSDB,Number=.,Type=String,Description="CLNDSDB annotation provided by ANNOVAR">
##INFO=<ID=CLNDSDBID,Number=.,Type=String,Description="CLNDSDBID annotation provided by ANNOVAR">
##INFO=<ID=PopFreqMax,Number=.,Type=String,Description="PopFreqMax annotation provided by ANNOVAR">
##INFO=<ID=Kaviar_AF,Number=.,Type=String,Description="Kaviar_AF annotation provided by ANNOVAR">
##INFO=<ID=Kaviar_AC,Number=.,Type=String,Description="Kaviar_AC annotation provided by ANNOVAR">
##INFO=<ID=Kaviar_AN,Number=.,Type=String,Description="Kaviar_AN annotation provided by ANNOVAR">
##INFO=<ID=ExAC_ALL,Number=.,Type=String,Description="ExAC_ALL annotation provided by ANNOVAR">
##INFO=<ID=ExAC_AFR,Number=.,Type=String,Description="ExAC_AFR annotation provided by ANNOVAR">
##INFO=<ID=ExAC_AMR,Number=.,Type=String,Description="ExAC_AMR annotation provided by ANNOVAR">
##INFO=<ID=ExAC_EAS,Number=.,Type=String,Description="ExAC_EAS annotation provided by ANNOVAR">
##INFO=<ID=ExAC_FIN,Number=.,Type=String,Description="ExAC_FIN annotation provided by ANNOVAR">
##INFO=<ID=ExAC_NFE,Number=.,Type=String,Description="ExAC_NFE annotation provided by ANNOVAR">
##INFO=<ID=ExAC_OTH,Number=.,Type=String,Description="ExAC_OTH annotation provided by ANNOVAR">
##INFO=<ID=ExAC_SAS,Number=.,Type=String,Description="ExAC_SAS annotation provided by ANNOVAR">
##INFO=<ID=1000g2014oct_all,Number=1,Type=Float,Description="1000g2014oct_all annotation provided by ANNOVAR">
##INFO=<ID=snp138,Number=.,Type=String,Description="snp138 annotation provided by ANNOVAR">
##INFO=<ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR">
##INFO=<ID=SIFT_converted_rankscore,Number=.,Type=String,Description="SIFT_converted_rankscore annotation provided by ANNOVAR">
##INFO=<ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR">
##INFO=<ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR">
##INFO=<ID=Polyphen2_HDIV_rankscore,Number=.,Type=String,Description="Polyphen2_HDIV_rankscore annotation provided by ANNOVAR">
##INFO=<ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR">
##INFO=<ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR">
##INFO=<ID=Polyphen2_HVAR_rankscore,Number=.,Type=String,Description="Polyphen2_HVAR_rankscore annotation provided by ANNOVAR">
##INFO=<ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR">
##INFO=<ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR">
##INFO=<ID=LRT_converted_rankscore,Number=.,Type=String,Description="LRT_converted_rankscore annotation provided by ANNOVAR">
##INFO=<ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR">
##INFO=<ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR">
##INFO=<ID=MutationTaster_converted_rankscore,Number=.,Type=String,Description="MutationTaster_converted_rankscore annotation provided by ANNOVAR">
##INFO=<ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR">
##INFO=<ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR">
##INFO=<ID=MutationAssessor_score_rankscore,Number=.,Type=String,Description="MutationAssessor_score_rankscore annotation provided by ANNOVAR">
##INFO=<ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR">
##INFO=<ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR">
##INFO=<ID=FATHMM_converted_rankscore,Number=.,Type=String,Description="FATHMM_converted_rankscore annotation provided by ANNOVAR">
##INFO=<ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR">
##INFO=<ID=PROVEAN_score,Number=.,Type=String,Description="PROVEAN_score annotation provided by ANNOVAR">
##INFO=<ID=PROVEAN_converted_rankscore,Number=.,Type=String,Description="PROVEAN_converted_rankscore annotation provided by ANNOVAR">
##INFO=<ID=PROVEAN_pred,Number=.,Type=String,Description="PROVEAN_pred annotation provided by ANNOVAR">
##INFO=<ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR">
##INFO=<ID=VEST3_rankscore,Number=.,Type=String,Description="VEST3_rankscore annotation provided by ANNOVAR">
##INFO=<ID=MetaSVM_score,Number=.,Type=String,Description="MetaSVM_score annotation provided by ANNOVAR">
##INFO=<ID=MetaSVM_rankscore,Number=.,Type=String,Description="MetaSVM_rankscore annotation provided by ANNOVAR">
##INFO=<ID=MetaSVM_pred,Number=.,Type=String,Description="MetaSVM_pred annotation provided by ANNOVAR">
##INFO=<ID=MetaLR_score,Number=.,Type=String,Description="MetaLR_score annotation provided by ANNOVAR">
##INFO=<ID=MetaLR_rankscore,Number=.,Type=String,Description="MetaLR_rankscore annotation provided by ANNOVAR">
##INFO=<ID=MetaLR_pred,Number=.,Type=String,Description="MetaLR_pred annotation provided by ANNOVAR">
##INFO=<ID=M-CAP_score,Number=.,Type=String,Description="M-CAP_score annotation provided by ANNOVAR">
##INFO=<ID=M-CAP_rankscore,Number=.,Type=String,Description="M-CAP_rankscore annotation provided by ANNOVAR">
##INFO=<ID=M-CAP_pred,Number=.,Type=String,Description="M-CAP_pred annotation provided by ANNOVAR">
##INFO=<ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR">
##INFO=<ID=CADD_raw_rankscore,Number=.,Type=String,Description="CADD_raw_rankscore annotation provided by ANNOVAR">
##INFO=<ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR">
##INFO=<ID=DANN_score,Number=.,Type=String,Description="DANN_score annotation provided by ANNOVAR">
##INFO=<ID=DANN_rankscore,Number=.,Type=String,Description="DANN_rankscore annotation provided by ANNOVAR">
##INFO=<ID=fathmm-MKL_coding_score,Number=.,Type=String,Description="fathmm-MKL_coding_score annotation provided by ANNOVAR">
##INFO=<ID=fathmm-MKL_coding_rankscore,Number=.,Type=String,Description="fathmm-MKL_coding_rankscore annotation provided by ANNOVAR">
##INFO=<ID=fathmm-MKL_coding_pred,Number=.,Type=String,Description="fathmm-MKL_coding_pred annotation provided by ANNOVAR">
##INFO=<ID=Eigen_coding_or_noncoding,Number=.,Type=String,Description="Eigen_coding_or_noncoding annotation provided by ANNOVAR">
##INFO=<ID=Eigen-raw,Number=.,Type=String,Description="Eigen-raw annotation provided by ANNOVAR">
##INFO=<ID=Eigen-PC-raw,Number=.,Type=String,Description="Eigen-PC-raw annotation provided by ANNOVAR">
##INFO=<ID=GenoCanyon_score,Number=.,Type=String,Description="GenoCanyon_score annotation provided by ANNOVAR">
##INFO=<ID=GenoCanyon_score_rankscore,Number=.,Type=String,Description="GenoCanyon_score_rankscore annotation provided by ANNOVAR">
##INFO=<ID=integrated_fitCons_score,Number=.,Type=String,Description="integrated_fitCons_score annotation provided by ANNOVAR">
##INFO=<ID=integrated_fitCons_score_rankscore,Number=.,Type=String,Description="integrated_fitCons_score_rankscore annotation provided by ANNOVAR">
##INFO=<ID=integrated_confidence_value,Number=.,Type=String,Description="integrated_confidence_value annotation provided by ANNOVAR">
##INFO=<ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR">
##INFO=<ID=GERP++_RS_rankscore,Number=.,Type=String,Description="GERP++_RS_rankscore annotation provided by ANNOVAR">
##INFO=<ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR">
##INFO=<ID=phyloP100way_vertebrate_rankscore,Number=.,Type=String,Description="phyloP100way_vertebrate_rankscore annotation provided by ANNOVAR">
##INFO=<ID=phyloP20way_mammalian,Number=.,Type=String,Description="phyloP20way_mammalian annotation provided by ANNOVAR">
##INFO=<ID=phyloP20way_mammalian_rankscore,Number=.,Type=String,Description="phyloP20way_mammalian_rankscore annotation provided by ANNOVAR">
##INFO=<ID=phastCons100way_vertebrate,Number=.,Type=String,Description="phastCons100way_vertebrate annotation provided by ANNOVAR">
##INFO=<ID=phastCons100way_vertebrate_rankscore,Number=.,Type=String,Description="phastCons100way_vertebrate_rankscore annotation provided by ANNOVAR">
##INFO=<ID=phastCons20way_mammalian,Number=.,Type=String,Description="phastCons20way_mammalian annotation provided by ANNOVAR">
##INFO=<ID=phastCons20way_mammalian_rankscore,Number=.,Type=String,Description="phastCons20way_mammalian_rankscore annotation provided by ANNOVAR">
##INFO=<ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR">
##INFO=<ID=SiPhy_29way_logOdds_rankscore,Number=.,Type=String,Description="SiPhy_29way_logOdds_rankscore annotation provided by ANNOVAR">
##INFO=<ID=Interpro_domain,Number=.,Type=String,Description="Interpro_domain annotation provided by ANNOVAR">
##INFO=<ID=GTEx_V6_gene,Number=.,Type=String,Description="GTEx_V6_gene annotation provided by ANNOVAR">
##INFO=<ID=GTEx_V6_tissue,Number=.,Type=String,Description="GTEx_V6_tissue annotation provided by ANNOVAR">
##INFO=<ID=dpsi_max_tissue,Number=.,Type=String,Description="dpsi_max_tissue annotation provided by ANNOVAR">
##INFO=<ID=dpsi_zscore,Number=.,Type=String,Description="dpsi_zscore annotation provided by ANNOVAR">
##INFO=<ID=dbscSNV_ADA_SCORE,Number=.,Type=String,Description="dbscSNV_ADA_SCORE annotation provided by ANNOVAR">
##INFO=<ID=dbscSNV_RF_SCORE,Number=.,Type=String,Description="dbscSNV_RF_SCORE annotation provided by ANNOVAR">
##INFO=<ID=MCAP,Number=.,Type=String,Description="MCAP annotation provided by ANNOVAR">
##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12
chr1 955440 rs569722974 GC G 253.12 LowGQ;R8;LowDP;SB BaseQRankSum=-0.751;FS=0;HRun=9;HaplotypeScore=104.656;MQ=36;MQ0=0;MQRankSum=-0.751;QD=18.36;ReadPosRankSum=0.751;SB=-62.47;DP=53;AN=10;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=upstream;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=upstream;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=upstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=0.0002689;Kaviar_AC=7;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:3,8:11:10.7:243,11,0:36:11:0.727 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:7,6:13:99:192,0,118:46:99:0.462 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/0:7,6:13:99:224,.,.:46:99:0.462 0/0:1,7:8:14.01:295,.,.:51:14:0.875 ./.:.:.:.:.:.:.:. 1/1:1,7:8:21.05:224,21,0:44:21:0.875
chr1 955440 rs569722974 GCC G 253.12 LowGQ;R8;LowDP;SB BaseQRankSum=-0.751;FS=0;HRun=9;HaplotypeScore=104.656;MQ=36;MQ0=0;MQRankSum=-0.751;QD=18.36;ReadPosRankSum=0.751;SB=-62.47;DP=53;AN=10;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=upstream;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=upstream;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=upstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.67;Kaviar_AF=0.12744;Kaviar_AC=3317;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.583067;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/0:3,8:11:10.7:243,.,.:36:11:0.727 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/0:7,6:13:99:192,.,.:46:99:0.462 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:7,6:13:99:224,0,219:46:99:0.462 1/1:1,7:8:14.01:295,14,0:51:14:0.875 ./.:.:.:.:.:.:.:. 0/0:1,7:8:21.05:224,.,.:44:21:0.875
chr1 955597 rs115173026 G T 457.02 PASS BaseQRankSum=0.104;Dels=0;FS=1.44;HRun=0;HaplotypeScore=9.0741;MQ=49;MQ0=0;MQRankSum=0.173;QD=13.44;ReadPosRankSum=-0.659;SB=-182.79;TI=NM_198576;GI=AGRN;FC=Synonymous_P15P;EXON;DP=129;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon1:c.G45T:p.P15P;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon1:c.G45T:p.P15P;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon1:c.G45T:p.P15P;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116272.4;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.53;Kaviar_AF=0.0646111;Kaviar_AC=9989;Kaviar_AN=154602;ExAC_ALL=0.4242;ExAC_AFR=0.4677;ExAC_AMR=0.4138;ExAC_EAS=0.2237;ExAC_FIN=.;ExAC_NFE=0.4509;ExAC_OTH=0.5312;ExAC_SAS=0.4170;1000g2014oct_all=0.282548;snp138=rs115173026;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:15,19:34:99:487,0,341:49:99:0.559 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:40,18:59:99:423,0,942:54:99:0.31 0/1:22,14:36:99:369,0,447:54:99:0.389 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 957898 rs2799064 G T 1742.14 PASS BaseQRankSum=1.083;Dels=0;FS=0;HRun=0;HaplotypeScore=25.3588;MQ=48;MQ0=0;MQRankSum=4.04;QD=15.48;ReadPosRankSum=1.837;SB=-349.98;TI=NM_198576;GI=AGRN;FC=Silent;DP=378;AN=8;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.42;Kaviar_AF=0.0627806;Kaviar_AC=9706;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.328474;snp138=rs2799064;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2638;dpsi_zscore=-0.798;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:44,53:97:99:1531,0,1211:48:99:0.546 ./.:.:.:.:.:.:.:. 0/1:33,42:75:99:1184,0,933:45:99:0.56 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:61,65:127:99:1772,0,1637:47:99:0.516 0/1:34,45:79:99:1387,0,978:48:99:0.57 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976289 . C G 73.68 SB;LowDP BaseQRankSum=-2.617;Dels=0;FS=2.737;HRun=4;HaplotypeScore=6.3496;MQ=51;MQ0=0;MQRankSum=-2.912;QD=3.35;ReadPosRankSum=-0.774;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=59;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.5375;dpsi_zscore=1.169;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:16,6:22:99:104,0,495:51:74:0.273 ./.:.:.:.:.:.:.:. 0/1:14,4:18:52.45:52,0,353:48:22:0.222 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:12,6:19:87.87:88,0,315:41:58:0.333 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976294 . A G 48.21 SB;LowDP;LowVariantFreq;LowGQX BaseQRankSum=-2.374;Dels=0;FS=0;HRun=4;HaplotypeScore=4.551;MQ=50;MQ0=0;MQRankSum=-2.374;QD=1.91;ReadPosRankSum=0.428;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=75;AN=8;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=6.5e-06;Kaviar_AC=1;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2438;dpsi_zscore=0.803;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:15,6:21:70.07:70,0,444:50:40:0.286 ./.:.:.:.:.:.:.:. 0/1:11,4:15:78.2:78,0,292:48:48:0.267 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:21,4:25:55.06:55,0,576:52:25:0.16 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:11,3:14:30.76:31,0,331:53:3:0.214
chr1 976299 . C G 48.37 SB;LowDP BaseQRankSum=-2.051;Dels=0;FS=0;HRun=4;HaplotypeScore=13.1341;MQ=47;MQ0=0;MQRankSum=-2.192;QD=3.24;ReadPosRankSum=-0.071;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=29;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.7989;dpsi_zscore=1.386;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:10,4:14:75.32:75,0,301:47:45:0.286 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:10,5:15:78.36:78,0,268:41:48:0.333 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976310 . A G 13.02 SB;LowDP BaseQRankSum=-1.333;Dels=0;FS=0;HRun=1;HaplotypeScore=13.0884;MQ=45;MQ0=0;MQRankSum=-1.867;QD=0.93;ReadPosRankSum=0.8;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=14;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=6.5e-06;Kaviar_AC=1;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3904;dpsi_zscore=-0.972;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:9,5:14:42.79:43,0,210:45:13:0.357 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976313 . T G 28.48 SB;LowDP BaseQRankSum=-1.485;Dels=0;FS=0;HRun=2;HaplotypeScore=13.9551;MQ=45;MQ0=0;MQRankSum=-1.626;QD=1.76;ReadPosRankSum=1.909;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=28;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.5105;dpsi_zscore=-1.101;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:10,4:14:54.69:55,0,267:45:25:0.286 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:9,5:14:58.47:58,0,267:47:28:0.357 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976316 . A G 30.67 SB;LowDP;LowGQX BaseQRankSum=-0.54;Dels=0;FS=0;HRun=2;HaplotypeScore=13.2024;MQ=44;MQ0=0;MQRankSum=-2.083;QD=2.36;ReadPosRankSum=1.312;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=38;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2348;dpsi_zscore=-0.750;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:9,4:13:60.66:61,0,207:44:31:0.308 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:10,3:13:31.25:31,0,204:39:4:0.231 0/1:6,6:12:56.76:57,0,165:45:27:0.5 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976318 . C G 4.86 LowGQX;SB;LowDP BaseQRankSum=-1.398;Dels=0;FS=0;HRun=1;HaplotypeScore=16.6976;MQ=43;MQ0=0;MQRankSum=-1.663;QD=0.44;ReadPosRankSum=1.769;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=11;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.4961;dpsi_zscore=-1.087;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:7,4:11:33.14:33,0,187:43:5:0.364 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976320 . A G 58.45 SB;LowDP;LowGQX BaseQRankSum=-2.588;Dels=0;FS=0;HRun=2;HaplotypeScore=11.736;MQ=45;MQ0=0;MQRankSum=-2.843;QD=1.09;ReadPosRankSum=2.843;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=31;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3533;dpsi_zscore=0.963;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:6,6:12:42.79:43,0,211:45:13:0.5 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:7,3:10:34.1:34,0,235:44:6:0.3 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:4,5:9:60.44:88,0,60:38:58:0.556 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976324 . T G 56.27 SB;LowDP;LowGQX;LowGQ BaseQRankSum=-1.466;Dels=0;FS=3.09;HRun=3;HaplotypeScore=9.7423;MQ=44;MQ0=0;MQRankSum=-1.312;QD=4.33;ReadPosRankSum=1.62;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=44;AN=8;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.4422;dpsi_zscore=-1.031;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:9,4:13:86.27:86,0,234:44:56:0.308 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:7,3:10:66.47:66,0,202:44:36:0.3 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:10,3:13:30.03:30,0,262:39:3:0.231 0/1:5,3:8:28.62:78,0,29:34:29:0.375 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976481 . C G 11.55 LowVariantFreq;SB;LowDP;LowGQX BaseQRankSum=0.118;Dels=0;FS=3.979;HRun=6;HaplotypeScore=28.6591;MQ=28;MQ0=0;MQRankSum=0.354;QD=1.05;ReadPosRankSum=1.061;SB=0;TI=NM_198576;GI=AGRN;FC=Silent;DP=22;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3929;dpsi_zscore=1.014;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:9,2:11:41.23:41,0,100:28:12:0.182 ./.:.:.:.:.:.:.:. 0/1:9,2:11:36.78:37,0,257:41:8:0.182 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976484 . A G 13.33 LowGQX;SB;LowDP BaseQRankSum=-1.271;Dels=0;FS=15.563;HRun=2;HaplotypeScore=2.6961;MQ=41;MQ0=0;MQRankSum=-1.271;QD=0.5;ReadPosRankSum=-0.48;SB=-1.25;TI=NM_198576;GI=AGRN;FC=Silent;DP=15;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.8204;dpsi_zscore=-1.358;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:8,2:11:34.02:34,0,226:41:5:0.2 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:2,2:4:43.11:43,0,44:32:13:0.5 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976486 . C G 18.9 SB;LowDP BaseQRankSum=1.214;Dels=0.23;FS=0;HRun=4;HaplotypeScore=21.849;MQ=27;MQ0=0;MQRankSum=-1.386;QD=1.3;ReadPosRankSum=-0.296;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=20;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4962;dpsi_zscore=1.129;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:7,3:10:46.79:47,0,177:27:17:0.3 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:4,2:7:48.84:49,0,96:29:19:0.333
chr1 976491 . C G 77.62 LowGQX;SB;LowDP;LowVariantFreq;LowGQ BaseQRankSum=-1.109;Dels=0;FS=9.7;HRun=4;HaplotypeScore=14.2983;MQ=28;MQ0=0;MQRankSum=1.294;QD=0.46;ReadPosRankSum=0.185;SB=0.02;TI=NM_198576;GI=AGRN;FC=Silent;DP=40;AN=8;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.7997;dpsi_zscore=1.386;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:9,3:12:34.07:34,0,181:28:6:0.25 ./.:.:.:.:.:.:.:. 0/1:8,5:13:99:108,0,179:27:78:0.385 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:9,2:11:39.8:40,0,200:29:10:0.182 ./.:.:.:.:.:.:.:. 1/1:2,2:4:6:58,6,0:32:6:0.5 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976495 . A G 34.53 SB;LowDP;LowGQX;LowGQ BaseQRankSum=-0.978;Dels=0;FS=14.472;HRun=3;HaplotypeScore=19.881;MQ=32;MQ0=0;MQRankSum=-1.092;QD=2.13;ReadPosRankSum=-0.817;SB=-2.04;TI=NM_198576;GI=AGRN;FC=Silent;DP=52;AN=10;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.6636;dpsi_zscore=-1.240;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:8,5:13:57.68:58,0,170:32:28:0.385 ./.:.:.:.:.:.:.:. 0/1:9,6:15:57.53:58,0,216:29:28:0.4 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:7,4:11:64.52:65,0,214:39:35:0.364 1/1:1,3:4:6.01:63,6,0:32:6:0.75 ./.:.:.:.:.:.:.:. 0/1:6,2:8:40.09:40,0,110:29:11:0.25
chr1 976497 . C G 50.17 SB;LowDP BaseQRankSum=-0.849;Dels=0;FS=20.792;HRun=4;HaplotypeScore=24.6497;MQ=32;MQ0=0;MQRankSum=-0.386;QD=3.86;ReadPosRankSum=-1.003;SB=-2.5;TI=NM_198576;GI=AGRN;FC=Silent;DP=35;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4631;dpsi_zscore=1.094;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:9,4:13:80.16:80,0,205:32:50:0.308 ./.:.:.:.:.:.:.:. 0/1:10,4:14:42.85:43,0,162:29:13:0.286 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:6,2:8:40.05:40,0,140:29:10:0.25
chr1 976499 . GGGC G 753.3 SB;LowDP BaseQRankSum=1.833;FS=2.682;HRun=0;HaplotypeScore=402.915;MQ=30;MQ0=0;MQRankSum=0.033;QD=28.97;ReadPosRankSum=2.9;SB=-2.91;TI=NM_198576;GI=AGRN;FC=Noncoding;DP=41;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:12,14:26:99:792,0,238:30:99:0.538 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:10,5:15:99:250,0,315:40:99:0.333 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976502 . C G 77.8 LowDP;SB BaseQRankSum=-1.398;Dels=0.2;FS=8.451;HRun=4;HaplotypeScore=44.5096;MQ=31;MQ0=0;MQRankSum=-0.678;QD=5.19;ReadPosRankSum=-0.278;SB=-20.44;TI=NM_198576;GI=AGRN;FC=Silent;DP=41;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=3.84e-05;Kaviar_AC=1;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.7991;dpsi_zscore=1.386;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:4,7:12:99:108,0,111:31:78:0.636 ./.:.:.:.:.:.:.:. 0/1:9,3:12:48.84:49,0,126:33:19:0.25 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:6,2:9:42:42,0,158:36:12:0.25 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976506 . A G 25.5 SB;LowDP;LowVariantFreq;LowGQX BaseQRankSum=-0.495;Dels=0;FS=3.802;HRun=3;HaplotypeScore=60.4531;MQ=31;MQ0=0;MQRankSum=-2.051;QD=1.7;ReadPosRankSum=-0.778;SB=-9.37;TI=NM_198576;GI=AGRN;FC=Silent;DP=77;AN=10;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.6637;dpsi_zscore=-1.240;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:10,4:15:55.48:55,0,225:31:26:0.286 ./.:.:.:.:.:.:.:. 0/1:6,5:12:42.07:42,0,119:32:12:0.455 0/1:24,5:29:39.99:40,0,656:31:10:0.172 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:6,4:10:48.81:49,0,139:46:19:0.4 ./.:.:.:.:.:.:.:. 0/1:7,2:9:31.07:31,0,179:36:4:0.222
chr1 976506 . AGCGGGGGC A 1605.4 PASS BaseQRankSum=-0.39;FS=21.819;HRun=0;HaplotypeScore=286.26;MQ=31;MQ0=0;MQRankSum=-1.904;QD=55.36;ReadPosRankSum=3.648;SB=-10.7;TI=NM_198576;GI=AGRN;FC=Noncoding;DP=29;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.0194823;Kaviar_AC=3012;Kaviar_AN=154602;ExAC_ALL=0.9388;ExAC_AFR=1;ExAC_AMR=.;ExAC_EAS=1;ExAC_FIN=.;ExAC_NFE=0.95;ExAC_OTH=1;ExAC_SAS=0.9329;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:15,14:29:99:1644,0,105:31:99:0.483 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976508 . C G 13.06 LowGQX;SB;LowDP;LowVariantFreq BaseQRankSum=-1.109;Dels=0.2;FS=5.441;HRun=5;HaplotypeScore=54.3681;MQ=34;MQ0=0;MQRankSum=-0.74;QD=0.24;ReadPosRankSum=0.185;SB=0.03;TI=NM_198576;GI=AGRN;FC=Silent;DP=41;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.;Kaviar_AF=6.5e-06;Kaviar_AC=1;Kaviar_AN=154602;ExAC_ALL=0;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=0;ExAC_SAS=0;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2776;dpsi_zscore=0.858;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:9,3:12:31.06:31,0,179:34:4:0.25 ./.:.:.:.:.:.:.:. 0/1:9,2:12:42.84:43,0,167:32:13:0.182 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:5,3:8:40.04:40,0,161:36:10:0.375 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976514 rs79290478 C A 445.2 LowGQ;LowDP;LowGQX;SB Dels=0.16;FS=0;HRun=0;HaplotypeScore=33.8862;MQ=36;MQ0=0;QD=15.65;SB=-116.06;TI=NM_198576;GI=AGRN;FC=Silent;BaseQRankSum=-0.193;MQRankSum=1.542;ReadPosRankSum=0.385;DP=211;AN=21;AC=17;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.0189584;Kaviar_AC=2931;Kaviar_AN=154602;ExAC_ALL=1;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=1;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=rs79290478;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4665;dpsi_zscore=1.098;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,12:16:27.08:329,27,0:36:27:1 1/1:1,17:19:8.69:477,9,0:47:9:0.944 1/1:0,11:15:27.05:313,27,0:39:27:1 1:2,12:18:33.1:.:35:33:0.857 0/1:12,6:23:99:155,0,260:48:99:0.333 0/1:13,5:19:99:104,0,320:46:74:0.278 ./.:.:.:.:.:.:.:. 1/0:0,10,3:13:52.71:342,77,53:39:53:1 0/1:3,11:15:42.8:197,0,43:45:43:0.786 1/1:0,12:14:30.09:370,30,0:48:30:1 1/1:0,10:11:21.07:279,21,0:45:21:1 1/1:0,10:12:24.07:304,24,0:42:24:1
chr1 976514 rs79290478 C G 445.2 LowGQ;LowDP;LowGQX;SB Dels=0.16;FS=0;HRun=0;HaplotypeScore=33.8862;MQ=36;MQ0=0;QD=15.65;SB=-116.06;TI=NM_198576;GI=AGRN;FC=Silent;BaseQRankSum=-0.193;MQRankSum=1.542;ReadPosRankSum=0.385;DP=211;AN=21;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.8013;dpsi_zscore=1.388;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/0:0,12:16:27.08:329,.,.:36:27:1 0/0:1,17:19:8.69:477,.,.:47:9:0.944 0/0:0,11:15:27.05:313,.,.:39:27:1 0:2,12:18:33.1:.:35:33:0.857 0/0:12,6:23:99:155,.,.:48:99:0.333 0/0:13,5:19:99:104,.,.:46:74:0.278 ./.:.:.:.:.:.:.:. 0/1:0,10,3:13:52.71:342,265,256:39:53:1 0/0:3,11:15:42.8:197,.,.:45:43:0.786 0/0:0,12:14:30.09:370,.,.:48:30:1 0/0:0,10:11:21.07:279,.,.:45:21:1 0/0:0,10:12:24.07:304,.,.:42:24:1
chr1 976554 rs191270495 C G 266.12 PASS BaseQRankSum=-0.655;Dels=0;FS=0;HRun=2;HaplotypeScore=1.7608;MQ=49;MQ0=0;MQRankSum=-0.243;QD=8.06;ReadPosRankSum=0.056;SB=-135.14;TI=NM_198576;GI=AGRN;FC=Unknown_243;EXON;DP=33;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon5:c.C729G:p.G243G;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon5:c.C729G:p.G243G;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon5:c.C729G:p.G243G;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000241878.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.065;Kaviar_AF=0.0023803;Kaviar_AC=368;Kaviar_AN=154602;ExAC_ALL=0.0149;ExAC_AFR=0.0568;ExAC_AMR=0;ExAC_EAS=0.0196;ExAC_FIN=.;ExAC_NFE=0.0123;ExAC_OTH=0;ExAC_SAS=0.0146;1000g2014oct_all=0.0255591;snp138=rs191270495;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0613;dpsi_zscore=0.347;dbscSNV_ADA_SCORE=0;dbscSNV_RF_SCORE=0;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:21,12:33:99:296,0,497:49:99:0.364 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976629 rs113789806 C T 614.86 PASS BaseQRankSum=1.772;Dels=0;FS=4.913;HRun=1;HaplotypeScore=0;MQ=49;MQ0=0;MQRankSum=0.553;QD=15.37;ReadPosRankSum=0.014;SB=-290.44;TI=NM_198576;GI=AGRN;FC=Synonymous_A268A;EXON;DP=40;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon5:c.C804T:p.A268A;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon5:c.C804T:p.A268A;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon5:c.C804T:p.A268A;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116282.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.23;Kaviar_AF=0.0056856;Kaviar_AC=879;Kaviar_AN=154602;ExAC_ALL=0.0100;ExAC_AFR=0.2317;ExAC_AMR=0.0714;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0047;ExAC_OTH=0.0089;ExAC_SAS=0.0007;1000g2014oct_all=0.0411342;snp138=rs113789806;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4789;dpsi_zscore=1.111;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:14,26:40:99:645,0,338:49:99:0.65 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 976838 . C T 1405.39 PASS BaseQRankSum=-2.404;Dels=0;FS=2.396;HRun=1;HaplotypeScore=7.6822;MQ=55;MQ0=0;MQRankSum=2.174;QD=11.52;ReadPosRankSum=0.965;SB=-662.66;TI=NM_198576;GI=AGRN;FC=Silent;DP=232;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.;Kaviar_AF=6.5e-06;Kaviar_AC=1;Kaviar_AN=154602;ExAC_ALL=0;ExAC_AFR=0;ExAC_AMR=0;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0;ExAC_OTH=0;ExAC_SAS=0;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3357;dpsi_zscore=-0.903;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:62,60:122:99:1435,0,1549:55:99:0.492 0/1:53,57:110:99:1352,0,1520:58:99:0.518 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 977330 rs2799066 T C 7141.71 PASS Dels=0;FS=0;HRun=2;HaplotypeScore=9.1217;MQ=55;MQ0=0;QD=27.48;SB=-3910.84;TI=NM_198576;GI=AGRN;FC=Silent;BaseQRankSum=1.173;MQRankSum=3.509;ReadPosRankSum=-0.466;DP=2476;AN=22;AC=20;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116254.2;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=1.;Kaviar_AF=0.0053428;Kaviar_AC=826;Kaviar_AN=154602;ExAC_ALL=0.9166;ExAC_AFR=0.7175;ExAC_AMR=0.9541;ExAC_EAS=0.9998;ExAC_FIN=0.9492;ExAC_NFE=0.9161;ExAC_OTH=0.9326;ExAC_SAS=0.9544;1000g2014oct_all=0.885184;snp138=rs2799066;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-3.9233;dpsi_zscore=-2.336;dbscSNV_ADA_SCORE=0;dbscSNV_RF_SCORE=0.002;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,222:222:99:6100,439,0:55:99:1 1/1:0,274:274:99:7142,512,0:53:99:1 1/1:0,188:188:99:5188,376,0:56:99:1 1/1:0,248:248:99:6771,491,0:55:99:1 0/1:129,105:235:99:2526,0,2825:55:99:0.449 0/1:139,154:294:99:3597,0,3195:56:99:0.526 ./.:.:.:.:.:.:.:. 1/1:0,193:193:99:5530,409,0:55:99:1 1/1:0,241:244:99:6806,497,0:55:99:1 1/1:0,199:199:99:5408,394,0:52:99:1 1/1:1,181:182:99:4659,328,0:50:99:0.995 1/1:0,196:197:99:5645,409,0:54:99:1
chr1 977570 rs2710876 G A 3281.71 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=1.8499;MQ=57;MQ0=0;QD=30.05;SB=-1389.89;TI=NM_198576;GI=AGRN;FC=Silent;BaseQRankSum=1.003;MQRankSum=-1.003;ReadPosRankSum=0.18;DP=977;AN=22;AC=18;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000251375.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.97;Kaviar_AF=0.820552;Kaviar_AC=126859;Kaviar_AN=154602;ExAC_ALL=0.8946;ExAC_AFR=0.4638;ExAC_AMR=0.9367;ExAC_EAS=0.9691;ExAC_FIN=0.9376;ExAC_NFE=0.9136;ExAC_OTH=0.9184;ExAC_SAS=0.9479;1000g2014oct_all=0.794129;snp138=rs2710876;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.5137;dpsi_zscore=-1.105;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,98:99:99:3008,223,0:57:99:1 0/1:39,64:104:99:1532,0,883:55:99:0.621 1/1:2,84:86:99:2561,151,0:56:99:0.977 1/1:0,75:75:99:2353,172,0:57:99:1 0/1:57,43:100:99:1027,0,1437:57:99:0.43 0/1:47,62:109:99:1620,0,1264:56:99:0.569 ./.:.:.:.:.:.:.:. 0/1:32,44:76:99:1105,0,782:56:99:0.579 1/1:0,106:106:99:3282,244,0:58:99:1 1/1:0,74:74:99:2231,166,0:53:99:1 1/1:0,80:80:99:2028,141,0:50:99:1 1/1:0,68:68:99:2113,159,0:54:99:1
chr1 978603 rs35881187 CCT C 10187.3 PASS FS=0;HRun=0;HaplotypeScore=229.841;MQ=55;MQ0=2;QD=52.95;SB=-2949.87;TI=NM_198576;GI=AGRN;FC=Noncoding;BaseQRankSum=2.651;MQRankSum=1.158;ReadPosRankSum=-0.03;DP=1519;AN=18;AC=13;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000244801.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.8;Kaviar_AF=0.0165134;Kaviar_AC=2553;Kaviar_AN=154602;ExAC_ALL=0.5609;ExAC_AFR=0.1336;ExAC_AMR=0.7041;ExAC_EAS=0.7856;ExAC_FIN=0.5674;ExAC_NFE=0.572;ExAC_OTH=0.5695;ExAC_SAS=0.5642;1000g2014oct_all=0.479233;snp138=rs35881187;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:3,145:147:99:7890,439,0:55:99:0.98 0/1:97,73:170:99:3411,0,4698:57:99:0.429 0/1:56,65:122:99:3216,0,2585:58:99:0.537 1/1:0,190:190:99:10187,572,0:59:99:1 0/1:98,109:208:99:5275,0,4725:55:99:0.527 0/1:104,88:192:99:4113,0,5028:56:99:0.458 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:102,78:180:99:3738,0,4982:54:99:0.433 1/1:2,149:149:99:7947,442,0:51:99:0.987 1/1:1,155:155:99:8454,467,0:56:99:0.994
chr1 979690 rs115413462 G A 2059.18 PASS BaseQRankSum=1.13;Dels=0;FS=0;HRun=0;HaplotypeScore=3.7252;MQ=56;MQ0=0;MQRankSum=0.671;QD=11.9;ReadPosRankSum=2.222;SB=-1541.87;TI=NM_198576;GI=AGRN;FC=Silent;DP=173;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.083;Kaviar_AF=0.0115781;Kaviar_AC=1790;Kaviar_AN=154602;ExAC_ALL=0.0128;ExAC_AFR=0.0657;ExAC_AMR=0.0062;ExAC_EAS=0.0311;ExAC_FIN=0.0196;ExAC_NFE=0.0038;ExAC_OTH=0.0117;ExAC_SAS=0.0084;1000g2014oct_all=0.0299521;snp138=rs115413462;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.6832;dpsi_zscore=-1.255;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:81,92:173:99:2089,0,2074:56:99:0.532 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 979748 rs113288277 A T 2818.68 PASS BaseQRankSum=0.969;Dels=0;FS=2.149;HRun=0;HaplotypeScore=8.0987;MQ=58;MQ0=0;MQRankSum=-0.809;QD=12.44;ReadPosRankSum=-0.665;SB=-1180.96;TI=NM_198576;GI=AGRN;FC=Missense_E728V;EXON;DP=369;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon12:c.A2183T:p.E728V;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon12:c.A2183T:p.E728V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon12:c.A2183T:p.E728V;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116256.2;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.047;Kaviar_AF=0.0295404;Kaviar_AC=4567;Kaviar_AN=154602;ExAC_ALL=0.0302;ExAC_AFR=0.0064;ExAC_AMR=0.0147;ExAC_EAS=0.0042;ExAC_FIN=0.0386;ExAC_NFE=0.0417;ExAC_OTH=0.0325;ExAC_SAS=0.0204;1000g2014oct_all=0.0183706;snp138=rs113288277;SIFT_score=0.036;SIFT_converted_rankscore=0.433;SIFT_pred=D;Polyphen2_HDIV_score=0.998;Polyphen2_HDIV_rankscore=0.715;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.986;Polyphen2_HVAR_rankscore=0.754;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_converted_rankscore=0.629;LRT_pred=D;MutationTaster_score=1;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=D;MutationAssessor_score=2.385;MutationAssessor_score_rankscore=0.689;MutationAssessor_pred=M;FATHMM_score=3.56;FATHMM_converted_rankscore=0.047;FATHMM_pred=T;PROVEAN_score=-3.83;PROVEAN_converted_rankscore=0.721;PROVEAN_pred=D;VEST3_score=0.36;VEST3_rankscore=0.421;MetaSVM_score=-1.203;MetaSVM_rankscore=0.001;MetaSVM_pred=T;MetaLR_score=0.013;MetaLR_rankscore=0.052;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=5.343;CADD_raw_rankscore=0.723;CADD_phred=25.9;DANN_score=0.992;DANN_rankscore=0.536;fathmm-MKL_coding_score=0.991;fathmm-MKL_coding_rankscore=0.912;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.531;Eigen-PC-raw=0.423;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.707;integrated_fitCons_score_rankscore=0.730;integrated_confidence_value=0;GERP++_RS=4.58;GERP++_RS_rankscore=0.559;phyloP100way_vertebrate=5.452;phyloP100way_vertebrate_rankscore=0.662;phyloP20way_mammalian=1.088;phyloP20way_mammalian_rankscore=0.866;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.866;phastCons20way_mammalian_rankscore=0.362;SiPhy_29way_logOdds=13.954;SiPhy_29way_logOdds_rankscore=0.635;Interpro_domain=Kazal_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3771;dpsi_zscore=-0.956;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:67,77:144:99:1821,0,1753:58:99:0.535 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:111,112:225:99:2849,0,2809:58:99:0.502 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 979835 rs114389542 G A 1656.62 PASS BaseQRankSum=-1.372;Dels=0;FS=2.654;HRun=0;HaplotypeScore=11.9653;MQ=53;MQ0=0;MQRankSum=1.846;QD=8.77;ReadPosRankSum=-0.099;SB=-974.94;TI=NM_198576;GI=AGRN;FC=Silent;DP=189;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000242021.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.085;Kaviar_AF=0.0107243;Kaviar_AC=1658;Kaviar_AN=154602;ExAC_ALL=0.0166;ExAC_AFR=0.0833;ExAC_AMR=0.0104;ExAC_EAS=0.0449;ExAC_FIN=0.028;ExAC_NFE=0.0051;ExAC_OTH=0.0163;ExAC_SAS=0.0098;1000g2014oct_all=0.0305511;snp138=rs114389542;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.7966;dpsi_zscore=1.384;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:115,74:189:99:1687,0,2612:53:99:0.392 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 980460 rs3128097 G A 8063.8 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=11.8071;MQ=57;MQ0=0;QD=28.26;SB=-4144.42;TI=NM_198576;GI=AGRN;FC=Silent;BaseQRankSum=-1.618;MQRankSum=1.965;ReadPosRankSum=-1.654;DP=2540;AN=22;AC=20;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.184086;Kaviar_AC=28460;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.911941;snp138=rs3128097;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2610;dpsi_zscore=-0.794;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,252:253:99:7149,524,0:57:99:1 1/1:0,244:245:99:6180,439,0:55:99:1 1/1:0,186:186:99:5308,382,0:57:99:1 1/1:0,239:241:99:6653,488,0:57:99:1 0/1:90,114:205:99:2897,0,2138:56:99:0.559 0/1:95,132:227:99:3127,0,2085:56:99:0.581 ./.:.:.:.:.:.:.:. 1/1:1,237:241:99:6575,479,0:56:99:0.996 1/1:3,284:287:99:8064,548,0:57:99:0.99 1/1:1,212:215:99:5789,421,0:55:99:0.995 1/1:0,221:222:99:5555,394,0:51:99:1 1/1:0,217:218:99:6034,439,0:56:99:1
chr1 980824 rs112039851 G C 3130.31 PASS BaseQRankSum=0.155;Dels=0;FS=2.632;HRun=0;HaplotypeScore=17.7932;MQ=55;MQ0=0;MQRankSum=2.514;QD=11.1;ReadPosRankSum=-1.475;SB=-2251.65;TI=NM_198576;GI=AGRN;FC=Synonymous_G819G;EXON;DP=282;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon14:c.G2457C:p.G819G;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon14:c.G2457C:p.G819G;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon14:c.G2457C:p.G819G;cytoBand=1p36.33;CLINSIG=other;CLNDBN=not_specified;CLNACC=RCV000246474.2;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.073;Kaviar_AF=0.0109507;Kaviar_AC=1693;Kaviar_AN=154602;ExAC_ALL=0.0121;ExAC_AFR=0.0593;ExAC_AMR=0.0054;ExAC_EAS=0.0309;ExAC_FIN=0.0193;ExAC_NFE=0.0038;ExAC_OTH=0.0115;ExAC_SAS=0.0084;1000g2014oct_all=0.0273562;snp138=rs112039851;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2784;dpsi_zscore=0.859;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:143,139:282:99:3160,0,3152:55:99:0.493 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 980948 rs183108359 C T 4405.25 PASS BaseQRankSum=0.121;Dels=0;FS=6.85;HRun=0;HaplotypeScore=16.7333;MQ=57;MQ0=0;MQRankSum=1.826;QD=11.75;ReadPosRankSum=-1.203;SB=-2707.88;TI=NM_198576;GI=AGRN;FC=Silent;DP=375;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Likely_benign;CLNDBN=not_specified;CLNACC=RCV000252843.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.048;Kaviar_AF=0.0103103;Kaviar_AC=1594;Kaviar_AN=154602;ExAC_ALL=0.0116;ExAC_AFR=0.0032;ExAC_AMR=0.0039;ExAC_EAS=0.0001;ExAC_FIN=0.0017;ExAC_NFE=0.0085;ExAC_OTH=0.0111;ExAC_SAS=0.0434;1000g2014oct_all=0.0107827;snp138=rs183108359;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0347;dpsi_zscore=0.223;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:198,177:375:99:4405,0,4769:57:99:0.472 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 980955 rs139005472 AC A 5894.6 PASS BaseQRankSum=1.047;FS=1.249;HRun=5;HaplotypeScore=446.671;MQ=55;MQ0=0;MQRankSum=1.343;QD=16.06;ReadPosRankSum=0.456;SB=-2936.8;TI=NM_198576;GI=AGRN;FC=Noncoding;DP=367;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.087;Kaviar_AF=0.0003234;Kaviar_AC=50;Kaviar_AN=154602;ExAC_ALL=0.0127;ExAC_AFR=0.0661;ExAC_AMR=0.0059;ExAC_EAS=0.0303;ExAC_FIN=0.0195;ExAC_NFE=0.0037;ExAC_OTH=0.0123;ExAC_SAS=0.0084;1000g2014oct_all=0.0311502;snp138=rs139005472;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:185,177:367:99:5895,0,5338:55:99:0.489 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 981087 rs3128098 A G 10908.9 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=8.1316;MQ=56;MQ0=0;QD=29.44;SB=-6038.51;TI=NM_198576;GI=AGRN;FC=Silent;BaseQRankSum=1.315;MQRankSum=1.16;ReadPosRankSum=-1.918;DP=3572;AN=22;AC=19;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000243014.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=1.;Kaviar_AF=0.894937;Kaviar_AC=138359;Kaviar_AN=154602;ExAC_ALL=0.9128;ExAC_AFR=0.6454;ExAC_AMR=0.9480;ExAC_EAS=0.9999;ExAC_FIN=0.9509;ExAC_NFE=0.9217;ExAC_OTH=0.9357;ExAC_SAS=0.9570;1000g2014oct_all=0.869409;snp138=rs3128098;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0850;dpsi_zscore=0.435;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,353:354:99:10423,764,0:56:99:1 1/1:0,353:353:99:9137,644,0:53:99:1 1/1:0,287:287:99:8217,593,0:55:99:1 1/1:0,378:380:99:10909,792,0:56:99:1 0/1:177,157:334:99:3793,0,4424:54:99:0.47 0/1:173,149:323:99:3662,0,4355:56:99:0.463 ./.:.:.:.:.:.:.:. 0/1:128,172:301:99:4612,0,3224:56:99:0.573 1/1:0,376:376:99:10676,771,0:56:99:1 1/1:0,241:243:99:7077,518,0:55:99:1 1/1:1,308:309:99:7773,518,0:51:99:0.997 1/1:0,312:312:99:9161,668,0:56:99:1
chr1 981131 rs9697293 A G 3834.89 PASS BaseQRankSum=2.187;Dels=0;FS=0.791;HRun=0;HaplotypeScore=12.0809;MQ=53;MQ0=0;MQRankSum=3.428;QD=10.48;ReadPosRankSum=0.077;SB=-2559.17;TI=NM_198576;GI=AGRN;FC=Missense_Q852R;EXON;DP=366;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon15:c.A2555G:p.Q852R;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon15:c.A2555G:p.Q852R;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon15:c.A2555G:p.Q852R;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000247794.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.1;Kaviar_AF=0.0127036;Kaviar_AC=1964;Kaviar_AN=154602;ExAC_ALL=0.0137;ExAC_AFR=0.0756;ExAC_AMR=0.0064;ExAC_EAS=0.0320;ExAC_FIN=0.0186;ExAC_NFE=0.0038;ExAC_OTH=0.0111;ExAC_SAS=0.0084;1000g2014oct_all=0.0345447;snp138=rs9697293;SIFT_score=0.371;SIFT_converted_rankscore=0.115;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.004;Polyphen2_HVAR_rankscore=0.093;Polyphen2_HVAR_pred=B;LRT_score=0.573;LRT_converted_rankscore=0.112;LRT_pred=N;MutationTaster_score=1;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=N;MutationAssessor_score=0.07;MutationAssessor_score_rankscore=0.083;MutationAssessor_pred=N;FATHMM_score=0.15;FATHMM_converted_rankscore=0.608;FATHMM_pred=T;PROVEAN_score=-0.39;PROVEAN_converted_rankscore=0.136;PROVEAN_pred=N;VEST3_score=0.015;VEST3_rankscore=0.002;MetaSVM_score=-1.091;MetaSVM_rankscore=0.053;MetaSVM_pred=T;MetaLR_score=0.002;MetaLR_rankscore=0.007;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=-0.029;CADD_raw_rankscore=0.091;CADD_phred=2.318;DANN_score=0.644;DANN_rankscore=0.073;fathmm-MKL_coding_score=0.021;fathmm-MKL_coding_rankscore=0.062;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.179;Eigen-PC-raw=-1.083;GenoCanyon_score=0.125;GenoCanyon_score_rankscore=0.170;integrated_fitCons_score=0.707;integrated_fitCons_score_rankscore=0.730;integrated_confidence_value=0;GERP++_RS=-0.622;GERP++_RS_rankscore=0.109;phyloP100way_vertebrate=-0.151;phyloP100way_vertebrate_rankscore=0.101;phyloP20way_mammalian=-0.492;phyloP20way_mammalian_rankscore=0.052;phastCons100way_vertebrate=0.000;phastCons100way_vertebrate_rankscore=0.063;phastCons20way_mammalian=0.431;phastCons20way_mammalian_rankscore=0.259;SiPhy_29way_logOdds=5.309;SiPhy_29way_logOdds_rankscore=0.150;Interpro_domain=Laminin_EGF_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0486;dpsi_zscore=0.292;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:196,170:366:99:3835,0,4528:53:99:0.464 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 981136 . G A 4399.5 PASS BaseQRankSum=-1.267;Dels=0;FS=1.312;HRun=0;HaplotypeScore=27.2697;MQ=53;MQ0=0;MQRankSum=3.42;QD=13.33;ReadPosRankSum=0.934;SB=-2659.02;TI=NM_198576;GI=AGRN;FC=Missense_A854T;EXON;DP=654;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon15:c.G2560A:p.A854T;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon15:c.G2560A:p.A854T;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon15:c.G2560A:p.A854T;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.0002;Kaviar_AF=5.82e-05;Kaviar_AC=9;Kaviar_AN=154602;ExAC_ALL=6.634e-05;ExAC_AFR=0;ExAC_AMR=0;ExAC_EAS=0;ExAC_FIN=0.0002;ExAC_NFE=9.084e-05;ExAC_OTH=0;ExAC_SAS=6.059e-05;1000g2014oct_all=.;snp138=.;SIFT_score=0.012;SIFT_converted_rankscore=0.546;SIFT_pred=D;Polyphen2_HDIV_score=0.979;Polyphen2_HDIV_rankscore=0.571;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.906;Polyphen2_HVAR_rankscore=0.626;Polyphen2_HVAR_pred=P;LRT_score=0.003;LRT_converted_rankscore=0.351;LRT_pred=N;MutationTaster_score=0.996;MutationTaster_converted_rankscore=0.432;MutationTaster_pred=D;MutationAssessor_score=1.305;MutationAssessor_score_rankscore=0.328;MutationAssessor_pred=L;FATHMM_score=0.12;FATHMM_converted_rankscore=0.611;FATHMM_pred=T;PROVEAN_score=-1.59;PROVEAN_converted_rankscore=0.383;PROVEAN_pred=N;VEST3_score=0.362;VEST3_rankscore=0.423;MetaSVM_score=-0.714;MetaSVM_rankscore=0.598;MetaSVM_pred=T;MetaLR_score=0.254;MetaLR_rankscore=0.624;MetaLR_pred=T;M-CAP_score=0.073;M-CAP_rankscore=0.719;M-CAP_pred=D;CADD_raw=6.072;CADD_raw_rankscore=0.836;CADD_phred=28.1;DANN_score=0.999;DANN_rankscore=0.981;fathmm-MKL_coding_score=0.603;fathmm-MKL_coding_rankscore=0.309;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.197;Eigen-PC-raw=0.125;GenoCanyon_score=0.771;GenoCanyon_score_rankscore=0.236;integrated_fitCons_score=0.707;integrated_fitCons_score_rankscore=0.730;integrated_confidence_value=0;GERP++_RS=3.38;GERP++_RS_rankscore=0.376;phyloP100way_vertebrate=2.361;phyloP100way_vertebrate_rankscore=0.436;phyloP20way_mammalian=1.045;phyloP20way_mammalian_rankscore=0.669;phastCons100way_vertebrate=0.979;phastCons100way_vertebrate_rankscore=0.349;phastCons20way_mammalian=0.610;phastCons20way_mammalian_rankscore=0.290;SiPhy_29way_logOdds=14.680;SiPhy_29way_logOdds_rankscore=0.685;Interpro_domain=Laminin_EGF_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1293;dpsi_zscore=-0.531;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=0.0734108263905;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:155,174:330:99:4399,0,3767:53:99:0.529 0/1:157,167:324:99:4082,0,3906:55:99:0.515 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 981931 rs2465128 A G 8190.91 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=45.1027;MQ=54;MQ0=0;QD=27.94;SB=-3456.77;TI=NM_198576;GI=AGRN;FC=Synonymous_S1022S;EXON;BaseQRankSum=2.29;MQRankSum=1.503;ReadPosRankSum=0.753;DP=3026;AN=24;AC=19;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon18:c.A3066G:p.S1022S;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon18:c.A3066G:p.S1022S;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon18:c.A3066G:p.S1022S;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116259.2;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.96;Kaviar_AF=0.0001164;Kaviar_AC=18;Kaviar_AN=154602;ExAC_ALL=0.8767;ExAC_AFR=0.5130;ExAC_AMR=0.9312;ExAC_EAS=0.9649;ExAC_FIN=0.9266;ExAC_NFE=0.9018;ExAC_OTH=0.8983;ExAC_SAS=0.8890;1000g2014oct_all=0.797724;snp138=rs2465128;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0298;dpsi_zscore=0.195;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,237:242:99:6761,509,0:54:99:1 0/1:143,141:292:99:3235,0,3134:54:99:0.496 1/1:1,186:190:99:5386,406,0:54:99:0.995 1/1:0,288:291:99:8188,608,0:54:99:1 0/1:138,148:290:99:3499,0,3372:53:99:0.517 0/1:121,150:278:99:3706,0,2927:53:99:0.554 0/1:142,147:295:99:3738,0,3427:55:99:0.509 0/1:123,120:250:99:2988,0,2996:55:99:0.494 1/1:0,280:284:99:8191,620,0:55:99:1 1/1:0,219:222:99:6306,472,0:54:99:1 1/1:0,184:185:99:4723,343,0:51:99:1 1/1:0,203:207:99:6012,463,0:52:99:1
chr1 982844 rs76264143 G C 5093.23 PASS BaseQRankSum=2.711;Dels=0;FS=1.722;HRun=0;HaplotypeScore=24.8501;MQ=57;MQ0=0;MQRankSum=0.806;QD=13.33;ReadPosRankSum=0.24;SB=-2841.38;TI=NM_198576;GI=AGRN;FC=Silent;DP=770;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=other;CLNDBN=not_specified;CLNACC=RCV000116263.4;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.083;Kaviar_AF=0.0565064;Kaviar_AC=8736;Kaviar_AN=154602;ExAC_ALL=0.0577;ExAC_AFR=0.0119;ExAC_AMR=0.0304;ExAC_EAS=0.0002;ExAC_FIN=0.0537;ExAC_NFE=0.0730;ExAC_OTH=0.0673;ExAC_SAS=0.0748;1000g2014oct_all=0.038738;snp138=rs76264143;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-4.8544;dpsi_zscore=-2.480;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:176,197:373:99:4972,0,4307:57:99:0.528 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:190,205:397:99:5093,0,4710:57:99:0.519 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 982941 rs3128102 T C 12394.9 PASS Dels=0.01;FS=0;HRun=3;HaplotypeScore=26.0448;MQ=56;MQ0=0;QD=28.48;SB=-7190.83;TI=NM_198576;GI=AGRN;FC=Silent;BaseQRankSum=0.362;MQRankSum=0.09;ReadPosRankSum=-2.042;DP=4132;AN=22;AC=18;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000246305.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.97;Kaviar_AF=0.842796;Kaviar_AC=130298;Kaviar_AN=154602;ExAC_ALL=0.8859;ExAC_AFR=0.4549;ExAC_AMR=0.9356;ExAC_EAS=0.9689;ExAC_FIN=0.9298;ExAC_NFE=0.9109;ExAC_OTH=0.9154;ExAC_SAS=0.9458;1000g2014oct_all=0.79992;snp138=rs3128102;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1338;dpsi_zscore=-0.543;dbscSNV_ADA_SCORE=0.0001;dbscSNV_RF_SCORE=0.014;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,395:396:99:11336,828,0:56:99:1 0/1:167,188:356:99:4411,0,3964:54:99:0.53 1/1:0,320:321:99:9256,674,0:55:99:1 1/1:0,427:429:99:12395,903,0:57:99:1 0/1:237,187:425:99:4420,0,5637:54:99:0.441 0/1:191,215:408:99:5388,0,4725:55:99:0.53 ./.:.:.:.:.:.:.:. 0/1:180,171:351:99:4403,0,4681:57:99:0.487 1/1:4,418:423:99:11923,775,0:58:99:0.991 1/1:2,367:369:99:9914,670,0:55:99:0.995 1/1:0,360:360:99:9066,632,0:50:99:1 1/1:1,284:285:99:8130,590,0:56:99:0.996
chr1 982994 rs10267 T C 12358.5 PASS BaseQRankSum=1.043;Dels=0;FS=3.506;HRun=1;HaplotypeScore=26.8093;MQ=55;MQ0=0;MQRankSum=1.206;QD=28.6;ReadPosRankSum=-1.084;SB=-7112.64;TI=NM_198576;GI=AGRN;FC=Synonymous_F1186F;EXON;DP=4098;AN=22;AC=19;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon21:c.T3558C:p.F1186F;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon21:c.T3558C:p.F1186F;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon21:c.T3558C:p.F1186F;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116264.2;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=1.;Kaviar_AF=0.881082;Kaviar_AC=136217;Kaviar_AN=154602;ExAC_ALL=0.8989;ExAC_AFR=0.5354;ExAC_AMR=0.9420;ExAC_EAS=0.9995;ExAC_FIN=0.9490;ExAC_NFE=0.9151;ExAC_OTH=0.9256;ExAC_SAS=0.9543;1000g2014oct_all=0.835863;snp138=rs10267;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0089;dpsi_zscore=-0.030;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:2,420:422:99:12068,844,0:55:99:0.995 1/1:1,378:379:99:10183,694,0:53:99:0.997 1/1:0,300:300:99:8652,629,0:56:99:1 1/1:1,420:421:99:12359,900,0:57:99:0.998 0/1:233,182:415:99:4316,0,5647:54:99:0.439 0/1:200,190:393:99:4882,0,4902:55:99:0.487 ./.:.:.:.:.:.:.:. 0/1:169,174:346:99:4433,0,4355:56:99:0.507 1/1:3,399:403:99:11612,772,0:57:99:0.993 1/1:2,346:348:99:9581,653,0:55:99:0.994 1/1:1,376:377:99:9532,644,0:50:99:0.997 1/1:1,293:294:99:8323,567,0:56:99:0.997
chr1 984202 rs115499153 A G 2375.15 PASS BaseQRankSum=2.384;Dels=0;FS=5.023;HRun=0;HaplotypeScore=46.9054;MQ=46;MQ0=0;MQRankSum=-1.244;QD=11.2;ReadPosRankSum=-1.496;SB=-1216.72;TI=NM_198576;GI=AGRN;FC=Silent;DP=374;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.2;Kaviar_AF=0.005291;Kaviar_AC=818;Kaviar_AN=154602;ExAC_ALL=0.0097;ExAC_AFR=0.2009;ExAC_AMR=0.0242;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0029;ExAC_OTH=0.0082;ExAC_SAS=0.0007;1000g2014oct_all=0.0567093;snp138=rs115499153;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1214;dpsi_zscore=0.545;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:118,92:212:99:2405,0,2784:46:99:0.438 0/1:85,74:162:99:1793,0,2291:44:99:0.465 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 984302 rs9442391 T C 8087.53 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=14.815;MQ=50;MQ0=0;QD=27.22;SB=-4352.17;TI=NM_198576;GI=AGRN;FC=Synonymous_T1387T;EXON;BaseQRankSum=2.474;MQRankSum=-1.455;ReadPosRankSum=-1.615;DP=2395;AN=18;AC=14;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon24:c.T4161C:p.T1387T;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon24:c.T4161C:p.T1387T;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon24:c.T4161C:p.T1387T;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116269.2;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.84;Kaviar_AF=0.459153;Kaviar_AC=70986;Kaviar_AN=154602;ExAC_ALL=0.6295;ExAC_AFR=0.3853;ExAC_AMR=0.7571;ExAC_EAS=0.8435;ExAC_FIN=0.6654;ExAC_NFE=0.6388;ExAC_OTH=0.5748;ExAC_SAS=0.5753;1000g2014oct_all=0.545727;snp138=rs9442391;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1599;dpsi_zscore=0.639;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,255:255:99:6942,536,0:50:99:1 1/1:0,298:298:99:7547,551,0:52:99:1 0/1:128,121:251:99:2696,0,2780:51:99:0.486 1/1:2,296:298:99:8088,584,0:51:99:0.993 0/1:138,140:279:99:3267,0,2864:50:99:0.504 0/1:140,167:309:99:3860,0,3026:51:99:0.544 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:127,134:262:99:2844,0,2772:52:99:0.513 1/1:0,213:213:99:5208,379,0:48:99:1 1/1:0,228:228:99:6192,478,0:50:99:1
chr1 984450 rs369279324 A G 11.52 LowVariantFreq;SB BaseQRankSum=-0.128;Dels=0;FS=7.868;HRun=4;HaplotypeScore=34.6032;MQ=48;MQ0=0;MQRankSum=-2.151;QD=0.17;ReadPosRankSum=-2.78;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=67;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.5036;dpsi_zscore=1.136;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:58,8:67:41.19:41,0,1643:48:12:0.121 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 984476 . T G 155.26 LowVariantFreq;SB;LowGQX BaseQRankSum=-1.674;Dels=0.02;FS=8.275;HRun=3;HaplotypeScore=32.3343;MQ=44;MQ0=0;MQRankSum=-2.502;QD=0.27;ReadPosRankSum=2.662;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=266;AN=12;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3263;dpsi_zscore=0.928;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:41,6:47:42.55:43,0,1051:44:13:0.128 0/1:32,10:43:99:185,0,867:43:99:0.238 0/1:31,5:37:37:37,0,774:41:8:0.139 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:34,7:42:93.83:94,0,794:37:64:0.171 0/1:47,10:57:85.96:86,0,1458:45:56:0.175 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:34,5:39:54.5:54,0,952:46:25:0.128
chr1 984480 . C G 91.16 LowVariantFreq;SB BaseQRankSum=-1.482;Dels=0;FS=3.01;HRun=4;HaplotypeScore=13.5832;MQ=43;MQ0=0;MQRankSum=-1.905;QD=0.5;ReadPosRankSum=0.953;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=262;AN=16;AC=8;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.6772;dpsi_zscore=1.294;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:17,3:20:39.45:39,0,437:43:10:0.15 0/1:35,7:42:91.5:92,0,946:44:62:0.167 0/1:29,9:38:99:121,0,638:42:91:0.237 0/1:25,7:33:53.04:53,0,625:41:23:0.219 0/1:31,9:40:70.34:70,0,866:41:40:0.225 ./.:.:.:.:.:.:.:. 0/1:32,7:41:92.17:92,0,640:37:62:0.179 ./.:.:.:.:.:.:.:. 0/1:17,4:21:68.95:69,0,488:41:39:0.19 0/1:23,4:27:39.33:39,0,528:42:10:0.148 ./.:.:.:.:.:.:.:.
chr1 984485 . A G 184 SB;LowDP;LowVariantFreq BaseQRankSum=-2.234;Dels=0.03;FS=0;HRun=4;HaplotypeScore=40.8838;MQ=41;MQ0=0;MQRankSum=-2.18;QD=0.37;ReadPosRankSum=1.588;SB=-18.73;TI=NM_198576;GI=AGRN;FC=Silent;DP=253;AN=18;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=6.5e-06;Kaviar_AC=1;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4905;dpsi_zscore=1.123;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:23,6:35:43.06:43,0,618:41:13:0.207 0/1:9,5:16:97.64:98,0,258:42:68:0.357 0/1:25,10:37:99:112,0,640:44:82:0.286 0/1:20,14:36:99:214,0,566:43:99:0.412 0/1:23,5:28:73.6:74,0,491:38:44:0.179 ./.:.:.:.:.:.:.:. 0/1:19,8:27:70.13:70,0,369:38:40:0.296 0/1:17,8:33:99:140,0,337:34:99:0.32 ./.:.:.:.:.:.:.:. 0/1:11,6:18:99:117,0,299:40:87:0.353 0/1:14,4:20:75.06:75,0,362:41:45:0.222 ./.:.:.:.:.:.:.:.
chr1 984489 . G T 130.24 PASS BaseQRankSum=1.25;Dels=0;FS=4.801;HRun=0;HaplotypeScore=37.7448;MQ=36;MQ0=0;MQRankSum=0.972;QD=4.82;ReadPosRankSum=1.861;SB=-42.23;TI=NM_198576;GI=AGRN;FC=Silent;DP=27;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.016;Kaviar_AF=8.41e-05;Kaviar_AC=13;Kaviar_AN=154602;ExAC_ALL=0.0019;ExAC_AFR=0.0156;ExAC_AMR=0;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0021;ExAC_OTH=.;ExAC_SAS=0;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3818;dpsi_zscore=1.000;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:18,8:27:99:160,0,388:36:99:0.308 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 984490 . A G 97.63 SB;LowDP;LowVariantFreq BaseQRankSum=0.072;Dels=0.06;FS=3.09;HRun=4;HaplotypeScore=13.6797;MQ=41;MQ0=0;MQRankSum=-1.083;QD=1.53;ReadPosRankSum=1.371;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=158;AN=12;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=6.5e-06;Kaviar_AC=1;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3215;dpsi_zscore=0.922;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:12,3:15:54.44:54,0,322:41:24:0.2 0/1:29,7:36:70.37:70,0,767:43:40:0.194 0/1:23,7:30:99:128,0,516:40:98:0.233 0/1:19,5:25:39.35:39,0,492:38:10:0.208 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:22,4:29:61.92:62,0,509:33:32:0.154 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:14,4:18:82.87:83,0,321:38:53:0.222 ./.:.:.:.:.:.:.:.
chr1 984491 . C G 223.28 LowGQX;LowVariantFreq;SB;LowDP BaseQRankSum=1.689;Dels=0.21;FS=6.56;HRun=3;HaplotypeScore=49.624;MQ=39;MQ0=0;MQRankSum=-1.689;QD=0.19;ReadPosRankSum=0.685;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=112;AN=10;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=6.5e-06;Kaviar_AC=1;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3146;dpsi_zscore=0.912;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:20,3:23:34.11:34,0,617:39:6:0.13 0/1:10,4:15:56.71:57,0,226:41:27:0.286 ./.:.:.:.:.:.:.:. 0/1:19,11:30:99:253,0,439:39:99:0.367 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:16,4:21:45.68:46,0,337:37:16:0.2 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:9,6:15:94.64:95,0,258:33:65:0.4 ./.:.:.:.:.:.:.:.
chr1 984493 . GGC G 786.03 PASS BaseQRankSum=-2.119;FS=3.16;HRun=0;HaplotypeScore=566.184;MQ=32;MQ0=1;MQRankSum=0.727;QD=25.36;ReadPosRankSum=-0.854;SB=-353.66;TI=NM_198576;GI=AGRN;FC=Noncoding;DP=31;AN=2;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=7.68e-05;Kaviar_AC=2;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:14,16:30:61.89:828,62,0:32:62:0.533 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 984494 rs558237106 GC G 861.41 PASS BaseQRankSum=-0.495;FS=3.358;HRun=1;HaplotypeScore=435.797;MQ=36;MQ0=0;MQRankSum=0.743;QD=23.59;ReadPosRankSum=-0.867;SB=-348.64;TI=NM_198576;GI=AGRN;FC=Noncoding;DP=85;AN=6;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.91;Kaviar_AF=0.142693;Kaviar_AC=3714;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.73762;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:21,8:30:66.6:750,67,0:36:67:0.276 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:10,21:31:78.76:903,79,0:40:79:0.677 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:5,17:24:64.71:732,65,0:39:65:0.773
chr1 984495 rs368088288 C G 436.16 LowGQ;LowDP;SB BaseQRankSum=1.917;Dels=0.07;FS=0;HRun=5;HaplotypeScore=16.5442;MQ=39;MQ0=0;MQRankSum=1.369;QD=24.66;ReadPosRankSum=-0.091;SB=-88.44;TI=NM_198576;GI=AGRN;FC=Silent;DP=190;AN=16;AC=11;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=0.0001921;Kaviar_AC=5;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=rs368088288;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.6883;dpsi_zscore=1.302;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 1/1:2,12:14:17.42:403,17,0:39:17:0.857 0/1:13,8:22:99:149,0,289:40:99:0.381 ./.:.:.:.:.:.:.:. 0/1:12,11:23:99:176,0,287:35:99:0.478 0/1:9,19:29:99:466,0,183:39:99:0.679 0/1:10,9:20:99:246,0,206:37:99:0.474 ./.:.:.:.:.:.:.:. 0/1:13,12:26:99:306,0,327:37:99:0.48 1/1:2,6:8:15.04:166,15,0:32:15:0.75 1/1:1,12:13:36.1:406,36,0:30:36:0.923 ./.:.:.:.:.:.:.:.
chr1 984501 . A G 287.85 LowDP;SB BaseQRankSum=0.528;Dels=0.12;FS=18.195;HRun=7;HaplotypeScore=53.5855;MQ=32;MQ0=0;MQRankSum=-1.936;QD=5.31;ReadPosRankSum=1.936;SB=-14.33;TI=NM_198576;GI=AGRN;FC=Silent;DP=289;AN=24;AC=12;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2722;dpsi_zscore=0.849;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:11,10:22:99:163,0,134:32:99:0.476 0/1:4,10:14:72.14:221,0,72:38:72:0.714 0/1:16,9:25:99:136,0,314:38:99:0.36 0/1:16,16:32:99:318,0,380:38:99:0.5 0/1:18,7:27:40.41:40,0,433:33:11:0.28 0/1:18,9:29:99:126,0,452:38:96:0.333 0/1:13,10:25:99:137,0,334:40:99:0.435 0/1:18,10:30:99:196,0,284:31:99:0.357 0/1:20,14:34:99:267,0,461:32:99:0.412 0/1:7,4:11:42.82:43,0,163:29:13:0.364 0/1:6,7:13:99:197,0,107:30:99:0.538 0/1:13,5:19:79.17:79,0,212:36:49:0.278
chr1 984509 . C G 3.59 LowGQX;LowVariantFreq;SB;LowDP BaseQRankSum=0.934;Dels=0.06;FS=5.441;HRun=7;HaplotypeScore=49.211;MQ=34;MQ0=0;MQRankSum=-1.104;QD=0.22;ReadPosRankSum=0.085;SB=0.04;TI=NM_198576;GI=AGRN;FC=Silent;DP=16;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.4047;dpsi_zscore=-0.989;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:13,2:15:31.08:31,0,172:34:4:0.133 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 984510 . C G 50.35 SB;LowDP;LowVariantFreq BaseQRankSum=0.182;Dels=0.06;FS=11.761;HRun=4;HaplotypeScore=54.5717;MQ=34;MQ0=0;MQRankSum=0.182;QD=1.32;ReadPosRankSum=2.243;SB=0.05;TI=NM_198576;GI=AGRN;FC=Silent;DP=147;AN=12;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.4077;dpsi_zscore=-0.992;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:12,4:17:53.67:54,0,239:34:24:0.25 0/1:22,5:27:64.01:64,0,490:38:34:0.185 0/1:26,7:33:56.07:56,0,539:37:26:0.212 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:27,8:35:71.2:71,0,697:33:41:0.229 ./.:.:.:.:.:.:.:. 0/1:9,5:14:80.34:80,0,221:30:50:0.357 0/1:12,3:16:49.76:50,0,315:36:20:0.2
chr1 984544 . G C 4.68 LowGQX;LowVariantFreq;SB BaseQRankSum=-1.309;Dels=0.02;FS=25.116;HRun=1;HaplotypeScore=39.2141;MQ=45;MQ0=0;MQRankSum=-2.617;QD=0.11;ReadPosRankSum=1.309;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=93;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3461;dpsi_zscore=0.954;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:35,5:41:32.86:33,0,892:45:5:0.125 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:44,7:51:32.38:32,0,1091:42:4:0.137 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 984545 . C G 67.5 SB;LowVariantFreq BaseQRankSum=-2.71;Dels=0.03;FS=39.428;HRun=5;HaplotypeScore=44.717;MQ=46;MQ0=0;MQRankSum=-2.92;QD=1.79;ReadPosRankSum=1.869;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=135;AN=8;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.8888;dpsi_zscore=1.451;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:25,8:33:91.01:91,0,832:46:61:0.242 ./.:.:.:.:.:.:.:. 0/1:36,7:43:97.5:97,0,916:43:68:0.163 ./.:.:.:.:.:.:.:. 0/1:28,7:35:95.06:95,0,721:41:65:0.2 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:19,4:23:61.2:61,0,539:44:31:0.174 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 984560 . A G 179.55 LowVariantFreq;SB;LowGQX BaseQRankSum=-1.594;Dels=0;FS=58.747;HRun=2;HaplotypeScore=33.9509;MQ=44;MQ0=0;MQRankSum=-2.829;QD=0.97;ReadPosRankSum=0.086;SB=0.1;TI=NM_198576;GI=AGRN;FC=Silent;DP=377;AN=16;AC=8;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1794;dpsi_zscore=0.681;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:42,9:51:79.44:79,0,1210:44:49:0.176 0/1:32,11:44:99:151,0,971:48:99:0.256 0/1:36,10:47:99:115,0,979:48:85:0.217 ./.:.:.:.:.:.:.:. 0/1:34,10:45:35.2:35,0,949:48:6:0.227 0/1:33,11:45:99:210,0,832:44:99:0.25 ./.:.:.:.:.:.:.:. 0/1:46,9:57:94.72:95,0,1284:47:65:0.164 0/1:49,12:62:99:138,0,1467:46:99:0.197 ./.:.:.:.:.:.:.:. 0/1:20,4:24:34.1:34,0,645:40:6:0.167 ./.:.:.:.:.:.:.:.
chr1 984563 . C G 20.78 SB BaseQRankSum=-3.419;Dels=0;FS=42.619;HRun=4;HaplotypeScore=48.1927;MQ=48;MQ0=0;MQRankSum=-2.937;QD=0.46;ReadPosRankSum=-0.894;SB=-0.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=45;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2261;dpsi_zscore=0.772;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:36,9:45:50.74:51,0,1094:48:21:0.2 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 984847 rs112917612 G C 4692.25 PASS BaseQRankSum=-0.077;Dels=0;FS=0;HRun=0;HaplotypeScore=37.1826;MQ=56;MQ0=0;MQRankSum=1.264;QD=11.88;ReadPosRankSum=0.721;SB=-3211.98;TI=NM_198576;GI=AGRN;FC=Silent;DP=704;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000253016.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.2;Kaviar_AF=0.0219531;Kaviar_AC=3394;Kaviar_AN=154602;ExAC_ALL=0.0240;ExAC_AFR=0.2002;ExAC_AMR=0.0146;ExAC_EAS=0;ExAC_FIN=0.0018;ExAC_NFE=0.0093;ExAC_OTH=0.0195;ExAC_SAS=0.0033;1000g2014oct_all=0.0611022;snp138=rs112917612;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-1.1293;dpsi_zscore=-1.544;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:196,199:395:99:4692,0,4690:56:99:0.504 0/1:143,165:309:99:3894,0,3589:54:99:0.536 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 984888 rs112331531 A G 4447.38 PASS BaseQRankSum=-2.32;Dels=0;FS=0.801;HRun=0;HaplotypeScore=26.4873;MQ=56;MQ0=0;MQRankSum=2.43;QD=12.18;ReadPosRankSum=-0.892;SB=-2846.81;TI=NM_198576;GI=AGRN;FC=Silent;DP=643;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.25;Kaviar_AF=0.0297372;Kaviar_AC=774;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0734824;snp138=rs112331531;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3669;dpsi_zscore=-0.944;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:177,188:365:99:4447,0,4464:56:99:0.515 0/1:134,143:278:99:3459,0,3398:55:99:0.516 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 985239 rs115192323 C T 3093.05 PASS BaseQRankSum=4.566;Dels=0;FS=5.003;HRun=0;HaplotypeScore=14.8473;MQ=56;MQ0=0;MQRankSum=0.624;QD=11.85;ReadPosRankSum=-0.394;SB=-2116.95;TI=NM_198576;GI=AGRN;FC=Silent;DP=454;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.15;Kaviar_AF=0.0132793;Kaviar_AC=2053;Kaviar_AN=154602;ExAC_ALL=0.0136;ExAC_AFR=0.1468;ExAC_AMR=0.0099;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0014;ExAC_OTH=0.0096;ExAC_SAS=0.0027;1000g2014oct_all=0.0415335;snp138=rs115192323;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4121;dpsi_zscore=1.036;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:125,135:261:99:3123,0,2995:56:99:0.519 0/1:104,89:193:99:2218,0,2578:53:99:0.461 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 985266 rs2275813 C T 6793.34 PASS BaseQRankSum=2.429;Dels=0;FS=0;HRun=0;HaplotypeScore=9.7081;MQ=55;MQ0=0;MQRankSum=0.957;QD=27.73;ReadPosRankSum=-0.155;SB=-4552.47;TI=NM_198576;GI=AGRN;FC=Silent;DP=1996;AN=18;AC=12;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000250964.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.82;Kaviar_AF=0.52522;Kaviar_AC=81200;Kaviar_AN=154602;ExAC_ALL=0.5436;ExAC_AFR=0.1637;ExAC_AMR=0.7253;ExAC_EAS=0.8084;ExAC_FIN=0.5250;ExAC_NFE=0.5312;ExAC_OTH=0.5426;ExAC_SAS=0.5470;1000g2014oct_all=0.495208;snp138=rs2275813;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-1.2813;dpsi_zscore=-1.619;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:2,243:245:99:6793,497,0:55:99:0.992 1/1:0,214:214:99:5907,427,0:54:99:1 0/1:99,77:176:99:1929,0,2504:54:99:0.438 0/1:148,112:260:99:2660,0,3526:56:99:0.431 0/1:154,115:269:99:2732,0,3609:54:99:0.428 0/1:115,102:217:99:2530,0,2826:56:99:0.47 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:105,101:206:99:2490,0,2482:53:99:0.49 1/1:2,204:206:99:5114,319,0:50:99:0.99 0/1:108,95:203:99:2219,0,2814:54:99:0.468
chr1 985377 rs113020870 C T 1089.65 PASS BaseQRankSum=1.467;Dels=0;FS=2.587;HRun=0;HaplotypeScore=18.7664;MQ=53;MQ0=0;MQRankSum=-0.668;QD=9.82;ReadPosRankSum=1.369;SB=-590.95;TI=NM_198576;GI=AGRN;FC=Synonymous_C1613C;EXON;DP=111;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon27:c.C4839T:p.C1613C;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon27:c.C4839T:p.C1613C;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon27:c.C4839T:p.C1613C;cytoBand=1p36.33;CLINSIG=Likely_benign;CLNDBN=not_specified;CLNACC=RCV000254107.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.0044;Kaviar_AF=0.0023609;Kaviar_AC=365;Kaviar_AN=154602;ExAC_ALL=0.0025;ExAC_AFR=0.0015;ExAC_AMR=0.0008;ExAC_EAS=0;ExAC_FIN=0.0044;ExAC_NFE=0.0036;ExAC_OTH=0.0042;ExAC_SAS=0.0005;1000g2014oct_all=0.00119808;snp138=rs113020870;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.5479;dpsi_zscore=-1.138;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:68,42:111:99:1120,0,1880:53:99:0.382
chr1 985443 rs374942603 AG A 2712.49 R8 BaseQRankSum=-0.739;FS=6.617;HRun=15;HaplotypeScore=442.275;MQ=50;MQ0=0;MQRankSum=0.818;QD=13.41;ReadPosRankSum=-0.719;SB=-268.69;TI=NM_198576;GI=AGRN;FC=Noncoding;DP=579;AN=14;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.0017;Kaviar_AF=0.0045342;Kaviar_AC=701;Kaviar_AN=154602;ExAC_ALL=0.3903;ExAC_AFR=0.7466;ExAC_AMR=0.3235;ExAC_EAS=0.6513;ExAC_FIN=0.2027;ExAC_NFE=0.3004;ExAC_OTH=0.4726;ExAC_SAS=0.4223;1000g2014oct_all=.;snp138=rs374942603;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:28,31:60:67.47:844,0,67:50:67:0.525 0/1:35,30:67:99:814,0,172:51:99:0.462 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:39,13,0:103:99:1935,429,251:47:99:0.25 1/1:17,78:98:99:2410,207,0:49:99:0.821 1/1:22,86:111:99:2755,261,0:52:99:0.796 0/1:34,33:69:99:894,0,169:51:99:0.493 ./.:.:.:.:.:.:.:. 0/1:46,23:71:99:652,0,331:51:99:0.333
chr1 985443 rs374942603 AGG A 2712.49 R8 BaseQRankSum=-0.739;FS=6.617;HRun=15;HaplotypeScore=442.275;MQ=50;MQ0=0;MQRankSum=0.818;QD=13.41;ReadPosRankSum=-0.719;SB=-268.69;TI=NM_198576;GI=AGRN;FC=Noncoding;DP=579;AN=14;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.0017;Kaviar_AF=0.001009;Kaviar_AC=156;Kaviar_AN=154602;ExAC_ALL=0.0009;ExAC_AFR=0.0169;ExAC_AMR=0.0037;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0002;ExAC_OTH=0;ExAC_SAS=0.0001;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/0:28,31:60:67.47:844,.,.:50:67:0.525 0/0:35,30:67:99:814,.,.:51:99:0.462 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/0:39,13,0:103:99:1935,716,641:47:99:0.25 0/0:17,78:98:99:2410,.,.:49:99:0.821 0/0:22,86:111:99:2755,.,.:52:99:0.796 0/0:34,33:69:99:894,.,.:51:99:0.493 ./.:.:.:.:.:.:.:. 0/0:46,23:71:99:652,.,.:51:99:0.333
chr1 985446 rs2275812 G T 1698.09 PASS BaseQRankSum=-0.921;Dels=0;FS=7.194;HRun=0;HaplotypeScore=24.3023;MQ=53;MQ0=0;MQRankSum=2.233;QD=25.73;ReadPosRankSum=-1.132;SB=-451.01;TI=NM_198576;GI=AGRN;FC=Silent;DP=633;AN=18;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000250684.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.51;Kaviar_AF=0.0005886;Kaviar_AC=91;Kaviar_AN=154602;ExAC_ALL=0.4567;ExAC_AFR=0.1015;ExAC_AMR=0.4140;ExAC_EAS=0.1155;ExAC_FIN=0.5109;ExAC_NFE=0.5014;ExAC_OTH=0.4068;ExAC_SAS=0.4851;1000g2014oct_all=0.335463;snp138=rs2275812;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.6126;dpsi_zscore=-1.197;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:7,58:66:72.17:1728,0,72:53:72:0.892 0/1:42,18:60:99:467,0,1218:50:99:0.3 0/1:41,25:67:99:567,0,1172:51:99:0.379 0/1:55,44:99:99:1158,0,1558:50:99:0.444 0/1:45,39:84:99:990,0,1238:49:99:0.464 0/1:47,38:85:99:964,0,1260:51:99:0.447 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:46,23:69:99:496,0,1296:51:99:0.333 0/1:6,25:31:77.41:601,0,77:44:77:0.806 0/1:36,35:72:99:792,0,1013:51:99:0.493
chr1 985449 rs2799067 G A 2096.73 SB;LowGQ;LowVariantFreq BaseQRankSum=1.619;Dels=0;FS=13.195;HRun=0;HaplotypeScore=21.7023;MQ=53;MQ0=0;MQRankSum=2.187;QD=21.65;ReadPosRankSum=-1.788;SB=-288.14;TI=NM_198576;GI=AGRN;FC=Silent;DP=739;AN=20;AC=10;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000242423.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.62;Kaviar_AF=0.0002587;Kaviar_AC=40;Kaviar_AN=154602;ExAC_ALL=0.5301;ExAC_AFR=0.2016;ExAC_AMR=0.4845;ExAC_EAS=0.25;ExAC_FIN=0.5385;ExAC_NFE=0.5704;ExAC_OTH=0.4508;ExAC_SAS=0.5568;1000g2014oct_all=0.525559;snp138=rs2799067;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.6018;dpsi_zscore=-1.187;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:13,56:71:99:1567,0,118:53:99:0.812 0/1:37,19:56:99:407,0,993:50:99:0.339 0/1:44,26:70:99:628,0,1212:51:99:0.371 0/1:16,80:96:72.2:2127,0,72:50:72:0.833 0/1:17,61:82:28.28:1690,0,28:49:28:0.782 0/1:21,67:88:99:1848,0,199:51:99:0.761 0/1:87,10:100:56.62:57,0,2652:45:27:0.103 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:44,24:69:99:462,0,1265:51:99:0.353 0/1:4,27:32:11.63:647,0,12:45:12:0.871 0/1:38,35:75:99:660,0,989:51:99:0.479
chr1 985450 rs397834473 G A 2592.89 PASS BaseQRankSum=-2.299;Dels=0;FS=5.704;HRun=0;HaplotypeScore=32.7875;MQ=50;MQ0=0;MQRankSum=-1.226;QD=13.25;ReadPosRankSum=1.114;SB=-247.8;TI=NM_198576;GI=AGRN;FC=Silent;DP=588;AN=14;AC=7;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.76;Kaviar_AF=0.0116557;Kaviar_AC=1802;Kaviar_AN=154602;ExAC_ALL=0.4975;ExAC_AFR=0.7640;ExAC_AMR=0.4868;ExAC_EAS=0.7163;ExAC_FIN=0.4318;ExAC_NFE=0.4426;ExAC_OTH=0.5735;ExAC_SAS=0.4862;1000g2014oct_all=0.446486;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.5706;dpsi_zscore=-1.159;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:26,31:58:99:798,0,679:50:99:0.544 0/1:37,34:71:99:898,0,1034:51:99:0.479 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:58,41:100:99:1091,0,1484:45:99:0.414 0/1:15,82:100:99:2053,0,177:49:99:0.845 0/1:17,95:114:99:2623,0,171:52:99:0.848 0/1:33,33:68:99:853,0,873:51:99:0.5 ./.:.:.:.:.:.:.:. 0/1:48,29:77:99:771,0,1352:51:99:0.377
chr1 985460 rs2275811 T C 1457.69 PASS BaseQRankSum=2.049;Dels=0;FS=1.898;HRun=0;HaplotypeScore=34.7141;MQ=47;MQ0=0;MQRankSum=2.009;QD=15.34;ReadPosRankSum=1.286;SB=-567.26;TI=NM_198576;GI=AGRN;FC=Silent;DP=269;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.58;Kaviar_AF=0.0784013;Kaviar_AC=12121;Kaviar_AN=154602;ExAC_ALL=0.1578;ExAC_AFR=0.5809;ExAC_AMR=0.3539;ExAC_EAS=0.5458;ExAC_FIN=0.1074;ExAC_NFE=0.0656;ExAC_OTH=0.1218;ExAC_SAS=0.1034;1000g2014oct_all=0.290535;snp138=rs2275811;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.9647;dpsi_zscore=-1.450;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:36,55:95:99:1488,0,827:47:99:0.604 0/1:57,41:99:99:1092,0,1630:50:99:0.418 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:43,29:75:99:831,0,1241:52:99:0.403
chr1 985797 rs142286944 A G 3181.55 PASS BaseQRankSum=1.697;Dels=0;FS=2.148;HRun=0;HaplotypeScore=13.9557;MQ=57;MQ0=0;MQRankSum=2.327;QD=12.48;ReadPosRankSum=1.178;SB=-1602.39;TI=NM_198576;GI=AGRN;FC=Silent;DP=255;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000247197.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.028;Kaviar_AF=0.0191265;Kaviar_AC=2957;Kaviar_AN=154602;ExAC_ALL=0.0192;ExAC_AFR=0.0052;ExAC_AMR=0.0083;ExAC_EAS=0;ExAC_FIN=0.0085;ExAC_NFE=0.0273;ExAC_OTH=0.0174;ExAC_SAS=0.0179;1000g2014oct_all=0.0107827;snp138=rs142286944;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=1.2097;dpsi_zscore=1.640;dbscSNV_ADA_SCORE=0;dbscSNV_RF_SCORE=0.004;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:137,118:255:99:3212,0,3483:57:99:0.463 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 985900 rs17160776 C T 2562.51 PASS BaseQRankSum=-0.264;Dels=0;FS=0;HRun=2;HaplotypeScore=12.6891;MQ=57;MQ0=0;MQRankSum=-0.445;QD=11.19;ReadPosRankSum=-0.393;SB=-1573.57;TI=NM_198576;GI=AGRN;FC=Synonymous_F1690F;EXON;DP=405;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon29:c.C5070T:p.F1690F;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon29:c.C5070T:p.F1690F;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon29:c.C5070T:p.F1690F;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116275.2;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.15;Kaviar_AF=0.0168368;Kaviar_AC=2603;Kaviar_AN=154602;ExAC_ALL=0.0171;ExAC_AFR=0.1322;ExAC_AMR=0.0107;ExAC_EAS=0;ExAC_FIN=0.0011;ExAC_NFE=0.0081;ExAC_OTH=0.0171;ExAC_SAS=0.0029;1000g2014oct_all=0.0447284;snp138=rs17160776;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.6183;dpsi_zscore=-1.202;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:120,108:229:99:2593,0,2998:57:99:0.474 0/1:85,90:176:99:2257,0,2231:55:99:0.514 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 985999 rs111726760 G T 2060.77 PASS BaseQRankSum=-0.147;Dels=0;FS=2.894;HRun=0;HaplotypeScore=7.2391;MQ=58;MQ0=0;MQRankSum=-0.829;QD=12.77;ReadPosRankSum=-0.378;SB=-969;TI=NM_198576;GI=AGRN;FC=Silent;DP=298;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.18;Kaviar_AF=0.015265;Kaviar_AC=2360;Kaviar_AN=154602;ExAC_ALL=0.0153;ExAC_AFR=0.1733;ExAC_AMR=0.0105;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0014;ExAC_OTH=0.0098;ExAC_SAS=0.0003;1000g2014oct_all=0.0503195;snp138=rs111726760;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4834;dpsi_zscore=1.116;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:82,74:156:99:2022,0,2183:58:99:0.474 0/1:64,77:142:99:2091,0,1659:56:99:0.546 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 986628 rs34708466 C T 2608.48 PASS BaseQRankSum=-0.059;Dels=0;FS=1.069;HRun=0;HaplotypeScore=8.9187;MQ=56;MQ0=0;MQRankSum=3.179;QD=12.3;ReadPosRankSum=0.127;SB=-1580.6;TI=NM_198576;GI=AGRN;FC=Silent;DP=212;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=unknown;AAChange.refGene=UNKNOWN;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.011;Kaviar_AF=0.0022574;Kaviar_AC=349;Kaviar_AN=154602;ExAC_ALL=0.0059;ExAC_AFR=0.0013;ExAC_AMR=0.0034;ExAC_EAS=0;ExAC_FIN=0.0095;ExAC_NFE=0.0113;ExAC_OTH=0;ExAC_SAS=0.0006;1000g2014oct_all=0.000599042;snp138=rs34708466;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.8154;dpsi_zscore=1.398;dbscSNV_ADA_SCORE=0;dbscSNV_RF_SCORE=0;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:102,110:212:99:2638,0,2558:56:99:0.519 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 986737 rs17160781 T C 2236.42 PASS BaseQRankSum=0.388;Dels=0;FS=2.104;HRun=0;HaplotypeScore=14.8131;MQ=56;MQ0=0;MQRankSum=1.815;QD=14.15;ReadPosRankSum=-0.515;SB=-1209.78;TI=NM_198576;GI=AGRN;FC=Synonymous_G1786G;EXON;DP=295;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon31:c.T5358C:p.G1786G;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon31:c.T5358C:p.G1786G;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon31:c.T5358C:p.G1786G;cytoBand=1p36.33;CLINSIG=other;CLNDBN=not_specified;CLNACC=RCV000116277.3;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.3;Kaviar_AF=0.0205948;Kaviar_AC=3184;Kaviar_AN=154602;ExAC_ALL=0.0500;ExAC_AFR=0.2964;ExAC_AMR=0.0503;ExAC_EAS=0.0006;ExAC_FIN=0.0057;ExAC_NFE=0.0161;ExAC_OTH=0.0213;ExAC_SAS=0.0039;1000g2014oct_all=0.0790735;snp138=rs17160781;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2354;dpsi_zscore=0.788;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:67,88:158:99:2266,0,1643:56:99:0.568 0/1:66,70:137:99:1735,0,1649:56:99:0.515 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 987200 rs9803031 C T 10869.7 PASS BaseQRankSum=1.723;Dels=0;FS=0;HRun=0;HaplotypeScore=28.7051;MQ=55;MQ0=0;MQRankSum=1.58;QD=27.89;ReadPosRankSum=0.128;SB=-6651.25;TI=NM_198576;GI=AGRN;FC=Silent;DP=3521;AN=22;AC=19;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116279.2;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=1.;Kaviar_AF=0.857764;Kaviar_AC=132612;Kaviar_AN=154602;ExAC_ALL=0.8757;ExAC_AFR=0.4520;ExAC_AMR=0.9366;ExAC_EAS=0.9968;ExAC_FIN=0.9443;ExAC_NFE=0.9055;ExAC_OTH=0.9101;ExAC_SAS=0.8844;1000g2014oct_all=0.788738;snp138=rs9803031;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.5381;dpsi_zscore=1.170;dbscSNV_ADA_SCORE=0.0002;dbscSNV_RF_SCORE=0.016;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,364:367:99:10234,740,0:55:99:0.997 1/1:0,357:358:99:9280,653,0:54:99:1 1/1:0,251:251:99:6978,500,0:55:99:1 1/1:0,342:342:99:9541,683,0:56:99:1 0/1:197,207:404:99:4744,0,4631:54:99:0.512 0/1:191,156:347:99:3645,0,4666:54:99:0.45 ./.:.:.:.:.:.:.:. 0/1:136,107:243:99:2630,0,3392:56:99:0.44 1/1:0,377:377:99:10870,792,0:57:99:1 1/1:0,300:301:99:7938,563,0:54:99:1 1/1:0,283:284:99:7135,500,0:50:99:1 1/1:0,246:247:99:6938,503,0:55:99:1
chr1 987253 rs113261977 C T 2617.48 PASS BaseQRankSum=-1.106;Dels=0;FS=0;HRun=0;HaplotypeScore=7.1509;MQ=54;MQ0=0;MQRankSum=2.057;QD=14.23;ReadPosRankSum=1.477;SB=-1599.53;TI=NM_198576;GI=AGRN;FC=Silent;DP=184;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.032;Kaviar_AF=0.0037774;Kaviar_AC=584;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.00838658;snp138=rs113261977;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0507;dpsi_zscore=0.301;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:73,111:184:99:2647,0,1726:54:99:0.603 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 990280 rs4275402 C T 6768.95 PASS BaseQRankSum=1.645;Dels=0;FS=0;HRun=0;HaplotypeScore=7.9053;MQ=58;MQ0=0;MQRankSum=-1.207;QD=30.39;ReadPosRankSum=-0.49;SB=-3199.2;TI=NM_198576;GI=AGRN;FC=Synonymous_D2019D;EXON;DP=1614;AN=18;AC=17;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGRN;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGRN:NM_198576:exon36:c.C6057T:p.D2019D;Func.knownGene=exonic;Gene.knownGene=AGRN;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGRN:uc001ack.2:exon36:c.C6057T:p.D2019D;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30551.1:CCDS30551.1:exon36:c.C6057T:p.D2019D;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000116281.2;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.82;Kaviar_AF=0.466301;Kaviar_AC=72091;Kaviar_AN=154602;ExAC_ALL=0.6376;ExAC_AFR=0.3518;ExAC_AMR=0.7745;ExAC_EAS=0.8173;ExAC_FIN=0.7258;ExAC_NFE=0.6998;ExAC_OTH=0.5978;ExAC_SAS=0.6154;1000g2014oct_all=0.585264;snp138=rs4275402;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,197:198:99:6016,448,0:58:99:0.995 1/1:1,170:171:99:4896,358,0:55:99:0.994 0/1:78,78:156:99:1972,0,1904:57:99:0.5 1/1:0,229:229:99:6769,500,0:57:99:1 1/1:0,213:214:99:6388,472,0:57:99:1 1/1:1,175:177:99:5378,403,0:56:99:0.994 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:1,151:152:99:4485,325,0:57:99:0.993 1/1:1,146:147:99:3715,233,0:52:99:0.993 1/1:1,169:170:99:4956,334,0:56:99:0.994
chr1 990380 rs3121561 C T 11372.2 PASS BaseQRankSum=-0.421;Dels=0;FS=0.502;HRun=0;HaplotypeScore=19.2762;MQ=55;MQ0=0;MQRankSum=-0.584;QD=10.9;ReadPosRankSum=-0.198;SB=-1526.21;TI=NM_198576;GI=AGRN;FC=Silent;EXON;DP=1168;AN=8;AC=7;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGRN;GeneDetail.refGene=NM_001305275:c.*19C>T\x3bNM_198576:c.*19C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGRN;GeneDetail.knownGene=uc001ack.2:c.*19C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000252490.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.56;Kaviar_AF=0.136027;Kaviar_AC=21030;Kaviar_AN=154602;ExAC_ALL=0.3334;ExAC_AFR=0.5610;ExAC_AMR=0.2791;ExAC_EAS=0.2212;ExAC_FIN=0.4643;ExAC_NFE=0.3195;ExAC_OTH=0.3765;ExAC_SAS=0.3068;1000g2014oct_all=0.34345;snp138=rs3121561;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:119,99:219:99:2417,0,2999:55:99:0.454 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,401:403:99:11372,828,0:56:99:1 1/1:2,210:212:99:6237,426,0:56:99:0.991 1/1:1,333:334:99:9732,713,0:57:99:0.997 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 990417 rs2465136 T C 12474.5 PASS BaseQRankSum=-0.682;Dels=0;FS=2.078;HRun=0;HaplotypeScore=17.3018;MQ=55;MQ0=0;MQRankSum=-0.027;QD=11.27;ReadPosRankSum=-2.03;SB=-1849.65;TI=NM_198576;GI=AGRN;FC=Silent;EXON;DP=1355;AN=8;AC=7;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGRN;GeneDetail.refGene=NM_001305275:c.*56T>C\x3bNM_198576:c.*56T>C;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGRN;GeneDetail.knownGene=uc001ack.2:c.*56T>C;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.65;Kaviar_AF=0.0103734;Kaviar_AC=270;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.383986;snp138=rs2465136;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:140,123:263:99:2993,0,3397:55:99:0.468 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:2,452:454:99:12474,861,0:56:99:0.996 1/1:2,248:250:99:7359,472,0:57:99:0.992 1/1:1,387:388:99:11175,782,0:56:99:0.997 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 990517 rs2710872 C T 10782.9 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=20.563;MQ=57;MQ0=0;QD=28.08;SB=-7209.97;TI=NM_198576;GI=AGRN;FC=Silent;EXON;BaseQRankSum=1.851;MQRankSum=1.083;ReadPosRankSum=-0.32;DP=3769;AN=24;AC=22;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGRN;GeneDetail.refGene=NM_001305275:c.*156C>T\x3bNM_198576:c.*156C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGRN;GeneDetail.knownGene=uc001ack.2:c.*156C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.150218;Kaviar_AC=23224;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.917931;snp138=rs2710872;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,384:384:99:10783,783,0:57:99:1 1/1:0,335:335:99:9158,656,0:56:99:1 1/1:0,221:221:99:6454,467,0:57:99:1 1/1:0,335:336:99:9666,695,0:57:99:1 0/1:189,170:360:99:3937,0,4419:56:99:0.474 0/1:168,157:326:99:3715,0,4034:55:99:0.483 1/1:1,381:383:99:10657,770,0:57:99:0.997 1/1:2,243:245:99:7412,548,0:56:99:0.992 1/1:1,369:371:99:10676,746,0:57:99:0.997 1/1:0,296:297:99:8243,590,0:57:99:1 1/1:0,250:251:99:6324,445,0:53:99:1 1/1:0,259:260:99:7407,536,0:55:99:1
chr1 990533 rs4308920 G A 4292.04 PASS BaseQRankSum=0.831;Dels=0;FS=5.397;HRun=1;HaplotypeScore=13.9902;MQ=57;MQ0=0;MQRankSum=2.675;QD=11.63;ReadPosRankSum=2.149;SB=-2362.29;TI=NM_198576;GI=AGRN;FC=Silent;EXON;DP=607;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGRN;GeneDetail.refGene=NM_001305275:c.*172G>A\x3bNM_198576:c.*172G>A;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGRN;GeneDetail.knownGene=uc001ack.2:c.*172G>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.43;Kaviar_AF=0.0415706;Kaviar_AC=1082;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.121805;snp138=rs4308920;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:190,179:369:99:4292,0,4655:57:99:0.485 0/1:117,121:238:99:3022,0,2880:56:99:0.508 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 990687 rs4308921 G A 3663.05 PASS BaseQRankSum=2.173;Dels=0;FS=2.054;HRun=0;HaplotypeScore=8.9369;MQ=58;MQ0=0;MQRankSum=1.034;QD=13.52;ReadPosRankSum=-0.716;SB=-2188.83;TI=NM_198576;GI=AGRN;FC=Silent;EXON;DP=507;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGRN;GeneDetail.refGene=NM_001305275:c.*326G>A\x3bNM_198576:c.*326G>A;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGRN;GeneDetail.knownGene=uc001ack.2:c.*326G>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.16;Kaviar_AF=0.0165207;Kaviar_AC=430;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0463259;snp138=rs4308921;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:124,147:271:99:3663,0,3338:58:99:0.542 0/1:127,109:236:99:2869,0,3200:55:99:0.462 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 990773 rs2799072 C T 9105.91 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=9.0375;MQ=57;MQ0=0;QD=28.72;SB=-4679.63;TI=NM_198576;GI=AGRN;FC=Silent;EXON;BaseQRankSum=-0.733;MQRankSum=1.7;ReadPosRankSum=0.721;DP=3168;AN=24;AC=22;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGRN;GeneDetail.refGene=NM_001305275:c.*412C>T\x3bNM_198576:c.*412C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGRN;GeneDetail.knownGene=uc001ack.2:c.*412C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.99;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.846046;snp138=rs2799072;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,267:267:99:7668,557,0:57:99:1 1/1:0,232:232:99:6142,436,0:54:99:1 1/1:0,217:217:99:6236,451,0:56:99:1 1/1:0,288:288:99:8412,611,0:58:99:1 0/1:130,146:277:99:3319,0,3205:56:99:0.529 0/1:129,142:271:99:3445,0,3017:57:99:0.524 1/1:0,300:300:99:8579,626,0:57:99:1 1/1:0,236:238:99:6800,503,0:56:99:1 1/1:0,317:317:99:9106,659,0:57:99:1 1/1:0,260:260:99:7191,518,0:55:99:1 1/1:1,283:285:99:7169,503,0:49:99:0.996 1/1:0,215:216:99:5983,433,0:55:99:1
chr1 990839 rs13129 C T 1905.65 PASS BaseQRankSum=1.148;Dels=0;FS=1.213;HRun=2;HaplotypeScore=8.1474;MQ=55;MQ0=0;MQRankSum=0.956;QD=11.34;ReadPosRankSum=1.238;SB=-1273.54;TI=NM_198576;GI=AGRN;FC=Silent;EXON;DP=168;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGRN;GeneDetail.refGene=NM_001305275:c.*478C>T\x3bNM_198576:c.*478C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGRN;GeneDetail.knownGene=uc001ack.2:c.*478C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.12;Kaviar_AF=0.0022639;Kaviar_AC=350;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.038738;snp138=rs13129;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:86,81:168:99:1936,0,2247:55:99:0.485 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 990882 rs4587516 C T 3324.81 PASS BaseQRankSum=1.012;Dels=0;FS=3.475;HRun=0;HaplotypeScore=10.978;MQ=57;MQ0=0;MQRankSum=1.145;QD=12.94;ReadPosRankSum=0.797;SB=-1734.2;TI=NM_198576;GI=AGRN;FC=Silent;EXON;DP=433;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGRN;GeneDetail.refGene=NM_001305275:c.*521C>T\x3bNM_198576:c.*521C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGRN;GeneDetail.knownGene=uc001ack.2:c.*521C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.17;Kaviar_AF=0.0029883;Kaviar_AC=462;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0489217;snp138=rs4587516;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:134,123:257:99:3325,0,3507:57:99:0.479 0/1:92,83:176:99:2324,0,2632:57:99:0.474 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 990984 rs8014 G A 7208.24 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=9.3087;MQ=56;MQ0=0;QD=29.92;SB=-3881.2;TI=NM_198576;GI=AGRN;FC=Silent;EXON;BaseQRankSum=1.661;MQRankSum=1.679;ReadPosRankSum=0.495;DP=2207;AN=24;AC=22;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGRN;GeneDetail.refGene=NM_001305275:c.*623G>A\x3bNM_198576:c.*623G>A;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGRN;GeneDetail.knownGene=uc001ack.2:c.*623G>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30551.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.33;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.892039;Kaviar_AC=23218;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.922324;snp138=rs8014;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,206:207:99:6193,454,0:56:99:1 1/1:0,173:173:99:4763,340,0:54:99:1 1/1:0,153:153:99:4556,331,0:56:99:1 1/1:1,195:196:99:6066,445,0:57:99:0.995 0/1:90,96:186:99:2162,0,2421:56:99:0.516 0/1:101,101:202:99:2620,0,2671:56:99:0.5 1/1:0,241:243:99:7208,527,0:56:99:1 1/1:0,172:173:99:5166,376,0:57:99:1 1/1:0,213:213:99:6336,461,0:58:99:1 1/1:1,168:169:99:4856,352,0:55:99:0.994 1/1:0,150:151:99:3781,265,0:54:99:1 1/1:1,140:141:99:4202,307,0:56:99:0.993
chr1 22149183 rs1049644 G C 3060.78 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=5.3945;MQ=55;MQ0=0;QD=31.01;SB=-1697.78;TI=NM_001013693,NM_005529;GI=LDLRAD2,HSPG2;FC=Silent,Silent;EXON;BaseQRankSum=0.19;MQRankSum=-0.19;ReadPosRankSum=1.079;DP=583;AN=12;AC=8;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=HSPG2\x3bLDLRAD2;GeneDetail.refGene=NM_005529:c.*626C>G\x3bNM_001291860:c.*626C>G\x3bNM_001013693:c.*475G>C;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=HSPG2\x3bLDLRAD2;GeneDetail.knownGene=uc001bfi.3:c.*626C>G\x3buc001bfj.3:c.*626C>G\x3buc009vqd.3:c.*626C>G\x3buc001bfg.1:c.*475G>C;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30624.1\x3bCCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000297630.1|RCV000354787.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.43;Kaviar_AF=0.0446695;Kaviar_AC=6906;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.319888;snp138=rs1049644;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 1/1:0,92:93:99:2917,223,0:55:99:1 1/1:2,95:98:99:3094,200,0:55:99:0.979 ./.:.:.:.:.:.:.:. 0/1:45,59:104:99:1647,0,1281:53:99:0.567 0/1:51,63:116:99:1564,0,1467:51:99:0.553 ./.:.:.:.:.:.:.:. 0/1:39,64:104:99:1830,0,993:55:99:0.621 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:28,40:68:99:999,0,719:50:99:0.588 ./.:.:.:.:.:.:.:.
chr1 22149418 rs146732517 C T 3048.68 PASS BaseQRankSum=1.85;Dels=0;FS=0;HRun=0;HaplotypeScore=3.7581;MQ=52;MQ0=0;MQRankSum=1.074;QD=10.66;ReadPosRankSum=-0.506;SB=-2262.97;TI=NM_001013693,NM_005529;GI=LDLRAD2,HSPG2;FC=Silent,Silent;EXON;DP=286;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=HSPG2\x3bLDLRAD2;GeneDetail.refGene=NM_005529:c.*391G>A\x3bNM_001291860:c.*391G>A\x3bNM_001013693:c.*710C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=HSPG2\x3bLDLRAD2;GeneDetail.knownGene=uc001bfi.3:c.*391G>A\x3buc001bfj.3:c.*391G>A\x3buc009vqd.3:c.*391G>A\x3buc001bfg.1:c.*710C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS30624.1\x3bCCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.022;Kaviar_AF=0.0013831;Kaviar_AC=36;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.00439297;snp138=rs146732517;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:147,139:286:99:3079,0,3313:52:99:0.486 ./.:.:.:.:.:.:.:.
chr1 22149935 rs897467 T C 5058.3 PASS BaseQRankSum=0.192;Dels=0;FS=4.058;HRun=2;HaplotypeScore=9.985;MQ=56;MQ0=0;MQRankSum=1.131;QD=31.14;ReadPosRankSum=-1.034;SB=-2064.94;TI=NM_001013693,NM_005529;GI=LDLRAD2,HSPG2;FC=Silent,Synonymous_S4350S;EXON;DP=1932;AN=24;AC=18;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon97:c.A13053G:p.S4351S\x3bHSPG2:NM_005529:exon97:c.A13050G:p.S4350S;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfi.3:exon11:c.A1101G:p.S367S\x3bHSPG2:uc001bfj.3:exon97:c.A13050G:p.S4350S\x3bHSPG2:uc009vqd.3:exon97:c.A13053G:p.S4351S;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon97:c.A13050G:p.S4350S;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000302221.1|RCV000359351.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.85;Kaviar_AF=0.760333;Kaviar_AC=117549;Kaviar_AN=154602;ExAC_ALL=0.8204;ExAC_AFR=0.7297;ExAC_AMR=0.7689;ExAC_EAS=0.8206;ExAC_FIN=0.8281;ExAC_NFE=0.8389;ExAC_OTH=0.8082;ExAC_SAS=0.8304;1000g2014oct_all=0.780351;snp138=rs897467;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,143:145:99:4516,303,0:56:99:0.993 1/1:0,181:181:99:5058,364,0:55:99:1 1/1:0,117:118:99:3531,262,0:56:99:1 1/1:0,151:152:99:4637,346,0:57:99:1 0/1:111,87:199:99:2126,0,2842:56:99:0.439 0/1:82,75:158:99:1902,0,2025:55:99:0.478 0/1:138,91:230:99:2239,0,3692:57:99:0.397 1/1:0,155:155:99:4936,370,0:57:99:1 0/1:98,120:220:99:3159,0,2621:56:99:0.55 1/1:0,138:139:99:4106,298,0:56:99:1 0/1:62,42:104:99:925,0,1496:51:99:0.404 0/1:77,53:131:99:1370,0,2046:54:99:0.408
chr1 22150118 rs1138469 C T 9245.6 PASS BaseQRankSum=0.319;Dels=0;FS=0;HRun=0;HaplotypeScore=12.9874;MQ=54;MQ0=0;MQRankSum=1.016;QD=26.27;ReadPosRankSum=-0.418;SB=-6398.77;TI=NM_001013693,NM_005529;GI=LDLRAD2,HSPG2;FC=Silent,Missense_V4332I;EXON;DP=626;AN=4;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon96:c.G12997A:p.V4333I\x3bHSPG2:NM_005529:exon96:c.G12994A:p.V4332I;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfi.3:exon10:c.G1045A:p.V349I\x3bHSPG2:uc001bfj.3:exon96:c.G12994A:p.V4332I\x3bHSPG2:uc009vqd.3:exon96:c.G12997A:p.V4333I;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon96:c.G12994A:p.V4332I;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000274764.1|RCV000318163.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.1;Kaviar_AF=0.0566357;Kaviar_AC=8756;Kaviar_AN=154602;ExAC_ALL=0.0585;ExAC_AFR=0.0298;ExAC_AMR=0.0237;ExAC_EAS=0.0002;ExAC_FIN=0.0567;ExAC_NFE=0.0655;ExAC_OTH=0.0689;ExAC_SAS=0.1037;1000g2014oct_all=0.0453275;snp138=rs1138469;SIFT_score=1.0;SIFT_converted_rankscore=0.010;SIFT_pred=T;Polyphen2_HDIV_score=0.001;Polyphen2_HDIV_rankscore=0.102;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.002;Polyphen2_HVAR_rankscore=0.063;Polyphen2_HVAR_pred=B;LRT_score=0.174;LRT_converted_rankscore=0.173;LRT_pred=N;MutationTaster_score=0.932;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=N;MutationAssessor_score=-0.31;MutationAssessor_score_rankscore=0.036;MutationAssessor_pred=N;FATHMM_score=-0.88;FATHMM_converted_rankscore=0.747;FATHMM_pred=T;PROVEAN_score=0.0;PROVEAN_converted_rankscore=0.070;PROVEAN_pred=N;VEST3_score=0.02;VEST3_rankscore=0.004;MetaSVM_score=-1.007;MetaSVM_rankscore=0.277;MetaSVM_pred=T;MetaLR_score=0.018;MetaLR_rankscore=0.073;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=-0.335;CADD_raw_rankscore=0.066;CADD_phred=0.552;DANN_score=0.860;DANN_rankscore=0.157;fathmm-MKL_coding_score=0.028;fathmm-MKL_coding_rankscore=0.075;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.968;Eigen-PC-raw=-1.951;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=-8.58;GERP++_RS_rankscore=0.008;phyloP100way_vertebrate=-2.578;phyloP100way_vertebrate_rankscore=0.010;phyloP20way_mammalian=-1.634;phyloP20way_mammalian_rankscore=0.008;phastCons100way_vertebrate=0.000;phastCons100way_vertebrate_rankscore=0.063;phastCons20way_mammalian=0.672;phastCons20way_mammalian_rankscore=0.303;SiPhy_29way_logOdds=15.012;SiPhy_29way_logOdds_rankscore=0.711;Interpro_domain=Concanavalin_A-like_lectin/glucanase_domain|Laminin_G_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1318;dpsi_zscore=-0.538;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 1/1:4,348:352:99:9246,579,0:54:99:0.989 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:135,139:274:99:3379,0,3464:56:99:0.507 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22150120 rs3736360 C T 7340.73 PASS BaseQRankSum=1.705;Dels=0;FS=0;HRun=1;HaplotypeScore=1.7608;MQ=55;MQ0=0;MQRankSum=0.903;QD=28.79;ReadPosRankSum=-0.808;SB=-4579.43;TI=NM_001013693,NM_005529;GI=LDLRAD2,HSPG2;FC=Silent,Missense_S4331N;EXON;DP=985;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon96:c.G12995A:p.S4332N\x3bHSPG2:NM_005529:exon96:c.G12992A:p.S4331N;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfi.3:exon10:c.G1043A:p.S348N\x3bHSPG2:uc001bfj.3:exon96:c.G12992A:p.S4331N\x3bHSPG2:uc009vqd.3:exon96:c.G12995A:p.S4332N;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon96:c.G12992A:p.S4331N;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000278239.1|RCV000375072.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.32;Kaviar_AF=0.178452;Kaviar_AC=27589;Kaviar_AN=154602;ExAC_ALL=0.1849;ExAC_AFR=0.0835;ExAC_AMR=0.1308;ExAC_EAS=0.1612;ExAC_FIN=0.2467;ExAC_NFE=0.1830;ExAC_OTH=0.15;ExAC_SAS=0.2836;1000g2014oct_all=0.176118;snp138=rs3736360;SIFT_score=0.684;SIFT_converted_rankscore=0.044;SIFT_pred=T;Polyphen2_HDIV_score=0.001;Polyphen2_HDIV_rankscore=0.067;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.004;Polyphen2_HVAR_rankscore=0.093;Polyphen2_HVAR_pred=B;LRT_score=0.248;LRT_converted_rankscore=0.156;LRT_pred=N;MutationTaster_score=0.897;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=P;MutationAssessor_score=0.135;MutationAssessor_score_rankscore=0.087;MutationAssessor_pred=N;FATHMM_score=-0.93;FATHMM_converted_rankscore=0.752;FATHMM_pred=T;PROVEAN_score=0.06;PROVEAN_converted_rankscore=0.063;PROVEAN_pred=N;VEST3_score=0.01;VEST3_rankscore=0.001;MetaSVM_score=-1.106;MetaSVM_rankscore=0.034;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.001;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=1.583;CADD_raw_rankscore=0.252;CADD_phred=13.76;DANN_score=0.873;DANN_rankscore=0.166;fathmm-MKL_coding_score=0.213;fathmm-MKL_coding_rankscore=0.211;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.872;Eigen-PC-raw=-0.745;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.401;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=2.03;GERP++_RS_rankscore=0.256;phyloP100way_vertebrate=0.009;phyloP100way_vertebrate_rankscore=0.130;phyloP20way_mammalian=-0.035;phyloP20way_mammalian_rankscore=0.126;phastCons100way_vertebrate=0.011;phastCons100way_vertebrate_rankscore=0.184;phastCons20way_mammalian=0.747;phastCons20way_mammalian_rankscore=0.321;SiPhy_29way_logOdds=5.376;SiPhy_29way_logOdds_rankscore=0.154;Interpro_domain=Concanavalin_A-like_lectin/glucanase_domain|Laminin_G_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1243;dpsi_zscore=0.552;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:1,254:255:99:7341,527,0:55:99:0.996 ./.:.:.:.:.:.:.:. 0/1:193,209:406:99:5158,0,4629:54:99:0.52 0/1:163,160:324:99:4153,0,4014:54:99:0.495 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22150160 rs3736358 G T 8071.25 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=7.1188;MQ=55;MQ0=0;QD=30.12;SB=-4759.8;TI=NM_001013693,NM_005529;GI=LDLRAD2,HSPG2;FC=Silent,Synonymous_R4318R;EXON;BaseQRankSum=2.626;MQRankSum=4.269;ReadPosRankSum=1.987;DP=1021;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon96:c.C12955A:p.R4319R\x3bHSPG2:NM_005529:exon96:c.C12952A:p.R4318R;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfi.3:exon10:c.C1003A:p.R335R\x3bHSPG2:uc001bfj.3:exon96:c.C12952A:p.R4318R\x3bHSPG2:uc009vqd.3:exon96:c.C12955A:p.R4319R;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon96:c.C12952A:p.R4318R;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000286377.1|RCV000339035.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.28;Kaviar_AF=0.169267;Kaviar_AC=26169;Kaviar_AN=154602;ExAC_ALL=0.1808;ExAC_AFR=0.0359;ExAC_AMR=0.1302;ExAC_EAS=0.1613;ExAC_FIN=0.2464;ExAC_NFE=0.1831;ExAC_OTH=0.1481;ExAC_SAS=0.2838;1000g2014oct_all=.;snp138=rs3736358;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-2.1320;dpsi_zscore=-1.941;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,268:268:99:8071,587,0:55:99:1 ./.:.:.:.:.:.:.:. 0/1:205,209:415:99:4998,0,4941:54:99:0.505 0/1:157,181:338:99:4540,0,3822:54:99:0.536 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22150257 rs3736357 C T 10540.1 PASS BaseQRankSum=1.625;Dels=0;FS=0;HRun=1;HaplotypeScore=19.1297;MQ=55;MQ0=0;MQRankSum=-0.049;QD=27.24;ReadPosRankSum=-1.625;SB=-6541.66;TI=NM_001013693,NM_005529;GI=LDLRAD2,HSPG2;FC=Silent,Silent;EXON;DP=2155;AN=12;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=LDLRAD2;GeneDetail.refGene=NM_001013693:c.*1549C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=LDLRAD2;GeneDetail.knownGene=uc001bfg.1:c.*1549C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.65;Kaviar_AF=0.429322;Kaviar_AC=66374;Kaviar_AN=154602;ExAC_ALL=0.4593;ExAC_AFR=0.1442;ExAC_AMR=0.5437;ExAC_EAS=0.6513;ExAC_FIN=0.4823;ExAC_NFE=0.4963;ExAC_OTH=0.4931;ExAC_SAS=0.3407;1000g2014oct_all=0.3752;snp138=rs3736357;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2961;dpsi_zscore=-0.847;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,386:387:99:10540,758,0:55:99:0.997 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,335:335:99:9409,683,0:57:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:210,204:414:99:4772,0,5006:57:99:0.493 0/1:170,129:299:99:3143,0,4201:56:99:0.431 0/1:218,198:416:99:4654,0,5180:57:99:0.476 1/1:0,302:304:99:8333,599,0:55:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22154436 rs147927082 T A 5003.93 PASS BaseQRankSum=2.545;Dels=0;FS=2.562;HRun=0;HaplotypeScore=24.4569;MQ=56;MQ0=0;MQRankSum=3.311;QD=11.8;ReadPosRankSum=1.183;SB=-3305.28;TI=NM_005529;GI=HSPG2;FC=Silent;DP=424;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.011;Kaviar_AF=0.0011255;Kaviar_AC=174;Kaviar_AN=154602;ExAC_ALL=0.0017;ExAC_AFR=0.0073;ExAC_AMR=0.0057;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0012;ExAC_OTH=0.0040;ExAC_SAS=0;1000g2014oct_all=0.00239617;snp138=rs147927082;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=2.4385;dpsi_zscore=2.098;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:216,206:424:99:5004,0,5229:56:99:0.488 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22154845 rs2228347 A G 10995.3 PASS BaseQRankSum=1.642;Dels=0;FS=0;HRun=0;HaplotypeScore=16.6431;MQ=55;MQ0=0;MQRankSum=-0.386;QD=25.99;ReadPosRankSum=-0.671;SB=-7899.16;TI=NM_005529;GI=HSPG2;FC=Synonymous_D4104D;EXON;DP=1780;AN=10;AC=7;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon89:c.T12315C:p.D4105D\x3bHSPG2:NM_005529:exon89:c.T12312C:p.D4104D;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfi.3:exon3:c.T363C:p.D121D\x3bHSPG2:uc001bfj.3:exon89:c.T12312C:p.D4104D\x3bHSPG2:uc009vqd.3:exon89:c.T12315C:p.D4105D;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon89:c.T12312C:p.D4104D;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000319755.1|RCV000353544.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.51;Kaviar_AF=0.292616;Kaviar_AC=45239;Kaviar_AN=154602;ExAC_ALL=0.2982;ExAC_AFR=0.1360;ExAC_AMR=0.1835;ExAC_EAS=0.1607;ExAC_FIN=0.3359;ExAC_NFE=0.3143;ExAC_OTH=0.2757;ExAC_SAS=0.4733;1000g2014oct_all=0.257188;snp138=rs2228347;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3451;dpsi_zscore=0.953;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 1/1:3,420:423:99:10995,700,0:55:99:0.993 1/1:0,266:266:99:7357,527,0:56:99:1 ./.:.:.:.:.:.:.:. 0/1:199,194:393:99:4886,0,4865:56:99:0.494 0/1:182,199:381:99:5085,0,4312:55:99:0.522 ./.:.:.:.:.:.:.:. 0/1:164,152:317:99:3877,0,4059:57:99:0.481 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22155353 rs74859884 G A 3356.72 PASS BaseQRankSum=0.776;Dels=0;FS=0.924;HRun=1;HaplotypeScore=24.0361;MQ=55;MQ0=0;MQRankSum=1.857;QD=11.37;ReadPosRankSum=0.675;SB=-2159.19;TI=NM_005529;GI=HSPG2;FC=Missense_A4071V;EXON;DP=547;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon88:c.C12215T:p.A4072V\x3bHSPG2:NM_005529:exon88:c.C12212T:p.A4071V;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfi.3:exon2:c.C263T:p.A88V\x3bHSPG2:uc001bfj.3:exon88:c.C12212T:p.A4071V\x3bHSPG2:uc009vqd.3:exon88:c.C12215T:p.A4072V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon88:c.C12212T:p.A4071V;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000261134.1|RCV000323342.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.15;Kaviar_AF=0.0137902;Kaviar_AC=2132;Kaviar_AN=154602;ExAC_ALL=0.0246;ExAC_AFR=0.0063;ExAC_AMR=0.0297;ExAC_EAS=0;ExAC_FIN=0.1538;ExAC_NFE=0.0360;ExAC_OTH=0.0412;ExAC_SAS=0.0191;1000g2014oct_all=0.0133786;snp138=rs74859884;SIFT_score=0.144;SIFT_converted_rankscore=0.252;SIFT_pred=T;Polyphen2_HDIV_score=0.083;Polyphen2_HDIV_rankscore=0.365;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.122;Polyphen2_HVAR_rankscore=0.425;Polyphen2_HVAR_pred=B;LRT_score=0.028;LRT_converted_rankscore=0.256;LRT_pred=N;MutationTaster_score=0.973;MutationTaster_converted_rankscore=0.256;MutationTaster_pred=N;MutationAssessor_score=0.48;MutationAssessor_score_rankscore=0.132;MutationAssessor_pred=N;FATHMM_score=-0.94;FATHMM_converted_rankscore=0.753;FATHMM_pred=T;PROVEAN_score=-1.48;PROVEAN_converted_rankscore=0.362;PROVEAN_pred=N;VEST3_score=0.087;VEST3_rankscore=0.083;MetaSVM_score=-0.858;MetaSVM_rankscore=0.514;MetaSVM_pred=T;MetaLR_score=0.070;MetaLR_rankscore=0.286;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=2.851;CADD_raw_rankscore=0.403;CADD_phred=21.6;DANN_score=0.996;DANN_rankscore=0.739;fathmm-MKL_coding_score=0.611;fathmm-MKL_coding_rankscore=0.311;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.110;Eigen-PC-raw=-0.020;GenoCanyon_score=0.013;GenoCanyon_score_rankscore=0.125;integrated_fitCons_score=0.707;integrated_fitCons_score_rankscore=0.730;integrated_confidence_value=0;GERP++_RS=5.08;GERP++_RS_rankscore=0.682;phyloP100way_vertebrate=2.462;phyloP100way_vertebrate_rankscore=0.445;phyloP20way_mammalian=0.953;phyloP20way_mammalian_rankscore=0.551;phastCons100way_vertebrate=0.393;phastCons100way_vertebrate_rankscore=0.259;phastCons20way_mammalian=0.965;phastCons20way_mammalian_rankscore=0.450;SiPhy_29way_logOdds=12.876;SiPhy_29way_logOdds_rankscore=0.572;Interpro_domain=Concanavalin_A-like_lectin/glucanase_domain|Laminin_G_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0379;dpsi_zscore=0.240;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:145,134:280:99:3213,0,3403:55:99:0.48 0/1:131,136:267:99:3357,0,3358:56:99:0.509 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22155841 rs12042189 T C 5788.89 PASS BaseQRankSum=2.219;Dels=0;FS=2.992;HRun=0;HaplotypeScore=12.935;MQ=57;MQ0=0;MQRankSum=1.896;QD=27.05;ReadPosRankSum=1.873;SB=-3742.84;TI=NM_005529;GI=HSPG2;FC=Silent;DP=845;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.31;Kaviar_AF=0.173937;Kaviar_AC=26891;Kaviar_AN=154602;ExAC_ALL=0.1821;ExAC_AFR=0.0356;ExAC_AMR=0.1319;ExAC_EAS=0.1607;ExAC_FIN=0.2471;ExAC_NFE=0.1846;ExAC_OTH=0.1506;ExAC_SAS=0.2833;1000g2014oct_all=0.15635;snp138=rs12042189;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0441;dpsi_zscore=-0.238;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:2,211:214:99:5789,364,0:57:99:0.991 ./.:.:.:.:.:.:.:. 0/1:172,149:321:99:3730,0,3964:55:99:0.464 0/1:159,150:310:99:3552,0,3895:55:99:0.485 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22155853 rs12023794 C T 6371.01 PASS BaseQRankSum=1.717;Dels=0;FS=0;HRun=0;HaplotypeScore=7.1861;MQ=57;MQ0=0;MQRankSum=1.702;QD=27.94;ReadPosRankSum=1.565;SB=-4146.89;TI=NM_005529;GI=HSPG2;FC=Silent;DP=905;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.3;Kaviar_AF=0.176647;Kaviar_AC=27310;Kaviar_AN=154602;ExAC_ALL=0.1847;ExAC_AFR=0.0859;ExAC_AMR=0.1316;ExAC_EAS=0.1674;ExAC_FIN=0.2468;ExAC_NFE=0.1831;ExAC_OTH=0.1477;ExAC_SAS=0.2751;1000g2014oct_all=0.171526;snp138=rs12023794;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0702;dpsi_zscore=-0.349;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:1,227:228:99:6371,451,0:57:99:0.996 ./.:.:.:.:.:.:.:. 0/1:191,163:356:99:4020,0,4536:55:99:0.46 0/1:165,156:321:99:3879,0,4020:55:99:0.486 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22157689 rs3736355 G A 8438.86 PASS BaseQRankSum=-1.337;Dels=0;FS=2.363;HRun=0;HaplotypeScore=26.0554;MQ=57;MQ0=0;MQRankSum=-0.142;QD=28.74;ReadPosRankSum=0.705;SB=-4506.58;TI=NM_005529;GI=HSPG2;FC=Silent;DP=2975;AN=22;AC=17;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.83;Kaviar_AF=0.773024;Kaviar_AC=119511;Kaviar_AN=154602;ExAC_ALL=0.7923;ExAC_AFR=0.6968;ExAC_AMR=0.7461;ExAC_EAS=0.8061;ExAC_FIN=0.8125;ExAC_NFE=0.8073;ExAC_OTH=0.7856;ExAC_SAS=0.8097;1000g2014oct_all=0.759185;snp138=rs3736355;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1746;dpsi_zscore=0.672;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:3,286:289:99:8307,542,0:57:99:0.99 1/1:1,244:245:99:6914,472,0:56:99:0.996 1/1:0,206:207:99:6131,448,0:57:99:1 1/1:0,289:289:99:8439,614,0:58:99:1 0/1:168,130:299:99:3207,0,4037:58:99:0.436 0/1:124,122:247:99:2981,0,3277:58:99:0.496 0/1:179,196:375:99:4882,0,4321:58:99:0.523 1/1:1,215:218:99:6520,459,0:57:99:0.995 0/1:196,178:374:99:4555,0,5069:58:99:0.476 1/1:0,214:215:99:6141,451,0:57:99:1 ./.:.:.:.:.:.:.:. 0/1:109,108:217:99:2711,0,2914:57:99:0.498
chr1 22157795 rs111866498 G A 2056.13 PASS BaseQRankSum=1.216;Dels=0;FS=6.241;HRun=1;HaplotypeScore=11.9981;MQ=55;MQ0=0;MQRankSum=3.326;QD=10.77;ReadPosRankSum=0.345;SB=-1194.39;TI=NM_005529;GI=HSPG2;FC=Synonymous_I3825I;EXON;DP=191;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon84:c.C11478T:p.I3826I\x3bHSPG2:NM_005529:exon84:c.C11475T:p.I3825I;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon84:c.C11475T:p.I3825I\x3bHSPG2:uc009vqd.3:exon84:c.C11478T:p.I3826I;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon84:c.C11475T:p.I3825I;cytoBand=1p36.12;CLINSIG=Uncertain_significance|Uncertain_significance|Uncertain_significance;CLNDBN=not_specified|Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000180423.1|RCV000270486.1|RCV000325486.1;CLNDSDB=MedGen|MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.011;Kaviar_AF=0.0026778;Kaviar_AC=414;Kaviar_AN=154602;ExAC_ALL=0.0023;ExAC_AFR=0.0006;ExAC_AMR=0.0014;ExAC_EAS=0;ExAC_FIN=0.0040;ExAC_NFE=0.0033;ExAC_OTH=0.0011;ExAC_SAS=0.0008;1000g2014oct_all=0.000998403;snp138=rs111866498;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0366;dpsi_zscore=-0.201;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:108,83:191:99:2086,0,2712:55:99:0.435
chr1 22158120 rs2270701 G T 4177.42 PASS BaseQRankSum=-0.134;Dels=0;FS=2.169;HRun=1;HaplotypeScore=7.2036;MQ=56;MQ0=0;MQRankSum=0.796;QD=29.21;ReadPosRankSum=0.19;SB=-2494.09;TI=NM_005529;GI=HSPG2;FC=Silent;DP=634;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.32;Kaviar_AF=0.176427;Kaviar_AC=27276;Kaviar_AN=154602;ExAC_ALL=0.1950;ExAC_AFR=0.0643;ExAC_AMR=0.1519;ExAC_EAS=0.1723;ExAC_FIN=0.2618;ExAC_NFE=0.1929;ExAC_OTH=0.1604;ExAC_SAS=0.2966;1000g2014oct_all=0.165136;snp138=rs2270701;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3401;dpsi_zscore=-0.909;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:3,140:143:99:4177,234,0:56:99:0.979 ./.:.:.:.:.:.:.:. 0/1:123,117:240:99:2763,0,3104:56:99:0.488 0/1:135,116:251:99:2928,0,3561:56:99:0.462 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22158157 rs2229488 A G 2353.2 PASS BaseQRankSum=2.912;Dels=0;FS=1.77;HRun=0;HaplotypeScore=10.8531;MQ=54;MQ0=0;MQRankSum=2.666;QD=11.88;ReadPosRankSum=-0.071;SB=-1469.32;TI=NM_005529;GI=HSPG2;FC=Synonymous_N3780N;EXON;DP=198;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon82:c.T11343C:p.N3781N\x3bHSPG2:NM_005529:exon82:c.T11340C:p.N3780N;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon82:c.T11340C:p.N3780N\x3bHSPG2:uc009vqd.3:exon82:c.T11343C:p.N3781N;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon82:c.T11340C:p.N3780N;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000296602.1|RCV000351453.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.18;Kaviar_AF=0.0745398;Kaviar_AC=11524;Kaviar_AN=154602;ExAC_ALL=0.0827;ExAC_AFR=0.1823;ExAC_AMR=0.0468;ExAC_EAS=0;ExAC_FIN=0.0435;ExAC_NFE=0.0811;ExAC_OTH=0.0657;ExAC_SAS=0.0977;1000g2014oct_all=0.0832668;snp138=rs2229488;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.7434;dpsi_zscore=1.345;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:102,96:198:99:2383,0,2435:54:99:0.485
chr1 22159008 rs2229487 C A 5832.49 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=9.4366;MQ=57;MQ0=0;QD=29.76;SB=-3766.83;TI=NM_005529;GI=HSPG2;FC=Synonymous_V3729V;EXON;BaseQRankSum=0.758;MQRankSum=3.95;ReadPosRankSum=-0.694;DP=781;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon81:c.G11190T:p.V3730V\x3bHSPG2:NM_005529:exon81:c.G11187T:p.V3729V;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon81:c.G11187T:p.V3729V\x3bHSPG2:uc009vqd.3:exon81:c.G11190T:p.V3730V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon81:c.G11187T:p.V3729V;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000302763.1|RCV000338946.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.29;Kaviar_AF=0.168685;Kaviar_AC=26079;Kaviar_AN=154602;ExAC_ALL=0.1731;ExAC_AFR=0.0602;ExAC_AMR=0.1288;ExAC_EAS=0.1621;ExAC_FIN=0.2218;ExAC_NFE=0.1739;ExAC_OTH=0.1339;ExAC_SAS=0.2601;1000g2014oct_all=0.157748;snp138=rs2229487;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.7263;dpsi_zscore=1.332;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,196:196:99:5832,421,0:57:99:1 ./.:.:.:.:.:.:.:. 0/1:137,133:271:99:3200,0,3153:55:99:0.493 0/1:133,181:314:99:4586,0,3259:55:99:0.576 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22159709 rs60718319 G A 2643.09 PASS BaseQRankSum=1.074;Dels=0;FS=0.462;HRun=1;HaplotypeScore=7.1473;MQ=56;MQ0=0;MQRankSum=2.832;QD=10.28;ReadPosRankSum=2.074;SB=-1632.53;TI=NM_005529;GI=HSPG2;FC=Silent;DP=257;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.14;Kaviar_AF=0.0060478;Kaviar_AC=935;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0457268;snp138=rs60718319;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.6471;dpsi_zscore=1.268;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:145,112:257:99:2673,0,3572:56:99:0.436
chr1 22159774 rs2229486 G A 3170.46 PASS BaseQRankSum=1.527;Dels=0;FS=0.433;HRun=0;HaplotypeScore=12.4057;MQ=55;MQ0=0;MQRankSum=0.638;QD=11.24;ReadPosRankSum=-1.543;SB=-1999.7;TI=NM_005529;GI=HSPG2;FC=Synonymous_P3694P;EXON;DP=282;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon80:c.C11085T:p.P3695P\x3bHSPG2:NM_005529:exon80:c.C11082T:p.P3694P;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon80:c.C11082T:p.P3694P\x3bHSPG2:uc009vqd.3:exon80:c.C11085T:p.P3695P;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon80:c.C11082T:p.P3694P;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000304022.1|RCV000393030.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.17;Kaviar_AF=0.0795656;Kaviar_AC=12301;Kaviar_AN=154602;ExAC_ALL=0.0792;ExAC_AFR=0.1712;ExAC_AMR=0.0372;ExAC_EAS=0;ExAC_FIN=0.0587;ExAC_NFE=0.0772;ExAC_OTH=0.0710;ExAC_SAS=0.1091;1000g2014oct_all=0.0858626;snp138=rs2229486;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1408;dpsi_zscore=0.595;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:155,126:282:99:3200,0,3897:55:99:0.448
chr1 22160020 rs17459097 C T 4216.64 PASS BaseQRankSum=0.024;Dels=0;FS=2.26;HRun=0;HaplotypeScore=9.1359;MQ=57;MQ0=0;MQRankSum=2.478;QD=11.68;ReadPosRankSum=0.622;SB=-2621.99;TI=NM_005529;GI=HSPG2;FC=Missense_V3640I;EXON;DP=361;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon79:c.G10921A:p.V3641I\x3bHSPG2:NM_005529:exon79:c.G10918A:p.V3640I;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon79:c.G10918A:p.V3640I\x3bHSPG2:uc009vqd.3:exon79:c.G10921A:p.V3641I;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon79:c.G10918A:p.V3640I;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000275039.1|RCV000330138.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.11;Kaviar_AF=0.042037;Kaviar_AC=6499;Kaviar_AN=154602;ExAC_ALL=0.0425;ExAC_AFR=0.0100;ExAC_AMR=0.0258;ExAC_EAS=0.0001;ExAC_FIN=0.1058;ExAC_NFE=0.0581;ExAC_OTH=0.0636;ExAC_SAS=0.0078;1000g2014oct_all=0.0217652;snp138=rs17459097;SIFT_score=0.257;SIFT_converted_rankscore=0.167;SIFT_pred=T;Polyphen2_HDIV_score=0.028;Polyphen2_HDIV_rankscore=0.184;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.034;Polyphen2_HVAR_rankscore=0.212;Polyphen2_HVAR_pred=B;LRT_score=0.056;LRT_converted_rankscore=0.226;LRT_pred=N;MutationTaster_score=0.819;MutationTaster_converted_rankscore=0.289;MutationTaster_pred=N;MutationAssessor_score=0.565;MutationAssessor_score_rankscore=0.153;MutationAssessor_pred=N;FATHMM_score=-0.65;FATHMM_converted_rankscore=0.722;FATHMM_pred=T;PROVEAN_score=-0.31;PROVEAN_converted_rankscore=0.121;PROVEAN_pred=N;VEST3_score=0.012;VEST3_rankscore=0.001;MetaSVM_score=-1.080;MetaSVM_rankscore=0.074;MetaSVM_pred=T;MetaLR_score=0.017;MetaLR_rankscore=0.071;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=1.784;CADD_raw_rankscore=0.275;CADD_phred=14.89;DANN_score=0.912;DANN_rankscore=0.198;fathmm-MKL_coding_score=0.872;fathmm-MKL_coding_rankscore=0.464;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.676;Eigen-PC-raw=-0.589;GenoCanyon_score=0.986;GenoCanyon_score_rankscore=0.310;integrated_fitCons_score=0.722;integrated_fitCons_score_rankscore=0.854;integrated_confidence_value=0;GERP++_RS=1.02;GERP++_RS_rankscore=0.190;phyloP100way_vertebrate=1.472;phyloP100way_vertebrate_rankscore=0.348;phyloP20way_mammalian=0.807;phyloP20way_mammalian_rankscore=0.329;phastCons100way_vertebrate=0.807;phastCons100way_vertebrate_rankscore=0.296;phastCons20way_mammalian=0.830;phastCons20way_mammalian_rankscore=0.347;SiPhy_29way_logOdds=8.957;SiPhy_29way_logOdds_rankscore=0.348;Interpro_domain=Concanavalin_A-like_lectin/glucanase_domain|Immunoglobulin_I-set|Immunoglobulin_subtype_2|Immunoglobulin-like_domain|Immunoglobulin-like_fold;GTEx_V6_gene=ENSG00000218510.3;GTEx_V6_tissue=Artery_Tibial;dpsi_max_tissue=0.0574;dpsi_zscore=0.330;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:191,169:361:99:4217,0,4781:57:99:0.469 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22160043 rs2229493 C T 3860.63 PASS BaseQRankSum=2.695;Dels=0;FS=5.974;HRun=1;HaplotypeScore=12.0938;MQ=56;MQ0=0;MQRankSum=0.478;QD=12.49;ReadPosRankSum=-0.566;SB=-2439.05;TI=NM_005529;GI=HSPG2;FC=Missense_R3632Q;EXON;DP=309;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon79:c.G10898A:p.R3633Q\x3bHSPG2:NM_005529:exon79:c.G10895A:p.R3632Q;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon79:c.G10895A:p.R3632Q\x3bHSPG2:uc009vqd.3:exon79:c.G10898A:p.R3633Q;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon79:c.G10895A:p.R3632Q;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000276227.1|RCV000389238.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.17;Kaviar_AF=0.0796173;Kaviar_AC=12309;Kaviar_AN=154602;ExAC_ALL=0.0795;ExAC_AFR=0.1733;ExAC_AMR=0.0372;ExAC_EAS=0;ExAC_FIN=0.0588;ExAC_NFE=0.0774;ExAC_OTH=0.0702;ExAC_SAS=0.1091;1000g2014oct_all=0.0858626;snp138=rs2229493;SIFT_score=0.399;SIFT_converted_rankscore=0.110;SIFT_pred=T;Polyphen2_HDIV_score=0.003;Polyphen2_HDIV_rankscore=0.237;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.015;Polyphen2_HVAR_rankscore=0.195;Polyphen2_HVAR_pred=B;LRT_score=0.965;LRT_converted_rankscore=0.082;LRT_pred=N;MutationTaster_score=1;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=P;MutationAssessor_score=0.93;MutationAssessor_score_rankscore=0.236;MutationAssessor_pred=L;FATHMM_score=-0.15;FATHMM_converted_rankscore=0.652;FATHMM_pred=T;PROVEAN_score=-1.51;PROVEAN_converted_rankscore=0.439;PROVEAN_pred=N;VEST3_score=0.132;VEST3_rankscore=0.152;MetaSVM_score=-1.067;MetaSVM_rankscore=0.102;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.001;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=0.200;CADD_raw_rankscore=0.113;CADD_phred=4.684;DANN_score=0.880;DANN_rankscore=0.171;fathmm-MKL_coding_score=0.191;fathmm-MKL_coding_rankscore=0.203;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.666;Eigen-PC-raw=-1.655;GenoCanyon_score=0.967;GenoCanyon_score_rankscore=0.289;integrated_fitCons_score=0.722;integrated_fitCons_score_rankscore=0.854;integrated_confidence_value=0;GERP++_RS=-1.15;GERP++_RS_rankscore=0.092;phyloP100way_vertebrate=0.057;phyloP100way_vertebrate_rankscore=0.140;phyloP20way_mammalian=-0.966;phyloP20way_mammalian_rankscore=0.023;phastCons100way_vertebrate=0.005;phastCons100way_vertebrate_rankscore=0.169;phastCons20way_mammalian=0.016;phastCons20way_mammalian_rankscore=0.126;SiPhy_29way_logOdds=8.850;SiPhy_29way_logOdds_rankscore=0.342;Interpro_domain=Immunoglobulin_I-set|Immunoglobulin_subtype_2|Immunoglobulin-like_domain|Immunoglobulin-like_fold;GTEx_V6_gene=ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12;GTEx_V6_tissue=Adipose_Subcutaneous|Lung|Nerve_Tibial|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg;dpsi_max_tissue=-0.8643;dpsi_zscore=-1.388;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:156,153:309:99:3861,0,3986:56:99:0.495
chr1 22160111 rs17459139 C T 7544.69 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=2.7041;MQ=56;MQ0=0;QD=29.47;SB=-4924.19;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=-1.057;MQRankSum=4.265;ReadPosRankSum=0.14;DP=877;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000281067.1|RCV000340788.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.32;Kaviar_AF=0.170056;Kaviar_AC=26291;Kaviar_AN=154602;ExAC_ALL=0.1757;ExAC_AFR=0.0608;ExAC_AMR=0.1288;ExAC_EAS=0.1629;ExAC_FIN=0.2233;ExAC_NFE=0.1756;ExAC_OTH=0.1376;ExAC_SAS=0.2693;1000g2014oct_all=0.164137;snp138=rs17459139;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.8406;dpsi_zscore=1.416;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,256:256:99:7545,545,0:56:99:1 ./.:.:.:.:.:.:.:. 0/1:156,169:325:99:4296,0,3936:56:99:0.52 0/1:120,176:296:99:4451,0,2896:56:99:0.595 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22160140 rs74060187 T C 2907.57 PASS BaseQRankSum=1.52;Dels=0;FS=2.325;HRun=2;HaplotypeScore=5.5186;MQ=56;MQ0=0;MQRankSum=2.334;QD=13.22;ReadPosRankSum=0.164;SB=-1841.2;TI=NM_005529;GI=HSPG2;FC=Silent;DP=220;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.14;Kaviar_AF=0.0261446;Kaviar_AC=4042;Kaviar_AN=154602;ExAC_ALL=0.0259;ExAC_AFR=0.1368;ExAC_AMR=0.0137;ExAC_EAS=0;ExAC_FIN=0.0116;ExAC_NFE=0.0214;ExAC_OTH=0.0124;ExAC_SAS=0.0054;1000g2014oct_all=0.0433307;snp138=rs74060187;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0384;dpsi_zscore=-0.210;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:108,112:220:99:2938,0,2696:56:99:0.509
chr1 22160148 rs7547731 C T 8400.33 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=13.4057;MQ=58;MQ0=0;QD=29.37;SB=-5289.09;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.71;MQRankSum=0.963;ReadPosRankSum=0.188;DP=1654;AN=12;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.65;Kaviar_AF=0.444845;Kaviar_AC=68774;Kaviar_AN=154602;ExAC_ALL=0.4552;ExAC_AFR=0.1446;ExAC_AMR=0.5390;ExAC_EAS=0.6478;ExAC_FIN=0.4775;ExAC_NFE=0.4902;ExAC_OTH=0.4932;ExAC_SAS=0.3335;1000g2014oct_all=0.375;snp138=rs7547731;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-2.3748;dpsi_zscore=-2.007;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,286:286:99:8400,608,0:58:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,273:273:99:8388,614,0:57:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:158,159:317:99:4259,0,4062:58:99:0.502 0/1:117,127:245:99:3267,0,3061:57:99:0.52 0/1:146,154:300:99:4240,0,3907:58:99:0.513 1/1:1,231:233:99:6825,494,0:57:99:0.996 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22161275 rs2229492 G A 7778.72 PASS BaseQRankSum=1.025;Dels=0;FS=0;HRun=1;HaplotypeScore=4.5356;MQ=54;MQ0=0;MQRankSum=0.53;QD=27.39;ReadPosRankSum=1.661;SB=-5132.7;TI=NM_005529;GI=HSPG2;FC=Synonymous_V3539V;EXON;DP=924;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon77:c.C10620T:p.V3540V\x3bHSPG2:NM_005529:exon77:c.C10617T:p.V3539V;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon77:c.C10617T:p.V3539V\x3bHSPG2:uc009vqd.3:exon77:c.C10620T:p.V3540V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon77:c.C10617T:p.V3539V;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000312313.1|RCV000392359.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.3;Kaviar_AF=0.169073;Kaviar_AC=26139;Kaviar_AN=154602;ExAC_ALL=0.1748;ExAC_AFR=0.0586;ExAC_AMR=0.1288;ExAC_EAS=0.1622;ExAC_FIN=0.2223;ExAC_NFE=0.1749;ExAC_OTH=0.1353;ExAC_SAS=0.2693;1000g2014oct_all=0.159545;snp138=rs2229492;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2857;dpsi_zscore=-0.832;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:3,281:284:99:7779,486,0:54:99:0.989 ./.:.:.:.:.:.:.:. 0/1:162,154:316:99:4007,0,4061:55:99:0.487 0/1:179,145:324:99:3705,0,4370:54:99:0.448 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22163390 rs35444472 G A 3513.72 PASS BaseQRankSum=1.632;Dels=0;FS=2.111;HRun=1;HaplotypeScore=11.803;MQ=55;MQ0=0;MQRankSum=0.386;QD=13.67;ReadPosRankSum=-0.204;SB=-1992.8;TI=NM_005529;GI=HSPG2;FC=Synonymous_H3420H;EXON;DP=257;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon75:c.C10263T:p.H3421H\x3bHSPG2:NM_005529:exon75:c.C10260T:p.H3420H;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon75:c.C10260T:p.H3420H\x3bHSPG2:uc009vqd.3:exon75:c.C10263T:p.H3421H;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon75:c.C10260T:p.H3420H;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000293149.1|RCV000352651.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.21;Kaviar_AF=0.0606849;Kaviar_AC=9382;Kaviar_AN=154602;ExAC_ALL=0.1274;ExAC_AFR=0.2079;ExAC_AMR=0.1172;ExAC_EAS=0;ExAC_FIN=0.1676;ExAC_NFE=0.1227;ExAC_OTH=0.0583;ExAC_SAS=0.1214;1000g2014oct_all=0.0860623;snp138=rs35444472;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0716;dpsi_zscore=0.387;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:119,138:257:99:3514,0,3144:55:99:0.537
chr1 22163402 rs41310390 G A 8675.56 PASS BaseQRankSum=1.721;Dels=0;FS=0;HRun=0;HaplotypeScore=13.6145;MQ=54;MQ0=0;MQRankSum=-0.981;QD=26.86;ReadPosRankSum=1.067;SB=-6283.88;TI=NM_005529;GI=HSPG2;FC=Synonymous_S3416S;EXON;DP=609;AN=4;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon75:c.C10251T:p.S3417S\x3bHSPG2:NM_005529:exon75:c.C10248T:p.S3416S;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon75:c.C10248T:p.S3416S\x3bHSPG2:uc009vqd.3:exon75:c.C10251T:p.S3417S;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon75:c.C10248T:p.S3416S;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000356605.1|RCV000391634.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.22;Kaviar_AF=0.0432401;Kaviar_AC=6685;Kaviar_AN=154602;ExAC_ALL=0.0976;ExAC_AFR=0.0414;ExAC_AMR=0.0680;ExAC_EAS=0;ExAC_FIN=0.2180;ExAC_NFE=0.1152;ExAC_OTH=0.0780;ExAC_SAS=0.1046;1000g2014oct_all=0.04373;snp138=rs41310390;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3091;dpsi_zscore=-0.866;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 1/1:1,322:323:99:8676,617,0:54:99:0.997 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:142,143:286:99:3689,0,3779:57:99:0.502 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22165901 rs2291826 A G 6185.75 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=14.9773;MQ=55;MQ0=0;QD=29.04;SB=-3706.67;TI=NM_005529;GI=HSPG2;FC=Synonymous_A3284A;EXON;BaseQRankSum=1.873;MQRankSum=1.413;ReadPosRankSum=0.021;DP=979;AN=8;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon73:c.T9855C:p.A3285A\x3bHSPG2:NM_005529:exon73:c.T9852C:p.A3284A;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon73:c.T9852C:p.A3284A\x3bHSPG2:uc009vqd.3:exon73:c.T9855C:p.A3285A;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon73:c.T9852C:p.A3284A;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000336014.1|RCV000399444.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.55;Kaviar_AF=0.282732;Kaviar_AC=43711;Kaviar_AN=154602;ExAC_ALL=0.2876;ExAC_AFR=0.5338;ExAC_AMR=0.1840;ExAC_EAS=0.1621;ExAC_FIN=0.2849;ExAC_NFE=0.2616;ExAC_OTH=0.2311;ExAC_SAS=0.3795;1000g2014oct_all=0.346046;snp138=rs2291826;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0728;dpsi_zscore=0.392;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,212:213:99:6186,451,0:55:99:1 ./.:.:.:.:.:.:.:. 0/1:114,176:291:99:4210,0,2613:54:99:0.607 0/1:116,147:264:99:3818,0,2895:57:99:0.559 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:86,124:211:99:3029,0,2133:55:99:0.59
chr1 22165963 rs139500146 T C 3431.72 PASS BaseQRankSum=1.972;Dels=0;FS=4.648;HRun=0;HaplotypeScore=7.9645;MQ=57;MQ0=0;MQRankSum=-0.57;QD=11.75;ReadPosRankSum=0.259;SB=-2023.64;TI=NM_005529;GI=HSPG2;FC=Missense_I3264V;EXON;DP=292;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon73:c.A9793G:p.I3265V\x3bHSPG2:NM_005529:exon73:c.A9790G:p.I3264V;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon73:c.A9790G:p.I3264V\x3bHSPG2:uc009vqd.3:exon73:c.A9793G:p.I3265V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon73:c.A9790G:p.I3264V;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000282161.1|RCV000337226.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.04;Kaviar_AF=0.0104656;Kaviar_AC=1618;Kaviar_AN=154602;ExAC_ALL=0.0108;ExAC_AFR=0.0018;ExAC_AMR=0.0038;ExAC_EAS=0;ExAC_FIN=0.0403;ExAC_NFE=0.0142;ExAC_OTH=0.0091;ExAC_SAS=0.0021;1000g2014oct_all=0.00579073;snp138=rs139500146;SIFT_score=0.547;SIFT_converted_rankscore=0.066;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.006;Polyphen2_HVAR_rankscore=0.112;Polyphen2_HVAR_pred=B;LRT_score=0.032;LRT_converted_rankscore=0.251;LRT_pred=N;MutationTaster_score=0.992;MutationTaster_converted_rankscore=0.239;MutationTaster_pred=N;MutationAssessor_score=-0.59;MutationAssessor_score_rankscore=0.022;MutationAssessor_pred=N;FATHMM_score=1.71;FATHMM_converted_rankscore=0.267;FATHMM_pred=T;PROVEAN_score=-0.16;PROVEAN_converted_rankscore=0.095;PROVEAN_pred=N;VEST3_score=0.036;VEST3_rankscore=0.016;MetaSVM_score=-0.999;MetaSVM_rankscore=0.301;MetaSVM_pred=T;MetaLR_score=0.012;MetaLR_rankscore=0.046;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=-1.265;CADD_raw_rankscore=0.023;CADD_phred=0.005;DANN_score=0.523;DANN_rankscore=0.046;fathmm-MKL_coding_score=0.438;fathmm-MKL_coding_rankscore=0.270;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.294;Eigen-PC-raw=-1.264;GenoCanyon_score=0.065;GenoCanyon_score_rankscore=0.153;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=-3.26;GERP++_RS_rankscore=0.047;phyloP100way_vertebrate=0.212;phyloP100way_vertebrate_rankscore=0.172;phyloP20way_mammalian=-0.219;phyloP20way_mammalian_rankscore=0.097;phastCons100way_vertebrate=0.965;phastCons100way_vertebrate_rankscore=0.337;phastCons20way_mammalian=0.907;phastCons20way_mammalian_rankscore=0.385;SiPhy_29way_logOdds=6.575;SiPhy_29way_logOdds_rankscore=0.216;Interpro_domain=Immunoglobulin_I-set|Immunoglobulin_subtype_2|Immunoglobulin-like_domain|Immunoglobulin-like_fold;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0864;dpsi_zscore=0.440;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:156,136:292:99:3432,0,3736:57:99:0.466 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22165987 rs2291827 G A 5587.95 PASS BaseQRankSum=-1.456;Dels=0;FS=3.429;HRun=0;HaplotypeScore=4.443;MQ=56;MQ0=0;MQRankSum=-0.129;QD=27.8;ReadPosRankSum=0.302;SB=-3419.57;TI=NM_005529;GI=HSPG2;FC=Missense_H3256Y;EXON;DP=761;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon73:c.C9769T:p.H3257Y\x3bHSPG2:NM_005529:exon73:c.C9766T:p.H3256Y;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon73:c.C9766T:p.H3256Y\x3bHSPG2:uc009vqd.3:exon73:c.C9769T:p.H3257Y;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon73:c.C9766T:p.H3256Y;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000341659.1|RCV000407535.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.3;Kaviar_AF=0.167456;Kaviar_AC=25889;Kaviar_AN=154602;ExAC_ALL=0.1728;ExAC_AFR=0.0356;ExAC_AMR=0.1285;ExAC_EAS=0.1616;ExAC_FIN=0.2291;ExAC_NFE=0.1744;ExAC_OTH=0.1373;ExAC_SAS=0.2698;1000g2014oct_all=0.152157;snp138=rs2291827;SIFT_score=0.651;SIFT_converted_rankscore=0.048;SIFT_pred=T;Polyphen2_HDIV_score=0.387;Polyphen2_HDIV_rankscore=0.327;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.194;Polyphen2_HVAR_rankscore=0.349;Polyphen2_HVAR_pred=B;LRT_score=0.001;LRT_converted_rankscore=0.403;LRT_pred=N;MutationTaster_score=0.000;MutationTaster_converted_rankscore=0.524;MutationTaster_pred=P;MutationAssessor_score=0.58;MutationAssessor_score_rankscore=0.154;MutationAssessor_pred=N;FATHMM_score=1.67;FATHMM_converted_rankscore=0.273;FATHMM_pred=T;PROVEAN_score=-3.52;PROVEAN_converted_rankscore=0.684;PROVEAN_pred=D;VEST3_score=0.269;VEST3_rankscore=0.327;MetaSVM_score=-1.097;MetaSVM_rankscore=0.044;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=4.117;CADD_raw_rankscore=0.552;CADD_phred=23.8;DANN_score=0.990;DANN_rankscore=0.496;fathmm-MKL_coding_score=0.918;fathmm-MKL_coding_rankscore=0.540;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.054;Eigen-PC-raw=0.139;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=5.5;GERP++_RS_rankscore=0.813;phyloP100way_vertebrate=6.178;phyloP100way_vertebrate_rankscore=0.717;phyloP20way_mammalian=1.045;phyloP20way_mammalian_rankscore=0.669;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.986;phastCons20way_mammalian_rankscore=0.517;SiPhy_29way_logOdds=17.962;SiPhy_29way_logOdds_rankscore=0.890;Interpro_domain=Immunoglobulin_I-set|Immunoglobulin_subtype_2|Immunoglobulin-like_domain|Immunoglobulin-like_fold;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0785;dpsi_zscore=0.413;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:1,200:201:99:5588,369,0:56:99:0.995 ./.:.:.:.:.:.:.:. 0/1:139,138:277:99:3313,0,3254:54:99:0.498 0/1:137,146:283:99:3542,0,3373:56:99:0.516 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22166108 rs74060191 C T 1833.74 PASS BaseQRankSum=1.071;Dels=0;FS=0;HRun=0;HaplotypeScore=10.9934;MQ=58;MQ0=0;MQRankSum=-1.015;QD=16.67;ReadPosRankSum=-0.868;SB=-756.04;TI=NM_005529;GI=HSPG2;FC=Silent;DP=110;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.14;Kaviar_AF=0.0304288;Kaviar_AC=792;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0461262;snp138=rs74060191;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3933;dpsi_zscore=-0.975;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:46,63:110:99:1864,0,1215:58:99:0.578
chr1 22167605 rs2228349 C T 1956.94 PASS BaseQRankSum=2.127;Dels=0;FS=2.956;HRun=0;HaplotypeScore=8.4695;MQ=56;MQ0=0;MQRankSum=1.445;QD=12.15;ReadPosRankSum=-0.801;SB=-788.23;TI=NM_005529;GI=HSPG2;FC=Missense_A3168T;EXON;DP=161;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon71:c.G9505A:p.A3169T\x3bHSPG2:NM_005529:exon71:c.G9502A:p.A3168T;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon71:c.G9502A:p.A3168T\x3bHSPG2:uc009vqd.3:exon71:c.G9505A:p.A3169T;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon71:c.G9502A:p.A3168T;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000259415.1|RCV000316947.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.23;Kaviar_AF=0.0731879;Kaviar_AC=11315;Kaviar_AN=154602;ExAC_ALL=0.1176;ExAC_AFR=0.2266;ExAC_AMR=0.0711;ExAC_EAS=0;ExAC_FIN=0.1124;ExAC_NFE=0.1144;ExAC_OTH=0.1;ExAC_SAS=0.1355;1000g2014oct_all=0.0836661;snp138=rs2228349;SIFT_score=0.271;SIFT_converted_rankscore=0.160;SIFT_pred=T;Polyphen2_HDIV_score=0.006;Polyphen2_HDIV_rankscore=0.126;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.027;Polyphen2_HVAR_rankscore=0.198;Polyphen2_HVAR_pred=B;LRT_score=0.510;LRT_converted_rankscore=0.118;LRT_pred=N;MutationTaster_score=1;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=P;MutationAssessor_score=0.925;MutationAssessor_score_rankscore=0.236;MutationAssessor_pred=L;FATHMM_score=-0.25;FATHMM_converted_rankscore=0.670;FATHMM_pred=T;PROVEAN_score=-1.16;PROVEAN_converted_rankscore=0.297;PROVEAN_pred=N;VEST3_score=0.028;VEST3_rankscore=0.009;MetaSVM_score=-1.066;MetaSVM_rankscore=0.104;MetaSVM_pred=T;MetaLR_score=0.001;MetaLR_rankscore=0.002;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=1.523;CADD_raw_rankscore=0.245;CADD_phred=13.43;DANN_score=0.936;DANN_rankscore=0.228;fathmm-MKL_coding_score=0.306;fathmm-MKL_coding_rankscore=0.239;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.024;Eigen-PC-raw=-1.018;GenoCanyon_score=0.001;GenoCanyon_score_rankscore=0.077;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=-0.426;GERP++_RS_rankscore=0.116;phyloP100way_vertebrate=0.959;phyloP100way_vertebrate_rankscore=0.286;phyloP20way_mammalian=-0.249;phyloP20way_mammalian_rankscore=0.090;phastCons100way_vertebrate=0.865;phastCons100way_vertebrate_rankscore=0.305;phastCons20way_mammalian=0.024;phastCons20way_mammalian_rankscore=0.140;SiPhy_29way_logOdds=10.313;SiPhy_29way_logOdds_rankscore=0.427;Interpro_domain=Immunoglobulin_I-set|Immunoglobulin_subtype_2|Immunoglobulin-like_domain|Immunoglobulin-like_fold;GTEx_V6_gene=ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12;GTEx_V6_tissue=Adipose_Subcutaneous|Esophagus_Mucosa|Lung|Nerve_Tibial|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg;dpsi_max_tissue=0.0503;dpsi_zscore=0.299;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:86,75:161:99:1987,0,2259:56:99:0.466
chr1 22167988 rs2270697 G T 6490.16 PASS BaseQRankSum=-1.67;Dels=0;FS=3.194;HRun=0;HaplotypeScore=3.6806;MQ=56;MQ0=0;MQRankSum=1.685;QD=29.23;ReadPosRankSum=-0.921;SB=-4085.49;TI=NM_005529;GI=HSPG2;FC=Silent;DP=863;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.3;Kaviar_AF=0.167559;Kaviar_AC=25905;Kaviar_AN=154602;ExAC_ALL=0.1734;ExAC_AFR=0.0355;ExAC_AMR=0.1276;ExAC_EAS=0.1720;ExAC_FIN=0.2210;ExAC_NFE=0.1750;ExAC_OTH=0.1366;ExAC_SAS=0.2689;1000g2014oct_all=0.152756;snp138=rs2270697;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0502;dpsi_zscore=0.299;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:1,221:222:99:6490,442,0:56:99:0.995 ./.:.:.:.:.:.:.:. 0/1:182,144:326:99:3377,0,4390:57:99:0.442 0/1:164,149:315:99:3656,0,4105:55:99:0.476 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22168216 rs7556412 C T 9718.69 PASS BaseQRankSum=-1.109;Dels=0;FS=3.654;HRun=1;HaplotypeScore=10.4416;MQ=55;MQ0=0;MQRankSum=0.773;QD=28.83;ReadPosRankSum=-1.384;SB=-4691.59;TI=NM_005529;GI=HSPG2;FC=Silent;DP=2625;AN=18;AC=13;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.82;Kaviar_AF=0.631648;Kaviar_AC=97654;Kaviar_AN=154602;ExAC_ALL=0.6516;ExAC_AFR=0.5011;ExAC_AMR=0.6314;ExAC_EAS=0.8165;ExAC_FIN=0.7010;ExAC_NFE=0.6644;ExAC_OTH=0.6505;ExAC_SAS=0.6042;1000g2014oct_all=0.623802;snp138=rs7556412;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3384;dpsi_zscore=0.944;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,288:289:99:8333,570,0:55:99:0.997 ./.:.:.:.:.:.:.:. 1/1:1,188:190:99:5617,380,0:54:99:0.995 1/1:0,330:331:99:9719,713,0:57:99:1 0/1:166,115:281:99:2676,0,4044:56:99:0.409 0/1:161,107:268:99:2733,0,3955:55:99:0.399 0/1:165,153:318:99:3451,0,4051:57:99:0.481 0/1:138,132:270:99:3449,0,3554:58:99:0.489 0/1:183,190:374:99:4668,0,4490:57:99:0.509 1/1:0,304:304:99:8303,593,0:56:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22168801 rs2229491 T C 3747.96 PASS BaseQRankSum=2.563;Dels=0;FS=2.48;HRun=1;HaplotypeScore=12.2022;MQ=55;MQ0=0;MQRankSum=0.205;QD=12.33;ReadPosRankSum=-2.054;SB=-2415.4;TI=NM_005529;GI=HSPG2;FC=Missense_S2995G;EXON;DP=304;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon68:c.A8986G:p.S2996G\x3bHSPG2:NM_005529:exon68:c.A8983G:p.S2995G;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon68:c.A8983G:p.S2995G\x3bHSPG2:uc009vqd.3:exon68:c.A8986G:p.S2996G;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon68:c.A8983G:p.S2995G;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000313160.1|RCV000370135.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.18;Kaviar_AF=0.0801219;Kaviar_AC=12387;Kaviar_AN=154602;ExAC_ALL=0.0812;ExAC_AFR=0.1832;ExAC_AMR=0.0383;ExAC_EAS=0;ExAC_FIN=0.0614;ExAC_NFE=0.0781;ExAC_OTH=0.0727;ExAC_SAS=0.1110;1000g2014oct_all=0.0886581;snp138=rs2229491;SIFT_score=1.0;SIFT_converted_rankscore=0.010;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.0;Polyphen2_HVAR_rankscore=0.013;Polyphen2_HVAR_pred=B;LRT_score=0.031;LRT_converted_rankscore=0.252;LRT_pred=N;MutationTaster_score=1;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=P;MutationAssessor_score=0.93;MutationAssessor_score_rankscore=0.236;MutationAssessor_pred=L;FATHMM_score=0.94;FATHMM_converted_rankscore=0.437;FATHMM_pred=T;PROVEAN_score=1.26;PROVEAN_converted_rankscore=0.010;PROVEAN_pred=N;VEST3_score=0.036;VEST3_rankscore=0.016;MetaSVM_score=-1.020;MetaSVM_rankscore=0.237;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=-1.372;CADD_raw_rankscore=0.020;CADD_phred=0.004;DANN_score=0.270;DANN_rankscore=0.013;fathmm-MKL_coding_score=0.011;fathmm-MKL_coding_rankscore=0.041;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.431;Eigen-PC-raw=-1.406;GenoCanyon_score=0.000;GenoCanyon_score_rankscore=0.044;integrated_fitCons_score=0.632;integrated_fitCons_score_rankscore=0.406;integrated_confidence_value=0;GERP++_RS=1.0;GERP++_RS_rankscore=0.189;phyloP100way_vertebrate=-0.183;phyloP100way_vertebrate_rankscore=0.096;phyloP20way_mammalian=-0.441;phyloP20way_mammalian_rankscore=0.057;phastCons100way_vertebrate=0.000;phastCons100way_vertebrate_rankscore=0.063;phastCons20way_mammalian=0.000;phastCons20way_mammalian_rankscore=0.016;SiPhy_29way_logOdds=1.546;SiPhy_29way_logOdds_rankscore=0.024;Interpro_domain=Immunoglobulin_subtype_2|Immunoglobulin-like_domain;GTEx_V6_gene=ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12|ENSG00000142798.12;GTEx_V6_tissue=Adipose_Subcutaneous|Lung|Nerve_Tibial|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg;dpsi_max_tissue=0.0640;dpsi_zscore=0.358;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:149,155:304:99:3748,0,3586:55:99:0.51
chr1 22169222 rs74060195 C T 2882.83 PASS BaseQRankSum=1.147;Dels=0;FS=0;HRun=0;HaplotypeScore=12.9605;MQ=55;MQ0=0;MQRankSum=1.152;QD=12.22;ReadPosRankSum=0.271;SB=-1822.54;TI=NM_005529;GI=HSPG2;FC=Silent;DP=236;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.16;Kaviar_AF=0.0286154;Kaviar_AC=4424;Kaviar_AN=154602;ExAC_ALL=0.0281;ExAC_AFR=0.1639;ExAC_AMR=0.0148;ExAC_EAS=0;ExAC_FIN=0.0114;ExAC_NFE=0.0220;ExAC_OTH=0.0145;ExAC_SAS=0.0053;1000g2014oct_all=0.0515176;snp138=rs74060195;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2155;dpsi_zscore=-0.717;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:114,120:236:99:2913,0,2770:55:99:0.513
chr1 22169453 rs41266009 G A 981.42 PASS BaseQRankSum=2.304;Dels=0;FS=0;HRun=0;HaplotypeScore=1.8663;MQ=58;MQ0=0;MQRankSum=1.396;QD=12.12;ReadPosRankSum=0.885;SB=-405.52;TI=NM_005529;GI=HSPG2;FC=Silent;DP=81;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.13;Kaviar_AF=0.0264292;Kaviar_AC=4086;Kaviar_AN=154602;ExAC_ALL=0.0261;ExAC_AFR=0.1347;ExAC_AMR=0.0140;ExAC_EAS=0;ExAC_FIN=0.0115;ExAC_NFE=0.0215;ExAC_OTH=0.0122;ExAC_SAS=0.0053;1000g2014oct_all=0.0429313;snp138=rs41266009;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0667;dpsi_zscore=-0.335;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:43,38:81:99:1011,0,1183:58:99:0.469
chr1 22169926 rs62642513 G A 1486.58 PASS BaseQRankSum=1.005;Dels=0;FS=4.41;HRun=0;HaplotypeScore=7.3089;MQ=55;MQ0=0;MQRankSum=0.521;QD=11.89;ReadPosRankSum=-0.985;SB=-727.16;TI=NM_005529;GI=HSPG2;FC=Synonymous_H2874H;EXON;DP=125;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon66:c.C8625T:p.H2875H\x3bHSPG2:NM_005529:exon66:c.C8622T:p.H2874H;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon66:c.C8622T:p.H2874H\x3bHSPG2:uc009vqd.3:exon66:c.C8625T:p.H2875H;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon66:c.C8622T:p.H2874H;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000294878.1|RCV000402417.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.17;Kaviar_AF=0.0283761;Kaviar_AC=4387;Kaviar_AN=154602;ExAC_ALL=0.0316;ExAC_AFR=0.1740;ExAC_AMR=0.0169;ExAC_EAS=0;ExAC_FIN=0.0149;ExAC_NFE=0.0239;ExAC_OTH=0.0123;ExAC_SAS=0.0059;1000g2014oct_all=0.0501198;snp138=rs62642513;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0890;dpsi_zscore=-0.415;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:63,62:125:99:1517,0,1619:55:99:0.496
chr1 22174426 rs2290501 T G 9917.55 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=18.6358;MQ=55;MQ0=0;QD=26.88;SB=-6864.57;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.404;MQRankSum=1.693;ReadPosRankSum=1.247;DP=1991;AN=12;AC=8;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.54;Kaviar_AF=0.331076;Kaviar_AC=51185;Kaviar_AN=154602;ExAC_ALL=0.3372;ExAC_AFR=0.5254;ExAC_AMR=0.2040;ExAC_EAS=0.1720;ExAC_FIN=0.3346;ExAC_NFE=0.3193;ExAC_OTH=0.2929;ExAC_SAS=0.4743;1000g2014oct_all=0.3748;snp138=rs2290501;SIFT_score=0.0;SIFT_converted_rankscore=0.912;SIFT_pred=D;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=1;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=P;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=0.97;FATHMM_converted_rankscore=0.425;FATHMM_pred=T;PROVEAN_score=1.99;PROVEAN_converted_rankscore=0.004;PROVEAN_pred=N;VEST3_score=0.164;VEST3_rankscore=0.198;MetaSVM_score=-0.929;MetaSVM_rankscore=0.443;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=0.444;CADD_raw_rankscore=0.137;CADD_phred=6.985;DANN_score=0.543;DANN_rankscore=0.050;fathmm-MKL_coding_score=0.013;fathmm-MKL_coding_rankscore=0.044;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.663;Eigen-PC-raw=-0.798;GenoCanyon_score=0.968;GenoCanyon_score_rankscore=0.290;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=2.45;GERP++_RS_rankscore=0.288;phyloP100way_vertebrate=-0.665;phyloP100way_vertebrate_rankscore=0.053;phyloP20way_mammalian=0.073;phyloP20way_mammalian_rankscore=0.181;phastCons100way_vertebrate=0.000;phastCons100way_vertebrate_rankscore=0.063;phastCons20way_mammalian=0.001;phastCons20way_mammalian_rankscore=0.043;SiPhy_29way_logOdds=3.671;SiPhy_29way_logOdds_rankscore=0.077;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4203;dpsi_zscore=1.045;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 1/1:0,366:369:99:9918,707,0:55:99:1 1/1:1,263:264:99:7526,517,0:54:99:0.996 ./.:.:.:.:.:.:.:. 0/1:171,211:384:99:5072,0,4039:55:99:0.552 0/1:167,213:380:99:5313,0,4129:55:99:0.561 ./.:.:.:.:.:.:.:. 0/1:138,184:322:99:4575,0,3428:56:99:0.571 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:136,136:272:99:3324,0,3408:54:99:0.5
chr1 22174600 rs3767138 A G 6225.14 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=4.7495;MQ=57;MQ0=0;QD=28.43;SB=-3466.64;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.049;MQRankSum=1.661;ReadPosRankSum=1.025;DP=2337;AN=22;AC=17;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000287463.1|RCV000379747.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.84;Kaviar_AF=0.0048318;Kaviar_AC=747;Kaviar_AN=154602;ExAC_ALL=0.8116;ExAC_AFR=0.7170;ExAC_AMR=0.7278;ExAC_EAS=0.8316;ExAC_FIN=0.8254;ExAC_NFE=0.8338;ExAC_OTH=0.7881;ExAC_SAS=0.8143;1000g2014oct_all=0.761981;snp138=rs3767138;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1265;dpsi_zscore=-0.524;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,219:219:99:6225,451,0:57:99:1 1/1:0,212:212:99:5757,412,0:55:99:1 1/1:1,146:147:99:4027,262,0:56:99:0.993 1/1:1,204:205:99:5925,430,0:56:99:0.995 0/1:92,116:208:99:2951,0,2191:55:99:0.558 0/1:117,113:231:99:2892,0,3013:56:99:0.491 0/1:124,124:248:99:3057,0,2999:57:99:0.5 1/1:0,198:198:99:6092,445,0:57:99:1 0/1:154,119:274:99:3026,0,3767:57:99:0.436 1/1:0,212:212:99:5834,421,0:55:99:1 ./.:.:.:.:.:.:.:. 0/1:94,89:183:99:2377,0,2434:56:99:0.486
chr1 22176500 rs6658388 G T 4858.1 PASS BaseQRankSum=1.148;Dels=0;FS=0;HRun=0;HaplotypeScore=6.1347;MQ=55;MQ0=0;MQRankSum=-1.382;QD=28.92;ReadPosRankSum=-0.431;SB=-2655.7;TI=NM_005529;GI=HSPG2;FC=Silent;DP=651;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.3;Kaviar_AF=0.16809;Kaviar_AC=25987;Kaviar_AN=154602;ExAC_ALL=0.1743;ExAC_AFR=0.0380;ExAC_AMR=0.1278;ExAC_EAS=0.1838;ExAC_FIN=0.2169;ExAC_NFE=0.1747;ExAC_OTH=0.1373;ExAC_SAS=0.2671;1000g2014oct_all=0.154952;snp138=rs6658388;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0068;dpsi_zscore=0.046;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:2,166:168:99:4858,313,0:55:99:0.988 ./.:.:.:.:.:.:.:. 0/1:143,134:277:99:3343,0,3501:57:99:0.484 0/1:95,111:206:99:2552,0,2486:56:99:0.539 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22176831 rs2290500 C T 5008.44 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=2.9662;MQ=57;MQ0=0;QD=28.78;SB=-3035.28;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.779;MQRankSum=-1.919;ReadPosRankSum=0.87;DP=654;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.3;Kaviar_AF=0.169247;Kaviar_AC=26166;Kaviar_AN=154602;ExAC_ALL=0.2057;ExAC_AFR=0.1952;ExAC_AMR=0.1577;ExAC_EAS=0.2000;ExAC_FIN=0.2489;ExAC_NFE=0.1916;ExAC_OTH=0.1447;ExAC_SAS=0.2774;1000g2014oct_all=0.194888;snp138=rs2290500;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1979;dpsi_zscore=-0.683;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,173:174:99:5008,367,0:57:99:1 ./.:.:.:.:.:.:.:. 0/1:136,138:274:99:3129,0,3129:56:99:0.504 0/1:110,95:206:99:2369,0,2798:56:99:0.463 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22180665 rs56123493 C T 2716.47 PASS BaseQRankSum=0.975;Dels=0;FS=2.43;HRun=0;HaplotypeScore=5.3988;MQ=56;MQ0=0;MQRankSum=1.618;QD=13.06;ReadPosRankSum=1.405;SB=-1317.99;TI=NM_005529;GI=HSPG2;FC=Silent;DP=208;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.026;Kaviar_AF=0.0045666;Kaviar_AC=706;Kaviar_AN=154602;ExAC_ALL=0.0146;ExAC_AFR=0.0017;ExAC_AMR=0.0049;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0262;ExAC_OTH=0.0105;ExAC_SAS=0.0051;1000g2014oct_all=0.00279553;snp138=rs56123493;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1187;dpsi_zscore=-0.503;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:103,103:208:99:2746,0,2511:56:99:0.5 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22181360 rs116788687 G C 3714.71 PASS BaseQRankSum=1.008;Dels=0;FS=3.749;HRun=0;HaplotypeScore=56.8443;MQ=55;MQ0=0;MQRankSum=1.393;QD=11.54;ReadPosRankSum=0.627;SB=-1828.64;TI=NM_005529;GI=HSPG2;FC=Missense_I2038M;EXON;DP=322;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon48:c.C6117G:p.I2039M\x3bHSPG2:NM_005529:exon48:c.C6114G:p.I2038M;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon48:c.C6114G:p.I2038M\x3bHSPG2:uc009vqd.3:exon48:c.C6117G:p.I2039M;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon48:c.C6114G:p.I2038M;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000300685.1|RCV000401298.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.075;Kaviar_AF=0.0167915;Kaviar_AC=2596;Kaviar_AN=154602;ExAC_ALL=0.0176;ExAC_AFR=0.0035;ExAC_AMR=0.0067;ExAC_EAS=0;ExAC_FIN=0.0750;ExAC_NFE=0.0225;ExAC_OTH=0.0258;ExAC_SAS=0.0026;1000g2014oct_all=0.00838658;snp138=rs116788687;SIFT_score=0.052;SIFT_converted_rankscore=0.390;SIFT_pred=T;Polyphen2_HDIV_score=0.136;Polyphen2_HDIV_rankscore=0.257;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.033;Polyphen2_HVAR_rankscore=0.210;Polyphen2_HVAR_pred=B;LRT_score=0.024;LRT_converted_rankscore=0.262;LRT_pred=N;MutationTaster_score=0.696;MutationTaster_converted_rankscore=0.334;MutationTaster_pred=D;MutationAssessor_score=1.635;MutationAssessor_score_rankscore=0.420;MutationAssessor_pred=L;FATHMM_score=-0.34;FATHMM_converted_rankscore=0.685;FATHMM_pred=T;PROVEAN_score=-1.23;PROVEAN_converted_rankscore=0.312;PROVEAN_pred=N;VEST3_score=0.104;VEST3_rankscore=0.109;MetaSVM_score=-0.926;MetaSVM_rankscore=0.447;MetaSVM_pred=T;MetaLR_score=0.093;MetaLR_rankscore=0.353;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=3.289;CADD_raw_rankscore=0.454;CADD_phred=22.8;DANN_score=0.969;DANN_rankscore=0.310;fathmm-MKL_coding_score=0.844;fathmm-MKL_coding_rankscore=0.432;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.485;Eigen-PC-raw=-0.391;GenoCanyon_score=0.673;GenoCanyon_score_rankscore=0.224;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=0.062;GERP++_RS_rankscore=0.136;phyloP100way_vertebrate=0.168;phyloP100way_vertebrate_rankscore=0.163;phyloP20way_mammalian=-0.675;phyloP20way_mammalian_rankscore=0.039;phastCons100way_vertebrate=0.976;phastCons100way_vertebrate_rankscore=0.346;phastCons20way_mammalian=0.722;phastCons20way_mammalian_rankscore=0.315;SiPhy_29way_logOdds=4.861;SiPhy_29way_logOdds_rankscore=0.129;Interpro_domain=Immunoglobulin_I-set|Immunoglobulin-like_domain|Immunoglobulin-like_fold;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0483;dpsi_zscore=-0.257;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:173,148:322:99:3715,0,4287:55:99:0.461 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22181723 rs77060492 G C 2125.17 PASS BaseQRankSum=1.694;Dels=0;FS=0;HRun=0;HaplotypeScore=10.1693;MQ=54;MQ0=0;MQRankSum=0.247;QD=27.96;ReadPosRankSum=0.74;SB=-929.79;TI=NM_005529;GI=HSPG2;FC=Silent;DP=457;AN=8;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.3;Kaviar_AF=0.18822;Kaviar_AC=4899;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.190296;snp138=rs77060492;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3200;dpsi_zscore=-0.882;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:2,73:76:99:2158,126,0:54:99:0.973 ./.:.:.:.:.:.:.:. 0/1:78,63:142:99:1587,0,1971:56:99:0.447 0/1:57,59:116:99:1643,0,1505:58:99:0.509 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:63,60:123:99:1663,0,1641:57:99:0.488
chr1 22182115 rs2229474 G A 4238.52 PASS BaseQRankSum=0.731;Dels=0;FS=9.026;HRun=0;HaplotypeScore=16.7437;MQ=57;MQ0=0;MQRankSum=0.614;QD=14.37;ReadPosRankSum=0.009;SB=-2570.53;TI=NM_005529;GI=HSPG2;FC=Missense_R1919C;EXON;DP=295;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon46:c.C5758T:p.R1920C\x3bHSPG2:NM_005529:exon46:c.C5755T:p.R1919C;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon46:c.C5755T:p.R1919C\x3bHSPG2:uc009vqd.3:exon46:c.C5758T:p.R1920C;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon46:c.C5755T:p.R1919C;cytoBand=1p36.12;CLINSIG=Benign|Likely_benign|Likely_benign;CLNDBN=not_specified|Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000178604.1|RCV000351708.1|RCV000400614.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=CN169374|C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.035;Kaviar_AF=0.0050064;Kaviar_AC=774;Kaviar_AN=154602;ExAC_ALL=0.0086;ExAC_AFR=0.0027;ExAC_AMR=0.0029;ExAC_EAS=0;ExAC_FIN=0.0353;ExAC_NFE=0.0144;ExAC_OTH=0.0035;ExAC_SAS=0;1000g2014oct_all=0.00199681;snp138=rs2229474;SIFT_score=0.01;SIFT_converted_rankscore=0.564;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_rankscore=0.899;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.999;Polyphen2_HVAR_rankscore=0.916;Polyphen2_HVAR_pred=D;LRT_score=0.022;LRT_converted_rankscore=0.268;LRT_pred=N;MutationTaster_score=0.987;MutationTaster_converted_rankscore=0.406;MutationTaster_pred=D;MutationAssessor_score=3.2;MutationAssessor_score_rankscore=0.893;MutationAssessor_pred=M;FATHMM_score=-0.4;FATHMM_converted_rankscore=0.693;FATHMM_pred=T;PROVEAN_score=-4.65;PROVEAN_converted_rankscore=0.794;PROVEAN_pred=D;VEST3_score=0.614;VEST3_rankscore=0.636;MetaSVM_score=0.146;MetaSVM_rankscore=0.850;MetaSVM_pred=D;MetaLR_score=0.461;MetaLR_rankscore=0.791;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=5.935;CADD_raw_rankscore=0.815;CADD_phred=27.6;DANN_score=0.999;DANN_rankscore=0.982;fathmm-MKL_coding_score=0.867;fathmm-MKL_coding_rankscore=0.457;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.593;Eigen-PC-raw=0.476;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.446;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=5.12;GERP++_RS_rankscore=0.693;phyloP100way_vertebrate=1.534;phyloP100way_vertebrate_rankscore=0.354;phyloP20way_mammalian=0.940;phyloP20way_mammalian_rankscore=0.530;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.398;phastCons20way_mammalian_rankscore=0.254;SiPhy_29way_logOdds=16.043;SiPhy_29way_logOdds_rankscore=0.804;Interpro_domain=Immunoglobulin_I-set|Immunoglobulin_subtype_2|Immunoglobulin-like_domain|Immunoglobulin-like_fold;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2016;dpsi_zscore=0.725;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:130,163:295:99:4239,0,3571:57:99:0.556 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22183471 rs12024579 A C 8016.44 PASS BaseQRankSum=3.015;Dels=0;FS=5.476;HRun=1;HaplotypeScore=7.6431;MQ=56;MQ0=0;MQRankSum=0.893;QD=13.29;ReadPosRankSum=1.072;SB=-1767.42;TI=NM_005529;GI=HSPG2;FC=Silent;DP=2675;AN=22;AC=17;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.83;Kaviar_AF=0.769705;Kaviar_AC=118998;Kaviar_AN=154602;ExAC_ALL=0.7910;ExAC_AFR=0.6629;ExAC_AMR=0.7139;ExAC_EAS=0.8154;ExAC_FIN=0.8271;ExAC_NFE=0.8159;ExAC_OTH=0.7819;ExAC_SAS=0.7985;1000g2014oct_all=0.749002;snp138=rs12024579;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.8000;dpsi_zscore=1.387;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:112,126:238:99:3193,0,2831:56:99:0.529 1/1:0,237:238:99:6339,451,0:55:99:1 1/1:0,153:154:99:4395,319,0:56:99:1 1/1:1,232:233:99:6536,475,0:57:99:0.996 0/1:140,134:274:99:3231,0,3298:55:99:0.489 0/1:127,139:268:99:3490,0,3241:56:99:0.523 0/1:170,133:303:99:3152,0,4125:57:99:0.439 1/1:1,204:206:99:6012,416,0:57:99:0.995 1/1:2,288:290:99:8016,572,0:57:99:0.993 1/1:3,236:241:99:6592,402,0:55:99:0.987 ./.:.:.:.:.:.:.:. 0/1:108,122:230:99:2996,0,2623:55:99:0.53
chr1 22183739 rs2305562 A G 9636.9 PASS BaseQRankSum=0.023;Dels=0;FS=0.342;HRun=1;HaplotypeScore=21.7572;MQ=57;MQ0=0;MQRankSum=1.653;QD=11.94;ReadPosRankSum=-0.093;SB=-3345.47;TI=NM_005529;GI=HSPG2;FC=Silent;DP=2303;AN=12;AC=8;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.56;Kaviar_AF=0.498266;Kaviar_AC=77033;Kaviar_AN=154602;ExAC_ALL=0.5031;ExAC_AFR=0.4214;ExAC_AMR=0.4920;ExAC_EAS=0.4540;ExAC_FIN=0.5556;ExAC_NFE=0.5481;ExAC_OTH=0.5221;ExAC_SAS=0.3836;1000g2014oct_all=0.446885;snp138=rs2305562;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.4344;dpsi_zscore=-1.022;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:224,228:453:99:5411,0,5560:57:99:0.504 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,336:336:99:9534,695,0:57:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:213,226:441:99:5592,0,5310:56:99:0.515 0/1:162,149:311:99:3848,0,4370:56:99:0.479 0/1:203,202:407:99:4977,0,5316:57:99:0.499 1/1:0,354:355:99:9637,689,0:54:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22186234 rs10917056 A G 11855.4 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=18.2784;MQ=58;MQ0=0;QD=28.72;SB=-5898.94;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.625;MQRankSum=1.7;ReadPosRankSum=1.078;DP=3732;AN=24;AC=22;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.164241;Kaviar_AC=25392;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.929313;snp138=rs10917056;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3635;dpsi_zscore=0.976;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,309:311:99:8933,647,0:58:99:1 1/1:0,314:314:99:9343,674,0:57:99:1 1/1:0,248:248:99:7539,551,0:56:99:1 1/1:1,322:323:99:9714,683,0:57:99:0.997 1/1:0,278:280:99:8155,593,0:56:99:1 1/1:0,329:331:99:9797,713,0:56:99:1 0/1:196,175:372:99:4482,0,5089:57:99:0.472 1/1:2,297:300:99:9098,632,0:56:99:0.993 1/1:0,400:400:99:11855,858,0:57:99:1 1/1:0,342:343:99:9953,722,0:56:99:1 0/1:145,116:261:99:2537,0,3369:53:99:0.444 1/1:0,248:249:99:7218,530,0:57:99:1
chr1 22188328 rs41311989 C T 6879.03 PASS BaseQRankSum=5.599;Dels=0;FS=2.581;HRun=0;HaplotypeScore=32.0068;MQ=56;MQ0=0;MQRankSum=6.517;QD=12.35;ReadPosRankSum=0.209;SB=-4504.59;TI=NM_005529;GI=HSPG2;FC=Missense_R1626H;EXON;DP=557;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon39:c.G4880A:p.R1627H\x3bHSPG2:NM_005529:exon39:c.G4877A:p.R1626H;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon39:c.G4877A:p.R1626H\x3bHSPG2:uc009vqd.3:exon39:c.G4880A:p.R1627H;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon39:c.G4877A:p.R1626H;cytoBand=1p36.12;CLINSIG=Uncertain_significance|Uncertain_significance|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1|not_specified;CLNACC=RCV000293392.1|RCV000385287.1|RCV000403852.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet|MedGen;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800|CN169374;PopFreqMax=0.011;Kaviar_AF=0.0013325;Kaviar_AC=206;Kaviar_AN=154602;ExAC_ALL=0.0014;ExAC_AFR=0.0080;ExAC_AMR=0.0025;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0008;ExAC_OTH=0.0023;ExAC_SAS=6.099e-05;1000g2014oct_all=0.00319489;snp138=rs41311989;SIFT_score=0.036;SIFT_converted_rankscore=0.433;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_rankscore=0.899;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.996;Polyphen2_HVAR_rankscore=0.832;Polyphen2_HVAR_pred=D;LRT_score=0.002;LRT_converted_rankscore=0.367;LRT_pred=N;MutationTaster_score=0.940;MutationTaster_converted_rankscore=0.373;MutationTaster_pred=D;MutationAssessor_score=0.925;MutationAssessor_score_rankscore=0.236;MutationAssessor_pred=L;FATHMM_score=-0.04;FATHMM_converted_rankscore=0.633;FATHMM_pred=T;PROVEAN_score=-2.58;PROVEAN_converted_rankscore=0.556;PROVEAN_pred=D;VEST3_score=0.381;VEST3_rankscore=0.441;MetaSVM_score=-0.677;MetaSVM_rankscore=0.615;MetaSVM_pred=T;MetaLR_score=0.163;MetaLR_rankscore=0.500;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=4.654;CADD_raw_rankscore=0.624;CADD_phred=24.5;DANN_score=0.999;DANN_rankscore=0.998;fathmm-MKL_coding_score=0.825;fathmm-MKL_coding_rankscore=0.414;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.509;Eigen-PC-raw=0.519;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.462;integrated_fitCons_score=0.722;integrated_fitCons_score_rankscore=0.854;integrated_confidence_value=0;GERP++_RS=4.94;GERP++_RS_rankscore=0.645;phyloP100way_vertebrate=2.386;phyloP100way_vertebrate_rankscore=0.438;phyloP20way_mammalian=0.935;phyloP20way_mammalian_rankscore=0.490;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=1.000;phastCons20way_mammalian_rankscore=0.888;SiPhy_29way_logOdds=9.134;SiPhy_29way_logOdds_rankscore=0.358;Interpro_domain=Laminin_EGF_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.9910;dpsi_zscore=-1.466;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:280,275:557:99:6879,0,6894:56:99:0.495 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22190541 rs141748265 C G 1108.85 PASS BaseQRankSum=0.569;Dels=0;FS=5.028;HRun=0;HaplotypeScore=2.7331;MQ=55;MQ0=0;MQRankSum=2.286;QD=10.17;ReadPosRankSum=-0.009;SB=-477.23;TI=NM_005529;GI=HSPG2;FC=Silent;DP=109;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.014;Kaviar_AF=0.0016623;Kaviar_AC=257;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.00419329;snp138=rs141748265;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2700;dpsi_zscore=-0.807;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:64,45:109:99:1139,0,1524:55:99:0.413 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22191454 rs897471 G A 6805.45 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=11.833;MQ=56;MQ0=0;QD=28.53;SB=-3623.33;TI=NM_005529;GI=HSPG2;FC=Missense_A1503V;EXON;BaseQRankSum=-1.005;MQRankSum=2.61;ReadPosRankSum=-0.75;DP=1903;AN=20;AC=16;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon36:c.C4511T:p.A1504V\x3bHSPG2:NM_005529:exon36:c.C4508T:p.A1503V;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon36:c.C4508T:p.A1503V\x3bHSPG2:uc009vqd.3:exon36:c.C4511T:p.A1504V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon36:c.C4508T:p.A1503V;cytoBand=1p36.12;CLINSIG=Benign|Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|not_specified|Dyssegmental_Dysplasia;CLNACC=RCV000274418.1|RCV000299057.1|RCV000371265.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|CN169374|C1857100:ORPHA1865;PopFreqMax=0.9;Kaviar_AF=0.675069;Kaviar_AC=104367;Kaviar_AN=154602;ExAC_ALL=0.7463;ExAC_AFR=0.6525;ExAC_AMR=0.8269;ExAC_EAS=0.9042;ExAC_FIN=0.7712;ExAC_NFE=0.7581;ExAC_OTH=0.7778;ExAC_SAS=0.6023;1000g2014oct_all=0.691494;snp138=rs897471;SIFT_score=0.056;SIFT_converted_rankscore=0.381;SIFT_pred=T;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_rankscore=0.899;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.997;Polyphen2_HVAR_rankscore=0.850;Polyphen2_HVAR_pred=D;LRT_score=0.002;LRT_converted_rankscore=0.381;LRT_pred=N;MutationTaster_score=0.999;MutationTaster_converted_rankscore=0.214;MutationTaster_pred=P;MutationAssessor_score=2.045;MutationAssessor_score_rankscore=0.562;MutationAssessor_pred=M;FATHMM_score=1.27;FATHMM_converted_rankscore=0.361;FATHMM_pred=T;PROVEAN_score=-3.11;PROVEAN_converted_rankscore=0.636;PROVEAN_pred=D;VEST3_score=0.088;VEST3_rankscore=0.084;MetaSVM_score=-1.100;MetaSVM_rankscore=0.041;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=3.682;CADD_raw_rankscore=0.500;CADD_phred=23.3;DANN_score=0.999;DANN_rankscore=0.972;fathmm-MKL_coding_score=0.459;fathmm-MKL_coding_rankscore=0.274;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.002;Eigen-PC-raw=-0.161;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.500;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=4.37;GERP++_RS_rankscore=0.517;phyloP100way_vertebrate=4.315;phyloP100way_vertebrate_rankscore=0.587;phyloP20way_mammalian=0.998;phyloP20way_mammalian_rankscore=0.613;phastCons100way_vertebrate=0.998;phastCons100way_vertebrate_rankscore=0.411;phastCons20way_mammalian=0.536;phastCons20way_mammalian_rankscore=0.277;SiPhy_29way_logOdds=12.819;SiPhy_29way_logOdds_rankscore=0.569;Interpro_domain=Laminin_IV;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2241;dpsi_zscore=-0.732;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,198:198:99:5649,412,0:56:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,186:186:99:5343,391,0:56:99:1 0/1:114,74:188:99:1827,0,2865:56:99:0.394 0/1:76,99:175:99:2733,0,1767:56:99:0.566 1/1:1,232:233:99:6805,465,0:57:99:0.996 0/1:84,103:187:99:2778,0,2068:57:99:0.551 0/1:119,94:214:99:2501,0,3035:57:99:0.441 1/1:0,187:187:99:5538,403,0:55:99:1 1/1:1,171:172:99:4539,293,0:53:99:0.994 1/1:0,163:163:99:4970,364,0:56:99:1
chr1 22199081 rs2501266 A T 5535.44 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=7.1761;MQ=56;MQ0=0;QD=28.09;SB=-2511.91;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.69;MQRankSum=0.997;ReadPosRankSum=-0.787;DP=1838;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.00011;Kaviar_AC=17;Kaviar_AN=154602;ExAC_ALL=0.9936;ExAC_AFR=0.9430;ExAC_AMR=0.9974;ExAC_EAS=1;ExAC_FIN=1;ExAC_NFE=0.9998;ExAC_OTH=0.9969;ExAC_SAS=0.9999;1000g2014oct_all=0.979832;snp138=rs2501266;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-1.5380;dpsi_zscore=-1.732;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,171:173:99:4859,352,0:56:99:1 1/1:0,147:149:99:4256,307,0:54:99:1 1/1:0,129:129:99:3802,277,0:55:99:1 1/1:0,141:142:99:4041,295,0:57:99:1 1/1:0,143:143:99:4187,307,0:56:99:1 1/1:1,164:166:99:4573,337,0:54:99:0.994 1/1:0,180:180:99:5535,409,0:58:99:1 1/1:0,136:137:99:4226,313,0:55:99:1 1/1:0,177:178:99:5430,403,0:59:99:1 1/1:0,145:146:99:4164,304,0:57:99:1 1/1:0,141:141:99:3537,247,0:50:99:1 1/1:0,153:154:99:4450,328,0:55:99:1
chr1 22199245 rs2229482 C T 6920.25 PASS BaseQRankSum=3.769;Dels=0;FS=2.577;HRun=0;HaplotypeScore=14.278;MQ=56;MQ0=0;MQRankSum=1.378;QD=14.72;ReadPosRankSum=0.928;SB=-1593.57;TI=NM_005529;GI=HSPG2;FC=Synonymous_V1299V;EXON;DP=1893;AN=20;AC=15;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon32:c.G3900A:p.V1300V\x3bHSPG2:NM_005529:exon32:c.G3897A:p.V1299V;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon32:c.G3897A:p.V1299V\x3bHSPG2:uc009vqd.3:exon32:c.G3900A:p.V1300V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon32:c.G3897A:p.V1299V;cytoBand=1p36.12;CLINSIG=Benign|Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|not_specified|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000269271.1|RCV000346655.1|RCV000366230.1;CLNDSDB=MedGen:Orphanet|MedGen|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|CN169374|C0036391:255800:ORPHA800;PopFreqMax=0.71;Kaviar_AF=0.523376;Kaviar_AC=80915;Kaviar_AN=154602;ExAC_ALL=0.6066;ExAC_AFR=0.3382;ExAC_AMR=0.5082;ExAC_EAS=0.5027;ExAC_FIN=0.7106;ExAC_NFE=0.6752;ExAC_OTH=0.6352;ExAC_SAS=0.5410;1000g2014oct_all=0.42492;snp138=rs2229482;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-2.9892;dpsi_zscore=-2.152;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:83,107:190:99:2826,0,2032:56:99:0.563 ./.:.:.:.:.:.:.:. 1/1:0,166:167:99:4951,361,0:55:99:1 1/1:0,165:166:99:4720,340,0:55:99:1 0/1:108,83:191:99:2139,0,2657:56:99:0.435 0/1:79,98:178:99:2313,0,2061:56:99:0.554 1/1:0,243:243:99:6920,500,0:58:99:1 0/1:86,83:169:99:2062,0,2204:57:99:0.491 1/1:2,225:227:99:6560,437,0:56:99:0.991 1/1:0,189:189:99:5397,391,0:56:99:1 0/1:78,94:173:99:2178,0,1684:51:99:0.547 ./.:.:.:.:.:.:.:.
chr1 22199821 rs2454290 G A 14400.1 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=21.7117;MQ=56;MQ0=0;QD=29.33;SB=-7475.01;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.624;MQRankSum=0.812;ReadPosRankSum=-1.173;DP=4281;AN=22;AC=20;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.98;Kaviar_AF=0.807092;Kaviar_AC=124778;Kaviar_AN=154602;ExAC_ALL=0.8192;ExAC_AFR=0.4888;ExAC_AMR=0.9240;ExAC_EAS=0.9776;ExAC_FIN=0.8641;ExAC_NFE=0.8483;ExAC_OTH=0.8271;ExAC_SAS=0.7353;1000g2014oct_all=0.742013;snp138=rs2454290;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-3.1830;dpsi_zscore=-2.194;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,409:410:99:12024,882,0:56:99:1 ./.:.:.:.:.:.:.:. 1/1:0,259:260:99:7585,545,0:58:99:1 1/1:0,449:451:99:12862,921,0:57:99:1 1/1:0,387:388:99:10681,764,0:55:99:1 1/1:0,399:402:99:11459,825,0:55:99:1 1/1:0,512:513:99:14400,1035,0:56:99:1 0/1:193,172:366:99:4543,0,4640:56:99:0.471 1/1:1,410:413:99:12158,879,0:58:99:0.998 1/1:0,417:418:99:11497,822,0:55:99:1 1/1:0,366:367:99:9484,665,0:51:99:1 0/1:167,123:291:99:3104,0,4065:55:99:0.424
chr1 22199982 rs34855688 G A 2616.48 PASS BaseQRankSum=0.264;Dels=0;FS=0.482;HRun=1;HaplotypeScore=12.058;MQ=56;MQ0=0;MQRankSum=2.908;QD=10.59;ReadPosRankSum=-0.801;SB=-1511.71;TI=NM_005529;GI=HSPG2;FC=Silent;DP=247;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.11;Kaviar_AF=0.0090232;Kaviar_AC=1395;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0327476;snp138=rs34855688;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0220;dpsi_zscore=-0.116;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:135,112:247:99:2646,0,3293:56:99:0.453 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22200835 rs2445135 C G 4861.75 PASS Dels=0;FS=0;HRun=3;HaplotypeScore=19.3424;MQ=54;MQ0=0;QD=27.86;SB=-1552.53;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.699;MQRankSum=0.445;ReadPosRankSum=-0.313;DP=1445;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.0003458;Kaviar_AC=9;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.978235;snp138=rs2445135;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2207;dpsi_zscore=-0.726;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,102:102:99:2874,214,0:54:99:1 1/1:1,104:105:99:2946,214,0:56:99:0.99 1/1:1,110:111:99:3209,235,0:55:99:0.991 1/1:0,104:104:99:2944,217,0:58:99:1 1/1:0,96:96:99:2789,205,0:54:99:1 1/1:0,142:142:99:4132,301,0:56:99:1 1/1:0,170:170:99:4862,355,0:57:99:1 1/1:0,135:135:99:4067,301,0:56:99:1 1/1:0,156:156:99:4695,346,0:57:99:1 1/1:0,101:101:99:2757,199,0:56:99:1 1/1:0,106:106:99:2796,199,0:53:99:1 1/1:0,117:117:99:3632,268,0:58:99:1
chr1 22200998 rs2229481 C T 2448.1 PASS BaseQRankSum=-1.732;Dels=0;FS=3.106;HRun=0;HaplotypeScore=19.8604;MQ=57;MQ0=0;MQRankSum=-0.038;QD=11.44;ReadPosRankSum=1.912;SB=-1405.36;TI=NM_005529;GI=HSPG2;FC=Missense_R1186Q;EXON;DP=214;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon28:c.G3560A:p.R1187Q\x3bHSPG2:NM_005529:exon28:c.G3557A:p.R1186Q;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon28:c.G3557A:p.R1186Q\x3bHSPG2:uc009vqd.3:exon28:c.G3560A:p.R1187Q;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon28:c.G3557A:p.R1186Q;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000305377.1|RCV000399591.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.2;Kaviar_AF=0.0372181;Kaviar_AC=5754;Kaviar_AN=154602;ExAC_ALL=0.0379;ExAC_AFR=0.1733;ExAC_AMR=0.0193;ExAC_EAS=0.0002;ExAC_FIN=0.0286;ExAC_NFE=0.0329;ExAC_OTH=0.0268;ExAC_SAS=0.0113;1000g2014oct_all=0.0638978;snp138=rs2229481;SIFT_score=0.595;SIFT_converted_rankscore=0.057;SIFT_pred=T;Polyphen2_HDIV_score=0.002;Polyphen2_HDIV_rankscore=0.090;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.005;Polyphen2_HVAR_rankscore=0.104;Polyphen2_HVAR_pred=B;LRT_score=0.861;LRT_converted_rankscore=0.089;LRT_pred=N;MutationTaster_score=0.998;MutationTaster_converted_rankscore=0.224;MutationTaster_pred=P;MutationAssessor_score=-0.085;MutationAssessor_score_rankscore=0.047;MutationAssessor_pred=N;FATHMM_score=0.07;FATHMM_converted_rankscore=0.617;FATHMM_pred=T;PROVEAN_score=-0.54;PROVEAN_converted_rankscore=0.166;PROVEAN_pred=N;VEST3_score=0.192;VEST3_rankscore=0.235;MetaSVM_score=-1.047;MetaSVM_rankscore=0.152;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=2.470;CADD_raw_rankscore=0.358;CADD_phred=19.28;DANN_score=0.963;DANN_rankscore=0.289;fathmm-MKL_coding_score=0.167;fathmm-MKL_coding_rankscore=0.193;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.076;Eigen-PC-raw=-0.962;GenoCanyon_score=0.898;GenoCanyon_score_rankscore=0.260;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=0.185;GERP++_RS_rankscore=0.143;phyloP100way_vertebrate=0.037;phyloP100way_vertebrate_rankscore=0.136;phyloP20way_mammalian=-0.461;phyloP20way_mammalian_rankscore=0.055;phastCons100way_vertebrate=0.056;phastCons100way_vertebrate_rankscore=0.214;phastCons20way_mammalian=0.952;phastCons20way_mammalian_rankscore=0.428;SiPhy_29way_logOdds=8.637;SiPhy_29way_logOdds_rankscore=0.329;Interpro_domain=Laminin_EGF_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-4.6030;dpsi_zscore=-2.440;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:113,99:214:99:2478,0,3009:57:99:0.467
chr1 22201331 rs2290494 C T 2436.66 PASS BaseQRankSum=-0.72;Dels=0;FS=1.277;HRun=0;HaplotypeScore=9.1094;MQ=58;MQ0=0;MQRankSum=0.935;QD=11.6;ReadPosRankSum=-0.645;SB=-1001.84;TI=NM_005529;GI=HSPG2;FC=Silent;DP=682;AN=10;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.6;Kaviar_AF=0.0416877;Kaviar_AC=6445;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.30012;snp138=rs2290494;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3777;dpsi_zscore=-0.956;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:88,69:158:99:1863,0,2226:58:99:0.439 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:81,80:162:99:2198,0,2181:58:99:0.497 0/1:82,94:176:99:2467,0,2280:58:99:0.534 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:31,54:85:99:1373,0,757:55:99:0.635 0/1:60,40:101:99:1191,0,1713:57:99:0.4
chr1 22201438 rs41307806 C T 1795.33 PASS BaseQRankSum=-1.195;Dels=0;FS=1.191;HRun=0;HaplotypeScore=8.4103;MQ=57;MQ0=0;MQRankSum=0.193;QD=9.97;ReadPosRankSum=-0.789;SB=-1053.51;TI=NM_005529;GI=HSPG2;FC=Synonymous_A1120A;EXON;DP=180;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon26:c.G3363A:p.A1121A\x3bHSPG2:NM_005529:exon26:c.G3360A:p.A1120A;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon26:c.G3360A:p.A1120A\x3bHSPG2:uc009vqd.3:exon26:c.G3363A:p.A1121A;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon26:c.G3360A:p.A1120A;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000259859.1|RCV000317371.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.15;Kaviar_AF=0.0547858;Kaviar_AC=8470;Kaviar_AN=154602;ExAC_ALL=0.0673;ExAC_AFR=0.0176;ExAC_AMR=0.0408;ExAC_EAS=0.0003;ExAC_FIN=0.1464;ExAC_NFE=0.0936;ExAC_OTH=0.0831;ExAC_SAS=0.0223;1000g2014oct_all=0.0309505;snp138=rs41307806;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1956;dpsi_zscore=-0.679;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:104,76:180:99:1825,0,2650:57:99:0.422 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22202109 rs2501265 C T 8280.42 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=13.5714;MQ=56;MQ0=0;QD=29.54;SB=-3393.99;TI=NM_005529;GI=HSPG2;FC=Silent;DP=2372;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000330637.1|RCV000387485.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=1.;Kaviar_AF=0.936288;Kaviar_AC=144752;Kaviar_AN=154602;ExAC_ALL=0.9837;ExAC_AFR=0.8242;ExAC_AMR=0.9922;ExAC_EAS=1;ExAC_FIN=1;ExAC_NFE=0.9992;ExAC_OTH=0.9934;ExAC_SAS=0.9995;1000g2014oct_all=0.942292;snp138=rs2501265;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0439;dpsi_zscore=-0.237;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,206:206:99:6085,445,0:56:99:1 1/1:0,177:177:99:4897,349,0:55:99:1 1/1:0,170:170:99:4946,358,0:54:99:1 1/1:0,209:209:99:6010,433,0:58:99:1 1/1:0,193:194:99:5544,403,0:56:99:1 1/1:0,225:225:99:6393,461,0:56:99:1 1/1:0,216:216:99:6170,442,0:58:99:1 1/1:0,192:192:99:5749,418,0:56:99:1 1/1:0,289:290:99:8280,596,0:58:99:1 1/1:0,176:176:99:4929,352,0:56:99:1 1/1:0,162:162:99:4271,304,0:52:99:1 1/1:0,155:155:99:4426,319,0:56:99:1
chr1 22204630 rs7513608 G A 2747.82 PASS BaseQRankSum=-0.611;Dels=0;FS=0;HRun=0;HaplotypeScore=15.5362;MQ=58;MQ0=0;MQRankSum=-0.23;QD=10.79;ReadPosRankSum=-0.305;SB=-1098.6;TI=NM_005529;GI=HSPG2;FC=Silent;DP=917;AN=10;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.61;Kaviar_AF=0.247739;Kaviar_AC=38301;Kaviar_AN=154602;ExAC_ALL=0.2667;ExAC_AFR=0.1647;ExAC_AMR=0.4426;ExAC_EAS=0.5844;ExAC_FIN=0.2136;ExAC_NFE=0.2143;ExAC_OTH=0.2768;ExAC_SAS=0.2668;1000g2014oct_all=0.309704;snp138=rs7513608;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.5792;dpsi_zscore=-1.167;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:113,89:202:99:2209,0,2841:58:99:0.441 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:98,77:175:99:1813,0,2462:55:99:0.44 0/1:96,106:202:99:2778,0,2377:56:99:0.525 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:91,70:161:99:1506,0,2032:53:99:0.435 0/1:88,89:177:99:2211,0,2199:56:99:0.503
chr1 22205408 rs2454294 T C 5805.44 PASS Dels=0;FS=0;HRun=2;HaplotypeScore=8.1984;MQ=57;MQ0=0;QD=30.48;SB=-2310.92;TI=NM_005529;GI=HSPG2;FC=Silent;DP=1821;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.160807;Kaviar_AC=24861;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.973642;snp138=rs2454294;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0743;dpsi_zscore=-0.364;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,156:156:99:4754,352,0:57:99:1 1/1:0,140:140:99:3926,283,0:56:99:1 1/1:0,120:120:99:3731,274,0:57:99:1 1/1:0,161:161:99:5234,388,0:57:99:1 1/1:0,164:164:99:4865,358,0:56:99:1 1/1:0,156:156:99:4605,337,0:57:99:1 1/1:0,188:188:99:5805,424,0:56:99:1 1/1:0,150:150:99:4656,349,0:58:99:1 1/1:0,162:162:99:4884,358,0:58:99:1 1/1:0,143:143:99:4336,316,0:57:99:1 1/1:0,116:116:99:2993,214,0:51:99:1 1/1:0,165:165:99:5006,367,0:55:99:1
chr1 22205466 rs2454293 T C 8071.45 PASS BaseQRankSum=1.691;Dels=0.03;FS=0;HRun=7;HaplotypeScore=29.8101;MQ=56;MQ0=0;MQRankSum=-1.18;QD=27.82;ReadPosRankSum=-0.683;SB=-3930.03;TI=NM_005529;GI=HSPG2;FC=Silent;DP=2744;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.939263;Kaviar_AC=145212;Kaviar_AN=154602;ExAC_ALL=0.9878;ExAC_AFR=0.8784;ExAC_AMR=0.9937;ExAC_EAS=0.9974;ExAC_FIN=0.9994;ExAC_NFE=0.9982;ExAC_OTH=0.9932;ExAC_SAS=0.9974;1000g2014oct_all=0.959465;snp138=rs2454293;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1341;dpsi_zscore=0.578;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,250:252:99:7261,527,0:56:99:0.996 1/1:0,192:192:99:5541,400,0:56:99:1 1/1:0,170:170:99:5178,376,0:56:99:1 1/1:0,261:261:99:7662,560,0:57:99:1 1/1:0,236:236:99:6884,503,0:56:99:1 1/1:0,212:212:99:6609,482,0:56:99:1 1/1:0,270:270:99:8071,590,0:56:99:1 1/1:0,202:203:99:6037,442,0:56:99:1 1/1:1,241:242:99:7395,539,0:57:99:0.996 1/1:0,222:222:99:6610,482,0:56:99:1 1/1:0,193:193:99:5062,358,0:51:99:1 1/1:0,212:212:99:6145,445,0:55:99:1
chr1 22206649 rs989994 T C 11651.7 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=10.0356;MQ=55;MQ0=0;QD=28.74;SB=-7092.99;TI=NM_005529;GI=HSPG2;FC=Missense_N765S;EXON;BaseQRankSum=1.721;MQRankSum=0.468;ReadPosRankSum=-0.935;DP=4086;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon17:c.A2297G:p.N766S\x3bHSPG2:NM_005529:exon17:c.A2294G:p.N765S;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon17:c.A2294G:p.N765S\x3bHSPG2:uc009vqd.3:exon17:c.A2297G:p.N766S;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon17:c.A2294G:p.N765S;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000317586.1|RCV000372262.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=1.;Kaviar_AF=0.930195;Kaviar_AC=143810;Kaviar_AN=154602;ExAC_ALL=0.9811;ExAC_AFR=0.7916;ExAC_AMR=0.9923;ExAC_EAS=1;ExAC_FIN=1;ExAC_NFE=0.9996;ExAC_OTH=0.9868;ExAC_SAS=0.9997;1000g2014oct_all=0.929912;snp138=rs989994;SIFT_score=0.246;SIFT_converted_rankscore=0.173;SIFT_pred=T;Polyphen2_HDIV_score=0.003;Polyphen2_HDIV_rankscore=0.102;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.016;Polyphen2_HVAR_rankscore=0.166;Polyphen2_HVAR_pred=B;LRT_score=0.016;LRT_converted_rankscore=0.281;LRT_pred=N;MutationTaster_score=0.002;MutationTaster_converted_rankscore=0.449;MutationTaster_pred=P;MutationAssessor_score=1.425;MutationAssessor_score_rankscore=0.359;MutationAssessor_pred=L;FATHMM_score=0.11;FATHMM_converted_rankscore=0.612;FATHMM_pred=T;PROVEAN_score=-1.88;PROVEAN_converted_rankscore=0.439;PROVEAN_pred=N;VEST3_score=0.082;VEST3_rankscore=0.075;MetaSVM_score=-0.967;MetaSVM_rankscore=0.378;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=2.117;CADD_raw_rankscore=0.315;CADD_phred=16.97;DANN_score=0.993;DANN_rankscore=0.594;fathmm-MKL_coding_score=0.821;fathmm-MKL_coding_rankscore=0.411;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.124;Eigen-PC-raw=0.050;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.707;integrated_fitCons_score_rankscore=0.730;integrated_confidence_value=0;GERP++_RS=5.38;GERP++_RS_rankscore=0.772;phyloP100way_vertebrate=0.800;phyloP100way_vertebrate_rankscore=0.265;phyloP20way_mammalian=0.964;phyloP20way_mammalian_rankscore=0.580;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=1.000;phastCons20way_mammalian_rankscore=0.888;SiPhy_29way_logOdds=13.348;SiPhy_29way_logOdds_rankscore=0.599;Interpro_domain=Laminin_EGF_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1142;dpsi_zscore=-0.491;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,371:371:99:10664,765,0:55:99:1 1/1:0,354:354:99:9811,698,0:56:99:1 1/1:0,241:242:99:7191,521,0:56:99:1 1/1:0,349:349:99:10198,734,0:58:99:1 1/1:1,325:326:99:9353,674,0:55:99:0.997 1/1:0,359:359:99:10677,771,0:57:99:1 1/1:0,392:392:99:11342,816,0:57:99:1 1/1:0,339:339:99:10238,740,0:57:99:1 1/1:0,400:400:99:11652,840,0:58:99:1 1/1:0,387:387:99:11061,792,0:56:99:1 1/1:0,260:260:99:6851,488,0:51:99:1 1/1:0,307:307:99:8991,647,0:56:99:1
chr1 22206942 rs1874793 G A 12137.3 PASS BaseQRankSum=1.722;Dels=0;FS=0;HRun=0;HaplotypeScore=16.1874;MQ=56;MQ0=0;MQRankSum=-0.443;QD=29.7;ReadPosRankSum=0.295;SB=-6785.28;TI=NM_005529;GI=HSPG2;FC=Synonymous_A703A;EXON;DP=3922;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon16:c.C2112T:p.A704A\x3bHSPG2:NM_005529:exon16:c.C2109T:p.A703A;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon16:c.C2109T:p.A703A\x3bHSPG2:uc009vqd.3:exon16:c.C2112T:p.A704A;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon16:c.C2109T:p.A703A;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000282418.1|RCV000318734.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=1.;Kaviar_AF=0.938099;Kaviar_AC=145032;Kaviar_AN=154602;ExAC_ALL=0.9812;ExAC_AFR=0.7924;ExAC_AMR=0.9923;ExAC_EAS=1;ExAC_FIN=1;ExAC_NFE=0.9996;ExAC_OTH=0.9867;ExAC_SAS=0.9998;1000g2014oct_all=0.929912;snp138=rs1874793;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0917;dpsi_zscore=0.458;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,351:352:99:10456,767,0:56:99:0.997 1/1:0,277:277:99:7856,566,0:55:99:1 1/1:0,273:274:99:8159,602,0:57:99:1 1/1:0,373:374:99:10831,795,0:58:99:1 1/1:0,374:376:99:10972,804,0:56:99:1 1/1:1,339:342:99:9846,725,0:55:99:0.997 1/1:1,404:406:99:12137,885,0:57:99:0.998 1/1:0,284:286:99:8897,662,0:57:99:1 1/1:1,362:364:99:10858,795,0:57:99:0.997 1/1:2,327:330:99:9401,686,0:55:99:0.994 1/1:0,268:268:99:7009,500,0:51:99:1 1/1:1,271:273:99:8040,590,0:56:99:0.996
chr1 22207235 rs1874792 T C 9759.76 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=13.1371;MQ=57;MQ0=0;QD=29.94;SB=-4007.98;TI=NM_005529;GI=HSPG2;FC=Missense_M638V;EXON;BaseQRankSum=1.666;MQRankSum=-1.325;ReadPosRankSum=-1.49;DP=3032;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon15:c.A1915G:p.M639V\x3bHSPG2:NM_005529:exon15:c.A1912G:p.M638V;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon15:c.A1912G:p.M638V\x3bHSPG2:uc009vqd.3:exon15:c.A1915G:p.M639V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon15:c.A1912G:p.M638V;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000260399.1|RCV000296869.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=1.;Kaviar_AF=0.933817;Kaviar_AC=144370;Kaviar_AN=154602;ExAC_ALL=0.9931;ExAC_AFR=0.9216;ExAC_AMR=0.9971;ExAC_EAS=1;ExAC_FIN=1;ExAC_NFE=0.9997;ExAC_OTH=0.9985;ExAC_SAS=1;1000g2014oct_all=0.973642;snp138=rs1874792;SIFT_score=1.0;SIFT_converted_rankscore=0.010;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.0;Polyphen2_HVAR_rankscore=0.013;Polyphen2_HVAR_pred=B;LRT_score=0.062;LRT_converted_rankscore=0.221;LRT_pred=N;MutationTaster_score=1.000;MutationTaster_converted_rankscore=0.198;MutationTaster_pred=P;MutationAssessor_score=-2.085;MutationAssessor_score_rankscore=0.002;MutationAssessor_pred=N;FATHMM_score=1.34;FATHMM_converted_rankscore=0.348;FATHMM_pred=T;PROVEAN_score=1.09;PROVEAN_converted_rankscore=0.013;PROVEAN_pred=N;VEST3_score=0.016;VEST3_rankscore=0.003;MetaSVM_score=-0.979;MetaSVM_rankscore=0.352;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=-1.579;CADD_raw_rankscore=0.015;CADD_phred=0.002;DANN_score=0.341;DANN_rankscore=0.021;fathmm-MKL_coding_score=0.174;fathmm-MKL_coding_rankscore=0.196;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.163;Eigen-PC-raw=-0.925;GenoCanyon_score=0.962;GenoCanyon_score_rankscore=0.286;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=3.56;GERP++_RS_rankscore=0.397;phyloP100way_vertebrate=1.148;phyloP100way_vertebrate_rankscore=0.310;phyloP20way_mammalian=-0.425;phyloP20way_mammalian_rankscore=0.059;phastCons100way_vertebrate=0.757;phastCons100way_vertebrate_rankscore=0.290;phastCons20way_mammalian=0.008;phastCons20way_mammalian_rankscore=0.104;SiPhy_29way_logOdds=7.569;SiPhy_29way_logOdds_rankscore=0.269;Interpro_domain=Laminin_IV;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4067;dpsi_zscore=1.030;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,254:254:99:7605,557,0:57:99:1 1/1:0,266:266:99:7511,545,0:56:99:1 1/1:0,203:203:99:5959,433,0:57:99:1 1/1:0,232:233:99:7134,521,0:57:99:1 1/1:0,280:280:99:8300,605,0:57:99:1 1/1:0,245:245:99:7502,551,0:57:99:1 1/1:1,314:315:99:9428,686,0:57:99:0.997 1/1:0,249:249:99:7535,554,0:55:99:1 1/1:0,332:333:99:9760,710,0:57:99:1 1/1:0,211:211:99:6177,448,0:57:99:1 1/1:2,185:187:99:4931,313,0:52:99:0.989 1/1:0,256:256:99:7662,557,0:55:99:1
chr1 22207381 rs141879728 C T 1775.66 PASS BaseQRankSum=0.495;Dels=0;FS=1.372;HRun=1;HaplotypeScore=0.8941;MQ=57;MQ0=0;MQRankSum=0.53;QD=12.96;ReadPosRankSum=0.499;SB=-1012.42;TI=NM_005529;GI=HSPG2;FC=Silent;DP=137;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.041;Kaviar_AF=0.0019987;Kaviar_AC=309;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0121805;snp138=rs141879728;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.5401;dpsi_zscore=1.172;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:62,75:137:99:1806,0,1465:57:99:0.547 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22207804 rs139046040 ACCCAGGGTGGCAG A 12942.8 PASS FS=0;HRun=0;HaplotypeScore=128.007;MQ=34;MQ0=0;QD=106.97;SB=-5827.98;TI=NM_005529;GI=HSPG2;FC=Noncoding;DP=1154;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.0290229;Kaviar_AC=4487;Kaviar_AN=154602;ExAC_ALL=0.9888;ExAC_AFR=0.8785;ExAC_AMR=0.9949;ExAC_EAS=0.9999;ExAC_FIN=0.9998;ExAC_NFE=0.9996;ExAC_OTH=0.9956;ExAC_SAS=0.9997;1000g2014oct_all=0.959665;snp138=rs139046040;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:32,88:121:99:12943,277,0:34:99:0.733 1/1:26,57:83:99:7639,178,0:36:99:0.687 1/1:22,48:70:99:6706,154,0:34:99:0.686 1/1:29,61:92:99:8821,193,0:34:99:0.678 1/1:23,70:93:99:9870,211,0:34:99:0.753 1/1:20,87:108:99:12343,265,0:35:99:0.813 1/1:35,79:114:99:10038,241,0:38:99:0.693 1/1:40,79:120:99:11641,253,0:38:99:0.664 1/1:40,85:125:99:11951,262,0:35:99:0.68 1/1:31,45:76:99:5284,135,0:37:99:0.592 1/1:23,28:51:84.28:3137,84,0:39:84:0.549 1/1:28,72:101:99:9894,223,0:34:99:0.72
chr1 22208030 rs921847 C T 4972.38 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=10.0789;MQ=55;MQ0=0;QD=28.58;SB=-2693.64;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.577;MQRankSum=0.804;ReadPosRankSum=0.526;DP=1736;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.955654;Kaviar_AC=147746;Kaviar_AN=154602;ExAC_ALL=0.9688;ExAC_AFR=0.7978;ExAC_AMR=0.9877;ExAC_EAS=1;ExAC_FIN=0.9718;ExAC_NFE=0.9848;ExAC_OTH=0.9722;ExAC_SAS=0.9806;1000g2014oct_all=0.925919;snp138=rs921847;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0343;dpsi_zscore=0.221;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,174:174:99:4972,373,0:55:99:1 1/1:0,136:137:99:3659,271,0:53:99:1 1/1:0,129:129:99:3695,277,0:55:99:1 1/1:0,147:148:99:4230,319,0:55:99:1 1/1:0,147:147:99:4259,316,0:52:99:1 1/1:0,179:179:99:4968,367,0:53:99:1 1/1:0,158:158:99:4575,349,0:54:99:1 1/1:0,119:119:99:3514,268,0:54:99:1 1/1:0,168:169:99:4831,364,0:54:99:1 1/1:1,111:112:99:3158,232,0:55:99:0.991 1/1:0,151:151:99:3922,277,0:54:99:1 1/1:1,112:113:99:3163,244,0:53:99:0.991
chr1 22211217 rs2290493 G A 3617.77 PASS BaseQRankSum=1.868;Dels=0;FS=3.039;HRun=0;HaplotypeScore=17.1942;MQ=57;MQ0=0;MQRankSum=-0.432;QD=13.28;ReadPosRankSum=0.378;SB=-1548.18;TI=NM_005529;GI=HSPG2;FC=Silent;DP=1005;AN=10;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.61;Kaviar_AF=0.253994;Kaviar_AC=39268;Kaviar_AN=154602;ExAC_ALL=0.2763;ExAC_AFR=0.1720;ExAC_AMR=0.4548;ExAC_EAS=0.5992;ExAC_FIN=0.2187;ExAC_NFE=0.2228;ExAC_OTH=0.2686;ExAC_SAS=0.2663;1000g2014oct_all=0.310703;snp138=rs2290493;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=1.4150;dpsi_zscore=1.740;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:108,117:225:99:3018,0,2971:57:99:0.52 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:128,103:232:99:2584,0,3364:56:99:0.446 0/1:114,131:246:99:3618,0,2838:57:99:0.535 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:89,55:144:99:1286,0,2038:53:99:0.382 0/1:80,78:158:99:2129,0,2207:58:99:0.494
chr1 22211222 rs4654994 T C 8670.84 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=17.0545;MQ=57;MQ0=0;QD=30.67;SB=-3768.07;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=1.596;MQRankSum=1.162;ReadPosRankSum=-0.754;DP=2437;AN=22;AC=22;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.96;Kaviar_AF=0.0052522;Kaviar_AC=812;Kaviar_AN=154602;ExAC_ALL=0.9126;ExAC_AFR=0.8516;ExAC_AMR=0.8739;ExAC_EAS=0.9639;ExAC_FIN=0.9131;ExAC_NFE=0.9266;ExAC_OTH=0.9185;ExAC_SAS=0.8951;1000g2014oct_all=0.896366;snp138=rs4654994;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.5063;dpsi_zscore=1.138;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,236:237:99:7268,542,0:57:99:1 ./.:.:.:.:.:.:.:. 1/1:0,162:162:99:4836,352,0:56:99:1 1/1:0,238:238:99:6965,509,0:57:99:1 1/1:0,237:238:99:7055,515,0:57:99:1 1/1:1,254:257:99:7685,572,0:57:99:0.996 1/1:0,295:296:99:8431,611,0:57:99:1 1/1:0,208:209:99:6239,463,0:56:99:1 1/1:0,286:286:99:8671,632,0:57:99:1 1/1:0,203:203:99:5763,418,0:56:99:1 1/1:0,151:153:99:4032,286,0:53:99:1 1/1:0,156:157:99:5013,370,0:58:99:1
chr1 22211680 rs113201880 C T 1519.04 PASS BaseQRankSum=-0.039;Dels=0;FS=2.412;HRun=1;HaplotypeScore=12.579;MQ=57;MQ0=0;MQRankSum=2.192;QD=12.45;ReadPosRankSum=-1.533;SB=-777.9;TI=NM_005529;GI=HSPG2;FC=Silent;DP=122;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.22;Kaviar_AF=0.0384083;Kaviar_AC=5938;Kaviar_AN=154602;ExAC_ALL=0.0424;ExAC_AFR=0.2023;ExAC_AMR=0.0229;ExAC_EAS=0.0001;ExAC_FIN=0.0283;ExAC_NFE=0.0370;ExAC_OTH=0.0312;ExAC_SAS=0.0121;1000g2014oct_all=0.0700879;snp138=rs113201880;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1742;dpsi_zscore=-0.634;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:63,58:122:99:1549,0,1680:57:99:0.479
chr1 22211856 rs145101074 G A 4000.61 PASS BaseQRankSum=1.316;Dels=0;FS=0;HRun=0;HaplotypeScore=17.3703;MQ=55;MQ0=0;MQRankSum=-1.077;QD=11.77;ReadPosRankSum=0.654;SB=-2663.99;TI=NM_005529;GI=HSPG2;FC=Synonymous_D389D;EXON;DP=340;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon10:c.C1167T:p.D389D\x3bHSPG2:NM_005529:exon10:c.C1167T:p.D389D;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon10:c.C1167T:p.D389D\x3bHSPG2:uc009vqd.3:exon10:c.C1167T:p.D389D;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon10:c.C1167T:p.D389D;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.013;Kaviar_AF=0.0078524;Kaviar_AC=1214;Kaviar_AN=154602;ExAC_ALL=0.0071;ExAC_AFR=0.0028;ExAC_AMR=0.0084;ExAC_EAS=0.0001;ExAC_FIN=0.0114;ExAC_NFE=0.0096;ExAC_OTH=0.0055;ExAC_SAS=0.0007;1000g2014oct_all=0.00479233;snp138=rs145101074;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0330;dpsi_zscore=-0.181;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:168,170:340:99:4001,0,4055:55:99:0.503 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22214046 rs41307868 C T 3658.01 PASS BaseQRankSum=-0.154;Dels=0;FS=4.784;HRun=0;HaplotypeScore=24.6388;MQ=57;MQ0=0;MQRankSum=3.151;QD=13.16;ReadPosRankSum=-0.65;SB=-2287.57;TI=NM_005529;GI=HSPG2;FC=Synonymous_L275L;EXON;DP=278;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon8:c.G825A:p.L275L\x3bHSPG2:NM_005529:exon8:c.G825A:p.L275L;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc009vqe.1:exon5:c.G521A:p.C174Y;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon8:c.G825A:p.L275L;cytoBand=1p36.12;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000310706.1|RCV000401276.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.099;Kaviar_AF=0.0576448;Kaviar_AC=8912;Kaviar_AN=154602;ExAC_ALL=0.0574;ExAC_AFR=0.0152;ExAC_AMR=0.0354;ExAC_EAS=0.0001;ExAC_FIN=0.0985;ExAC_NFE=0.0804;ExAC_OTH=0.0678;ExAC_SAS=0.0195;1000g2014oct_all=0.0309505;snp138=rs41307868;SIFT_score=0.0;SIFT_converted_rankscore=0.912;SIFT_pred=D;Polyphen2_HDIV_score=0.046;Polyphen2_HDIV_rankscore=0.205;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.032;Polyphen2_HVAR_rankscore=0.208;Polyphen2_HVAR_pred=B;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=1.000;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=N;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=0.57;FATHMM_converted_rankscore=0.544;FATHMM_pred=T;PROVEAN_score=-1.26;PROVEAN_converted_rankscore=0.318;PROVEAN_pred=N;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=-1.085;MetaSVM_rankscore=0.064;MetaSVM_pred=T;MetaLR_score=0.004;MetaLR_rankscore=0.013;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=0.727;CADD_raw_rankscore=0.163;CADD_phred=9.000;DANN_score=0.960;DANN_rankscore=0.280;fathmm-MKL_coding_score=0.171;fathmm-MKL_coding_rankscore=0.195;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.844;Eigen-PC-raw=-0.901;GenoCanyon_score=0.998;GenoCanyon_score_rankscore=0.367;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=0.549;GERP++_RS_rankscore=0.163;phyloP100way_vertebrate=2.221;phyloP100way_vertebrate_rankscore=0.423;phyloP20way_mammalian=0.932;phyloP20way_mammalian_rankscore=0.445;phastCons100way_vertebrate=0.006;phastCons100way_vertebrate_rankscore=0.172;phastCons20way_mammalian=0.061;phastCons20way_mammalian_rankscore=0.171;SiPhy_29way_logOdds=4.851;SiPhy_29way_logOdds_rankscore=0.128;Interpro_domain=.;GTEx_V6_gene=ENSG00000218510.3;GTEx_V6_tissue=Artery_Tibial;dpsi_max_tissue=0.1223;dpsi_zscore=0.547;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:133,145:278:99:3658,0,3359:57:99:0.522 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22214127 rs2229478 A G 8975.29 PASS BaseQRankSum=1.162;Dels=0;FS=3.681;HRun=0;HaplotypeScore=14.7395;MQ=55;MQ0=0;MQRankSum=2.686;QD=12.49;ReadPosRankSum=-1.702;SB=-3340.49;TI=NM_005529;GI=HSPG2;FC=Synonymous_L248L;EXON;DP=2079;AN=12;AC=8;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon8:c.T744C:p.L248L\x3bHSPG2:NM_005529:exon8:c.T744C:p.L248L;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc009vqe.1:exon5:c.T440C:p.L147S;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon8:c.T744C:p.L248L;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000267416.1|RCV000317902.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=0.71;Kaviar_AF=0.408222;Kaviar_AC=63112;Kaviar_AN=154602;ExAC_ALL=0.4175;ExAC_AFR=0.6406;ExAC_AMR=0.5977;ExAC_EAS=0.6264;ExAC_FIN=0.3508;ExAC_NFE=0.3354;ExAC_OTH=0.4011;ExAC_SAS=0.4014;1000g2014oct_all=0.536342;snp138=rs2229478;SIFT_score=0.0;SIFT_converted_rankscore=0.912;SIFT_pred=D;Polyphen2_HDIV_score=0.001;Polyphen2_HDIV_rankscore=0.067;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_rankscore=0.040;Polyphen2_HVAR_pred=B;LRT_score=0.682;LRT_converted_rankscore=0.102;LRT_pred=N;MutationTaster_score=1.000;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=P;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=0.45;FATHMM_converted_rankscore=0.565;FATHMM_pred=T;PROVEAN_score=0.18;PROVEAN_converted_rankscore=0.050;PROVEAN_pred=N;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=-0.946;MetaSVM_rankscore=0.417;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=-0.843;CADD_raw_rankscore=0.038;CADD_phred=0.034;DANN_score=0.896;DANN_rankscore=0.184;fathmm-MKL_coding_score=0.061;fathmm-MKL_coding_rankscore=0.120;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.402;Eigen-PC-raw=-1.444;GenoCanyon_score=0.998;GenoCanyon_score_rankscore=0.365;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=0.117;GERP++_RS_rankscore=0.139;phyloP100way_vertebrate=-1.838;phyloP100way_vertebrate_rankscore=0.018;phyloP20way_mammalian=-0.948;phyloP20way_mammalian_rankscore=0.024;phastCons100way_vertebrate=0.000;phastCons100way_vertebrate_rankscore=0.063;phastCons20way_mammalian=0.000;phastCons20way_mammalian_rankscore=0.016;SiPhy_29way_logOdds=0.623;SiPhy_29way_logOdds_rankscore=0.007;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2294;dpsi_zscore=0.777;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:197,214:412:99:5145,0,4639:55:99:0.521 1/1:2,330:332:99:8975,603,0:55:99:0.994 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:225,176:401:99:4060,0,5260:54:99:0.439 0/1:193,162:355:99:3908,0,4673:54:99:0.456 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:164,161:326:99:3345,0,3503:50:99:0.495 1/1:1,252:253:99:7260,497,0:54:99:0.996
chr1 22214371 rs74062203 T C 3813.03 PASS BaseQRankSum=2.387;Dels=0;FS=0;HRun=0;HaplotypeScore=17.0087;MQ=57;MQ0=0;MQRankSum=2.684;QD=12.54;ReadPosRankSum=-0.326;SB=-1993.28;TI=NM_005529;GI=HSPG2;FC=Silent;DP=537;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.082;Kaviar_AF=0.001824;Kaviar_AC=282;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0301518;snp138=rs74062203;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0815;dpsi_zscore=0.423;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:151,153:304:99:3813,0,3733:57:99:0.503 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:132,101:233:99:2190,0,2875:50:99:0.433 ./.:.:.:.:.:.:.:.
chr1 22216398 rs191661170 G A 1818.44 PASS BaseQRankSum=1.308;Dels=0;FS=0;HRun=1;HaplotypeScore=8.3599;MQ=56;MQ0=0;MQRankSum=2.088;QD=12.72;ReadPosRankSum=-0.059;SB=-805.19;TI=NM_005529;GI=HSPG2;FC=Silent;DP=143;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.0043;Kaviar_AF=0.00152;Kaviar_AC=235;Kaviar_AN=154602;ExAC_ALL=0.0015;ExAC_AFR=0.0004;ExAC_AMR=0.0016;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0023;ExAC_OTH=0.0011;ExAC_SAS=6.286e-05;1000g2014oct_all=0.00119808;snp138=rs191661170;SIFT_score=0.0;SIFT_converted_rankscore=0.912;SIFT_pred=D;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=1.000;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=N;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=0.76;FATHMM_converted_rankscore=0.499;FATHMM_pred=T;PROVEAN_score=-1.23;PROVEAN_converted_rankscore=0.312;PROVEAN_pred=N;VEST3_score=0.118;VEST3_rankscore=0.130;MetaSVM_score=-0.976;MetaSVM_rankscore=0.360;MetaSVM_pred=T;MetaLR_score=0.092;MetaLR_rankscore=0.351;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=0.334;CADD_raw_rankscore=0.126;CADD_phred=6.020;DANN_score=0.961;DANN_rankscore=0.281;fathmm-MKL_coding_score=0.170;fathmm-MKL_coding_rankscore=0.194;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.540;Eigen-PC-raw=-0.706;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.473;integrated_fitCons_score=0.461;integrated_fitCons_score_rankscore=0.090;integrated_confidence_value=0;GERP++_RS=1.01;GERP++_RS_rankscore=0.190;phyloP100way_vertebrate=0.115;phyloP100way_vertebrate_rankscore=0.153;phyloP20way_mammalian=0.912;phyloP20way_mammalian_rankscore=0.422;phastCons100way_vertebrate=0.010;phastCons100way_vertebrate_rankscore=0.182;phastCons20way_mammalian=0.083;phastCons20way_mammalian_rankscore=0.182;SiPhy_29way_logOdds=5.682;SiPhy_29way_logOdds_rankscore=0.169;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0809;dpsi_zscore=-0.388;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:75,68:143:99:1848,0,1948:56:99:0.476 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22216574 rs2254358 C A 13096.3 PASS BaseQRankSum=3.66;Dels=0;FS=0.351;HRun=0;HaplotypeScore=29.322;MQ=55;MQ0=0;MQRankSum=4.795;QD=12.33;ReadPosRankSum=-0.603;SB=-3511.83;TI=NM_005529;GI=HSPG2;FC=Synonymous_G158G;EXON;DP=3894;AN=20;AC=16;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon6:c.G474T:p.G158G\x3bHSPG2:NM_005529:exon6:c.G474T:p.G158G;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc009vqe.1:exon3:c.G170T:p.G57V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon6:c.G474T:p.G158G;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000282698.1|RCV000374875.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.68;Kaviar_AF=0.574812;Kaviar_AC=88867;Kaviar_AN=154602;ExAC_ALL=0.5769;ExAC_AFR=0.2937;ExAC_AMR=0.3974;ExAC_EAS=0.3736;ExAC_FIN=0.6489;ExAC_NFE=0.6655;ExAC_OTH=0.5960;ExAC_SAS=0.6000;1000g2014oct_all=0.444489;snp138=rs2254358;SIFT_score=0.183;SIFT_converted_rankscore=0.217;SIFT_pred=T;Polyphen2_HDIV_score=0.617;Polyphen2_HDIV_rankscore=0.379;Polyphen2_HDIV_pred=P;Polyphen2_HVAR_score=0.226;Polyphen2_HVAR_rankscore=0.363;Polyphen2_HVAR_pred=B;LRT_score=0.043;LRT_converted_rankscore=0.238;LRT_pred=N;MutationTaster_score=0.998;MutationTaster_converted_rankscore=0.221;MutationTaster_pred=P;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=0.39;FATHMM_converted_rankscore=0.574;FATHMM_pred=T;PROVEAN_score=-1.35;PROVEAN_converted_rankscore=0.336;PROVEAN_pred=N;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=-0.960;MetaSVM_rankscore=0.391;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=1.249;CADD_raw_rankscore=0.215;CADD_phred=12.00;DANN_score=0.983;DANN_rankscore=0.394;fathmm-MKL_coding_score=0.222;fathmm-MKL_coding_rankscore=0.215;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.489;Eigen-PC-raw=-0.557;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.454;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=0.36;GERP++_RS_rankscore=0.153;phyloP100way_vertebrate=-0.592;phyloP100way_vertebrate_rankscore=0.058;phyloP20way_mammalian=-0.351;phyloP20way_mammalian_rankscore=0.070;phastCons100way_vertebrate=0.000;phastCons100way_vertebrate_rankscore=0.063;phastCons20way_mammalian=0.003;phastCons20way_mammalian_rankscore=0.074;SiPhy_29way_logOdds=3.784;SiPhy_29way_logOdds_rankscore=0.082;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.9251;dpsi_zscore=1.475;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:213,210:424:99:5227,0,4929:55:99:0.496 ./.:.:.:.:.:.:.:. 1/1:0,295:295:99:8568,620,0:56:99:1 1/1:0,421:422:99:12116,873,0:56:99:1 0/1:186,230:416:99:5356,0,4355:54:99:0.553 0/1:214,207:422:99:5178,0,5012:55:99:0.492 1/1:0,447:447:99:13096,948,0:57:99:1 1/1:1,336:338:99:10008,731,0:55:99:0.997 1/1:3,397:400:99:11343,745,0:56:99:0.993 1/1:0,365:365:99:10038,716,0:56:99:1 0/1:162,203:365:99:4540,0,3477:49:99:0.556 ./.:.:.:.:.:.:.:.
chr1 22216604 rs2254357 C G 12254 PASS BaseQRankSum=0.296;Dels=0;FS=0;HRun=0;HaplotypeScore=29.5569;MQ=55;MQ0=0;MQRankSum=1.762;QD=11.68;ReadPosRankSum=-2.006;SB=-3220.07;TI=NM_005529;GI=HSPG2;FC=Synonymous_L148L;EXON;DP=3833;AN=20;AC=16;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon6:c.G444C:p.L148L\x3bHSPG2:NM_005529:exon6:c.G444C:p.L148L;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=HSPG2:uc009vqe.1:exon3:c.G140C:p.W47S;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon6:c.G444C:p.L148L;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Schwartz_Jampel_syndrome_type_1|Dyssegmental_Dysplasia;CLNACC=RCV000295447.1|RCV000352676.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet;CLNDSDBID=C0036391:255800:ORPHA800|C1857100:ORPHA1865;PopFreqMax=0.68;Kaviar_AF=0.574559;Kaviar_AC=88828;Kaviar_AN=154602;ExAC_ALL=0.5770;ExAC_AFR=0.2937;ExAC_AMR=0.3976;ExAC_EAS=0.3732;ExAC_FIN=0.6487;ExAC_NFE=0.6657;ExAC_OTH=0.5960;ExAC_SAS=0.6000;1000g2014oct_all=0.444489;snp138=rs2254357;SIFT_score=0.243;SIFT_converted_rankscore=0.175;SIFT_pred=T;Polyphen2_HDIV_score=0.946;Polyphen2_HDIV_rankscore=0.514;Polyphen2_HDIV_pred=P;Polyphen2_HVAR_score=0.509;Polyphen2_HVAR_rankscore=0.461;Polyphen2_HVAR_pred=P;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=0.000;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=P;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=0.56;FATHMM_converted_rankscore=0.546;FATHMM_pred=T;PROVEAN_score=0.76;PROVEAN_converted_rankscore=0.020;PROVEAN_pred=N;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=-1.050;MetaSVM_rankscore=0.143;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=1.275;CADD_raw_rankscore=0.218;CADD_phred=12.14;DANN_score=0.917;DANN_rankscore=0.204;fathmm-MKL_coding_score=0.915;fathmm-MKL_coding_rankscore=0.533;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.227;Eigen-PC-raw=0.286;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=4.5;GERP++_RS_rankscore=0.542;phyloP100way_vertebrate=1.139;phyloP100way_vertebrate_rankscore=0.309;phyloP20way_mammalian=0.935;phyloP20way_mammalian_rankscore=0.490;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.992;phastCons20way_mammalian_rankscore=0.562;SiPhy_29way_logOdds=14.050;SiPhy_29way_logOdds_rankscore=0.641;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3724;dpsi_zscore=0.988;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:207,202:410:99:4789,0,5120:55:99:0.494 ./.:.:.:.:.:.:.:. 1/1:0,270:271:99:7879,572,0:56:99:1 1/1:0,412:412:99:11516,834,0:56:99:1 0/1:207,225:432:99:5224,0,5187:55:99:0.521 0/1:198,196:395:99:4806,0,4876:55:99:0.497 1/1:0,429:431:99:12254,894,0:56:99:1 1/1:3,326:331:99:9396,674,0:55:99:0.991 1/1:4,411:415:99:11571,766,0:57:99:0.99 1/1:0,368:369:99:9838,704,0:55:99:1 0/1:157,207:367:99:4633,0,3369:48:99:0.569 ./.:.:.:.:.:.:.:.
chr1 22217108 rs2501260 G A 13503.3 PASS Dels=0;FS=0;HRun=2;HaplotypeScore=19.7714;MQ=56;MQ0=0;QD=28.47;SB=-8559.6;TI=NM_005529;GI=HSPG2;FC=Synonymous_F108F;EXON;BaseQRankSum=1.626;MQRankSum=-1.422;ReadPosRankSum=0.086;DP=4759;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=HSPG2:NM_001291860:exon4:c.C324T:p.F108F\x3bHSPG2:NM_005529:exon4:c.C324T:p.F108F;Func.knownGene=exonic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=HSPG2:uc001bfj.3:exon4:c.C324T:p.F108F\x3bHSPG2:uc009vqd.3:exon4:c.C324T:p.F108F;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS30625.1:CCDS30625.1:exon4:c.C324T:p.F108F;cytoBand=1p36.12;CLINSIG=Benign|Benign;CLNDBN=Dyssegmental_Dysplasia|Schwartz_Jampel_syndrome_type_1;CLNACC=RCV000289547.1|RCV000406389.1;CLNDSDB=MedGen:Orphanet|MedGen:OMIM:Orphanet;CLNDSDBID=C1857100:ORPHA1865|C0036391:255800:ORPHA800;PopFreqMax=1.;Kaviar_AF=0.935188;Kaviar_AC=144582;Kaviar_AN=154602;ExAC_ALL=0.9861;ExAC_AFR=0.8475;ExAC_AMR=0.9944;ExAC_EAS=1;ExAC_FIN=1;ExAC_NFE=0.9996;ExAC_OTH=0.9879;ExAC_SAS=0.9998;1000g2014oct_all=0.948083;snp138=rs2501260;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0601;dpsi_zscore=0.342;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,463:463:99:13180,957,0:56:99:1 1/1:1,424:425:99:11174,798,0:55:99:0.998 1/1:0,313:313:99:8844,650,0:54:99:1 1/1:0,395:398:99:11108,816,0:56:99:1 1/1:0,436:437:99:11870,861,0:54:99:1 1/1:0,354:354:99:10226,749,0:55:99:1 1/1:0,445:448:99:12405,912,0:56:99:1 1/1:1,348:349:99:10351,770,0:55:99:0.997 1/1:1,463:467:99:13503,984,0:57:99:0.998 1/1:0,401:401:99:10936,783,0:55:99:1 1/1:1,377:378:99:9703,689,0:51:99:0.997 1/1:2,323:326:99:9315,659,0:57:99:0.994
chr1 22263612 . G C 5.06 LowGQX;LowGQ;SB;LowDP Dels=0;FS=0;HRun=5;HaplotypeScore=0;MQ=29;MQ0=0;QD=5.06;SB=-0.01;TI=NM_005529;GI=HSPG2;FC=Silent;DP=1;AN=2;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,1:1:3.01:33,3,0:29:3:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22263618 . G C 24.85 LowGQX;LowGQ;SB;LowDP Dels=0;FS=0;HRun=6;HaplotypeScore=0;MQ=29;MQ0=0;QD=5.06;SB=-0.01;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=-1.026;MQRankSum=-1.026;ReadPosRankSum=-1.026;DP=16;AN=8;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,1:1:3.01:33,3,0:29:3:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:2,2:4:54.83:55,0,61:31:25:0.5 0/1:2,4:6:18.66:49,0,19:42:19:0.667 0/1:3,2:5:44.09:44,0,73:40:14:0.4 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22263621 . C T 4.59 LowGQX;LowDP BaseQRankSum=0.358;Dels=0;FS=0;HRun=0;HaplotypeScore=1.9663;MQ=40;MQ0=0;MQRankSum=0.358;QD=0.92;ReadPosRankSum=0.358;SB=-30.99;TI=NM_005529;GI=HSPG2;FC=Silent;DP=5;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:3,2:5:32.73:33,0,95:40:5:0.4 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22263625 . G C 42.69 LowGQX;LowGQ;SB;LowDP Dels=0;FS=0;HRun=6;HaplotypeScore=0;MQ=29;MQ0=0;QD=5.06;SB=-0.01;TI=NM_005529;GI=HSPG2;FC=Silent;BaseQRankSum=0;MQRankSum=-1.026;ReadPosRankSum=-1.026;DP=18;AN=8;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,1:1:3.01:33,3,0:29:3:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:2,2:4:54.83:55,0,57:31:25:0.5 0/1:3,4:7:72.68:73,0,79:40:43:0.571 0/1:4,2:6:51.82:52,0,104:38:22:0.333 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 22263630 . T C 12.33 SB;LowDP BaseQRankSum=-1.38;Dels=0;FS=3.31;HRun=4;HaplotypeScore=7.4966;MQ=42;MQ0=0;MQRankSum=0.72;QD=2.06;ReadPosRankSum=-0.72;SB=-0.01;TI=NM_005529;GI=HSPG2;FC=Silent;DP=6;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=HSPG2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=HSPG2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS30625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.12;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:4,2:6:42.07:42,0,120:42:12:0.333 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 26126680 rs12121707 T C 112.58 LowGQ;LowDP;LowGQX;SB Dels=0;FS=0;HRun=1;HaplotypeScore=0.8941;MQ=44;MQ0=0;QD=22.52;SB=-40.01;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Silent,Silent;EXON;DP=19;AN=12;AC=12;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR5;Gene.refGene=SEPN1;GeneDetail.refGene=NM_020451:c.-42T>C\x3bNM_206926:c.-42T>C;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR5;Gene.knownGene=SEPN1;GeneDetail.knownGene=uc021ojk.1:c.-42T>C\x3buc021ojl.1:c.-42T>C;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=upstream;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=Benign|Uncertain_significance;CLNDBN=not_specified|SEPN1-Related_Disorders;CLNACC=RCV000249922.1|RCV000377725.1;CLNDSDB=MedGen|MedGen;CLNDSDBID=CN169374|CN239420;PopFreqMax=0.;Kaviar_AF=0.0036739;Kaviar_AC=568;Kaviar_AN=154602;ExAC_ALL=0;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=rs12121707;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,5:5:12.04:145,12,0:44:12:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,3:4:9.03:106,9,0:37:9:1 1/1:0,1:1:3.01:38,3,0:60:3:1 1/1:0,3:3:9.03:113,9,0:35:9:1 1/1:0,3:3:6.02:67,6,0:29:6:1 1/1:0,3:3:9.03:112,9,0:44:9:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 26126785 . G C 5.06 LowGQX;LowGQ;SB;LowDP Dels=0;FS=0;HRun=3;HaplotypeScore=0;MQ=29;MQ0=0;QD=5.06;SB=-0.01;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Missense_A22P,Missense_A22P;EXON;DP=1;AN=2;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=SEPN1;GeneDetail.refGene=.;ExonicFunc.refGene=unknown;AAChange.refGene=UNKNOWN;Func.knownGene=exonic;Gene.knownGene=SEPN1;GeneDetail.knownGene=.;ExonicFunc.knownGene=unknown;AAChange.knownGene=UNKNOWN;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=unknown;AAChange.ccdsGene=UNKNOWN;cytoBand=1p36.11;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=0.356;SIFT_converted_rankscore=0.120;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.0;Polyphen2_HVAR_rankscore=0.013;Polyphen2_HVAR_pred=B;LRT_score=0.932;LRT_converted_rankscore=0.084;LRT_pred=N;MutationTaster_score=1;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=N;MutationAssessor_score=0.755;MutationAssessor_score_rankscore=0.192;MutationAssessor_pred=N;FATHMM_score=-2.38;FATHMM_converted_rankscore=0.883;FATHMM_pred=D;PROVEAN_score=-0.59;PROVEAN_converted_rankscore=0.199;PROVEAN_pred=N;VEST3_score=0.199;VEST3_rankscore=0.245;MetaSVM_score=-0.755;MetaSVM_rankscore=0.577;MetaSVM_pred=T;MetaLR_score=0.371;MetaLR_rankscore=0.731;MetaLR_pred=T;M-CAP_score=0.746;M-CAP_rankscore=0.980;M-CAP_pred=D;CADD_raw=1.538;CADD_raw_rankscore=0.247;CADD_phred=13.52;DANN_score=0.700;DANN_rankscore=0.089;fathmm-MKL_coding_score=0.030;fathmm-MKL_coding_rankscore=0.078;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.260;Eigen-PC-raw=-1.265;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.455;integrated_fitCons_score_rankscore=0.088;integrated_confidence_value=0;GERP++_RS=1.03;GERP++_RS_rankscore=0.191;phyloP100way_vertebrate=1.127;phyloP100way_vertebrate_rankscore=0.308;phyloP20way_mammalian=0.511;phyloP20way_mammalian_rankscore=0.281;phastCons100way_vertebrate=0.002;phastCons100way_vertebrate_rankscore=0.151;phastCons20way_mammalian=0.891;phastCons20way_mammalian_rankscore=0.375;SiPhy_29way_logOdds=6.246;SiPhy_29way_logOdds_rankscore=0.199;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=0.74649391802;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,1:1:3.01:33,3,0:29:3:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 26131654 rs7349185 G A 10771.8 PASS BaseQRankSum=1.671;Dels=0;FS=0;HRun=0;HaplotypeScore=19.9902;MQ=56;MQ0=0;MQRankSum=0.853;QD=28.29;ReadPosRankSum=0.611;SB=-5836.99;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Missense_C142Y,Missense_C108Y;EXON;DP=3509;AN=22;AC=21;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=SEPN1;GeneDetail.refGene=.;ExonicFunc.refGene=unknown;AAChange.refGene=UNKNOWN;Func.knownGene=exonic;Gene.knownGene=SEPN1;GeneDetail.knownGene=.;ExonicFunc.knownGene=unknown;AAChange.knownGene=UNKNOWN;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=unknown;AAChange.ccdsGene=UNKNOWN;cytoBand=1p36.11;CLINSIG=Benign|Benign;CLNDBN=not_specified|SEPN1-Related_Disorders;CLNACC=RCV000082016.8|RCV000371932.1;CLNDSDB=MedGen|MedGen;CLNDSDBID=CN169374|CN239420;PopFreqMax=0.94;Kaviar_AF=0.793819;Kaviar_AC=122726;Kaviar_AN=154602;ExAC_ALL=0.8144;ExAC_AFR=0.7804;ExAC_AMR=0.9150;ExAC_EAS=0.9416;ExAC_FIN=0.7282;ExAC_NFE=0.7777;ExAC_OTH=0.8158;ExAC_SAS=0.8805;1000g2014oct_all=0.841853;snp138=rs7349185;SIFT_score=1.0;SIFT_converted_rankscore=0.010;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.0;Polyphen2_HVAR_rankscore=0.013;Polyphen2_HVAR_pred=B;LRT_score=0.076;LRT_converted_rankscore=0.212;LRT_pred=N;MutationTaster_score=1;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=P;MutationAssessor_score=1.1;MutationAssessor_score_rankscore=0.281;MutationAssessor_pred=L;FATHMM_score=0.68;FATHMM_converted_rankscore=0.520;FATHMM_pred=T;PROVEAN_score=2.8;PROVEAN_converted_rankscore=0.002;PROVEAN_pred=N;VEST3_score=0.07;VEST3_rankscore=0.236;MetaSVM_score=-0.907;MetaSVM_rankscore=0.472;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=-0.989;CADD_raw_rankscore=0.032;CADD_phred=0.017;DANN_score=0.318;DANN_rankscore=0.018;fathmm-MKL_coding_score=0.008;fathmm-MKL_coding_rankscore=0.031;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.121;Eigen-PC-raw=-1.048;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.517;integrated_fitCons_score=0.696;integrated_fitCons_score_rankscore=0.567;integrated_confidence_value=0;GERP++_RS=1.58;GERP++_RS_rankscore=0.224;phyloP100way_vertebrate=0.869;phyloP100way_vertebrate_rankscore=0.275;phyloP20way_mammalian=0.241;phyloP20way_mammalian_rankscore=0.266;phastCons100way_vertebrate=0.358;phastCons100way_vertebrate_rankscore=0.256;phastCons20way_mammalian=0.906;phastCons20way_mammalian_rankscore=0.385;SiPhy_29way_logOdds=0.970;SiPhy_29way_logOdds_rankscore=0.013;Interpro_domain=.;GTEx_V6_gene=ENSG00000272478.1|ENSG00000117640.13|ENSG00000117640.13|ENSG00000272478.1|ENSG00000117640.13|ENSG00000162430.12|ENSG00000228172.1|ENSG00000162430.12;GTEx_V6_tissue=Artery_Tibial|Artery_Tibial|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Muscle_Skeletal|Muscle_Skeletal|Thyroid;dpsi_max_tissue=0.3116;dpsi_zscore=0.908;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,342:343:99:9704,701,0:56:99:0.997 1/1:1,344:345:99:9445,674,0:54:99:0.997 0/1:134,112:247:99:2905,0,3267:56:99:0.455 1/1:0,363:364:99:10463,752,0:56:99:1 1/1:1,303:304:99:8645,596,0:55:99:0.997 1/1:0,295:295:99:8404,608,0:55:99:1 1/1:2,352:355:99:10293,714,0:56:99:0.994 1/1:0,258:258:99:7583,554,0:55:99:1 1/1:0,366:366:99:10772,786,0:57:99:1 1/1:0,323:324:99:9182,662,0:55:99:1 1/1:0,304:306:99:7655,536,0:51:99:1 ./.:.:.:.:.:.:.:.
chr1 26135116 rs115852080 G A 4463.37 PASS BaseQRankSum=-0.363;Dels=0;FS=3.824;HRun=0;HaplotypeScore=19.9217;MQ=55;MQ0=0;MQRankSum=2.637;QD=11.13;ReadPosRankSum=-1.895;SB=-2617.84;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Missense_A195T,Missense_A161T;EXON;DP=401;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=SEPN1;GeneDetail.refGene=.;ExonicFunc.refGene=unknown;AAChange.refGene=UNKNOWN;Func.knownGene=exonic;Gene.knownGene=SEPN1;GeneDetail.knownGene=.;ExonicFunc.knownGene=unknown;AAChange.knownGene=UNKNOWN;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=unknown;AAChange.ccdsGene=UNKNOWN;cytoBand=1p36.11;CLINSIG=other;CLNDBN=not_specified;CLNACC=RCV000082019.8;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.015;Kaviar_AF=0.0099675;Kaviar_AC=1541;Kaviar_AN=154602;ExAC_ALL=0.0101;ExAC_AFR=0.0050;ExAC_AMR=0.0065;ExAC_EAS=0.0001;ExAC_FIN=0.0022;ExAC_NFE=0.0137;ExAC_OTH=0.0068;ExAC_SAS=0.0093;1000g2014oct_all=0.00638978;snp138=rs115852080;SIFT_score=0.054;SIFT_converted_rankscore=0.386;SIFT_pred=T;Polyphen2_HDIV_score=0.972;Polyphen2_HDIV_rankscore=0.554;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.374;Polyphen2_HVAR_rankscore=0.419;Polyphen2_HVAR_pred=B;LRT_score=0.001;LRT_converted_rankscore=0.434;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=D;MutationAssessor_score=1.15;MutationAssessor_score_rankscore=0.294;MutationAssessor_pred=L;FATHMM_score=-2.34;FATHMM_converted_rankscore=0.880;FATHMM_pred=D;PROVEAN_score=-1.13;PROVEAN_converted_rankscore=0.324;PROVEAN_pred=N;VEST3_score=0.249;VEST3_rankscore=0.497;MetaSVM_score=-0.179;MetaSVM_rankscore=0.782;MetaSVM_pred=T;MetaLR_score=0.338;MetaLR_rankscore=0.705;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=1.662;CADD_raw_rankscore=0.261;CADD_phred=14.19;DANN_score=0.987;DANN_rankscore=0.441;fathmm-MKL_coding_score=0.970;fathmm-MKL_coding_rankscore=0.718;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.048;Eigen-PC-raw=-0.044;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.707;integrated_fitCons_score_rankscore=0.730;integrated_confidence_value=0;GERP++_RS=4.02;GERP++_RS_rankscore=0.458;phyloP100way_vertebrate=3.245;phyloP100way_vertebrate_rankscore=0.509;phyloP20way_mammalian=1.036;phyloP20way_mammalian_rankscore=0.656;phastCons100way_vertebrate=0.983;phastCons100way_vertebrate_rankscore=0.354;phastCons20way_mammalian=0.053;phastCons20way_mammalian_rankscore=0.166;SiPhy_29way_logOdds=13.338;SiPhy_29way_logOdds_rankscore=0.598;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.8979;dpsi_zscore=1.457;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:216,184:401:99:4463,0,5337:55:99:0.46 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 26136282 rs147587542 C T 4546.13 PASS BaseQRankSum=0.551;Dels=0;FS=5.766;HRun=0;HaplotypeScore=23.036;MQ=55;MQ0=0;MQRankSum=2.55;QD=11.39;ReadPosRankSum=2.258;SB=-2939.77;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Synonymous_R327R,Synonymous_R293R;EXON;DP=399;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=SEPN1;GeneDetail.refGene=.;ExonicFunc.refGene=unknown;AAChange.refGene=UNKNOWN;Func.knownGene=exonic;Gene.knownGene=SEPN1;GeneDetail.knownGene=.;ExonicFunc.knownGene=unknown;AAChange.knownGene=UNKNOWN;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=unknown;AAChange.ccdsGene=UNKNOWN;cytoBand=1p36.11;CLINSIG=other|Likely_benign;CLNDBN=not_specified|SEPN1-Related_Disorders;CLNACC=RCV000082021.8|RCV000406527.1;CLNDSDB=MedGen|MedGen;CLNDSDBID=CN169374|CN239420;PopFreqMax=0.042;Kaviar_AF=0.0262351;Kaviar_AC=4056;Kaviar_AN=154602;ExAC_ALL=0.0251;ExAC_AFR=0.0085;ExAC_AMR=0.0195;ExAC_EAS=0;ExAC_FIN=0.0144;ExAC_NFE=0.0379;ExAC_OTH=0.0167;ExAC_SAS=0.0052;1000g2014oct_all=0.0101837;snp138=rs147587542;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-2.1141;dpsi_zscore=-1.936;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:207,192:399:99:4546,0,5217:55:99:0.481 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 26138136 rs760598 C A 11774.3 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=17.4334;MQ=56;MQ0=0;QD=29.73;SB=-6443.33;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Silent,Silent;BaseQRankSum=2.912;MQRankSum=1.486;ReadPosRankSum=-1.852;DP=3747;AN=22;AC=18;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=SEPN1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=SEPN1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000251176.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.97;Kaviar_AF=0.760546;Kaviar_AC=117582;Kaviar_AN=154602;ExAC_ALL=0.7861;ExAC_AFR=0.4765;ExAC_AMR=0.8925;ExAC_EAS=0.9645;ExAC_FIN=0.7543;ExAC_NFE=0.7686;ExAC_OTH=0.8025;ExAC_SAS=0.8786;1000g2014oct_all=0.747005;snp138=rs760598;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.4815;dpsi_zscore=-1.073;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,368:369:99:10971,801,0:56:99:1 1/1:0,327:327:99:9172,659,0:55:99:1 0/1:129,114:243:99:3100,0,3302:56:99:0.469 1/1:0,357:360:99:10666,782,0:57:99:1 0/1:183,179:362:99:4463,0,4456:56:99:0.494 0/1:163,155:318:99:3949,0,4080:55:99:0.487 1/1:1,409:410:99:11774,849,0:57:99:0.998 0/1:173,111:284:99:2871,0,4374:56:99:0.391 1/1:0,385:386:99:11382,834,0:58:99:1 1/1:1,363:364:99:10286,737,0:56:99:0.997 1/1:0,324:324:99:8421,593,0:51:99:1 ./.:.:.:.:.:.:.:.
chr1 26138262 rs760597 T C 10164.3 PASS Dels=0;FS=0;HRun=2;HaplotypeScore=12.7027;MQ=57;MQ0=0;QD=29.96;SB=-5443.59;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Synonymous_P391P,Synonymous_P357P;EXON;BaseQRankSum=2.798;MQRankSum=0.205;ReadPosRankSum=-0.48;DP=2965;AN=22;AC=21;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=SEPN1;GeneDetail.refGene=.;ExonicFunc.refGene=unknown;AAChange.refGene=UNKNOWN;Func.knownGene=exonic;Gene.knownGene=SEPN1;GeneDetail.knownGene=.;ExonicFunc.knownGene=unknown;AAChange.knownGene=UNKNOWN;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=unknown;AAChange.ccdsGene=UNKNOWN;cytoBand=1p36.11;CLINSIG=Benign|Benign;CLNDBN=not_specified|SEPN1-Related_Disorders;CLNACC=RCV000082009.7|RCV000358370.1;CLNDSDB=MedGen|MedGen;CLNDSDBID=CN169374|CN239420;PopFreqMax=0.97;Kaviar_AF=0.750915;Kaviar_AC=116093;Kaviar_AN=154602;ExAC_ALL=0.8132;ExAC_AFR=0.6368;ExAC_AMR=0.9016;ExAC_EAS=0.9641;ExAC_FIN=0.7717;ExAC_NFE=0.7917;ExAC_OTH=0.8045;ExAC_SAS=0.8825;1000g2014oct_all=0.791933;snp138=rs760597;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.6707;dpsi_zscore=-1.245;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,289:289:99:8659,629,0:57:99:1 1/1:0,262:262:99:7400,533,0:55:99:1 0/1:102,102:205:99:2536,0,2666:57:99:0.5 1/1:0,311:311:99:9030,653,0:57:99:1 1/1:0,264:266:99:7555,551,0:57:99:1 1/1:0,281:281:99:8304,605,0:56:99:1 1/1:2,289:291:99:8598,593,0:57:99:0.993 1/1:0,238:239:99:7214,530,0:57:99:1 1/1:0,332:332:99:10164,740,0:58:99:1 1/1:0,268:268:99:7558,542,0:55:99:1 1/1:0,221:221:99:5679,397,0:53:99:1 ./.:.:.:.:.:.:.:.
chr1 26139137 rs10902685 C T 6247.62 PASS BaseQRankSum=2.659;Dels=0.01;FS=2.848;HRun=0;HaplotypeScore=42.0343;MQ=50;MQ0=0;MQRankSum=2.197;QD=27.41;ReadPosRankSum=2.509;SB=-2421.75;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Silent,Silent;DP=1943;AN=22;AC=20;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=SEPN1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=SEPN1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000242697.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.97;Kaviar_AF=0.0045989;Kaviar_AC=711;Kaviar_AN=154602;ExAC_ALL=0.7944;ExAC_AFR=0.3388;ExAC_AMR=0.9000;ExAC_EAS=0.9663;ExAC_FIN=0.7738;ExAC_NFE=0.7923;ExAC_OTH=0.8223;ExAC_SAS=0.8834;1000g2014oct_all=0.697684;snp138=rs10902685;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1099;dpsi_zscore=0.512;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:3,171:175:99:4824,332,0:50:99:0.983 1/1:8,197:205:99:5430,300,0:51:99:0.961 0/1:76,77:153:99:1850,0,1844:53:99:0.503 1/1:6,163:169:99:4763,335,0:52:99:0.964 1/1:2,151:153:99:4372,306,0:52:99:0.987 1/1:1,156:158:99:4437,343,0:52:99:0.994 1/1:2,219:222:99:6198,452,0:48:99:0.991 0/1:85,73:159:99:1795,0,2133:49:99:0.462 1/1:5,228:233:99:6248,452,0:52:99:0.979 1/1:1,154:156:99:4448,337,0:49:99:0.994 1/1:1,158:159:99:4104,298,0:46:99:0.994 ./.:.:.:.:.:.:.:.
chr1 26140573 rs2294228 C A 12617.6 PASS BaseQRankSum=2.899;Dels=0;FS=3.133;HRun=2;HaplotypeScore=11.9088;MQ=56;MQ0=0;MQRankSum=0.631;QD=29.14;ReadPosRankSum=1.007;SB=-7445.84;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Missense_N502K,Missense_N468K;EXON;DP=4204;AN=22;AC=20;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=SEPN1;GeneDetail.refGene=.;ExonicFunc.refGene=unknown;AAChange.refGene=UNKNOWN;Func.knownGene=exonic;Gene.knownGene=SEPN1;GeneDetail.knownGene=.;ExonicFunc.knownGene=unknown;AAChange.knownGene=UNKNOWN;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=unknown;AAChange.ccdsGene=UNKNOWN;cytoBand=1p36.11;CLINSIG=Benign|Benign;CLNDBN=not_specified|SEPN1-Related_Disorders;CLNACC=RCV000082012.7|RCV000299948.1;CLNDSDB=MedGen|MedGen;CLNDSDBID=CN169374|CN239420;PopFreqMax=0.97;Kaviar_AF=0.764182;Kaviar_AC=118144;Kaviar_AN=154602;ExAC_ALL=0.7747;ExAC_AFR=0.2938;ExAC_AMR=0.8902;ExAC_EAS=0.9643;ExAC_FIN=0.7486;ExAC_NFE=0.7769;ExAC_OTH=0.7964;ExAC_SAS=0.8804;1000g2014oct_all=0.697484;snp138=rs2294228;SIFT_score=0.053;SIFT_converted_rankscore=0.491;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_rankscore=0.040;Polyphen2_HVAR_pred=B;LRT_score=0.054;LRT_converted_rankscore=0.228;LRT_pred=N;MutationTaster_score=0.999;MutationTaster_converted_rankscore=0.361;MutationTaster_pred=P;MutationAssessor_score=1.525;MutationAssessor_score_rankscore=0.387;MutationAssessor_pred=L;FATHMM_score=-2.36;FATHMM_converted_rankscore=0.882;FATHMM_pred=D;PROVEAN_score=-1.8;PROVEAN_converted_rankscore=0.526;PROVEAN_pred=N;VEST3_score=0.012;VEST3_rankscore=0.071;MetaSVM_score=-0.998;MetaSVM_rankscore=0.306;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=2.958;CADD_raw_rankscore=0.416;CADD_phred=22.1;DANN_score=0.978;DANN_rankscore=0.356;fathmm-MKL_coding_score=0.368;fathmm-MKL_coding_rankscore=0.254;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.749;Eigen-PC-raw=-0.748;GenoCanyon_score=0.983;GenoCanyon_score_rankscore=0.304;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=2.58;GERP++_RS_rankscore=0.299;phyloP100way_vertebrate=0.140;phyloP100way_vertebrate_rankscore=0.158;phyloP20way_mammalian=0.023;phyloP20way_mammalian_rankscore=0.146;phastCons100way_vertebrate=0.718;phastCons100way_vertebrate_rankscore=0.286;phastCons20way_mammalian=0.032;phastCons20way_mammalian_rankscore=0.149;SiPhy_29way_logOdds=7.686;SiPhy_29way_logOdds_rankscore=0.275;Interpro_domain=.;GTEx_V6_gene=ENSG00000117640.13|ENSG00000272478.1|ENSG00000117640.13|ENSG00000272478.1|ENSG00000117640.13|ENSG00000162430.12|ENSG00000117640.13|ENSG00000272478.1|ENSG00000117640.13|ENSG00000272478.1|ENSG00000162430.12|ENSG00000117640.13|ENSG00000228172.1|ENSG00000272478.1|ENSG00000117640.13;GTEx_V6_tissue=Adrenal_Gland|Adrenal_Gland|Artery_Aorta|Artery_Tibial|Artery_Tibial|Brain_Cerebellum|Heart_Atrial_Appendage|Heart_Atrial_Appendage|Heart_Left_Ventricle|Heart_Left_Ventricle|Muscle_Skeletal|Muscle_Skeletal|Muscle_Skeletal|Thyroid|Thyroid;dpsi_max_tissue=-0.6479;dpsi_zscore=-1.227;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:3,402:407:99:11862,843,0:56:99:0.993 1/1:1,392:393:99:10829,777,0:54:99:0.997 0/1:127,139:267:99:3300,0,3239:55:99:0.523 1/1:1,397:400:99:11510,840,0:56:99:0.997 1/1:1,373:377:99:10483,755,0:55:99:0.997 1/1:2,397:402:99:11314,783,0:55:99:0.995 1/1:1,443:444:99:12618,921,0:57:99:0.998 0/1:190,167:357:99:4118,0,4835:56:99:0.468 1/1:1,418:420:99:12407,900,0:57:99:0.998 1/1:0,353:354:99:9901,716,0:55:99:1 1/1:0,382:382:99:9554,671,0:50:99:1 ./.:.:.:.:.:.:.:.
chr1 26142357 . A G 5334.2 PASS BaseQRankSum=1.488;Dels=0;FS=0.353;HRun=1;HaplotypeScore=29.9443;MQ=55;MQ0=0;MQRankSum=2.919;QD=12.46;ReadPosRankSum=-0.413;SB=-3857.01;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Silent,Silent;EXON;DP=428;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=SEPN1;GeneDetail.refGene=NM_020451:c.*148A>G\x3bNM_206926:c.*148A>G;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=SEPN1;GeneDetail.knownGene=uc021ojk.1:c.*148A>G\x3buc021ojl.1:c.*148A>G;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:192,235:428:99:5334,0,4454:55:99:0.55 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 26142989 rs11556312 C T 4023.06 PASS BaseQRankSum=-1.144;Dels=0;FS=0;HRun=0;HaplotypeScore=9.9944;MQ=57;MQ0=0;MQRankSum=2.312;QD=12.08;ReadPosRankSum=1.52;SB=-2255.21;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Silent,Silent;EXON;DP=333;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=SEPN1;GeneDetail.refGene=NM_020451:c.*780C>T\x3bNM_206926:c.*780C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=SEPN1;GeneDetail.knownGene=uc021ojk.1:c.*780C>T\x3buc021ojl.1:c.*780C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS41282.1\x3bCCDS41283.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=Likely_benign;CLNDBN=SEPN1-Related_Disorders;CLNACC=RCV000301368.1;CLNDSDB=MedGen;CLNDSDBID=CN239420;PopFreqMax=0.082;Kaviar_AF=0.0065698;Kaviar_AC=171;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0221645;snp138=rs11556312;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:180,153:333:99:4023,0,4591:57:99:0.459 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 26143566 . A C 61.66 LowVariantFreq;SB;LowGQX BaseQRankSum=-5.2;Dels=0;FS=156.649;HRun=4;HaplotypeScore=84.8902;MQ=45;MQ0=0;MQRankSum=-7.494;QD=0.19;ReadPosRankSum=-2.159;SB=-0.01;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Silent,Silent;EXON;DP=549;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=SEPN1;GeneDetail.refGene=NM_020451:c.*1357A>C\x3bNM_206926:c.*1357A>C;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=SEPN1;GeneDetail.knownGene=uc021ojk.1:c.*1357A>C\x3buc021ojl.1:c.*1357A>C;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intergenic;Gene.ccdsGene=CCDS41283.1\x3bCCDS44089.1;GeneDetail.ccdsGene=dist\x3d1357\x3bdist\x3d6030;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:277,38:319:91.65:92,0,7992:45:62:0.121 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:200,25:229:31.32:31,0,6068:46:4:0.111
chr1 26143704 rs3033477 A ATTTTG 20728.3 PASS BaseQRankSum=1.031;FS=0;HRun=0;HaplotypeScore=279.639;MQ=53;MQ0=1;MQRankSum=1.339;QD=51.23;ReadPosRankSum=-0.414;SB=-7828.1;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Noncoding,Noncoding;EXON;DP=3156;AN=22;AC=21;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=SEPN1;GeneDetail.refGene=NM_020451:c.*1495_*1496insTTTTG\x3bNM_206926:c.*1495_*1496insTTTTG;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=SEPN1;GeneDetail.knownGene=uc021ojk.1:c.*1495_*1496insTTTTG\x3buc021ojl.1:c.*1495_*1496insTTTTG;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intergenic;Gene.ccdsGene=CCDS41283.1\x3bCCDS44089.1;GeneDetail.ccdsGene=dist\x3d1495\x3bdist\x3d5892;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.011;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=rs3033477;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:112,222:337:99:17316,671,0:53:99:0.665 1/1:96,176:272:99:14019,458,0:53:99:0.647 0/1:140,73:213:99:4733,0,7318:53:99:0.343 1/1:76,217:294:99:16085,683,0:54:99:0.741 1/1:103,170:272:99:13730,521,0:53:99:0.623 1/1:79,186:267:99:13885,590,0:54:99:0.702 1/1:82,282:369:99:20728,744,0:55:99:0.775 1/1:51,184:237:99:13897,590,0:54:99:0.783 1/1:87,260:347:99:19321,816,0:55:99:0.749 1/1:68,200:273:99:14367,479,0:55:99:0.746 1/1:89,178:268:99:12634,406,0:53:99:0.667 ./.:.:.:.:.:.:.:.
chr1 26144437 rs11319301 TC T 12663 PASS FS=0;HRun=8;HaplotypeScore=296.34;MQ=57;MQ0=0;QD=31.87;SB=-4778.8;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Noncoding,Noncoding;EXON;BaseQRankSum=-1.176;MQRankSum=-0.014;ReadPosRankSum=0.503;DP=3424;AN=24;AC=22;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=SEPN1;GeneDetail.refGene=NM_020451:c.*2229delC\x3bNM_206926:c.*2229delC;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=SEPN1;GeneDetail.knownGene=uc021ojk.1:c.*2229delC\x3buc021ojl.1:c.*2229delC;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intergenic;Gene.ccdsGene=CCDS41283.1\x3bCCDS44089.1;GeneDetail.ccdsGene=dist\x3d2229\x3bdist\x3d5158;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=Uncertain_significance;CLNDBN=SEPN1-Related_Disorders;CLNACC=RCV000351112.1;CLNDSDB=MedGen;CLNDSDBID=CN239420;PopFreqMax=.;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.766573;snp138=rs11319301;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:12,296:312:99:9945,890,0:57:99:0.961 1/1:31,252:288:99:8821,747,0:54:99:0.89 0/1:97,91:192:99:2519,0,2365:58:99:0.484 1/1:20,267:299:99:9108,825,0:58:99:0.93 1/1:35,250:286:99:9078,815,0:55:99:0.877 1/1:12,286:299:99:9640,863,0:57:99:0.96 1/1:23,336:361:99:11357,1021,0:58:99:0.936 1/1:13,240:256:99:8136,733,0:57:99:0.949 1/1:29,370:402:99:12663,1140,0:57:99:0.927 1/1:10,236:251:99:7961,716,0:57:99:0.959 1/1:9,221:232:99:7469,672,0:54:99:0.961 0/1:125,115:243:99:3208,0,3132:56:99:0.479
chr1 26144545 rs1044183 A T 4038.23 PASS BaseQRankSum=1.827;Dels=0;FS=0.817;HRun=0;HaplotypeScore=18.6618;MQ=56;MQ0=0;MQRankSum=0.594;QD=11.88;ReadPosRankSum=-0.573;SB=-2911.01;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Silent,Silent;EXON;DP=340;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=SEPN1;GeneDetail.refGene=NM_020451:c.*2336A>T\x3bNM_206926:c.*2336A>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=SEPN1;GeneDetail.knownGene=uc021ojk.1:c.*2336A>T\x3buc021ojl.1:c.*2336A>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intergenic;Gene.ccdsGene=CCDS41283.1\x3bCCDS44089.1;GeneDetail.ccdsGene=dist\x3d2336\x3bdist\x3d5051;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=Likely_benign;CLNDBN=SEPN1-Related_Disorders;CLNACC=RCV000397931.1;CLNDSDB=MedGen;CLNDSDBID=CN239420;PopFreqMax=0.061;Kaviar_AF=0.0055239;Kaviar_AC=854;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0179712;snp138=rs1044183;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:165,174:340:99:4038,0,4117:56:99:0.513 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 26144674 rs6872 G A 13255.7 PASS BaseQRankSum=-3.346;Dels=0;FS=0.356;HRun=0;HaplotypeScore=14.6833;MQ=54;MQ0=0;MQRankSum=2.184;QD=11.84;ReadPosRankSum=0.768;SB=-3287.13;TI=NM_020451,NM_206926;GI=SEPN1,SEPN1;FC=Silent,Silent;EXON;DP=1269;AN=6;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=SEPN1;GeneDetail.refGene=NM_020451:c.*2465G>A\x3bNM_206926:c.*2465G>A;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=SEPN1;GeneDetail.knownGene=uc021ojk.1:c.*2465G>A\x3buc021ojl.1:c.*2465G>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intergenic;Gene.ccdsGene=CCDS41283.1\x3bCCDS44089.1;GeneDetail.ccdsGene=dist\x3d2465\x3bdist\x3d4922;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p36.11;CLINSIG=Benign;CLNDBN=SEPN1-Related_Disorders;CLNACC=RCV000310137.1;CLNDSDB=MedGen;CLNDSDBID=CN239420;PopFreqMax=0.31;Kaviar_AF=0.0074151;Kaviar_AC=193;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.162939;snp138=rs6872;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:206,213:419:99:4959,0,4767:54:99:0.508 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:2,463:467:99:13256,931,0:56:99:0.996 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,383:383:99:10506,755,0:54:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 46655100 rs113174528 T C 4568.08 PASS BaseQRankSum=0.987;Dels=0;FS=2.128;HRun=2;HaplotypeScore=22.1054;MQ=56;MQ0=0;MQRankSum=0.799;QD=11.54;ReadPosRankSum=0.562;SB=-2958.51;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Silent,Silent;DP=396;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p34.1;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000242379.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.15;Kaviar_AF=0.0349737;Kaviar_AC=5407;Kaviar_AN=154602;ExAC_ALL=0.0380;ExAC_AFR=0.1325;ExAC_AMR=0.0115;ExAC_EAS=0.0155;ExAC_FIN=0.0662;ExAC_NFE=0.0228;ExAC_OTH=0.0334;ExAC_SAS=0.0591;1000g2014oct_all=0.0638978;snp138=rs113174528;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=1.1059;dpsi_zscore=1.583;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:209,186:396:99:4568,0,5168:56:99:0.471 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 46655158 rs6659553 T C 14673.2 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=17.2363;MQ=56;MQ0=0;QD=27.58;SB=-8216.06;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Missense_M623V,Silent;EXON;BaseQRankSum=1.715;MQRankSum=0.031;ReadPosRankSum=0.519;DP=4831;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=POMGNT1:NM_001290129:exon20:c.A1801G:p.M601V\x3bPOMGNT1:NM_001290130:exon20:c.A1438G:p.M480V\x3bPOMGNT1:NM_001243766:exon21:c.A1867G:p.M623V\x3bPOMGNT1:NM_017739:exon21:c.A1867G:p.M623V;Func.knownGene=exonic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=POMGNT1:uc001cpf.3:exon18:c.A868G:p.M290V\x3bPOMGNT1:uc010olx.2:exon20:c.A1801G:p.M601V\x3bPOMGNT1:uc010olz.2:exon20:c.A1438G:p.M480V\x3bPOMGNT1:uc001cpe.3:exon21:c.A1867G:p.M623V\x3bPOMGNT1:uc001cpg.3:exon21:c.A1867G:p.M623V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS531.1:CCDS531.1:exon20:c.A1867G:p.M623V\x3bCCDS57995.1:CCDS57995.1:exon20:c.A1867G:p.M623V;cytoBand=1p34.1;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000153758.3;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=1.;Kaviar_AF=0.9422;Kaviar_AC=145666;Kaviar_AN=154602;ExAC_ALL=0.9838;ExAC_AFR=0.8219;ExAC_AMR=0.9926;ExAC_EAS=1;ExAC_FIN=1;ExAC_NFE=0.9997;ExAC_OTH=0.9911;ExAC_SAS=0.9998;1000g2014oct_all=0.942492;snp138=rs6659553;SIFT_score=1.0;SIFT_converted_rankscore=0.010;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.0;Polyphen2_HVAR_rankscore=0.013;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.629;LRT_pred=N;MutationTaster_score=0.999;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=P;MutationAssessor_score=-0.625;MutationAssessor_score_rankscore=0.021;MutationAssessor_pred=N;FATHMM_score=-1.76;FATHMM_converted_rankscore=0.836;FATHMM_pred=D;PROVEAN_score=1.3;PROVEAN_converted_rankscore=0.010;PROVEAN_pred=N;VEST3_score=0.046;VEST3_rankscore=0.486;MetaSVM_score=-0.926;MetaSVM_rankscore=0.448;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=0.266;CADD_raw_rankscore=0.120;CADD_phred=5.360;DANN_score=0.858;DANN_rankscore=0.156;fathmm-MKL_coding_score=0.183;fathmm-MKL_coding_rankscore=0.200;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.667;Eigen-PC-raw=-0.308;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.732;integrated_fitCons_score_rankscore=0.924;integrated_confidence_value=0;GERP++_RS=5.92;GERP++_RS_rankscore=0.955;phyloP100way_vertebrate=5.829;phyloP100way_vertebrate_rankscore=0.688;phyloP20way_mammalian=0.069;phyloP20way_mammalian_rankscore=0.176;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.998;phastCons20way_mammalian_rankscore=0.697;SiPhy_29way_logOdds=15.028;SiPhy_29way_logOdds_rankscore=0.712;Interpro_domain=Nucleotide-diphospho-sugar_transferases;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-1.1906;dpsi_zscore=-1.575;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,425:425:99:11722,843,0:56:99:1 1/1:0,413:413:99:11111,786,0:53:99:1 1/1:0,243:243:99:7031,506,0:55:99:1 1/1:0,416:416:99:11925,861,0:57:99:1 1/1:0,428:429:99:11852,849,0:56:99:1 1/1:1,396:398:99:11279,810,0:54:99:0.997 1/1:0,537:537:99:14673,1053,0:57:99:1 1/1:0,317:317:99:9294,677,0:56:99:1 1/1:0,495:495:99:13887,999,0:56:99:1 1/1:0,394:394:99:10906,780,0:54:99:1 1/1:0,432:432:99:10594,734,0:49:99:1 1/1:0,328:330:99:9434,677,0:55:99:1
chr1 46655495 rs78405727 G T 4718.31 PASS BaseQRankSum=2.22;Dels=0;FS=0.79;HRun=2;HaplotypeScore=22.6263;MQ=55;MQ0=0;MQRankSum=1.809;QD=12.52;ReadPosRankSum=-0.226;SB=-2674.75;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Silent,Silent;DP=377;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p34.1;CLINSIG=Likely_benign;CLNDBN=not_specified;CLNACC=RCV000254414.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.14;Kaviar_AF=0.0303618;Kaviar_AC=4694;Kaviar_AN=154602;ExAC_ALL=0.0331;ExAC_AFR=0.1217;ExAC_AMR=0.0112;ExAC_EAS=0.0006;ExAC_FIN=0.0668;ExAC_NFE=0.0226;ExAC_OTH=0.0292;ExAC_SAS=0.0387;1000g2014oct_all=0.0549121;snp138=rs78405727;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0469;dpsi_zscore=-0.251;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:183,194:377:99:4718,0,4296:55:99:0.515 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 46655645 rs74374973 C T 4796.55 PASS BaseQRankSum=2.917;Dels=0;FS=4.117;HRun=1;HaplotypeScore=18.4026;MQ=54;MQ0=0;MQRankSum=-1.48;QD=13.29;ReadPosRankSum=-0.668;SB=-3192.82;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Missense_D556N,Silent;EXON;DP=361;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=POMGNT1:NM_001290129:exon19:c.G1600A:p.D534N\x3bPOMGNT1:NM_001290130:exon19:c.G1237A:p.D413N\x3bPOMGNT1:NM_001243766:exon20:c.G1666A:p.D556N\x3bPOMGNT1:NM_017739:exon20:c.G1666A:p.D556N;Func.knownGene=exonic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=POMGNT1:uc001cpf.3:exon17:c.G667A:p.D223N\x3bPOMGNT1:uc010olx.2:exon19:c.G1600A:p.D534N\x3bPOMGNT1:uc010olz.2:exon19:c.G1237A:p.D413N\x3bPOMGNT1:uc001cpe.3:exon20:c.G1666A:p.D556N\x3bPOMGNT1:uc001cpg.3:exon20:c.G1666A:p.D556N;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS531.1:CCDS531.1:exon19:c.G1666A:p.D556N\x3bCCDS57995.1:CCDS57995.1:exon19:c.G1666A:p.D556N;cytoBand=1p34.1;CLINSIG=Pathogenic|other;CLNDBN=Limb-girdle_muscular_dystrophy-dystroglycanopathy,_type_C3|not_specified;CLNACC=RCV000004204.3|RCV000081801.9;CLNDSDB=MedGen:OMIM:Orphanet|MedGen;CLNDSDBID=C3150417:613157:ORPHA206564|CN169374;PopFreqMax=0.018;Kaviar_AF=0.0095148;Kaviar_AC=1471;Kaviar_AN=154602;ExAC_ALL=0.0091;ExAC_AFR=0.0025;ExAC_AMR=0.0074;ExAC_EAS=0;ExAC_FIN=0.0185;ExAC_NFE=0.0126;ExAC_OTH=0.0104;ExAC_SAS=0.0010;1000g2014oct_all=0.00519169;snp138=rs74374973;SIFT_score=0.046;SIFT_converted_rankscore=0.405;SIFT_pred=D;Polyphen2_HDIV_score=0.998;Polyphen2_HDIV_rankscore=0.715;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.895;Polyphen2_HVAR_rankscore=0.631;Polyphen2_HVAR_pred=P;LRT_score=0.000;LRT_converted_rankscore=0.843;LRT_pred=D;MutationTaster_score=1;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=A;MutationAssessor_score=1.825;MutationAssessor_score_rankscore=0.480;MutationAssessor_pred=L;FATHMM_score=-1.59;FATHMM_converted_rankscore=0.821;FATHMM_pred=D;PROVEAN_score=-3.1;PROVEAN_converted_rankscore=0.637;PROVEAN_pred=D;VEST3_score=0.148;VEST3_rankscore=0.271;MetaSVM_score=0.009;MetaSVM_rankscore=0.824;MetaSVM_pred=D;MetaLR_score=0.483;MetaLR_rankscore=0.803;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=5.763;CADD_raw_rankscore=0.788;CADD_phred=27.0;DANN_score=0.999;DANN_rankscore=0.986;fathmm-MKL_coding_score=0.983;fathmm-MKL_coding_rankscore=0.817;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.730;Eigen-PC-raw=0.763;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.706;integrated_fitCons_score_rankscore=0.609;integrated_confidence_value=0;GERP++_RS=6.06;GERP++_RS_rankscore=0.983;phyloP100way_vertebrate=5.832;phyloP100way_vertebrate_rankscore=0.688;phyloP20way_mammalian=0.935;phyloP20way_mammalian_rankscore=0.490;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=1.000;phastCons20way_mammalian_rankscore=0.888;SiPhy_29way_logOdds=20.621;SiPhy_29way_logOdds_rankscore=0.995;Interpro_domain=Nucleotide-diphospho-sugar_transferases;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1357;dpsi_zscore=-0.547;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:161,200:361:99:4797,0,3847:54:99:0.554 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 46658217 rs41292143 C T 3544.58 PASS BaseQRankSum=0.001;Dels=0;FS=0.407;HRun=0;HaplotypeScore=8.451;MQ=56;MQ0=0;MQRankSum=0.311;QD=10.97;ReadPosRankSum=1.245;SB=-2280.19;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Synonymous_L419L,Silent;EXON;DP=323;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=POMGNT1:NM_001290129:exon14:c.G1191A:p.L397L\x3bPOMGNT1:NM_001290130:exon14:c.G828A:p.L276L\x3bPOMGNT1:NM_001243766:exon15:c.G1257A:p.L419L\x3bPOMGNT1:NM_017739:exon15:c.G1257A:p.L419L;Func.knownGene=exonic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=POMGNT1:uc001cpi.1:exon4:c.G258A:p.L86L\x3bPOMGNT1:uc001cpf.3:exon12:c.G258A:p.L86L\x3bPOMGNT1:uc010olx.2:exon14:c.G1191A:p.L397L\x3bPOMGNT1:uc010olz.2:exon14:c.G828A:p.L276L\x3bPOMGNT1:uc001cpe.3:exon15:c.G1257A:p.L419L\x3bPOMGNT1:uc001cpg.3:exon15:c.G1257A:p.L419L;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS531.1:CCDS531.1:exon14:c.G1257A:p.L419L\x3bCCDS57995.1:CCDS57995.1:exon14:c.G1257A:p.L419L;cytoBand=1p34.1;CLINSIG=other;CLNDBN=not_specified;CLNACC=RCV000118028.4;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.017;Kaviar_AF=0.0098511;Kaviar_AC=1523;Kaviar_AN=154602;ExAC_ALL=0.0090;ExAC_AFR=0.0034;ExAC_AMR=0.0022;ExAC_EAS=0;ExAC_FIN=0.0020;ExAC_NFE=0.0148;ExAC_OTH=0.0067;ExAC_SAS=0.0016;1000g2014oct_all=0.00279553;snp138=rs41292143;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0713;dpsi_zscore=0.386;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:172,150:323:99:3545,0,4423:56:99:0.466
chr1 46658328 rs2292484 A G 10207.7 PASS BaseQRankSum=1.199;Dels=0;FS=0;HRun=1;HaplotypeScore=4.563;MQ=57;MQ0=0;MQRankSum=1.672;QD=29.63;ReadPosRankSum=2.409;SB=-4778.42;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Silent,Silent;DP=1917;AN=14;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p34.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.43;Kaviar_AF=0.0678064;Kaviar_AC=10483;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.333466;snp138=rs2292484;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2162;dpsi_zscore=0.753;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:2,304:306:99:9068,620,0:57:99:0.993 ./.:.:.:.:.:.:.:. 0/1:87,77:164:99:2065,0,2353:59:99:0.47 0/1:114,150:264:99:3969,0,2949:58:99:0.568 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:164,141:305:99:3777,0,4482:58:99:0.462 ./.:.:.:.:.:.:.:. 1/1:0,328:329:99:10208,752,0:58:99:1 0/1:153,158:311:99:3795,0,3962:56:99:0.508 ./.:.:.:.:.:.:.:. 0/1:114,124:238:99:3246,0,2971:57:99:0.521
chr1 46658910 rs2292486 G A 4154.53 PASS BaseQRankSum=3.655;Dels=0;FS=0.375;HRun=0;HaplotypeScore=18.9609;MQ=55;MQ0=0;MQRankSum=1.381;QD=10.85;ReadPosRankSum=-0.588;SB=-2828.98;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Silent,Silent;DP=383;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p34.1;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000243209.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.34;Kaviar_AF=0.0636344;Kaviar_AC=9838;Kaviar_AN=154602;ExAC_ALL=0.0701;ExAC_AFR=0.0248;ExAC_AMR=0.0523;ExAC_EAS=0.3412;ExAC_FIN=0.0163;ExAC_NFE=0.0161;ExAC_OTH=0.0738;ExAC_SAS=0.2090;1000g2014oct_all=0.128594;snp138=rs2292486;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.5390;dpsi_zscore=1.171;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:200,183:383:99:4155,0,4630:55:99:0.478 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 46659104 rs7527668 T C 13904.4 PASS Dels=0;FS=0;HRun=3;HaplotypeScore=18.4961;MQ=56;MQ0=0;QD=28.26;SB=-9525.63;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Silent,Silent;BaseQRankSum=1.867;MQRankSum=0.736;ReadPosRankSum=0.714;DP=3043;AN=14;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR5;Gene.knownGene=POMGNT1;GeneDetail.knownGene=uc001cpf.3:c.-17A>G\x3buc001cpi.1:c.-17A>G;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p34.1;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000252026.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.46;Kaviar_AF=0.345759;Kaviar_AC=53455;Kaviar_AN=154602;ExAC_ALL=0.3805;ExAC_AFR=0.4587;ExAC_AMR=0.4293;ExAC_EAS=0.1562;ExAC_FIN=0.3999;ExAC_NFE=0.3689;ExAC_OTH=0.3549;ExAC_SAS=0.4489;1000g2014oct_all=0.367013;snp138=rs7527668;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.9370;dpsi_zscore=1.483;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,491:492:99:13904,996,0:56:99:1 ./.:.:.:.:.:.:.:. 0/1:146,166:312:99:4198,0,3308:55:99:0.532 0/1:207,247:454:99:6107,0,4952:56:99:0.544 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:266,271:539:99:6687,0,6399:57:99:0.505 ./.:.:.:.:.:.:.:. 1/1:5,481:486:99:13747,850,0:56:99:0.99 0/1:216,206:422:99:4734,0,5087:55:99:0.488 ./.:.:.:.:.:.:.:. 0/1:176,158:335:99:4114,0,4295:55:99:0.473
chr1 46659363 rs7527935 T C 12073.8 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=10.9627;MQ=56;MQ0=0;QD=29.67;SB=-7162.83;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Silent,Silent;BaseQRankSum=2.745;MQRankSum=1.041;ReadPosRankSum=0.229;DP=2460;AN=14;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR5;Gene.knownGene=POMGNT1;GeneDetail.knownGene=uc001cpf.3:c.-276A>G\x3buc001cpi.1:c.-276A>G;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p34.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.44;Kaviar_AF=0.342822;Kaviar_AC=53001;Kaviar_AN=154602;ExAC_ALL=0.3560;ExAC_AFR=0.3464;ExAC_AMR=0.3940;ExAC_EAS=0.1494;ExAC_FIN=0.3886;ExAC_NFE=0.3524;ExAC_OTH=0.3452;ExAC_SAS=0.4419;1000g2014oct_all=0.333466;snp138=rs7527935;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.4925;dpsi_zscore=1.125;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,406:407:99:12074,879,0:56:99:1 ./.:.:.:.:.:.:.:. 0/1:135,110:245:99:2838,0,3456:56:99:0.449 0/1:180,172:352:99:4629,0,4669:58:99:0.489 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:246,196:445:99:4892,0,6114:58:99:0.443 ./.:.:.:.:.:.:.:. 1/1:4,340:344:99:10527,704,0:57:99:0.988 0/1:226,143:370:99:3446,0,5580:56:99:0.388 ./.:.:.:.:.:.:.:. 0/1:152,145:297:99:3733,0,3991:56:99:0.488
chr1 46659636 rs115804669 C G 5412.5 PASS BaseQRankSum=0.357;Dels=0;FS=3.776;HRun=0;HaplotypeScore=18.7764;MQ=55;MQ0=0;MQRankSum=2.774;QD=13.57;ReadPosRankSum=0.374;SB=-3595.8;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Silent,Silent;DP=399;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p34.1;CLINSIG=Likely_benign;CLNDBN=not_specified;CLNACC=RCV000242341.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.068;Kaviar_AF=0.0243917;Kaviar_AC=3771;Kaviar_AN=154602;ExAC_ALL=0.0273;ExAC_AFR=0.0441;ExAC_AMR=0.0074;ExAC_EAS=0.0006;ExAC_FIN=0.0678;ExAC_NFE=0.0231;ExAC_OTH=0.0303;ExAC_SAS=0.0448;1000g2014oct_all=0.0319489;snp138=rs115804669;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0425;dpsi_zscore=-0.230;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:175,224:399:99:5412,0,4086:55:99:0.561 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 46660295 rs2292487 T C 11423.9 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=5.4702;MQ=56;MQ0=0;QD=29.16;SB=-6487.83;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Synonymous_K227K,Silent;EXON;BaseQRankSum=1.491;MQRankSum=0.584;ReadPosRankSum=-1.26;DP=2422;AN=14;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=POMGNT1:NM_001290129:exon7:c.A615G:p.K205K\x3bPOMGNT1:NM_001290130:exon7:c.A252G:p.K84K\x3bPOMGNT1:NM_001243766:exon8:c.A681G:p.K227K\x3bPOMGNT1:NM_017739:exon8:c.A681G:p.K227K;Func.knownGene=exonic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=POMGNT1:uc010olx.2:exon7:c.A615G:p.K205K\x3bPOMGNT1:uc010olz.2:exon7:c.A252G:p.K84K\x3bPOMGNT1:uc001cpe.3:exon8:c.A681G:p.K227K\x3bPOMGNT1:uc001cpg.3:exon8:c.A681G:p.K227K;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS531.1:CCDS531.1:exon7:c.A681G:p.K227K\x3bCCDS57995.1:CCDS57995.1:exon7:c.A681G:p.K227K;cytoBand=1p34.1;CLINSIG=other|Likely_benign|Likely_benign;CLNDBN=not_specified|Limb-Girdle_Muscular_Dystrophy,_Recessive|Congenital_Muscular_Dystrophy,_alpha-dystroglycan_related;CLNACC=RCV000081805.9|RCV000304915.1|RCV000343385.1;CLNDSDB=MedGen|MedGen|MedGen;CLNDSDBID=CN169374|CN239352|CN239202;PopFreqMax=0.44;Kaviar_AF=0.349763;Kaviar_AC=54074;Kaviar_AN=154602;ExAC_ALL=0.3549;ExAC_AFR=0.3476;ExAC_AMR=0.3922;ExAC_EAS=0.1471;ExAC_FIN=0.3838;ExAC_NFE=0.3521;ExAC_OTH=0.3436;ExAC_SAS=0.4422;1000g2014oct_all=0.333466;snp138=rs2292487;SIFT_score=0.018;SIFT_converted_rankscore=0.506;SIFT_pred=D;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=0.999;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=P;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=-0.14;PROVEAN_converted_rankscore=0.092;PROVEAN_pred=N;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=-1.001;MetaSVM_rankscore=0.295;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=0.373;CADD_raw_rankscore=0.130;CADD_phred=6.375;DANN_score=0.970;DANN_rankscore=0.314;fathmm-MKL_coding_score=0.237;fathmm-MKL_coding_rankscore=0.219;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.047;Eigen-PC-raw=0.020;GenoCanyon_score=0.997;GenoCanyon_score_rankscore=0.349;integrated_fitCons_score=0.732;integrated_fitCons_score_rankscore=0.924;integrated_confidence_value=0;GERP++_RS=3.73;GERP++_RS_rankscore=0.418;phyloP100way_vertebrate=0.397;phyloP100way_vertebrate_rankscore=0.205;phyloP20way_mammalian=-0.302;phyloP20way_mammalian_rankscore=0.080;phastCons100way_vertebrate=0.993;phastCons100way_vertebrate_rankscore=0.376;phastCons20way_mammalian=0.997;phastCons20way_mammalian_rankscore=0.653;SiPhy_29way_logOdds=10.333;SiPhy_29way_logOdds_rankscore=0.428;Interpro_domain=.;GTEx_V6_gene=ENSG00000171357.5|ENSG00000171357.5|ENSG00000232022.2|ENSG00000232022.2|ENSG00000232022.2|ENSG00000232022.2|ENSG00000117480.11|ENSG00000171357.5|ENSG00000117481.6|ENSG00000232022.2|ENSG00000171357.5|ENSG00000232022.2;GTEx_V6_tissue=Adipose_Subcutaneous|Adipose_Visceral_Omentum|Brain_Caudate_basal_ganglia|Brain_Cerebellum|Brain_Hypothalamus|Brain_Nucleus_accumbens_basal_ganglia|Esophagus_Mucosa|Lung|Muscle_Skeletal|Nerve_Tibial|Skin_Sun_Exposed_Lower_leg|Thyroid;dpsi_max_tissue=-3.7965;dpsi_zscore=-2.313;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,365:365:99:10645,771,0:56:99:1 ./.:.:.:.:.:.:.:. 0/1:117,153:270:99:3717,0,2747:55:99:0.567 0/1:165,176:342:99:4320,0,4019:57:99:0.516 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:198,200:398:99:4911,0,4846:57:99:0.503 ./.:.:.:.:.:.:.:. 1/1:4,385:389:99:11424,750,0:58:99:0.99 0/1:185,172:357:99:4044,0,4495:56:99:0.482 ./.:.:.:.:.:.:.:. 0/1:145,153:298:99:3639,0,3641:57:99:0.513
chr1 46661776 rs76693406 G A 6233.14 PASS BaseQRankSum=4.75;Dels=0;FS=2.455;HRun=1;HaplotypeScore=22.6572;MQ=56;MQ0=0;MQRankSum=1.922;QD=13.55;ReadPosRankSum=1.078;SB=-3761.69;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Silent,Silent;DP=460;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p34.1;CLINSIG=Likely_benign;CLNDBN=not_specified;CLNACC=RCV000250875.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.094;Kaviar_AF=0.0286154;Kaviar_AC=4424;Kaviar_AN=154602;ExAC_ALL=0.0304;ExAC_AFR=0.0873;ExAC_AMR=0.0091;ExAC_EAS=0.0006;ExAC_FIN=0.0659;ExAC_NFE=0.0224;ExAC_OTH=0.0290;ExAC_SAS=0.0434;1000g2014oct_all=0.0441294;snp138=rs76693406;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0600;dpsi_zscore=0.342;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:215,243:460:99:6233,0,4942:56:99:0.531 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 46662456 rs150576537 C T 3007.42 PASS BaseQRankSum=0.839;Dels=0;FS=0.835;HRun=0;HaplotypeScore=11.2299;MQ=51;MQ0=0;MQRankSum=-1.045;QD=9;ReadPosRankSum=0.799;SB=-2209.93;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Missense_V101I,Silent;EXON;DP=334;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=POMGNT1:NM_001290129:exon3:c.G235A:p.V79I\x3bPOMGNT1:NM_001243766:exon4:c.G301A:p.V101I\x3bPOMGNT1:NM_017739:exon4:c.G301A:p.V101I;Func.knownGene=exonic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=POMGNT1:uc001cpj.3:exon3:c.G301A:p.V101I\x3bPOMGNT1:uc010olx.2:exon3:c.G235A:p.V79I\x3bPOMGNT1:uc001cpe.3:exon4:c.G301A:p.V101I\x3bPOMGNT1:uc001cpg.3:exon4:c.G301A:p.V101I;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS531.1:CCDS531.1:exon3:c.G301A:p.V101I\x3bCCDS57995.1:CCDS57995.1:exon3:c.G301A:p.V101I;cytoBand=1p34.1;CLINSIG=other|Uncertain_significance|Uncertain_significance;CLNDBN=not_specified|Limb-Girdle_Muscular_Dystrophy,_Recessive|Congenital_Muscular_Dystrophy,_alpha-dystroglycan_related;CLNACC=RCV000081803.5|RCV000312026.1|RCV000369008.1;CLNDSDB=MedGen|MedGen|MedGen;CLNDSDBID=CN169374|CN239352|CN239202;PopFreqMax=0.0048;Kaviar_AF=0.0026908;Kaviar_AC=416;Kaviar_AN=154602;ExAC_ALL=0.0030;ExAC_AFR=9.625e-05;ExAC_AMR=0.0012;ExAC_EAS=0;ExAC_FIN=0.0008;ExAC_NFE=0.0048;ExAC_OTH=0.0011;ExAC_SAS=0.0008;1000g2014oct_all=0.000798722;snp138=rs150576537;SIFT_score=1.0;SIFT_converted_rankscore=0.025;SIFT_pred=T;Polyphen2_HDIV_score=0.005;Polyphen2_HDIV_rankscore=0.190;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.003;Polyphen2_HVAR_rankscore=0.104;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.843;LRT_pred=D;MutationTaster_score=0.759;MutationTaster_converted_rankscore=0.340;MutationTaster_pred=D;MutationAssessor_score=-0.505;MutationAssessor_score_rankscore=0.026;MutationAssessor_pred=N;FATHMM_score=-0.85;FATHMM_converted_rankscore=0.744;FATHMM_pred=T;PROVEAN_score=0.41;PROVEAN_converted_rankscore=0.036;PROVEAN_pred=N;VEST3_score=0.048;VEST3_rankscore=0.030;MetaSVM_score=-0.871;MetaSVM_rankscore=0.505;MetaSVM_pred=T;MetaLR_score=0.137;MetaLR_rankscore=0.454;MetaLR_pred=T;M-CAP_score=0.017;M-CAP_rankscore=0.393;M-CAP_pred=T;CADD_raw=1.023;CADD_raw_rankscore=0.192;CADD_phred=10.79;DANN_score=0.816;DANN_rankscore=0.133;fathmm-MKL_coding_score=0.813;fathmm-MKL_coding_rankscore=0.404;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.431;Eigen-PC-raw=-0.194;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.707;integrated_fitCons_score_rankscore=0.730;integrated_confidence_value=0;GERP++_RS=5.1;GERP++_RS_rankscore=0.688;phyloP100way_vertebrate=4.441;phyloP100way_vertebrate_rankscore=0.595;phyloP20way_mammalian=0.852;phyloP20way_mammalian_rankscore=0.362;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.990;phastCons20way_mammalian_rankscore=0.544;SiPhy_29way_logOdds=9.330;SiPhy_29way_logOdds_rankscore=0.370;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0771;dpsi_zscore=0.407;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=0.0174172712213;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:187,147:334:99:3037,0,4141:51:99:0.44 ./.:.:.:.:.:.:.:.
chr1 46662609 rs41309197 A C 5240.53 PASS BaseQRankSum=2.209;Dels=0;FS=1.518;HRun=0;HaplotypeScore=22.2855;MQ=57;MQ0=0;MQRankSum=-0.182;QD=11.67;ReadPosRankSum=1.177;SB=-3374.08;TI=NM_017739,NR_024332;GI=POMGNT1,POMGNT1;FC=Silent,Silent;DP=449;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=POMGNT1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=POMGNT1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS531.1\x3bCCDS57995.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p34.1;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000253882.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.094;Kaviar_AF=0.0285443;Kaviar_AC=4413;Kaviar_AN=154602;ExAC_ALL=0.0302;ExAC_AFR=0.0865;ExAC_AMR=0.0091;ExAC_EAS=0.0006;ExAC_FIN=0.0656;ExAC_NFE=0.0223;ExAC_OTH=0.0286;ExAC_SAS=0.0433;1000g2014oct_all=0.0441294;snp138=rs41309197;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-3.3318;dpsi_zscore=-2.226;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:236,213:449:99:5241,0,5941:57:99:0.474 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 46685792 rs62620990 A G 6049.52 PASS BaseQRankSum=2.82;Dels=0;FS=0.916;HRun=0;HaplotypeScore=5.7866;MQ=57;MQ0=0;MQRankSum=1.612;QD=13.03;ReadPosRankSum=-0.666;SB=-2285.19;TI=NR_024332,NM_001013615;GI=POMGNT1,C1orf190;FC=Silent,Missense_Q207R;EXON;DP=1606;AN=8;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=LURAP1;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=LURAP1:NM_001013615:exon2:c.A620G:p.Q207R;Func.knownGene=exonic;Gene.knownGene=LURAP1;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=LURAP1:uc010oma.2:exon2:c.A620G:p.Q207R;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS30703.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS30703.1:CCDS30703.1:exon2:c.A620G:p.Q207R;cytoBand=1p34.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.044;Kaviar_AF=0.0269337;Kaviar_AC=4164;Kaviar_AN=154602;ExAC_ALL=0.0265;ExAC_AFR=0.0076;ExAC_AMR=0.0172;ExAC_EAS=0;ExAC_FIN=0.0265;ExAC_NFE=0.0390;ExAC_OTH=0.0277;ExAC_SAS=0.0085;1000g2014oct_all=0.0129792;snp138=rs62620990;SIFT_score=0.088;SIFT_converted_rankscore=0.323;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_rankscore=0.040;Polyphen2_HVAR_pred=B;LRT_score=0.032;LRT_converted_rankscore=0.018;LRT_pred=N;MutationTaster_score=1.000;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=N;MutationAssessor_score=2.2;MutationAssessor_score_rankscore=0.622;MutationAssessor_pred=M;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=0.3;PROVEAN_converted_rankscore=0.041;PROVEAN_pred=N;VEST3_score=0.017;VEST3_rankscore=0.003;MetaSVM_score=-1.066;MetaSVM_rankscore=0.102;MetaSVM_pred=T;MetaLR_score=0.016;MetaLR_rankscore=0.064;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=-0.408;CADD_raw_rankscore=0.061;CADD_phred=0.370;DANN_score=0.791;DANN_rankscore=0.121;fathmm-MKL_coding_score=0.070;fathmm-MKL_coding_rankscore=0.129;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.054;Eigen-PC-raw=-1.060;GenoCanyon_score=0.657;GenoCanyon_score_rankscore=0.222;integrated_fitCons_score=0.615;integrated_fitCons_score_rankscore=0.372;integrated_confidence_value=0;GERP++_RS=-3.09;GERP++_RS_rankscore=0.050;phyloP100way_vertebrate=0.463;phyloP100way_vertebrate_rankscore=0.215;phyloP20way_mammalian=1.088;phyloP20way_mammalian_rankscore=0.866;phastCons100way_vertebrate=0.000;phastCons100way_vertebrate_rankscore=0.063;phastCons20way_mammalian=0.989;phastCons20way_mammalian_rankscore=0.536;SiPhy_29way_logOdds=5.747;SiPhy_29way_logOdds_rankscore=0.173;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:136,142:278:99:3624,0,3404:57:99:0.511 0/1:220,203:425:99:5128,0,5253:57:99:0.48 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:226,235:461:99:6050,0,5688:58:99:0.51 0/1:219,222:442:99:5360,0,5106:56:99:0.503 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 53662823 rs72673121 C A 2052.86 PASS BaseQRankSum=-2.006;Dels=0;FS=0.894;HRun=2;HaplotypeScore=5.4409;MQ=55;MQ0=0;MQRankSum=1.491;QD=14.53;ReadPosRankSum=0.928;SB=-509.45;TI=NM_000098;GI=CPT2;FC=Silent;DP=286;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CPT2;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CPT2;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS575.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p32.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.21;Kaviar_AF=0.0289776;Kaviar_AC=4480;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0888578;snp138=rs72673121;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:35,47:83:99:1236,0,832:55:99:0.573 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:70,51:121:99:1147,0,1766:57:99:0.421 ./.:.:.:.:.:.:.:. 1/1:0,82:82:99:2086,147,0:52:99:1 ./.:.:.:.:.:.:.:.
chr1 53675857 rs2229292 C T 7029.52 PASS BaseQRankSum=0.916;Dels=0;FS=0.965;HRun=2;HaplotypeScore=21.4839;MQ=57;MQ0=0;MQRankSum=0.91;QD=12.27;ReadPosRankSum=0.044;SB=-4711.45;TI=NM_000098;GI=CPT2;FC=Synonymous_L171L;EXON;DP=573;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CPT2;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=CPT2:NM_000098:exon4:c.C511T:p.L171L;Func.knownGene=exonic;Gene.knownGene=CPT2;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=CPT2:uc001cvb.4:exon4:c.C511T:p.L171L;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS575.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS575.1:CCDS575.1:exon4:c.C511T:p.L171L;cytoBand=1p32.3;CLINSIG=Benign|Likely_benign;CLNDBN=not_specified|Carnitine_palmitoyltransferase_II_deficiency;CLNACC=RCV000178037.1|RCV000385074.1;CLNDSDB=MedGen|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|C0342790:ORPHA157:238002005;PopFreqMax=0.076;Kaviar_AF=0.0060349;Kaviar_AC=933;Kaviar_AN=154602;ExAC_ALL=0.0065;ExAC_AFR=0.0712;ExAC_AMR=0.0029;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0001;ExAC_OTH=0.0033;ExAC_SAS=0;1000g2014oct_all=0.0205671;snp138=rs2229292;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0101;dpsi_zscore=0.069;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:285,288:573:99:7030,0,7064:57:99:0.503 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 53676448 rs1799821 G A 10743.5 PASS BaseQRankSum=1.072;Dels=0;FS=1.614;HRun=0;HaplotypeScore=17.2226;MQ=54;MQ0=0;MQRankSum=2.161;QD=11.73;ReadPosRankSum=1.308;SB=-3365.38;TI=NM_000098;GI=CPT2;FC=Missense_V368I;EXON;DP=2222;AN=10;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CPT2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=CPT2:NM_000098:exon4:c.G1102A:p.V368I;Func.knownGene=exonic;Gene.knownGene=CPT2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=CPT2:uc001cvb.4:exon4:c.G1102A:p.V368I;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS575.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS575.1:CCDS575.1:exon4:c.G1102A:p.V368I;cytoBand=1p32.3;CLINSIG=other|Benign|Benign;CLNDBN=Encephalopathy,_acute,_infection-induced,_4,_susceptibility_to|not_specified|Carnitine_palmitoyltransferase_II_deficiency;CLNACC=RCV000023026.3|RCV000078116.6|RCV000202483.2;CLNDSDB=MedGen:OMIM:Orphanet|MedGen|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=C3280160:614212:ORPHA263524|CN169374|C0342790:ORPHA157:238002005;PopFreqMax=0.73;Kaviar_AF=0.483609;Kaviar_AC=74767;Kaviar_AN=154602;ExAC_ALL=0.4841;ExAC_AFR=0.2836;ExAC_AMR=0.4291;ExAC_EAS=0.7326;ExAC_FIN=0.5312;ExAC_NFE=0.5438;ExAC_OTH=0.4493;ExAC_SAS=0.2609;1000g2014oct_all=0.413139;snp138=rs1799821;SIFT_score=1.0;SIFT_converted_rankscore=0.010;SIFT_pred=T;Polyphen2_HDIV_score=0.011;Polyphen2_HDIV_rankscore=0.147;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.004;Polyphen2_HVAR_rankscore=0.093;Polyphen2_HVAR_pred=B;LRT_score=0.005;LRT_converted_rankscore=0.330;LRT_pred=N;MutationTaster_score=0.999;MutationTaster_converted_rankscore=0.218;MutationTaster_pred=P;MutationAssessor_score=-0.74;MutationAssessor_score_rankscore=0.017;MutationAssessor_pred=N;FATHMM_score=-2.47;FATHMM_converted_rankscore=0.890;FATHMM_pred=D;PROVEAN_score=0.11;PROVEAN_converted_rankscore=0.057;PROVEAN_pred=N;VEST3_score=0.077;VEST3_rankscore=0.068;MetaSVM_score=-0.955;MetaSVM_rankscore=0.402;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=-1.832;CADD_raw_rankscore=0.010;CADD_phred=0.002;DANN_score=0.719;DANN_rankscore=0.095;fathmm-MKL_coding_score=0.110;fathmm-MKL_coding_rankscore=0.162;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-1.380;Eigen-PC-raw=-1.312;GenoCanyon_score=0.002;GenoCanyon_score_rankscore=0.095;integrated_fitCons_score=0.732;integrated_fitCons_score_rankscore=0.924;integrated_confidence_value=0;GERP++_RS=-0.261;GERP++_RS_rankscore=0.123;phyloP100way_vertebrate=-0.048;phyloP100way_vertebrate_rankscore=0.118;phyloP20way_mammalian=0.073;phyloP20way_mammalian_rankscore=0.181;phastCons100way_vertebrate=0.000;phastCons100way_vertebrate_rankscore=0.063;phastCons20way_mammalian=0.594;phastCons20way_mammalian_rankscore=0.287;SiPhy_29way_logOdds=10.737;SiPhy_29way_logOdds_rankscore=0.451;Interpro_domain=.;GTEx_V6_gene=ENSG00000162384.9|ENSG00000162384.9|ENSG00000162384.9|ENSG00000162384.9;GTEx_V6_tissue=Artery_Tibial|Esophagus_Muscularis|Muscle_Skeletal|Thyroid;dpsi_max_tissue=-0.5085;dpsi_zscore=-1.099;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:202,202:404:99:4737,0,4719:54:99:0.5 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:246,197:444:99:4707,0,5990:55:99:0.445 0/1:204,202:406:99:4954,0,4999:55:99:0.498 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:277,262:540:99:6525,0,7187:57:99:0.486 ./.:.:.:.:.:.:.:. 1/1:0,428:428:99:10744,746,0:50:99:1 ./.:.:.:.:.:.:.:.
chr1 53676718 rs147276580 A C 3891.66 PASS BaseQRankSum=1.864;Dels=0;FS=0;HRun=0;HaplotypeScore=13.7638;MQ=56;MQ0=0;MQRankSum=3.813;QD=11.15;ReadPosRankSum=0.921;SB=-2365.08;TI=NM_000098;GI=CPT2;FC=Missense_K458Q;EXON;DP=349;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CPT2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=CPT2:NM_000098:exon4:c.A1372C:p.K458Q;Func.knownGene=exonic;Gene.knownGene=CPT2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=CPT2:uc001cvb.4:exon4:c.A1372C:p.K458Q;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS575.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS575.1:CCDS575.1:exon4:c.A1372C:p.K458Q;cytoBand=1p32.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.011;Kaviar_AF=0.000304;Kaviar_AC=47;Kaviar_AN=154602;ExAC_ALL=0.0003;ExAC_AFR=0.0036;ExAC_AMR=8.684e-05;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=4.508e-05;ExAC_OTH=0;ExAC_SAS=0;1000g2014oct_all=0.000998403;snp138=rs147276580;SIFT_score=0.422;SIFT_converted_rankscore=0.098;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.002;Polyphen2_HVAR_rankscore=0.063;Polyphen2_HVAR_pred=B;LRT_score=0.009;LRT_converted_rankscore=0.308;LRT_pred=N;MutationTaster_score=0.994;MutationTaster_converted_rankscore=0.422;MutationTaster_pred=D;MutationAssessor_score=0.94;MutationAssessor_score_rankscore=0.237;MutationAssessor_pred=L;FATHMM_score=-4.19;FATHMM_converted_rankscore=0.969;FATHMM_pred=D;PROVEAN_score=-0.29;PROVEAN_converted_rankscore=0.117;PROVEAN_pred=N;VEST3_score=0.14;VEST3_rankscore=0.163;MetaSVM_score=-0.026;MetaSVM_rankscore=0.817;MetaSVM_pred=T;MetaLR_score=0.665;MetaLR_rankscore=0.884;MetaLR_pred=D;M-CAP_score=0.035;M-CAP_rankscore=0.564;M-CAP_pred=D;CADD_raw=0.030;CADD_raw_rankscore=0.096;CADD_phred=2.881;DANN_score=0.728;DANN_rankscore=0.098;fathmm-MKL_coding_score=0.917;fathmm-MKL_coding_rankscore=0.538;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.477;Eigen-PC-raw=-0.323;GenoCanyon_score=0.011;GenoCanyon_score_rankscore=0.121;integrated_fitCons_score=0.732;integrated_fitCons_score_rankscore=0.924;integrated_confidence_value=0;GERP++_RS=2.01;GERP++_RS_rankscore=0.254;phyloP100way_vertebrate=2.853;phyloP100way_vertebrate_rankscore=0.478;phyloP20way_mammalian=0.155;phyloP20way_mammalian_rankscore=0.242;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.983;phastCons20way_mammalian_rankscore=0.502;SiPhy_29way_logOdds=8.887;SiPhy_29way_logOdds_rankscore=0.344;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.8867;dpsi_zscore=-1.402;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=0.0353398318678;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:188,161:349:99:3892,0,4747:56:99:0.461 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 53676857 rs368311455 C T 4446.95 PASS BaseQRankSum=1.393;Dels=0;FS=0.364;HRun=0;HaplotypeScore=13.7935;MQ=56;MQ0=0;MQRankSum=0.699;QD=10.79;ReadPosRankSum=0.258;SB=-2631.78;TI=NM_000098;GI=CPT2;FC=Missense_P504L;EXON;DP=412;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CPT2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=CPT2:NM_000098:exon4:c.C1511T:p.P504L;Func.knownGene=exonic;Gene.knownGene=CPT2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=CPT2:uc001cvb.4:exon4:c.C1511T:p.P504L;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS575.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS575.1:CCDS575.1:exon4:c.C1511T:p.P504L;cytoBand=1p32.3;CLINSIG=Pathogenic;CLNDBN=not_provided;CLNACC=RCV000185833.1;CLNDSDB=MedGen;CLNDSDBID=CN221809;PopFreqMax=0.0001;Kaviar_AF=2.59e-05;Kaviar_AC=4;Kaviar_AN=154602;ExAC_ALL=3.596e-05;ExAC_AFR=0;ExAC_AMR=0;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=6.46e-05;ExAC_OTH=0;ExAC_SAS=0;1000g2014oct_all=.;snp138=rs368311455;SIFT_score=0.002;SIFT_converted_rankscore=0.721;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_rankscore=0.899;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.999;Polyphen2_HVAR_rankscore=0.916;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_converted_rankscore=0.843;LRT_pred=D;MutationTaster_score=1;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=D;MutationAssessor_score=3.23;MutationAssessor_score_rankscore=0.897;MutationAssessor_pred=M;FATHMM_score=-2.56;FATHMM_converted_rankscore=0.896;FATHMM_pred=D;PROVEAN_score=-7.61;PROVEAN_converted_rankscore=0.954;PROVEAN_pred=D;VEST3_score=0.969;VEST3_rankscore=0.969;MetaSVM_score=0.924;MetaSVM_rankscore=0.960;MetaSVM_pred=D;MetaLR_score=0.864;MetaLR_rankscore=0.955;MetaLR_pred=D;M-CAP_score=0.123;M-CAP_rankscore=0.805;M-CAP_pred=D;CADD_raw=5.471;CADD_raw_rankscore=0.743;CADD_phred=26.2;DANN_score=0.999;DANN_rankscore=0.956;fathmm-MKL_coding_score=0.990;fathmm-MKL_coding_rankscore=0.893;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.719;Eigen-PC-raw=0.582;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=5.29;GERP++_RS_rankscore=0.743;phyloP100way_vertebrate=7.905;phyloP100way_vertebrate_rankscore=0.864;phyloP20way_mammalian=0.852;phyloP20way_mammalian_rankscore=0.362;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.673;phastCons20way_mammalian_rankscore=0.303;SiPhy_29way_logOdds=18.941;SiPhy_29way_logOdds_rankscore=0.925;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0706;dpsi_zscore=-0.350;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=0.122858907605;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:228,183:412:99:4447,0,5822:56:99:0.445 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 53679229 rs1799822 A G 10435.3 PASS BaseQRankSum=3.419;Dels=0;FS=0;HRun=0;HaplotypeScore=10.355;MQ=55;MQ0=0;MQRankSum=0.97;QD=10.43;ReadPosRankSum=1.029;SB=-3441.09;TI=NM_000098;GI=CPT2;FC=Missense_M647V;EXON;DP=1396;AN=6;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CPT2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=CPT2:NM_000098:exon5:c.A1939G:p.M647V;Func.knownGene=exonic;Gene.knownGene=CPT2;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=CPT2:uc001cvb.4:exon5:c.A1939G:p.M647V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS575.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS575.1:CCDS575.1:exon5:c.A1939G:p.M647V;cytoBand=1p32.3;CLINSIG=Benign|other;CLNDBN=not_specified|Carnitine_palmitoyltransferase_II_deficiency;CLNACC=RCV000078120.6|RCV000202533.2;CLNDSDB=MedGen|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|C0342790:ORPHA157:238002005;PopFreqMax=0.23;Kaviar_AF=0.164817;Kaviar_AC=25481;Kaviar_AN=154602;ExAC_ALL=0.1620;ExAC_AFR=0.0452;ExAC_AMR=0.1211;ExAC_EAS=0.0854;ExAC_FIN=0.1325;ExAC_NFE=0.2154;ExAC_OTH=0.1501;ExAC_SAS=0.1007;1000g2014oct_all=0.100439;snp138=rs1799822;SIFT_score=0.021;SIFT_converted_rankscore=0.491;SIFT_pred=D;Polyphen2_HDIV_score=0.002;Polyphen2_HDIV_rankscore=0.090;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.009;Polyphen2_HVAR_rankscore=0.133;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.559;LRT_pred=D;MutationTaster_score=0.002;MutationTaster_converted_rankscore=0.442;MutationTaster_pred=P;MutationAssessor_score=0.885;MutationAssessor_score_rankscore=0.217;MutationAssessor_pred=L;FATHMM_score=-2.62;FATHMM_converted_rankscore=0.900;FATHMM_pred=D;PROVEAN_score=1.15;PROVEAN_converted_rankscore=0.012;PROVEAN_pred=N;VEST3_score=0.168;VEST3_rankscore=0.203;MetaSVM_score=-1.058;MetaSVM_rankscore=0.123;MetaSVM_pred=T;MetaLR_score=0.001;MetaLR_rankscore=0.002;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=3.420;CADD_raw_rankscore=0.469;CADD_phred=23.0;DANN_score=0.984;DANN_rankscore=0.403;fathmm-MKL_coding_score=0.993;fathmm-MKL_coding_rankscore=0.935;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.075;Eigen-PC-raw=0.291;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.672;integrated_fitCons_score_rankscore=0.522;integrated_confidence_value=0;GERP++_RS=5.9;GERP++_RS_rankscore=0.949;phyloP100way_vertebrate=7.431;phyloP100way_vertebrate_rankscore=0.794;phyloP20way_mammalian=1.199;phyloP20way_mammalian_rankscore=0.960;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.999;phastCons20way_mammalian_rankscore=0.750;SiPhy_29way_logOdds=16.332;SiPhy_29way_logOdds_rankscore=0.828;Interpro_domain=.;GTEx_V6_gene=ENSG00000157184.5;GTEx_V6_tissue=Artery_Tibial;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:247,214:463:99:4828,0,5761:55:99:0.464 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:256,253:509:99:6380,0,6563:57:99:0.497 ./.:.:.:.:.:.:.:. 1/1:1,423:424:99:10435,691,0:49:99:0.998 ./.:.:.:.:.:.:.:.
chr1 53679874 rs14829 G T 4444.96 PASS BaseQRankSum=1.872;Dels=0;FS=2.312;HRun=2;HaplotypeScore=5.4678;MQ=56;MQ0=0;MQRankSum=-0.227;QD=10.39;ReadPosRankSum=1.494;SB=-1442.87;TI=NM_017887;GI=C1orf123;FC=Silent;EXON;DP=910;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=C1orf123;GeneDetail.refGene=NM_017887:c.*457C>A\x3bNM_001304760:c.*457C>A\x3bNM_001304759:c.*457C>A;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=C1orf123;GeneDetail.knownGene=uc001cvd.3:c.*457C>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS575.1\x3bCCDS576.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p32.3;CLINSIG=Likely_benign;CLNDBN=Carnitine_palmitoyltransferase_II_deficiency;CLNACC=RCV000299911.1;CLNDSDB=MedGen:Orphanet:SNOMED_CT;CLNDSDBID=C0342790:ORPHA157:238002005;PopFreqMax=0.041;Kaviar_AF=0.0104887;Kaviar_AC=273;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0133786;snp138=rs14829;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:126,96:223:99:2348,0,3381:56:99:0.432 ./.:.:.:.:.:.:.:. 0/1:170,185:355:99:4445,0,4008:55:99:0.521 0/1:189,143:332:99:3552,0,4814:55:99:0.431 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 53679878 rs1056438 T C 4688.3 PASS BaseQRankSum=1.319;Dels=0;FS=0;HRun=1;HaplotypeScore=20.7344;MQ=55;MQ0=0;MQRankSum=0.979;QD=10.86;ReadPosRankSum=0.833;SB=-2571.41;TI=NM_017887;GI=C1orf123;FC=Silent;EXON;DP=666;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=C1orf123;GeneDetail.refGene=NM_017887:c.*453A>G\x3bNM_001304760:c.*453A>G\x3bNM_001304759:c.*453A>G;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=C1orf123;GeneDetail.knownGene=uc001cvd.3:c.*453A>G;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS575.1\x3bCCDS576.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p32.3;CLINSIG=Benign;CLNDBN=Carnitine_palmitoyltransferase_II_deficiency;CLNACC=RCV000354722.1;CLNDSDB=MedGen:Orphanet:SNOMED_CT;CLNDSDBID=C0342790:ORPHA157:238002005;PopFreqMax=0.49;Kaviar_AF=0.048641;Kaviar_AC=7520;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.228235;snp138=rs1056438;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:185,158:343:99:3725,0,4475:55:99:0.461 0/1:142,181:323:99:4688,0,3578:56:99:0.56 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 64089432 rs77043134 G A 6539.77 PASS BaseQRankSum=-1.439;Dels=0;FS=4.916;HRun=0;HaplotypeScore=18.4221;MQ=57;MQ0=0;MQRankSum=1.723;QD=12.7;ReadPosRankSum=0.882;SB=-3823.92;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;DP=927;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=splicing;Gene.refGene=PGM1;GeneDetail.refGene=NM_001172818:exon1:c.300+1G>A;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=splicing;Gene.knownGene=PGM1;GeneDetail.knownGene=uc010ooz.2:exon1:c.300+1G>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=splicing;Gene.ccdsGene=CCDS53323.1;GeneDetail.ccdsGene=CCDS53323.1:exon1:c.300+1G>A;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.016;Kaviar_AF=0.0096894;Kaviar_AC=1498;Kaviar_AN=154602;ExAC_ALL=0.0103;ExAC_AFR=0.0016;ExAC_AMR=0.0028;ExAC_EAS=0;ExAC_FIN=0.0076;ExAC_NFE=0.0161;ExAC_OTH=0.0134;ExAC_SAS=0.0030;1000g2014oct_all=0.00359425;snp138=rs77043134;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=1;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=D;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=5.209;CADD_raw_rankscore=0.703;CADD_phred=25.5;DANN_score=0.995;DANN_rankscore=0.680;fathmm-MKL_coding_score=0.987;fathmm-MKL_coding_rankscore=0.859;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=1.205;Eigen-PC-raw=1.050;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.164;integrated_fitCons_score_rankscore=0.030;integrated_confidence_value=0;GERP++_RS=4.98;GERP++_RS_rankscore=0.655;phyloP100way_vertebrate=9.556;phyloP100way_vertebrate_rankscore=0.972;phyloP20way_mammalian=1.048;phyloP20way_mammalian_rankscore=0.713;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=1.000;phastCons20way_mammalian_rankscore=0.888;SiPhy_29way_logOdds=19.149;SiPhy_29way_logOdds_rankscore=0.934;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=1.0000;dbscSNV_RF_SCORE=0.94;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:239,275:515:99:6540,0,5808:57:99:0.535 ./.:.:.:.:.:.:.:. 0/1:206,205:412:99:4490,0,4594:53:99:0.499 ./.:.:.:.:.:.:.:.
chr1 64095042 rs855313 G T 4193.33 PASS BaseQRankSum=1.366;Dels=0;FS=0;HRun=0;HaplotypeScore=13.8456;MQ=57;MQ0=0;MQRankSum=0.489;QD=13.61;ReadPosRankSum=0.837;SB=-2115.3;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;DP=963;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=PGM1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=PGM1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS53323.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.17;Kaviar_AF=0.0201679;Kaviar_AC=3118;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0904553;snp138=rs855313;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0280;dpsi_zscore=-0.153;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:143,164:308:99:4193,0,3885:57:99:0.534 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:159,184:343:99:4001,0,3497:51:99:0.536 0/1:153,159:312:99:3963,0,3909:55:99:0.51
chr1 64095111 rs855314 A G 4684.83 PASS BaseQRankSum=2.367;Dels=0;FS=0.811;HRun=0;HaplotypeScore=12.6738;MQ=57;MQ0=0;MQRankSum=-1.866;QD=13.09;ReadPosRankSum=-0.242;SB=-2849.51;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Missense_I88V,Silent,Missense_I106V;EXON;DP=1078;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=PGM1;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=PGM1:NM_001172818:exon2:c.A316G:p.I106V\x3bPGM1:NM_002633:exon2:c.A262G:p.I88V;Func.knownGene=exonic;Gene.knownGene=PGM1;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=PGM1:uc001dbh.3:exon2:c.A262G:p.I88V\x3bPGM1:uc010ooz.2:exon2:c.A316G:p.I106V;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS53323.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS53323.1:CCDS53323.1:exon2:c.A316G:p.I106V\x3bCCDS625.1:CCDS625.1:exon2:c.A262G:p.I88V;cytoBand=1p31.3;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Congenital_disorder_of_glycosylation_type_1t|Congenital_disorder_of_glycosylation;CLNACC=RCV000350881.1|RCV000389349.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=C2752015:614921:ORPHA319646|C0282577:ORPHA137:238049009;PopFreqMax=0.25;Kaviar_AF=0.130419;Kaviar_AC=20163;Kaviar_AN=154602;ExAC_ALL=0.1304;ExAC_AFR=0.2477;ExAC_AMR=0.0584;ExAC_EAS=0.0068;ExAC_FIN=0.1355;ExAC_NFE=0.1488;ExAC_OTH=0.1222;ExAC_SAS=0.0959;1000g2014oct_all=0.129792;snp138=rs855314;SIFT_score=1.0;SIFT_converted_rankscore=0.010;SIFT_pred=T;Polyphen2_HDIV_score=0.022;Polyphen2_HDIV_rankscore=0.245;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.037;Polyphen2_HVAR_rankscore=0.252;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.629;LRT_pred=D;MutationTaster_score=0.182;MutationTaster_converted_rankscore=0.810;MutationTaster_pred=P;MutationAssessor_score=-0.745;MutationAssessor_score_rankscore=0.017;MutationAssessor_pred=N;FATHMM_score=0.02;FATHMM_converted_rankscore=0.623;FATHMM_pred=T;PROVEAN_score=-0.03;PROVEAN_converted_rankscore=0.075;PROVEAN_pred=N;VEST3_score=0.156;VEST3_rankscore=0.306;MetaSVM_score=-1.049;MetaSVM_rankscore=0.147;MetaSVM_pred=T;MetaLR_score=0.042;MetaLR_rankscore=0.180;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=3.281;CADD_raw_rankscore=0.453;CADD_phred=22.8;DANN_score=0.968;DANN_rankscore=0.305;fathmm-MKL_coding_score=0.988;fathmm-MKL_coding_rankscore=0.873;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.233;Eigen-PC-raw=0.044;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.732;integrated_fitCons_score_rankscore=0.924;integrated_confidence_value=0;GERP++_RS=5.48;GERP++_RS_rankscore=0.806;phyloP100way_vertebrate=9.197;phyloP100way_vertebrate_rankscore=0.941;phyloP20way_mammalian=1.199;phyloP20way_mammalian_rankscore=0.960;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.999;phastCons20way_mammalian_rankscore=0.750;SiPhy_29way_logOdds=15.892;SiPhy_29way_logOdds_rankscore=0.790;Interpro_domain=Alpha-D-phosphohexomutase,_alpha/beta/alpha_I/II/III|Alpha-D-phosphohexomutase,_alpha/beta/alpha_domain_I;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0497;dpsi_zscore=0.296;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:170,187:358:99:4685,0,4566:57:99:0.524 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:191,204:396:99:4537,0,3947:51:99:0.516 0/1:164,159:324:99:4012,0,4190:57:99:0.492
chr1 64095248 rs1126727 T C 4935.31 PASS BaseQRankSum=1.058;Dels=0;FS=1.619;HRun=0;HaplotypeScore=14.1175;MQ=55;MQ0=0;MQRankSum=-0.078;QD=12.19;ReadPosRankSum=0.882;SB=-3449.97;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Synonymous_I133I,Silent,Synonymous_I151I;EXON;DP=405;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=PGM1;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=PGM1:NM_001172818:exon2:c.T453C:p.I151I\x3bPGM1:NM_002633:exon2:c.T399C:p.I133I;Func.knownGene=exonic;Gene.knownGene=PGM1;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=PGM1:uc001dbh.3:exon2:c.T399C:p.I133I\x3bPGM1:uc010ooz.2:exon2:c.T453C:p.I151I;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS53323.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS53323.1:CCDS53323.1:exon2:c.T453C:p.I151I\x3bCCDS625.1:CCDS625.1:exon2:c.T399C:p.I133I;cytoBand=1p31.3;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Congenital_disorder_of_glycosylation|Congenital_disorder_of_glycosylation_type_1t;CLNACC=RCV000292719.1|RCV000349872.1;CLNDSDB=MedGen:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet;CLNDSDBID=C0282577:ORPHA137:238049009|C2752015:614921:ORPHA319646;PopFreqMax=0.1;Kaviar_AF=0.0075419;Kaviar_AC=1166;Kaviar_AN=154602;ExAC_ALL=0.0075;ExAC_AFR=0.0833;ExAC_AMR=0.0050;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0002;ExAC_OTH=0.0111;ExAC_SAS=0.0001;1000g2014oct_all=0.0297524;snp138=rs1126727;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2000;dpsi_zscore=-0.687;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:194,210:405:99:4935,0,4618:55:99:0.52 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 64097432 rs1126728 C T 10646.8 PASS BaseQRankSum=-0.21;Dels=0;FS=0;HRun=0;HaplotypeScore=9.8855;MQ=55;MQ0=0;MQRankSum=-1.104;QD=27.65;ReadPosRankSum=-1.014;SB=-7365.38;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Missense_R221C,Missense_R24C,Missense_R239C;EXON;DP=1965;AN=10;AC=7;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=PGM1;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=PGM1:NM_001172818:exon4:c.C715T:p.R239C\x3bPGM1:NM_001172819:exon4:c.C70T:p.R24C\x3bPGM1:NM_002633:exon4:c.C661T:p.R221C;Func.knownGene=exonic;Gene.knownGene=PGM1;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=PGM1:uc001dbh.3:exon4:c.C661T:p.R221C\x3bPGM1:uc010ooy.2:exon4:c.C70T:p.R24C\x3bPGM1:uc010ooz.2:exon4:c.C715T:p.R239C;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS53324.1:CCDS53324.1:exon1:c.C70T:p.R24C\x3bCCDS53323.1:CCDS53323.1:exon4:c.C715T:p.R239C\x3bCCDS625.1:CCDS625.1:exon4:c.C661T:p.R221C;cytoBand=1p31.3;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Congenital_disorder_of_glycosylation|Congenital_disorder_of_glycosylation_type_1t;CLNACC=RCV000344184.1|RCV000399244.1;CLNDSDB=MedGen:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet;CLNDSDBID=C0282577:ORPHA137:238049009|C2752015:614921:ORPHA319646;PopFreqMax=0.3;Kaviar_AF=0.238056;Kaviar_AC=36804;Kaviar_AN=154602;ExAC_ALL=0.2428;ExAC_AFR=0.1976;ExAC_AMR=0.2151;ExAC_EAS=0.2527;ExAC_FIN=0.2713;ExAC_NFE=0.2355;ExAC_OTH=0.2808;ExAC_SAS=0.3017;1000g2014oct_all=0.241414;snp138=rs1126728;SIFT_score=0.247;SIFT_converted_rankscore=0.196;SIFT_pred=T;Polyphen2_HDIV_score=0.465;Polyphen2_HDIV_rankscore=0.394;Polyphen2_HDIV_pred=P;Polyphen2_HVAR_score=0.031;Polyphen2_HVAR_rankscore=0.321;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.843;LRT_pred=D;MutationTaster_score=0.000;MutationTaster_converted_rankscore=0.588;MutationTaster_pred=P;MutationAssessor_score=1.395;MutationAssessor_score_rankscore=0.354;MutationAssessor_pred=L;FATHMM_score=-0.0;FATHMM_converted_rankscore=0.626;FATHMM_pred=T;PROVEAN_score=-1.61;PROVEAN_converted_rankscore=0.387;PROVEAN_pred=N;VEST3_score=0.327;VEST3_rankscore=0.599;MetaSVM_score=-0.970;MetaSVM_rankscore=0.372;MetaSVM_pred=T;MetaLR_score=0.107;MetaLR_rankscore=0.389;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=6.939;CADD_raw_rankscore=0.934;CADD_phred=33;DANN_score=0.999;DANN_rankscore=0.982;fathmm-MKL_coding_score=0.963;fathmm-MKL_coding_rankscore=0.685;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.152;Eigen-PC-raw=0.302;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.706;integrated_fitCons_score_rankscore=0.609;integrated_confidence_value=0;GERP++_RS=5.75;GERP++_RS_rankscore=0.904;phyloP100way_vertebrate=2.613;phyloP100way_vertebrate_rankscore=0.458;phyloP20way_mammalian=0.935;phyloP20way_mammalian_rankscore=0.490;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.997;phastCons20way_mammalian_rankscore=0.653;SiPhy_29way_logOdds=20.327;SiPhy_29way_logOdds_rankscore=0.987;Interpro_domain=Alpha-D-phosphohexomutase,_alpha/beta/alpha_I/II/III|Alpha-D-phosphohexomutase,_alpha/beta/alpha_domain_I\x3bAlpha-D-phosphohexomutase,_alpha/beta/alpha_I/II/III|Alpha-D-phosphohexomutase,_alpha/beta/alpha_domain_II;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1321;dpsi_zscore=-0.538;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:4,381:385:99:10647,681,0:55:99:0.99 1/1:0,342:342:99:9937,713,0:56:99:1 ./.:.:.:.:.:.:.:. 0/1:165,171:336:99:4418,0,4184:55:99:0.509 0/1:221,266:488:99:6787,0,5380:57:99:0.546 ./.:.:.:.:.:.:.:. 0/1:241,172:414:99:3618,0,5156:50:99:0.416 ./.:.:.:.:.:.:.:.
chr1 64100478 rs6588052 A T 13437.3 PASS BaseQRankSum=0.561;Dels=0;FS=3.082;HRun=3;HaplotypeScore=9.9276;MQ=54;MQ0=0;MQRankSum=-0.574;QD=11.07;ReadPosRankSum=0.004;SB=-3148.62;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;DP=3002;AN=14;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=PGM1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=PGM1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.68;Kaviar_AF=0.0002911;Kaviar_AC=45;Kaviar_AN=154602;ExAC_ALL=0.4141;ExAC_AFR=0.5728;ExAC_AMR=0.3901;ExAC_EAS=0.6782;ExAC_FIN=0.4373;ExAC_NFE=0.3605;ExAC_OTH=0.4412;ExAC_SAS=0.3993;1000g2014oct_all=0.5002;snp138=rs6588052;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3117;dpsi_zscore=0.908;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:215,204:420:99:4650,0,5147:54:99:0.487 ./.:.:.:.:.:.:.:. 0/1:224,207:432:99:5078,0,5696:56:99:0.48 1/1:1,481:482:99:13437,960,0:54:99:0.998 1/1:0,386:387:99:11088,804,0:55:99:1 ./.:.:.:.:.:.:.:. 0/1:184,190:375:99:4838,0,4574:56:99:0.508 0/1:254,243:497:99:6139,0,6453:56:99:0.489 ./.:.:.:.:.:.:.:. 0/1:199,210:409:99:4494,0,4385:51:99:0.513 ./.:.:.:.:.:.:.:.
chr1 64102114 rs2269248 A G 5352.71 PASS BaseQRankSum=2.928;Dels=0;FS=0;HRun=0;HaplotypeScore=11.2403;MQ=52;MQ0=0;MQRankSum=4.154;QD=12.89;ReadPosRankSum=3.988;SB=-3703.98;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;DP=2724;AN=14;AC=7;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=PGM1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=PGM1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.67;Kaviar_AF=0.0732655;Kaviar_AC=11327;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.49401;snp138=rs2269248;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0116;dpsi_zscore=-0.049;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:185,229:414:99:5336,0,4279:52:99:0.553 ./.:.:.:.:.:.:.:. 0/1:219,194:413:99:4647,0,5420:56:99:0.47 0/1:183,174:357:99:3857,0,4431:54:99:0.487 0/1:189,180:369:99:4405,0,4527:54:99:0.488 ./.:.:.:.:.:.:.:. 0/1:193,170:363:99:4150,0,4885:56:99:0.468 0/1:211,219:430:99:5353,0,5056:57:99:0.509 ./.:.:.:.:.:.:.:. 0/1:195,183:378:99:3903,0,4093:49:99:0.484 ./.:.:.:.:.:.:.:.
chr1 64114301 rs11208257 T C 6243.99 PASS BaseQRankSum=0.276;Dels=0;FS=2.533;HRun=0;HaplotypeScore=10.1944;MQ=54;MQ0=0;MQRankSum=2.199;QD=11.57;ReadPosRankSum=1.579;SB=-3258.02;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Missense_Y420H,Missense_Y223H,Missense_Y438H;EXON;DP=1384;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=PGM1;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=PGM1:NM_001172818:exon8:c.T1312C:p.Y438H\x3bPGM1:NM_001172819:exon8:c.T667C:p.Y223H\x3bPGM1:NM_002633:exon8:c.T1258C:p.Y420H;Func.knownGene=exonic;Gene.knownGene=PGM1;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=PGM1:uc001dbh.3:exon8:c.T1258C:p.Y420H\x3bPGM1:uc010ooy.2:exon8:c.T667C:p.Y223H\x3bPGM1:uc010ooz.2:exon8:c.T1312C:p.Y438H;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS53324.1:CCDS53324.1:exon5:c.T667C:p.Y223H\x3bCCDS53323.1:CCDS53323.1:exon8:c.T1312C:p.Y438H\x3bCCDS625.1:CCDS625.1:exon8:c.T1258C:p.Y420H;cytoBand=1p31.3;CLINSIG=Benign|Benign;CLNDBN=Congenital_disorder_of_glycosylation_type_1t|Congenital_disorder_of_glycosylation;CLNACC=RCV000277905.1|RCV000367456.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=C2752015:614921:ORPHA319646|C0282577:ORPHA137:238049009;PopFreqMax=0.44;Kaviar_AF=0.21937;Kaviar_AC=33915;Kaviar_AN=154602;ExAC_ALL=0.2240;ExAC_AFR=0.1777;ExAC_AMR=0.4449;ExAC_EAS=0.1996;ExAC_FIN=0.3302;ExAC_NFE=0.1911;ExAC_OTH=0.2230;ExAC_SAS=0.2012;1000g2014oct_all=0.225839;snp138=rs11208257;SIFT_score=0.015;SIFT_converted_rankscore=0.586;SIFT_pred=D;Polyphen2_HDIV_score=0.414;Polyphen2_HDIV_rankscore=0.334;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.365;Polyphen2_HVAR_rankscore=0.416;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.491;LRT_pred=D;MutationTaster_score=0.051;MutationTaster_converted_rankscore=0.376;MutationTaster_pred=P;MutationAssessor_score=2.785;MutationAssessor_score_rankscore=0.815;MutationAssessor_pred=M;FATHMM_score=0.56;FATHMM_converted_rankscore=0.546;FATHMM_pred=T;PROVEAN_score=-4.22;PROVEAN_converted_rankscore=0.758;PROVEAN_pred=D;VEST3_score=0.182;VEST3_rankscore=0.265;MetaSVM_score=-0.766;MetaSVM_rankscore=0.571;MetaSVM_pred=T;MetaLR_score=0.155;MetaLR_rankscore=0.487;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=3.888;CADD_raw_rankscore=0.524;CADD_phred=23.5;DANN_score=0.995;DANN_rankscore=0.677;fathmm-MKL_coding_score=0.971;fathmm-MKL_coding_rankscore=0.724;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.075;Eigen-PC-raw=0.169;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.706;integrated_fitCons_score_rankscore=0.609;integrated_confidence_value=0;GERP++_RS=4.77;GERP++_RS_rankscore=0.603;phyloP100way_vertebrate=6.277;phyloP100way_vertebrate_rankscore=0.724;phyloP20way_mammalian=1.061;phyloP20way_mammalian_rankscore=0.807;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.998;phastCons20way_mammalian_rankscore=0.697;SiPhy_29way_logOdds=13.260;SiPhy_29way_logOdds_rankscore=0.594;Interpro_domain=Alpha-D-phosphohexomutase,_C-terminal\x3bAlpha-D-phosphohexomutase,_C-terminal|Alpha-D-phosphohexomutase,_alpha/beta/alpha_I/II/III|Alpha-D-phosphohexomutase,_alpha/beta/alpha_domain_III\x3bAlpha-D-phosphohexomutase,_alpha/beta/alpha_I/II/III|Alpha-D-phosphohexomutase,_alpha/beta/alpha_domain_II;GTEx_V6_gene=ENSG00000244256.2;GTEx_V6_tissue=Thyroid;dpsi_max_tissue=-0.0455;dpsi_zscore=-0.244;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:209,211:420:99:4860,0,4938:54:99:0.502 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:227,258:485:99:6244,0,5590:57:99:0.532 ./.:.:.:.:.:.:.:. 0/1:250,228:479:99:6095,0,6014:57:99:0.477 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 64117537 rs2269238 G T 5957.23 PASS BaseQRankSum=0.799;Dels=0;FS=1.986;HRun=0;HaplotypeScore=13.4739;MQ=54;MQ0=0;MQRankSum=3.585;QD=11.78;ReadPosRankSum=-0.655;SB=-3429.25;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;DP=983;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=PGM1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=PGM1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=Benign|Benign;CLNDBN=Congenital_disorder_of_glycosylation|Congenital_disorder_of_glycosylation_type_1t;CLNACC=RCV000285149.1|RCV000335537.1;CLNDSDB=MedGen:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet;CLNDSDBID=C0282577:ORPHA137:238049009|C2752015:614921:ORPHA319646;PopFreqMax=0.45;Kaviar_AF=0.231608;Kaviar_AC=35807;Kaviar_AN=154602;ExAC_ALL=0.2365;ExAC_AFR=0.3274;ExAC_AMR=0.4477;ExAC_EAS=0.1991;ExAC_FIN=0.3300;ExAC_NFE=0.1905;ExAC_OTH=0.2258;ExAC_SAS=0.2000;1000g2014oct_all=0.276158;snp138=rs2269238;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0040;dpsi_zscore=0.002;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:215,238:453:99:5335,0,4907:54:99:0.525 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:280,247:530:99:5957,0,6849:58:99:0.469 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 64125234 rs11208265 G T 6138.95 PASS BaseQRankSum=1.906;Dels=0;FS=5.33;HRun=0;HaplotypeScore=17.0774;MQ=53;MQ0=0;MQRankSum=1.485;QD=11.58;ReadPosRankSum=1.58;SB=-2838.18;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;DP=1278;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=PGM1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=PGM1;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.44;Kaviar_AF=0.258004;Kaviar_AC=39888;Kaviar_AN=154602;ExAC_ALL=0.2644;ExAC_AFR=0.3944;ExAC_AMR=0.3737;ExAC_EAS=0.2418;ExAC_FIN=0.3224;ExAC_NFE=0.2288;ExAC_OTH=0.2599;ExAC_SAS=0.2386;1000g2014oct_all=0.320088;snp138=rs11208265;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:183,187:370:99:4283,0,4274:53:99:0.505 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:304,257:561:99:6139,0,7274:56:99:0.458 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:190,157:347:99:3379,0,4167:52:99:0.452 ./.:.:.:.:.:.:.:.
chr1 64125368 rs8294 C T 3814.09 PASS BaseQRankSum=0.739;Dels=0;FS=0.751;HRun=0;HaplotypeScore=21.6067;MQ=54;MQ0=0;MQRankSum=4.028;QD=9.08;ReadPosRankSum=1.326;SB=-2597.27;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;EXON;DP=420;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=PGM1;GeneDetail.refGene=NM_002633:c.*22C>T\x3bNM_001172819:c.*22C>T\x3bNM_001172818:c.*22C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=PGM1;GeneDetail.knownGene=uc001dbh.3:c.*22C>T\x3buc010ooy.2:c.*22C>T\x3buc010ooz.2:c.*22C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Congenital_disorder_of_glycosylation|Congenital_disorder_of_glycosylation_type_1t;CLNACC=RCV000307972.1|RCV000400984.1;CLNDSDB=MedGen:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet;CLNDSDBID=C0282577:ORPHA137:238049009|C2752015:614921:ORPHA319646;PopFreqMax=0.34;Kaviar_AF=0.192921;Kaviar_AC=29826;Kaviar_AN=154602;ExAC_ALL=0.1989;ExAC_AFR=0.0869;ExAC_AMR=0.3443;ExAC_EAS=0.1977;ExAC_FIN=0.2810;ExAC_NFE=0.1851;ExAC_OTH=0.2016;ExAC_SAS=0.1914;1000g2014oct_all=0.184505;snp138=rs8294;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:250,170:420:99:3814,0,5577:54:99:0.405 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 64125383 rs61765314 G A 4164.44 PASS BaseQRankSum=5.207;Dels=0;FS=5.639;HRun=0;HaplotypeScore=26.5934;MQ=54;MQ0=0;MQRankSum=1.969;QD=9.94;ReadPosRankSum=-0.465;SB=-2656.23;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;EXON;DP=419;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=PGM1;GeneDetail.refGene=NM_002633:c.*37G>A\x3bNM_001172819:c.*37G>A\x3bNM_001172818:c.*37G>A;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=PGM1;GeneDetail.knownGene=uc001dbh.3:c.*37G>A\x3buc010ooy.2:c.*37G>A\x3buc010ooz.2:c.*37G>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Congenital_disorder_of_glycosylation|Congenital_disorder_of_glycosylation_type_1t;CLNACC=RCV000271623.1|RCV000362631.1;CLNDSDB=MedGen:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet;CLNDSDBID=C0282577:ORPHA137:238049009|C2752015:614921:ORPHA319646;PopFreqMax=0.052;Kaviar_AF=0.0263063;Kaviar_AC=4067;Kaviar_AN=154602;ExAC_ALL=0.0266;ExAC_AFR=0.0122;ExAC_AMR=0.0142;ExAC_EAS=0;ExAC_FIN=0.0517;ExAC_NFE=0.0365;ExAC_OTH=0.0384;ExAC_SAS=0.0076;1000g2014oct_all=0.0163738;snp138=rs61765314;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:239,180:419:99:4164,0,5386:54:99:0.43 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 64125439 rs4643 A C 3919.06 PASS BaseQRankSum=2.357;Dels=0;FS=10.839;HRun=0;HaplotypeScore=13.7707;MQ=54;MQ0=0;MQRankSum=2.158;QD=10;ReadPosRankSum=0.632;SB=-2413.55;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;EXON;DP=392;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=PGM1;GeneDetail.refGene=NM_002633:c.*93A>C\x3bNM_001172819:c.*93A>C\x3bNM_001172818:c.*93A>C;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=PGM1;GeneDetail.knownGene=uc001dbh.3:c.*93A>C\x3buc010ooy.2:c.*93A>C\x3buc010ooz.2:c.*93A>C;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Congenital_disorder_of_glycosylation_type_1t|Congenital_disorder_of_glycosylation;CLNACC=RCV000267936.1|RCV000322974.1;CLNDSDB=MedGen:OMIM:Orphanet|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=C2752015:614921:ORPHA319646|C0282577:ORPHA137:238049009;PopFreqMax=0.33;Kaviar_AF=0.0384018;Kaviar_AC=5937;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.184704;snp138=rs4643;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:219,173:392:99:3919,0,5396:54:99:0.441 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 64125544 rs10909 C T 5954.87 PASS BaseQRankSum=2.747;Dels=0;FS=5.193;HRun=0;HaplotypeScore=19.1266;MQ=55;MQ0=0;MQRankSum=2.05;QD=12.85;ReadPosRankSum=-0.776;SB=-3913.2;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;EXON;DP=2145;AN=10;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=PGM1;GeneDetail.refGene=NM_002633:c.*198C>T\x3bNM_001172819:c.*198C>T\x3bNM_001172818:c.*198C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=PGM1;GeneDetail.knownGene=uc001dbh.3:c.*198C>T\x3buc010ooy.2:c.*198C>T\x3buc010ooz.2:c.*198C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Congenital_disorder_of_glycosylation|Congenital_disorder_of_glycosylation_type_1t;CLNACC=RCV000319415.1|RCV000373952.1;CLNDSDB=MedGen:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet;CLNDSDBID=C0282577:ORPHA137:238049009|C2752015:614921:ORPHA319646;PopFreqMax=0.33;Kaviar_AF=0.0221731;Kaviar_AC=3428;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.152157;snp138=rs10909;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:221,241:462:99:5937,0,5195:55:99:0.522 0/1:190,181:371:99:4433,0,4445:56:99:0.488 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:243,246:489:99:5955,0,5636:55:99:0.503 0/1:222,207:430:99:4395,0,4765:52:99:0.483 0/1:212,181:393:99:4459,0,5166:55:99:0.461
chr1 64125752 rs11557104 T C 5120.06 PASS BaseQRankSum=0.224;Dels=0;FS=1.116;HRun=0;HaplotypeScore=6.8321;MQ=56;MQ0=0;MQRankSum=0.33;QD=11.16;ReadPosRankSum=-0.267;SB=-1439.37;TI=NM_002633,NM_001172819,NM_001172818;GI=PGM1,PGM1,PGM1;FC=Silent,Silent,Silent;EXON;DP=604;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=PGM1;GeneDetail.refGene=NM_002633:c.*406T>C\x3bNM_001172819:c.*406T>C\x3bNM_001172818:c.*406T>C;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=PGM1;GeneDetail.knownGene=uc001dbh.3:c.*406T>C\x3buc010ooy.2:c.*406T>C\x3buc010ooz.2:c.*406T>C;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS53323.1\x3bCCDS53324.1\x3bCCDS625.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p31.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.016;Kaviar_AF=0.0029236;Kaviar_AC=452;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.00738818;snp138=rs11557104;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:103,93:196:99:2218,0,2596:56:99:0.474 0/1:209,199:408:99:5120,0,5094:56:99:0.488 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 100316589 rs2307130 A G 12800 PASS BaseQRankSum=2.84;Dels=0;FS=3.155;HRun=1;HaplotypeScore=11.7289;MQ=56;MQ0=0;MQRankSum=1.575;QD=11.59;ReadPosRankSum=0.857;SB=-3669.39;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646;GI=AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent;EXON;DP=3450;AN=16;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=splicing;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=splicing;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=upstream;Gene.ccdsGene=CCDS759.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign|Benign;CLNDBN=not_specified|Glycogen_storage_disease_type_III;CLNACC=RCV000175636.2|RCV000287312.1;CLNDSDB=MedGen|MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.54;Kaviar_AF=0.452523;Kaviar_AC=69961;Kaviar_AN=154602;ExAC_ALL=0.4687;ExAC_AFR=0.2631;ExAC_AMR=0.4420;ExAC_EAS=0.5336;ExAC_FIN=0.4371;ExAC_NFE=0.4829;ExAC_OTH=0.4637;ExAC_SAS=0.5363;1000g2014oct_all=0.427117;snp138=rs2307130;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-8.2899;dpsi_zscore=-2.807;dbscSNV_ADA_SCORE=0.0002;dbscSNV_RF_SCORE=0;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:276,252:528:99:6118,0,6886:56:99:0.477 ./.:.:.:.:.:.:.:. 0/1:108,81:189:99:2110,0,2646:57:99:0.429 1/1:2,444:447:99:12800,895,0:56:99:0.996 0/1:233,232:465:99:5527,0,5697:54:99:0.499 0/1:200,196:396:99:4884,0,4912:56:99:0.495 0/1:270,269:539:99:6840,0,6602:56:99:0.499 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:263,241:504:99:5751,0,6135:55:99:0.478 0/1:204,177:381:99:3767,0,4467:50:99:0.465 ./.:.:.:.:.:.:.:.
chr1 100318245 rs145049634 T G 3597.09 PASS BaseQRankSum=1.128;Dels=0;FS=2.304;HRun=0;HaplotypeScore=19.9706;MQ=52;MQ0=0;MQRankSum=-0.249;QD=10.25;ReadPosRankSum=2.817;SB=-2510.83;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646;GI=AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Missense_I7S;EXON;DP=351;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=AGL:NM_000646:exon2:c.T20G:p.I7S;Func.knownGene=exonic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=AGL:uc001dsm.1:exon2:c.T20G:p.I7S;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS760.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS760.1:CCDS760.1:exon1:c.T20G:p.I7S;cytoBand=1p21.2;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.042;Kaviar_AF=0.0154526;Kaviar_AC=2389;Kaviar_AN=154602;ExAC_ALL=0.0174;ExAC_AFR=0.0022;ExAC_AMR=0.0069;ExAC_EAS=0.0001;ExAC_FIN=0.0421;ExAC_NFE=0.0248;ExAC_OTH=0.0221;ExAC_SAS=0.0040;1000g2014oct_all=0.00878594;snp138=rs145049634;SIFT_score=0.035;SIFT_converted_rankscore=0.437;SIFT_pred=D;Polyphen2_HDIV_score=0.026;Polyphen2_HDIV_rankscore=0.181;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.005;Polyphen2_HVAR_rankscore=0.104;Polyphen2_HVAR_pred=B;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=1;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=N;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=-0.79;FATHMM_converted_rankscore=0.737;FATHMM_pred=T;PROVEAN_score=-0.76;PROVEAN_converted_rankscore=0.212;PROVEAN_pred=N;VEST3_score=0.049;VEST3_rankscore=0.030;MetaSVM_score=-0.993;MetaSVM_rankscore=0.318;MetaSVM_pred=T;MetaLR_score=0.109;MetaLR_rankscore=0.394;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=0.476;CADD_raw_rankscore=0.140;CADD_phred=7.249;DANN_score=0.936;DANN_rankscore=0.229;fathmm-MKL_coding_score=0.019;fathmm-MKL_coding_rankscore=0.057;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.871;Eigen-PC-raw=-0.962;GenoCanyon_score=0.996;GenoCanyon_score_rankscore=0.346;integrated_fitCons_score=0.554;integrated_fitCons_score_rankscore=0.283;integrated_confidence_value=0;GERP++_RS=1.11;GERP++_RS_rankscore=0.195;phyloP100way_vertebrate=0.358;phyloP100way_vertebrate_rankscore=0.198;phyloP20way_mammalian=0.363;phyloP20way_mammalian_rankscore=0.274;phastCons100way_vertebrate=0.003;phastCons100way_vertebrate_rankscore=0.159;phastCons20way_mammalian=0.340;phastCons20way_mammalian_rankscore=0.244;SiPhy_29way_logOdds=3.459;SiPhy_29way_logOdds_rankscore=0.070;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2079;dpsi_zscore=0.738;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:184,166:351:99:3597,0,4304:52:99:0.474 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 100327026 rs2307129 C T 5513.74 PASS BaseQRankSum=2.483;Dels=0;FS=3.465;HRun=0;HaplotypeScore=14.7279;MQ=56;MQ0=0;MQRankSum=2.201;QD=12.14;ReadPosRankSum=-0.672;SB=-3467.04;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;EXON;DP=2361;AN=12;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR5;Gene.refGene=AGL;GeneDetail.refGene=NM_000645:c.-2C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR5;Gene.knownGene=AGL;GeneDetail.knownGene=uc001dsn.1:c.-2C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000248220.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.42;Kaviar_AF=0.185192;Kaviar_AC=28631;Kaviar_AN=154602;ExAC_ALL=0.1962;ExAC_AFR=0.4009;ExAC_AMR=0.1257;ExAC_EAS=0.1212;ExAC_FIN=0.1997;ExAC_NFE=0.1863;ExAC_OTH=0.1847;ExAC_SAS=0.1928;1000g2014oct_all=0.227236;snp138=rs2307129;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2430;dpsi_zscore=0.801;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:227,227:454:99:5514,0,5383:56:99:0.5 0/1:178,163:341:99:3627,0,4103:54:99:0.478 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:198,180:379:99:4333,0,4745:55:99:0.476 0/1:158,165:324:99:4200,0,3871:55:99:0.511 ./.:.:.:.:.:.:.:. 0/1:182,152:335:99:4039,0,4695:57:99:0.455 0/1:297,231:528:99:5370,0,7330:57:99:0.438 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 100327183 rs2230305 T C 6033.91 PASS BaseQRankSum=0.91;Dels=0;FS=3.311;HRun=2;HaplotypeScore=15.9222;MQ=55;MQ0=0;MQRankSum=3.852;QD=12.29;ReadPosRankSum=-0.499;SB=-4239.39;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Synonymous_N69N,Synonymous_N69N,Synonymous_N69N,Synonymous_N69N,Synonymous_N53N,Synonymous_N52N;EXON;DP=491;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGL:NM_000645:exon1:c.T156C:p.N52N\x3bAGL:NM_000028:exon3:c.T207C:p.N69N\x3bAGL:NM_000642:exon3:c.T207C:p.N69N\x3bAGL:NM_000643:exon3:c.T207C:p.N69N\x3bAGL:NM_000644:exon3:c.T207C:p.N69N\x3bAGL:NM_000646:exon3:c.T159C:p.N53N;Func.knownGene=exonic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGL:uc001dsn.1:exon1:c.T156C:p.N52N\x3bAGL:uc001dsi.1:exon3:c.T207C:p.N69N\x3bAGL:uc001dsj.1:exon3:c.T207C:p.N69N\x3bAGL:uc001dsk.1:exon3:c.T207C:p.N69N\x3bAGL:uc001dsl.1:exon3:c.T207C:p.N69N\x3bAGL:uc001dsm.1:exon3:c.T159C:p.N53N;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS761.1:CCDS761.1:exon1:c.T156C:p.N52N\x3bCCDS759.1:CCDS759.1:exon2:c.T207C:p.N69N\x3bCCDS760.1:CCDS760.1:exon2:c.T159C:p.N53N;cytoBand=1p21.2;CLINSIG=Benign|Likely_benign;CLNDBN=not_specified|Glycogen_storage_disease_type_III;CLNACC=RCV000244020.1|RCV000356965.1;CLNDSDB=MedGen|MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.04;Kaviar_AF=0.0157825;Kaviar_AC=2440;Kaviar_AN=154602;ExAC_ALL=0.0162;ExAC_AFR=0.0021;ExAC_AMR=0.0066;ExAC_EAS=0.0001;ExAC_FIN=0.0401;ExAC_NFE=0.0228;ExAC_OTH=0.0221;ExAC_SAS=0.0037;1000g2014oct_all=0.00878594;snp138=rs2230305;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0447;dpsi_zscore=0.273;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:232,258:491:99:6034,0,5356:55:99:0.527 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 100335883 rs903126 A G 7637.45 PASS BaseQRankSum=-0.892;Dels=0;FS=6.303;HRun=0;HaplotypeScore=11.0061;MQ=56;MQ0=0;MQRankSum=0.446;QD=10.44;ReadPosRankSum=0.282;SB=-1971.07;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;DP=2185;AN=16;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.47;Kaviar_AF=0.0003074;Kaviar_AC=8;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.373003;snp138=rs903126;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1446;dpsi_zscore=0.603;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:201,157:358:99:3736,0,4884:56:99:0.439 ./.:.:.:.:.:.:.:. 0/1:83,59:143:99:1447,0,1992:55:99:0.415 1/1:0,274:274:99:7637,551,0:57:99:1 0/1:98,128:228:99:3045,0,2264:56:99:0.566 0/1:123,133:256:99:3353,0,2798:56:99:0.52 0/1:188,177:366:99:4259,0,4557:57:99:0.485 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:139,150:290:99:3687,0,3126:55:99:0.519 0/1:168,102:270:99:2179,0,3544:51:99:0.378 ./.:.:.:.:.:.:.:.
chr1 100335977 rs17121403 A G 4402.23 PASS BaseQRankSum=0.786;Dels=0;FS=0.757;HRun=2;HaplotypeScore=8.9752;MQ=54;MQ0=0;MQRankSum=2.146;QD=10.95;ReadPosRankSum=-0.756;SB=-2985.27;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Missense_Q229R,Missense_Q229R,Missense_Q229R,Missense_Q229R,Missense_Q213R,Missense_Q212R;EXON;DP=402;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=AGL:NM_000645:exon4:c.A635G:p.Q212R\x3bAGL:NM_000028:exon6:c.A686G:p.Q229R\x3bAGL:NM_000642:exon6:c.A686G:p.Q229R\x3bAGL:NM_000643:exon6:c.A686G:p.Q229R\x3bAGL:NM_000644:exon6:c.A686G:p.Q229R\x3bAGL:NM_000646:exon6:c.A638G:p.Q213R;Func.knownGene=exonic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=AGL:uc001dsn.1:exon4:c.A635G:p.Q212R\x3bAGL:uc001dsi.1:exon6:c.A686G:p.Q229R\x3bAGL:uc001dsj.1:exon6:c.A686G:p.Q229R\x3bAGL:uc001dsk.1:exon6:c.A686G:p.Q229R\x3bAGL:uc001dsl.1:exon6:c.A686G:p.Q229R\x3bAGL:uc001dsm.1:exon6:c.A638G:p.Q213R;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS761.1:CCDS761.1:exon4:c.A635G:p.Q212R\x3bCCDS759.1:CCDS759.1:exon5:c.A686G:p.Q229R\x3bCCDS760.1:CCDS760.1:exon5:c.A638G:p.Q213R;cytoBand=1p21.2;CLINSIG=Benign|Likely_benign;CLNDBN=not_specified|Glycogen_storage_disease_type_III;CLNACC=RCV000244905.1|RCV000332902.1;CLNDSDB=MedGen|MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.11;Kaviar_AF=0.0315908;Kaviar_AC=4884;Kaviar_AN=154602;ExAC_ALL=0.0326;ExAC_AFR=0.0918;ExAC_AMR=0.1142;ExAC_EAS=0.0280;ExAC_FIN=0.0048;ExAC_NFE=0.0156;ExAC_OTH=0.0232;ExAC_SAS=0.0207;1000g2014oct_all=0.0483227;snp138=rs17121403;SIFT_score=0.857;SIFT_converted_rankscore=0.027;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_rankscore=0.040;Polyphen2_HVAR_pred=B;LRT_score=0.009;LRT_converted_rankscore=0.304;LRT_pred=N;MutationTaster_score=0.987;MutationTaster_converted_rankscore=0.245;MutationTaster_pred=N;MutationAssessor_score=0.715;MutationAssessor_score_rankscore=0.187;MutationAssessor_pred=N;FATHMM_score=-1.74;FATHMM_converted_rankscore=0.834;FATHMM_pred=D;PROVEAN_score=-0.4;PROVEAN_converted_rankscore=0.138;PROVEAN_pred=N;VEST3_score=0.035;VEST3_rankscore=0.020;MetaSVM_score=-1.008;MetaSVM_rankscore=0.277;MetaSVM_pred=T;MetaLR_score=0.102;MetaLR_rankscore=0.377;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=0.854;CADD_raw_rankscore=0.175;CADD_phred=9.795;DANN_score=0.699;DANN_rankscore=0.088;fathmm-MKL_coding_score=0.316;fathmm-MKL_coding_rankscore=0.242;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.595;Eigen-PC-raw=-0.407;GenoCanyon_score=0.000;GenoCanyon_score_rankscore=0.058;integrated_fitCons_score=0.615;integrated_fitCons_score_rankscore=0.372;integrated_confidence_value=0;GERP++_RS=4.23;GERP++_RS_rankscore=0.492;phyloP100way_vertebrate=1.677;phyloP100way_vertebrate_rankscore=0.370;phyloP20way_mammalian=0.117;phyloP20way_mammalian_rankscore=0.209;phastCons100way_vertebrate=0.311;phastCons100way_vertebrate_rankscore=0.252;phastCons20way_mammalian=0.997;phastCons20way_mammalian_rankscore=0.653;SiPhy_29way_logOdds=3.389;SiPhy_29way_logOdds_rankscore=0.068;Interpro_domain=Glycogen_debranching_enzyme,_glucanotransferase_domain|Glycoside_hydrolase_superfamily|Glycoside_hydrolase,_catalytic_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0871;dpsi_zscore=0.443;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:208,193:402:99:4402,0,4844:54:99:0.481 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 100336119 . A C 4196.7 PASS BaseQRankSum=0.943;Dels=0;FS=2.759;HRun=0;HaplotypeScore=1.7882;MQ=54;MQ0=0;MQRankSum=3.664;QD=11.5;ReadPosRankSum=1.999;SB=-2965.97;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Missense_E276D,Missense_E276D,Missense_E276D,Missense_E276D,Missense_E260D,Missense_E259D;EXON;DP=365;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=AGL:NM_000645:exon4:c.A777C:p.E259D\x3bAGL:NM_000028:exon6:c.A828C:p.E276D\x3bAGL:NM_000642:exon6:c.A828C:p.E276D\x3bAGL:NM_000643:exon6:c.A828C:p.E276D\x3bAGL:NM_000644:exon6:c.A828C:p.E276D\x3bAGL:NM_000646:exon6:c.A780C:p.E260D;Func.knownGene=exonic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=AGL:uc001dsn.1:exon4:c.A777C:p.E259D\x3bAGL:uc001dsi.1:exon6:c.A828C:p.E276D\x3bAGL:uc001dsj.1:exon6:c.A828C:p.E276D\x3bAGL:uc001dsk.1:exon6:c.A828C:p.E276D\x3bAGL:uc001dsl.1:exon6:c.A828C:p.E276D\x3bAGL:uc001dsm.1:exon6:c.A780C:p.E260D;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS761.1:CCDS761.1:exon4:c.A777C:p.E259D\x3bCCDS759.1:CCDS759.1:exon5:c.A828C:p.E276D\x3bCCDS760.1:CCDS760.1:exon5:c.A780C:p.E260D;cytoBand=1p21.2;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=0.222;SIFT_converted_rankscore=0.192;SIFT_pred=T;Polyphen2_HDIV_score=0.036;Polyphen2_HDIV_rankscore=0.194;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.03;Polyphen2_HVAR_rankscore=0.205;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.497;LRT_pred=D;MutationTaster_score=0.929;MutationTaster_converted_rankscore=0.369;MutationTaster_pred=D;MutationAssessor_score=1.3;MutationAssessor_score_rankscore=0.327;MutationAssessor_pred=L;FATHMM_score=-1.84;FATHMM_converted_rankscore=0.842;FATHMM_pred=D;PROVEAN_score=-0.94;PROVEAN_converted_rankscore=0.251;PROVEAN_pred=N;VEST3_score=0.152;VEST3_rankscore=0.227;MetaSVM_score=-0.744;MetaSVM_rankscore=0.583;MetaSVM_pred=T;MetaLR_score=0.293;MetaLR_rankscore=0.665;MetaLR_pred=T;M-CAP_score=0.025;M-CAP_rankscore=0.484;M-CAP_pred=D;CADD_raw=1.614;CADD_raw_rankscore=0.255;CADD_phred=13.93;DANN_score=0.984;DANN_rankscore=0.405;fathmm-MKL_coding_score=0.817;fathmm-MKL_coding_rankscore=0.408;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.264;Eigen-PC-raw=-0.154;GenoCanyon_score=0.000;GenoCanyon_score_rankscore=0.029;integrated_fitCons_score=0.615;integrated_fitCons_score_rankscore=0.372;integrated_confidence_value=0;GERP++_RS=1.84;GERP++_RS_rankscore=0.242;phyloP100way_vertebrate=2.067;phyloP100way_vertebrate_rankscore=0.408;phyloP20way_mammalian=1.199;phyloP20way_mammalian_rankscore=0.960;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=1.000;phastCons20way_mammalian_rankscore=0.888;SiPhy_29way_logOdds=8.641;SiPhy_29way_logOdds_rankscore=0.330;Interpro_domain=Glycogen_debranching_enzyme,_glucanotransferase_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0907;dpsi_zscore=0.455;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=0.0252715314176;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:181,184:365:99:4197,0,4395:54:99:0.504
chr1 100336361 rs2230306 C T 13994.6 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=17.7861;MQ=56;MQ0=0;QD=27.77;SB=-9453.83;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Synonymous_L298L,Synonymous_L298L,Synonymous_L298L,Synonymous_L298L,Synonymous_L282L,Synonymous_L281L;EXON;BaseQRankSum=1.705;MQRankSum=-1.125;ReadPosRankSum=-0.054;DP=4312;AN=22;AC=19;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=AGL:NM_000645:exon5:c.C843T:p.L281L\x3bAGL:NM_000028:exon7:c.C894T:p.L298L\x3bAGL:NM_000642:exon7:c.C894T:p.L298L\x3bAGL:NM_000643:exon7:c.C894T:p.L298L\x3bAGL:NM_000644:exon7:c.C894T:p.L298L\x3bAGL:NM_000646:exon7:c.C846T:p.L282L;Func.knownGene=exonic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=AGL:uc001dsn.1:exon5:c.C843T:p.L281L\x3bAGL:uc001dsi.1:exon7:c.C894T:p.L298L\x3bAGL:uc001dsj.1:exon7:c.C894T:p.L298L\x3bAGL:uc001dsk.1:exon7:c.C894T:p.L298L\x3bAGL:uc001dsl.1:exon7:c.C894T:p.L298L\x3bAGL:uc001dsm.1:exon7:c.C846T:p.L282L;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS761.1:CCDS761.1:exon5:c.C843T:p.L281L\x3bCCDS759.1:CCDS759.1:exon6:c.C894T:p.L298L\x3bCCDS760.1:CCDS760.1:exon6:c.C846T:p.L282L;cytoBand=1p21.2;CLINSIG=Benign|Benign;CLNDBN=not_specified|Glycogen_storage_disease_type_III;CLNACC=RCV000179774.2|RCV000327447.1;CLNDSDB=MedGen|MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.93;Kaviar_AF=0.000194;Kaviar_AC=30;Kaviar_AN=154602;ExAC_ALL=0.7214;ExAC_AFR=0.9144;ExAC_AMR=0.6901;ExAC_EAS=0.6811;ExAC_FIN=0.6795;ExAC_NFE=0.7011;ExAC_OTH=0.6998;ExAC_SAS=0.7494;1000g2014oct_all=0.76258;snp138=rs2230306;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0552;dpsi_zscore=0.321;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,503:504:99:13995,1002,0:56:99:1 1/1:1,387:388:99:10125,713,0:54:99:0.997 0/1:74,94:169:99:2248,0,1900:55:99:0.56 1/1:0,376:377:99:10506,755,0:57:99:1 1/1:0,359:359:99:9677,695,0:54:99:1 1/1:0,361:363:99:10176,740,0:55:99:1 1/1:1,464:465:99:12644,906,0:56:99:0.998 1/1:0,322:323:99:9275,668,0:55:99:1 0/1:233,270:504:99:6662,0,5741:57:99:0.537 1/1:1,440:442:99:11937,852,0:55:99:0.998 0/1:199,219:418:99:4764,0,4237:50:99:0.524 ./.:.:.:.:.:.:.:.
chr1 100340225 rs634880 G A 12280.4 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=6.4651;MQ=55;MQ0=0;QD=29.13;SB=-6384.61;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;BaseQRankSum=-0.295;MQRankSum=-0.506;ReadPosRankSum=-0.652;DP=3913;AN=22;AC=20;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000246437.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.87;Kaviar_AF=0.711905;Kaviar_AC=110062;Kaviar_AN=154602;ExAC_ALL=0.7314;ExAC_AFR=0.8473;ExAC_AMR=0.6927;ExAC_EAS=0.7163;ExAC_FIN=0.7176;ExAC_NFE=0.7217;ExAC_OTH=0.7117;ExAC_SAS=0.7370;1000g2014oct_all=0.743411;snp138=rs634880;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0320;dpsi_zscore=-0.176;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,399:399:99:11624,843,0:55:99:1 1/1:0,355:355:99:9690,689,0:53:99:1 1/1:0,181:181:99:5262,376,0:55:99:1 1/1:0,315:316:99:9090,656,0:57:99:1 1/1:0,364:364:99:10312,740,0:56:99:1 1/1:2,335:337:99:10009,687,0:56:99:0.994 1/1:0,434:435:99:12280,879,0:56:99:1 1/1:0,330:331:99:9767,713,0:56:99:1 0/1:196,234:430:99:5795,0,4849:57:99:0.544 1/1:0,395:395:99:11063,792,0:56:99:1 0/1:214,154:370:99:3315,0,4868:52:99:0.418 ./.:.:.:.:.:.:.:.
chr1 100343153 rs2291638 A G 9503.57 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=0.9998;MQ=57;MQ0=0;QD=29.18;SB=-3651.71;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;BaseQRankSum=0.276;MQRankSum=1.952;ReadPosRankSum=0.452;DP=2443;AN=14;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000252556.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.45;Kaviar_AF=0.342272;Kaviar_AC=52916;Kaviar_AN=154602;ExAC_ALL=0.3488;ExAC_AFR=0.0906;ExAC_AMR=0.3733;ExAC_EAS=0.4487;ExAC_FIN=0.3472;ExAC_NFE=0.3815;ExAC_OTH=0.3652;ExAC_SAS=0.3069;1000g2014oct_all=0.284345;snp138=rs2291638;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=1.2038;dpsi_zscore=1.636;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,210:210:99:6127,439,0:57:99:1 1/1:0,334:334:99:9504,680,0:58:99:1 0/1:204,177:382:99:4215,0,4843:56:99:0.465 0/1:200,130:330:99:3057,0,4974:55:99:0.394 0/1:221,197:418:99:4589,0,5490:57:99:0.471 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:241,177:418:99:4065,0,5735:54:99:0.423 0/1:195,156:351:99:3258,0,4206:51:99:0.444 ./.:.:.:.:.:.:.:.
chr1 100345409 rs2392077 C G 8136.66 PASS BaseQRankSum=0.189;Dels=0;FS=0.837;HRun=0;HaplotypeScore=10.1413;MQ=56;MQ0=0;MQRankSum=0.954;QD=13.09;ReadPosRankSum=0.694;SB=-2434.75;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;DP=2330;AN=18;AC=12;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.68;Kaviar_AF=0.104585;Kaviar_AC=16169;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.534545;snp138=rs2392077;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0523;dpsi_zscore=0.308;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:161,182:344:99:4502,0,3835:56:99:0.531 ./.:.:.:.:.:.:.:. 1/1:0,113:113:99:3357,241,0:56:99:1 1/1:1,247:249:99:6885,491,0:57:99:0.996 0/1:132,154:288:99:3558,0,3266:56:99:0.538 0/1:140,134:274:99:3300,0,3326:57:99:0.489 1/1:0,280:281:99:8137,584,0:58:99:1 0/1:113,118:233:99:3123,0,2920:57:99:0.511 ./.:.:.:.:.:.:.:. 0/1:157,154:311:99:3738,0,3681:55:99:0.495 0/1:95,140:237:99:3010,0,1962:52:99:0.596 ./.:.:.:.:.:.:.:.
chr1 100346741 rs3736296 T C 14566.9 PASS BaseQRankSum=2.343;Dels=0;FS=1.103;HRun=0;HaplotypeScore=18.0788;MQ=56;MQ0=0;MQRankSum=-0.926;QD=12.23;ReadPosRankSum=0.439;SB=-3377.38;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;DP=3559;AN=18;AC=12;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign|Benign;CLNDBN=not_specified|Glycogen_storage_disease_type_III;CLNACC=RCV000254071.1|RCV000351044.1;CLNDSDB=MedGen|MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.68;Kaviar_AF=0.546351;Kaviar_AC=84467;Kaviar_AN=154602;ExAC_ALL=0.5517;ExAC_AFR=0.4316;ExAC_AMR=0.6338;ExAC_EAS=0.6648;ExAC_FIN=0.5117;ExAC_NFE=0.5362;ExAC_OTH=0.5364;ExAC_SAS=0.5905;1000g2014oct_all=0.558506;snp138=rs3736296;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-8.1003;dpsi_zscore=-2.793;dbscSNV_ADA_SCORE=0;dbscSNV_RF_SCORE=0.002;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:229,221:452:99:5526,0,5648:56:99:0.491 ./.:.:.:.:.:.:.:. 1/1:1,125:126:99:3735,271,0:55:99:0.992 1/1:1,335:336:99:10055,697,0:58:99:0.997 0/1:224,204:428:99:4946,0,5260:55:99:0.477 0/1:209,190:400:99:4825,0,5128:57:99:0.476 1/1:2,510:512:99:14567,1018,0:56:99:0.996 0/1:167,203:370:99:5205,0,4273:56:99:0.549 ./.:.:.:.:.:.:.:. 0/1:258,247:505:99:5678,0,6099:55:99:0.489 0/1:212,218:430:99:4823,0,4658:51:99:0.507 ./.:.:.:.:.:.:.:.
chr1 100353675 rs555929 G A 13974 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=10.0186;MQ=55;MQ0=1;QD=28.81;SB=-8587.41;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;BaseQRankSum=0.474;MQRankSum=0.69;ReadPosRankSum=1.264;DP=3808;AN=20;AC=17;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign|Benign;CLNDBN=not_specified|Glycogen_storage_disease_type_III;CLNACC=RCV000250101.1|RCV000272751.1;CLNDSDB=MedGen|MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.76;Kaviar_AF=0.682773;Kaviar_AC=105558;Kaviar_AN=154602;ExAC_ALL=0.6898;ExAC_AFR=0.5885;ExAC_AMR=0.7245;ExAC_EAS=0.6923;ExAC_FIN=0.6858;ExAC_NFE=0.6893;ExAC_OTH=0.6861;ExAC_SAS=0.7320;1000g2014oct_all=0.68111;snp138=rs555929;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0356;dpsi_zscore=-0.196;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,455:455:99:13110,942,0:55:99:1 ./.:.:.:.:.:.:.:. 1/1:0,117:117:99:3561,259,0:56:99:1 1/1:0,339:339:99:10123,731,0:57:99:1 1/1:3,395:398:99:10871,713,0:56:99:0.992 1/1:0,338:338:99:9832,707,0:55:99:1 1/1:1,493:494:99:13974,970,0:56:99:0.998 1/1:3,372:375:99:11093,739,0:56:99:0.992 0/1:230,229:460:99:5818,0,5689:57:99:0.499 0/1:227,197:424:99:4764,0,5599:54:99:0.465 0/1:204,204:408:99:4477,0,4458:50:99:0.5 ./.:.:.:.:.:.:.:.
chr1 100357141 rs2035961 T A 13720.5 PASS BaseQRankSum=2.086;Dels=0;FS=0;HRun=0;HaplotypeScore=16.2843;MQ=56;MQ0=0;MQRankSum=2.083;QD=11.34;ReadPosRankSum=0.549;SB=-3588.92;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;DP=3403;AN=18;AC=12;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000249993.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.68;Kaviar_AF=0.002749;Kaviar_AC=425;Kaviar_AN=154602;ExAC_ALL=0.5331;ExAC_AFR=0.3826;ExAC_AMR=0.6252;ExAC_EAS=0.6644;ExAC_FIN=0.4744;ExAC_NFE=0.5164;ExAC_OTH=0.5099;ExAC_SAS=0.5868;1000g2014oct_all=0.534345;snp138=rs2035961;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2775;dpsi_zscore=-0.819;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:254,223:478:99:5422,0,6200:56:99:0.468 ./.:.:.:.:.:.:.:. 1/1:0,148:148:99:4542,328,0:57:99:1 1/1:0,339:339:99:9863,710,0:58:99:1 0/1:213,205:418:99:5071,0,5033:56:99:0.49 0/1:184,202:386:99:5261,0,4645:56:99:0.523 1/1:0,496:496:99:13720,984,0:56:99:1 0/1:144,139:283:99:3681,0,3797:56:99:0.491 ./.:.:.:.:.:.:.:. 0/1:218,226:445:99:5292,0,5126:55:99:0.509 0/1:215,195:410:99:4209,0,4719:50:99:0.476 ./.:.:.:.:.:.:.:.
chr1 100358103 rs3753494 C T 6720.57 PASS BaseQRankSum=4.802;Dels=0;FS=2.076;HRun=0;HaplotypeScore=18.6115;MQ=55;MQ0=0;MQRankSum=2.648;QD=11.33;ReadPosRankSum=0.259;SB=-4462.13;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Missense_P1067S,Missense_P1067S,Missense_P1067S,Missense_P1067S,Missense_P1051S,Missense_P1050S;EXON;DP=2317;AN=10;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=AGL:NM_000645:exon22:c.C3148T:p.P1050S\x3bAGL:NM_000028:exon24:c.C3199T:p.P1067S\x3bAGL:NM_000642:exon24:c.C3199T:p.P1067S\x3bAGL:NM_000643:exon24:c.C3199T:p.P1067S\x3bAGL:NM_000644:exon24:c.C3199T:p.P1067S\x3bAGL:NM_000646:exon24:c.C3151T:p.P1051S;Func.knownGene=exonic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=AGL:uc001dsn.1:exon22:c.C3148T:p.P1050S\x3bAGL:uc001dsi.1:exon24:c.C3199T:p.P1067S\x3bAGL:uc001dsj.1:exon24:c.C3199T:p.P1067S\x3bAGL:uc001dsk.1:exon24:c.C3199T:p.P1067S\x3bAGL:uc001dsl.1:exon24:c.C3199T:p.P1067S\x3bAGL:uc001dsm.1:exon24:c.C3151T:p.P1051S;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS761.1:CCDS761.1:exon22:c.C3148T:p.P1050S\x3bCCDS759.1:CCDS759.1:exon23:c.C3199T:p.P1067S\x3bCCDS760.1:CCDS760.1:exon23:c.C3151T:p.P1051S;cytoBand=1p21.2;CLINSIG=Benign|Likely_benign;CLNDBN=not_specified|Glycogen_storage_disease_type_III;CLNACC=RCV000241565.1|RCV000363737.1;CLNDSDB=MedGen|MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.17;Kaviar_AF=0.134073;Kaviar_AC=20728;Kaviar_AN=154602;ExAC_ALL=0.1361;ExAC_AFR=0.1216;ExAC_AMR=0.0904;ExAC_EAS=0.0289;ExAC_FIN=0.1749;ExAC_NFE=0.1539;ExAC_OTH=0.1490;ExAC_SAS=0.1453;1000g2014oct_all=0.110623;snp138=rs3753494;SIFT_score=0.027;SIFT_converted_rankscore=0.473;SIFT_pred=D;Polyphen2_HDIV_score=0.12;Polyphen2_HDIV_rankscore=0.262;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.047;Polyphen2_HVAR_rankscore=0.292;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.629;LRT_pred=D;MutationTaster_score=0.000;MutationTaster_converted_rankscore=0.588;MutationTaster_pred=P;MutationAssessor_score=1.635;MutationAssessor_score_rankscore=0.420;MutationAssessor_pred=L;FATHMM_score=-0.88;FATHMM_converted_rankscore=0.748;FATHMM_pred=T;PROVEAN_score=-2.69;PROVEAN_converted_rankscore=0.574;PROVEAN_pred=D;VEST3_score=0.254;VEST3_rankscore=0.430;MetaSVM_score=-0.592;MetaSVM_rankscore=0.652;MetaSVM_pred=T;MetaLR_score=0.282;MetaLR_rankscore=0.654;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=2.294;CADD_raw_rankscore=0.337;CADD_phred=18.13;DANN_score=0.972;DANN_rankscore=0.324;fathmm-MKL_coding_score=0.978;fathmm-MKL_coding_rankscore=0.772;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=-0.021;Eigen-PC-raw=0.034;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.747;integrated_fitCons_score=0.732;integrated_fitCons_score_rankscore=0.924;integrated_confidence_value=0;GERP++_RS=5.2;GERP++_RS_rankscore=0.716;phyloP100way_vertebrate=7.280;phyloP100way_vertebrate_rankscore=0.778;phyloP20way_mammalian=0.883;phyloP20way_mammalian_rankscore=0.387;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.361;phastCons20way_mammalian_rankscore=0.248;SiPhy_29way_logOdds=19.102;SiPhy_29way_logOdds_rankscore=0.932;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2369;dpsi_zscore=-0.753;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:298,295:593:99:6721,0,7194:55:99:0.497 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:225,192:418:99:4438,0,5093:55:99:0.46 0/1:232,187:419:99:4574,0,5362:54:99:0.446 ./.:.:.:.:.:.:.:. 0/1:195,179:375:99:4665,0,4956:56:99:0.479 0/1:262,250:512:99:6317,0,6241:57:99:0.488 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 100358200 rs594249 G A 10990.8 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=5.4688;MQ=55;MQ0=0;QD=27.55;SB=-6742.21;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;BaseQRankSum=0.333;MQRankSum=0.253;ReadPosRankSum=-0.702;DP=3101;AN=20;AC=17;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000246558.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.76;Kaviar_AF=0.675127;Kaviar_AC=104376;Kaviar_AN=154602;ExAC_ALL=0.6912;ExAC_AFR=0.5888;ExAC_AMR=0.7252;ExAC_EAS=0.6951;ExAC_FIN=0.6852;ExAC_NFE=0.6900;ExAC_OTH=0.6895;ExAC_SAS=0.7364;1000g2014oct_all=0.68151;snp138=rs594249;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0474;dpsi_zscore=0.286;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,399:399:99:10991,786,0:55:99:1 ./.:.:.:.:.:.:.:. 1/1:0,107:107:99:3141,226,0:56:99:1 1/1:2,304:306:99:8952,611,0:57:99:0.993 1/1:0,305:305:99:8662,623,0:54:99:1 1/1:0,326:326:99:9291,668,0:53:99:1 1/1:0,339:339:99:9836,716,0:56:99:1 1/1:1,287:288:99:8495,620,0:56:99:0.997 0/1:197,195:392:99:4809,0,4916:58:99:0.497 0/1:187,143:331:99:3284,0,4616:54:99:0.433 0/1:168,140:308:99:2942,0,3599:49:99:0.455 ./.:.:.:.:.:.:.:.
chr1 100361822 rs17121560 T C 4161.67 PASS BaseQRankSum=1.388;Dels=0;FS=1.186;HRun=0;HaplotypeScore=10.4877;MQ=55;MQ0=0;MQRankSum=2.394;QD=10.46;ReadPosRankSum=1.122;SB=-2660.49;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;DP=398;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000243104.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.016;Kaviar_AF=0.001119;Kaviar_AC=173;Kaviar_AN=154602;ExAC_ALL=0.0012;ExAC_AFR=0.0128;ExAC_AMR=0.0007;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=4.497e-05;ExAC_OTH=0;ExAC_SAS=0;1000g2014oct_all=0.00439297;snp138=rs17121560;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0787;dpsi_zscore=-0.380;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:213,185:398:99:4162,0,4920:55:99:0.465 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 100376448 rs2274570 G A 8276.18 PASS BaseQRankSum=1.203;Dels=0;FS=5.988;HRun=3;HaplotypeScore=12.7964;MQ=56;MQ0=0;MQRankSum=0.305;QD=11.24;ReadPosRankSum=-0.098;SB=-2242.28;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;DP=2499;AN=16;AC=10;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000248824.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.58;Kaviar_AF=0.468733;Kaviar_AC=72467;Kaviar_AN=154602;ExAC_ALL=0.4744;ExAC_AFR=0.3714;ExAC_AMR=0.5775;ExAC_EAS=0.5453;ExAC_FIN=0.4859;ExAC_NFE=0.4889;ExAC_OTH=0.4707;ExAC_SAS=0.3690;1000g2014oct_all=0.461262;snp138=rs2274570;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0243;dpsi_zscore=-0.131;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:205,175:380:99:4272,0,5120:56:99:0.461 ./.:.:.:.:.:.:.:. 1/1:4,149:153:99:4535,261,0:55:99:0.974 1/1:0,287:287:99:8276,596,0:57:99:1 0/1:147,175:322:99:3952,0,3660:54:99:0.543 0/1:158,113:271:99:2721,0,4089:55:99:0.417 0/1:198,201:400:99:4826,0,4790:56:99:0.504 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:211,172:383:99:4077,0,5371:54:99:0.449 0/1:156,145:302:99:3086,0,3480:51:99:0.482 ./.:.:.:.:.:.:.:.
chr1 100376456 rs1541041 T A 7674.72 PASS BaseQRankSum=2.98;Dels=0;FS=8.054;HRun=0;HaplotypeScore=17.1716;MQ=56;MQ0=0;MQRankSum=1.019;QD=11.07;ReadPosRankSum=-0.303;SB=-1963.12;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;DP=2368;AN=16;AC=10;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.57;Kaviar_AF=0.0984075;Kaviar_AC=15214;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.459864;snp138=rs1541041;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0649;dpsi_zscore=-0.328;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:194,161:355:99:3931,0,4763:56:99:0.454 ./.:.:.:.:.:.:.:. 1/1:3,144:148:99:4231,237,0:55:99:0.98 1/1:2,261:264:99:7675,523,0:57:99:0.992 0/1:141,161:302:99:3581,0,3500:55:99:0.533 0/1:151,108:259:99:2586,0,3818:55:99:0.417 0/1:190,192:383:99:4504,0,4608:56:99:0.503 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:205,167:372:99:3874,0,5064:54:99:0.449 0/1:143,142:285:99:3047,0,3160:51:99:0.498 ./.:.:.:.:.:.:.:.
chr1 100381109 rs558245707 A AT 2219.58 R8;LowVariantFreq BaseQRankSum=2.16;FS=3.121;HRun=13;HaplotypeScore=682.401;MQ=54;MQ0=0;MQRankSum=0.364;QD=4.92;ReadPosRankSum=-0.245;SB=-767.2;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Noncoding,Noncoding,Noncoding,Noncoding,Noncoding,Noncoding;DP=2186;AN=18;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.49;Kaviar_AF=0.0001921;Kaviar_AC=5;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.396166;snp138=rs11438303;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:218,91:370:99:1865,0,3105:54:99:0.294 0/1:167,30:223:99:180,0,3123:54:99:0.152 1/0:39,50,18:115:99:1281,139,184:55:99:0.636 0/1:67,93:196:99:2259,0,203:54:99:0.581 0/1:127,73:242:99:1370,0,2083:55:99:0.365 0/1:118,74:215:99:1339,0,1521:54:99:0.385 0/1:178,71:286:99:1405,0,2443:55:99:0.285 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:152,91:289:99:1615,0,2317:54:99:0.374 0/1:119,93:245:99:1892,0,1189:52:99:0.439 ./.:.:.:.:.:.:.:.
chr1 100381109 rs558245707 A ATT 2219.58 R8;LowVariantFreq BaseQRankSum=2.16;FS=3.121;HRun=13;HaplotypeScore=682.401;MQ=54;MQ0=0;MQRankSum=0.364;QD=4.92;ReadPosRankSum=-0.245;SB=-767.2;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Noncoding,Noncoding,Noncoding,Noncoding,Noncoding,Noncoding;DP=2186;AN=18;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=AGL;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=AGL;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=0.0001537;Kaviar_AC=4;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/0:218,91:370:99:1865,.,.:54:99:0.294 0/0:167,30:223:99:180,.,.:54:99:0.152 0/1:39,50,18:115:99:1281,665,972:55:99:0.636 0/0:67,93:196:99:2259,.,.:54:99:0.581 0/0:127,73:242:99:1370,.,.:55:99:0.365 0/0:118,74:215:99:1339,.,.:54:99:0.385 0/0:178,71:286:99:1405,.,.:55:99:0.285 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/0:152,91:289:99:1615,.,.:54:99:0.374 0/0:119,93:245:99:1892,.,.:52:99:0.439 ./.:.:.:.:.:.:.:.
chr1 100387479 rs1804808 G T 8490.57 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=3.6789;MQ=55;MQ0=0;QD=29.97;SB=-2527.27;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;EXON;BaseQRankSum=1.672;MQRankSum=0.012;ReadPosRankSum=-1.72;DP=2256;AN=14;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGL;GeneDetail.refGene=NM_000642:c.*272G>T\x3bNM_000643:c.*272G>T\x3bNM_000028:c.*272G>T\x3bNM_000644:c.*272G>T\x3bNM_000646:c.*272G>T\x3bNM_000645:c.*272G>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGL;GeneDetail.knownGene=uc001dsi.1:c.*272G>T\x3buc001dsj.1:c.*272G>T\x3buc001dsk.1:c.*272G>T\x3buc001dsl.1:c.*272G>T\x3buc001dsm.1:c.*272G>T\x3buc001dsn.1:c.*272G>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=Glycogen_storage_disease_type_III;CLNACC=RCV000407316.1;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.55;Kaviar_AF=0.0001537;Kaviar_AC=4;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.332069;snp138=rs1804808;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 1/1:0,146:146:99:4376,316,0:55:99:1 1/1:1,287:288:99:8491,592,0:57:99:0.997 0/1:190,155:346:99:3748,0,4714:55:99:0.449 0/1:164,161:326:99:4198,0,4249:57:99:0.495 0/1:186,187:375:99:4696,0,4748:57:99:0.501 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:209,204:413:99:4827,0,4932:54:99:0.494 0/1:194,168:362:99:3768,0,4147:52:99:0.464 ./.:.:.:.:.:.:.:.
chr1 100387939 rs3766600 C T 13439.6 PASS Dels=0;FS=0;HRun=1;HaplotypeScore=13.513;MQ=56;MQ0=0;QD=29.73;SB=-8780.66;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;EXON;BaseQRankSum=1.606;MQRankSum=0.114;ReadPosRankSum=-1.049;DP=3548;AN=20;AC=15;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGL;GeneDetail.refGene=NM_000642:c.*732C>T\x3bNM_000643:c.*732C>T\x3bNM_000028:c.*732C>T\x3bNM_000644:c.*732C>T\x3bNM_000646:c.*732C>T\x3bNM_000645:c.*732C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGL;GeneDetail.knownGene=uc001dsi.1:c.*732C>T\x3buc001dsj.1:c.*732C>T\x3buc001dsk.1:c.*732C>T\x3buc001dsl.1:c.*732C>T\x3buc001dsm.1:c.*732C>T\x3buc001dsn.1:c.*732C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS759.1\x3bCCDS760.1\x3bCCDS761.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=Glycogen_storage_disease_type_III;CLNACC=RCV000355131.1;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.66;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.590455;snp138=rs3766600;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,452:452:99:13440,972,0:56:99:1 ./.:.:.:.:.:.:.:. 1/1:1,136:137:99:4124,269,0:54:99:0.993 1/1:0,299:299:99:9029,659,0:58:99:1 1/1:0,327:329:99:9262,665,0:55:99:1 1/1:1,320:321:99:9305,644,0:56:99:0.997 0/1:232,211:443:99:5391,0,5377:56:99:0.476 0/1:175,187:362:99:4719,0,4511:57:99:0.517 0/1:221,198:419:99:4739,0,5445:57:99:0.473 0/1:216,203:419:99:4853,0,4945:54:99:0.484 0/1:167,200:367:99:4591,0,3500:51:99:0.545 ./.:.:.:.:.:.:.:.
chr1 100388235 rs3766601 C T 9215.82 PASS BaseQRankSum=3.367;Dels=0;FS=2.713;HRun=0;HaplotypeScore=9.4682;MQ=56;MQ0=0;MQRankSum=1.628;QD=11.05;ReadPosRankSum=0.152;SB=-3820.35;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;EXON;DP=2929;AN=16;AC=10;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGL;GeneDetail.refGene=NM_000642:c.*1028C>T\x3bNM_000643:c.*1028C>T\x3bNM_000028:c.*1028C>T\x3bNM_000644:c.*1028C>T\x3bNM_000646:c.*1028C>T\x3bNM_000645:c.*1028C>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGL;GeneDetail.knownGene=uc001dsi.1:c.*1028C>T\x3buc001dsj.1:c.*1028C>T\x3buc001dsk.1:c.*1028C>T\x3buc001dsl.1:c.*1028C>T\x3buc001dsm.1:c.*1028C>T\x3buc001dsn.1:c.*1028C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intergenic;Gene.ccdsGene=CCDS759.1\x3bCCDS60204.1;GeneDetail.ccdsGene=dist\x3d1028\x3bdist\x3d47858;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=Glycogen_storage_disease_type_III;CLNACC=RCV000294197.1;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.57;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.468251;snp138=rs3766601;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:284,236:520:99:5748,0,7124:56:99:0.454 ./.:.:.:.:.:.:.:. 1/1:2,144:147:99:4135,236,0:55:99:0.986 1/1:1,310:311:99:9216,641,0:56:99:0.997 0/1:202,158:360:99:3795,0,4852:55:99:0.439 0/1:220,137:357:99:3393,0,5739:55:99:0.384 0/1:208,194:402:99:5094,0,5040:57:99:0.483 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:206,221:427:99:5441,0,5098:55:99:0.518 0/1:228,177:405:99:3820,0,4993:49:99:0.437 ./.:.:.:.:.:.:.:.
chr1 100388503 rs1804809 A C 10531.7 PASS BaseQRankSum=2.867;Dels=0;FS=6.091;HRun=0;HaplotypeScore=16.962;MQ=55;MQ0=0;MQRankSum=2.631;QD=13.16;ReadPosRankSum=-0.311;SB=-3938.32;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;EXON;DP=3324;AN=16;AC=10;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGL;GeneDetail.refGene=NM_000642:c.*1296A>C\x3bNM_000643:c.*1296A>C\x3bNM_000028:c.*1296A>C\x3bNM_000644:c.*1296A>C\x3bNM_000646:c.*1296A>C\x3bNM_000645:c.*1296A>C;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGL;GeneDetail.knownGene=uc001dsi.1:c.*1296A>C\x3buc001dsj.1:c.*1296A>C\x3buc001dsk.1:c.*1296A>C\x3buc001dsl.1:c.*1296A>C\x3buc001dsm.1:c.*1296A>C\x3buc001dsn.1:c.*1296A>C;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intergenic;Gene.ccdsGene=CCDS759.1\x3bCCDS60204.1;GeneDetail.ccdsGene=dist\x3d1296\x3bdist\x3d47590;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=Glycogen_storage_disease_type_III;CLNACC=RCV000398834.1;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.55;Kaviar_AF=0.436953;Kaviar_AC=11373;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.375799;snp138=rs1804809;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:247,262:509:99:6697,0,6014:55:99:0.515 ./.:.:.:.:.:.:.:. 1/1:0,186:186:99:5254,373,0:56:99:1 1/1:5,365:371:99:10532,687,0:57:99:0.986 0/1:246,243:489:99:5562,0,5986:55:99:0.497 0/1:204,176:380:99:4437,0,5107:55:99:0.463 0/1:236,257:494:99:6495,0,5841:56:99:0.521 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:219,242:461:99:5773,0,5155:55:99:0.525 0/1:195,239:434:99:5166,0,4157:50:99:0.551 ./.:.:.:.:.:.:.:.
chr1 100388748 rs3766603 T C 13254.7 PASS BaseQRankSum=0.093;Dels=0;FS=8.203;HRun=0;HaplotypeScore=21.667;MQ=56;MQ0=0;MQRankSum=-1.879;QD=11.93;ReadPosRankSum=-1.861;SB=-4200.78;TI=NM_000642,NM_000028,NM_000643,NM_000644,NM_000646,NM_000645;GI=AGL,AGL,AGL,AGL,AGL,AGL;FC=Silent,Silent,Silent,Silent,Silent,Silent;EXON;DP=3610;AN=16;AC=10;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=AGL;GeneDetail.refGene=NM_000642:c.*1541T>C\x3bNM_000643:c.*1541T>C\x3bNM_000028:c.*1541T>C\x3bNM_000644:c.*1541T>C\x3bNM_000646:c.*1541T>C\x3bNM_000645:c.*1541T>C;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=AGL;GeneDetail.knownGene=uc001dsi.1:c.*1541T>C\x3buc001dsj.1:c.*1541T>C\x3buc001dsk.1:c.*1541T>C\x3buc001dsl.1:c.*1541T>C\x3buc001dsm.1:c.*1541T>C\x3buc001dsn.1:c.*1541T>C;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intergenic;Gene.ccdsGene=CCDS759.1\x3bCCDS60204.1;GeneDetail.ccdsGene=dist\x3d1541\x3bdist\x3d47345;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1p21.2;CLINSIG=Benign;CLNDBN=Glycogen_storage_disease_type_III;CLNACC=RCV000286279.1;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C0017922:232400:ORPHA308684:66937008;PopFreqMax=0.55;Kaviar_AF=0.44479;Kaviar_AC=11577;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.401757;snp138=rs3766603;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:283,284:567:99:6764,0,6942:56:99:0.501 ./.:.:.:.:.:.:.:. 1/1:0,192:192:99:5648,406,0:56:99:1 1/1:4,455:459:99:13255,877,0:57:99:0.991 0/1:207,231:438:99:5836,0,4521:55:99:0.527 0/1:199,238:439:99:6006,0,4930:55:99:0.545 0/1:256,254:510:99:6349,0,6314:56:99:0.498 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:262,270:532:99:6238,0,6058:54:99:0.508 0/1:214,259:473:99:5518,0,4551:50:99:0.548 ./.:.:.:.:.:.:.:.
chr1 154134557 rs3196889 A C 9903.57 PASS BaseQRankSum=0.119;Dels=0;FS=0.388;HRun=1;HaplotypeScore=16.3026;MQ=57;MQ0=0;MQRankSum=3.603;QD=12.19;ReadPosRankSum=1.101;SB=-2354.1;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Silent,Silent,Silent,Silent,Silent;EXON;DP=2018;AN=14;AC=8;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=TPM3;GeneDetail.refGene=NM_152263:c.*5856T>G;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=TPM3;GeneDetail.knownGene=uc001fec.2:c.*5856T>G;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=Benign|Benign;CLNDBN=Congenital_fiber-type_disproportion|Nemaline_myopathy;CLNACC=RCV000304879.1|RCV000395347.1;CLNDSDB=MedGen|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=CN235628|C0206157:ORPHA607:75072002;PopFreqMax=0.5;Kaviar_AF=0.34728;Kaviar_AC=9039;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.321486;snp138=rs3196889;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:187,186:373:99:4546,0,4591:57:99:0.499 ./.:.:.:.:.:.:.:. 0/1:81,81:162:99:2146,0,1964:57:99:0.5 0/1:149,143:292:99:3448,0,3470:58:99:0.49 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:122,157:279:99:3732,0,2945:56:99:0.563 1/1:4,353:357:99:9904,613,0:57:99:0.989 0/1:173,157:330:99:3713,0,4209:56:99:0.476 ./.:.:.:.:.:.:.:. 0/1:110,113:224:99:2825,0,2675:57:99:0.507
chr1 154134862 . C A 134.14 LowVariantFreq;SB;LowGQX BaseQRankSum=-1.773;Dels=0.01;FS=48.063;HRun=21;HaplotypeScore=40.4167;MQ=45;MQ0=0;MQRankSum=-1.801;QD=1.34;ReadPosRankSum=-1.402;SB=-0.01;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Silent,Silent,Silent,Silent,Silent;EXON;DP=583;AN=8;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=TPM3;GeneDetail.refGene=NM_152263:c.*5551G>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=TPM3;GeneDetail.knownGene=uc001fec.2:c.*5551G>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=3.84e-05;Kaviar_AC=1;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:83,16:99:99:164,0,2272:45:99:0.162 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:140,27:168:34.91:35,0,3728:45:6:0.162 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:135,22:157:99:119,0,3534:45:89:0.14 ./.:.:.:.:.:.:.:. 0/1:123,25:150:99:144,0,3392:42:99:0.169
chr1 154135267 rs78724071 C T 5571.85 PASS BaseQRankSum=3.509;Dels=0;FS=1.449;HRun=0;HaplotypeScore=14.5927;MQ=56;MQ0=0;MQRankSum=1.063;QD=11.17;ReadPosRankSum=1.969;SB=-3818.09;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Silent,Silent,Silent,Silent,Silent;EXON;DP=499;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=TPM3;GeneDetail.refGene=NM_152263:c.*5146G>A;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=TPM3;GeneDetail.knownGene=uc001fec.2:c.*5146G>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.028;Kaviar_AF=0.0200937;Kaviar_AC=523;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.00838658;snp138=rs78724071;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:264,234:499:99:5572,0,6171:56:99:0.47 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 154136005 rs190755789 C A 5735.51 PASS BaseQRankSum=-0.108;Dels=0;FS=0.313;HRun=5;HaplotypeScore=23.2194;MQ=51;MQ0=0;MQRankSum=0.466;QD=10.88;ReadPosRankSum=3.137;SB=-4371.66;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Silent,Silent,Silent,Silent,Silent;EXON;DP=527;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=TPM3;GeneDetail.refGene=NM_152263:c.*4408G>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=TPM3;GeneDetail.knownGene=uc001fec.2:c.*4408G>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.014;Kaviar_AF=0.0052251;Kaviar_AC=136;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.00479233;snp138=rs190755789;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:260,266:527:99:5736,0,5519:51:99:0.506 ./.:.:.:.:.:.:.:.
chr1 154136591 rs12063890 C A 4213.94 PASS BaseQRankSum=-2.689;Dels=0;FS=0;HRun=0;HaplotypeScore=11.6466;MQ=54;MQ0=0;MQRankSum=4.264;QD=10.59;ReadPosRankSum=0.747;SB=-2736.01;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Silent,Silent,Silent,Silent,Silent;EXON;DP=682;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=TPM3;GeneDetail.refGene=NM_152263:c.*3822G>T;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=TPM3;GeneDetail.knownGene=uc001fec.2:c.*3822G>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=Benign|Benign;CLNDBN=Congenital_fiber-type_disproportion|Nemaline_myopathy;CLNACC=RCV000268480.1|RCV000358489.1;CLNDSDB=MedGen|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=CN235628|C0206157:ORPHA607:75072002;PopFreqMax=0.39;Kaviar_AF=0.0957815;Kaviar_AC=2493;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.175319;snp138=rs12063890;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:214,182:398:99:4214,0,5022:54:99:0.46 0/1:153,131:284:99:3150,0,3736:54:99:0.461 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 154137165 rs12026177 C T 5817.26 PASS BaseQRankSum=-1.894;Dels=0;FS=1.184;HRun=0;HaplotypeScore=9.3411;MQ=54;MQ0=0;MQRankSum=3.629;QD=10.72;ReadPosRankSum=1.337;SB=-2948.79;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Silent,Silent,Silent,Silent,Silent;EXON;DP=1355;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=TPM3;GeneDetail.refGene=NM_152263:c.*3248G>A;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=TPM3;GeneDetail.knownGene=uc001fec.2:c.*3248G>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=Likely_benign|Likely_benign;CLNDBN=Congenital_fiber-type_disproportion|Nemaline_myopathy;CLNACC=RCV000295269.1|RCV000345474.1;CLNDSDB=MedGen|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=CN235628|C0206157:ORPHA607:75072002;PopFreqMax=0.33;Kaviar_AF=0.134355;Kaviar_AC=3497;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.202077;snp138=rs12026177;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:208,187:395:99:4233,0,4904:54:99:0.473 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:290,245:536:99:5817,0,7322:56:99:0.458 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:207,216:424:99:4822,0,4652:50:99:0.511 ./.:.:.:.:.:.:.:.
chr1 154139165 rs373439338 C CT 3796.11 R8;LowVariantFreq BaseQRankSum=1.219;FS=1.797;HRun=12;HaplotypeScore=369.893;MQ=55;MQ0=0;MQRankSum=-1.301;QD=6.37;ReadPosRankSum=-1.645;SB=-772.87;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Noncoding,Noncoding,Noncoding,Noncoding,Noncoding;EXON;DP=2415;AN=22;AC=8;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=TPM3;GeneDetail.refGene=NM_152263:c.*1247_*1248insA;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=TPM3;GeneDetail.knownGene=uc001fec.2:c.*1247_*1248insA;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=Likely_benign|Likely_benign,Benign|Benign;CLNDBN=Congenital_fiber-type_disproportion|Nemaline_myopathy,Congenital_fiber-type_disproportion|Nemaline_myopathy;CLNACC=RCV000307028.1|RCV000398242.1,RCV000315274.1|RCV000369925.1;CLNDSDB=MedGen|MedGen:Orphanet:SNOMED_CT,MedGen|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=CN235628|C0206157:ORPHA607:75072002,CN235628|C0206157:ORPHA607:75072002;PopFreqMax=0.41;Kaviar_AF=0.0011142;Kaviar_AC=29;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.340855;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:129,82:251:99:1637,0,1702:55:99:0.389 1/0:84,63,39:202:99:3040,872,864:52:99:0.548 0/1:53,68:143:99:1597,0,289:55:99:0.562 0/1:123,46:208:99:1139,0,1323:55:99:0.272 ./.:.:.:.:.:.:.:. 0/0:179,35:247:99:473,.,.:55:99:0.164 0/0:138,64:284:99:1982,.,.:54:99:0.317 1/0:74,75,21:177:50.75:2079,51,265:53:51:0.565 1/0:98,66,85:274:99:3796,1422,1500:55:99:0.606 0/1:158,48:241:99:1190,0,2030:54:99:0.233 0/0:101,42:186:99:1160,.,.:51:99:0.294 0/1:103,48:200:99:1041,0,1214:54:99:0.318
chr1 154139165 rs373439338 C CTT 3796.11 R8;LowVariantFreq BaseQRankSum=1.219;FS=1.797;HRun=12;HaplotypeScore=369.893;MQ=55;MQ0=0;MQRankSum=-1.301;QD=6.37;ReadPosRankSum=-1.645;SB=-772.87;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Noncoding,Noncoding,Noncoding,Noncoding,Noncoding;EXON;DP=2415;AN=22;AC=5;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=TPM3;GeneDetail.refGene=NM_152263:c.*1247_*1248insAA;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=TPM3;GeneDetail.knownGene=uc001fec.2:c.*1247_*1248insAA;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=Likely_benign|Likely_benign,Benign|Benign;CLNDBN=Congenital_fiber-type_disproportion|Nemaline_myopathy,Congenital_fiber-type_disproportion|Nemaline_myopathy;CLNACC=RCV000307028.1|RCV000398242.1,RCV000315274.1|RCV000369925.1;CLNDSDB=MedGen|MedGen:Orphanet:SNOMED_CT,MedGen|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=CN235628|C0206157:ORPHA607:75072002,CN235628|C0206157:ORPHA607:75072002;PopFreqMax=0.19;Kaviar_AF=0.0167128;Kaviar_AC=435;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.125399;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/0:129,82:251:99:1637,.,.:55:99:0.389 0/1:84,63,39:202:99:3040,1217,1596:52:99:0.548 0/0:53,68:143:99:1597,.,.:55:99:0.562 0/0:123,46:208:99:1139,.,.:55:99:0.272 ./.:.:.:.:.:.:.:. 0/0:179,35:247:99:473,.,.:55:99:0.164 0/1:138,64:284:99:1982,0,2583:54:99:0.317 0/1:74,75,21:177:50.75:2079,1150,1865:53:51:0.565 0/1:98,66,85:274:99:3796,1027,1555:55:99:0.606 0/0:158,48:241:99:1190,.,.:54:99:0.233 0/1:101,42:186:99:1160,0,1705:51:99:0.294 0/0:103,48:200:99:1041,.,.:54:99:0.318
chr1 154139165 rs373439338 CT C 3796.11 R8;LowVariantFreq BaseQRankSum=1.219;FS=1.797;HRun=12;HaplotypeScore=369.893;MQ=55;MQ0=0;MQRankSum=-1.301;QD=6.37;ReadPosRankSum=-1.645;SB=-772.87;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Noncoding,Noncoding,Noncoding,Noncoding,Noncoding;EXON;DP=2415;AN=22;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=UTR3;Gene.refGene=TPM3;GeneDetail.refGene=NM_152263:c.*1247delA;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=TPM3;GeneDetail.knownGene=uc001fec.2:c.*1247delA;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=0.0001153;Kaviar_AC=3;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/0:129,82:251:99:1637,.,.:55:99:0.389 0/0:84,63,39:202:99:3040,.,.:52:99:0.548 0/0:53,68:143:99:1597,.,.:55:99:0.562 0/0:123,46:208:99:1139,.,.:55:99:0.272 ./.:.:.:.:.:.:.:. 0/1:179,35:247:99:473,0,3079:55:99:0.164 0/0:138,64:284:99:1982,.,.:54:99:0.317 0/0:74,75,21:177:50.75:2079,.,.:53:51:0.565 0/0:98,66,85:274:99:3796,.,.:55:99:0.606 0/0:158,48:241:99:1190,.,.:54:99:0.233 0/0:101,42:186:99:1160,.,.:51:99:0.294 0/0:103,48:200:99:1041,.,.:54:99:0.318
chr1 154141908 rs4845364 A G 10107.7 PASS BaseQRankSum=0.333;Dels=0;FS=1.816;HRun=1;HaplotypeScore=19.1811;MQ=56;MQ0=0;MQRankSum=0.452;QD=11.7;ReadPosRankSum=1.436;SB=-2300.7;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Silent,Silent,Silent,Silent,Silent;DP=2844;AN=20;AC=14;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=TPM3;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=TPM3;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS41403.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000246581.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.88;Kaviar_AF=0.589371;Kaviar_AC=91118;Kaviar_AN=154602;ExAC_ALL=0.6077;ExAC_AFR=0.8050;ExAC_AMR=0.7283;ExAC_EAS=0.8769;ExAC_FIN=0.5552;ExAC_NFE=0.5164;ExAC_OTH=0.6460;ExAC_SAS=0.6437;1000g2014oct_all=0.732228;snp138=rs4845364;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.6411;dpsi_zscore=1.263;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:174,175:351:99:4106,0,4112:56:99:0.501 1/1:0,304:304:99:8406,599,0:56:99:1 1/1:1,155:156:99:4582,296,0:55:99:0.994 0/1:155,129:285:99:3181,0,3822:56:99:0.454 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:204,184:388:99:4276,0,5018:57:99:0.474 1/1:0,211:212:99:6482,476,0:58:99:1 1/1:2,352:355:99:10108,687,0:58:99:0.994 0/1:180,123:303:99:2850,0,4393:56:99:0.406 0/1:133,138:271:99:3012,0,2786:50:99:0.509 0/1:102,117:219:99:2976,0,2502:56:99:0.534
chr1 154145532 rs28372838 C G 7083.14 PASS BaseQRankSum=1.395;Dels=0;FS=0.335;HRun=1;HaplotypeScore=26.3913;MQ=54;MQ0=0;MQRankSum=1.141;QD=11.86;ReadPosRankSum=-0.581;SB=-3872.35;TI=NM_001043353,NM_001043351,NM_001043352,NM_153649,NM_152263;GI=TPM3,TPM3,TPM3,TPM3,TPM3;FC=Silent,Silent,Silent,Silent,Silent;DP=1422;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=TPM3;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=TPM3;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1060.1\x3bCCDS41400.1\x3bCCDS41401.1\x3bCCDS41402.1\x3bCCDS41403.1\x3bCCDS60274.1\x3bCCDS60275.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=Benign;CLNDBN=not_specified;CLNACC=RCV000246097.1;CLNDSDB=MedGen;CLNDSDBID=CN169374;PopFreqMax=0.38;Kaviar_AF=0.134028;Kaviar_AC=20721;Kaviar_AN=154602;ExAC_ALL=0.1375;ExAC_AFR=0.2285;ExAC_AMR=0.0529;ExAC_EAS=0.3782;ExAC_FIN=0.1788;ExAC_NFE=0.1048;ExAC_OTH=0.1322;ExAC_SAS=0.1295;1000g2014oct_all=0.202077;snp138=rs28372838;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.8790;dpsi_zscore=1.444;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:226,241:469:99:5562,0,5201:54:99:0.516 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:280,295:575:99:7083,0,6734:56:99:0.513 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:193,185:378:99:3964,0,4262:51:99:0.489 ./.:.:.:.:.:.:.:.
chr1 154163596 rs557037818 G A 2715.7 PASS BaseQRankSum=-0.74;Dels=0;FS=5.357;HRun=0;HaplotypeScore=8.1523;MQ=56;MQ0=0;MQRankSum=1.027;QD=10.91;ReadPosRankSum=0.419;SB=-1301.08;TI=NM_152263;GI=TPM3;FC=Silent;DP=249;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=TPM3;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=TPM3;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS41403.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q21.3;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.022;Kaviar_AF=3.23e-05;Kaviar_AC=5;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.000399361;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.6537;dpsi_zscore=1.274;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:133,116:249:99:2746,0,3298:56:99:0.466 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 155113004 rs41264901 T C 5090.16 PASS BaseQRankSum=4.567;Dels=0;FS=0.35;HRun=0;HaplotypeScore=22.8663;MQ=57;MQ0=0;MQRankSum=1.062;QD=11.41;ReadPosRankSum=1.158;SB=-2985.33;DP=446;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=upstream;Gene.refGene=DPM3;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=upstream;Gene.knownGene=DPM3;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=upstream;Gene.ccdsGene=CCDS1094.1\x3bCCDS1095.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q22;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.002;Kaviar_AF=0.0024205;Kaviar_AC=63;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.000998403;snp138=rs41264901;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:244,202:446:99:5090,0,6035:57:99:0.453 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 156095848 rs2475758 C T 3621.01 PASS BaseQRankSum=-0.113;Dels=0;FS=0.901;HRun=0;HaplotypeScore=14.6122;MQ=56;MQ0=0;MQRankSum=0.874;QD=11.87;ReadPosRankSum=1.17;SB=-1770.67;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Silent,Silent,Silent;DP=491;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=LMNA;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q22;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.32;Kaviar_AF=0.0110089;Kaviar_AC=1702;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.11242;snp138=rs2475758;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:162,143:305:99:3621,0,4032:56:99:0.469 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:85,101:186:99:2627,0,2026:55:99:0.543
chr1 156104375 rs11264442 G T 2393.43 PASS BaseQRankSum=-1.202;Dels=0;FS=4.03;HRun=0;HaplotypeScore=13.9819;MQ=59;MQ0=0;MQRankSum=0.74;QD=11.45;ReadPosRankSum=-2.775;SB=-1224.09;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Silent,Silent,Silent;DP=209;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=LMNA;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1\x3bCCDS58038.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q22;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.19;Kaviar_AF=0.007335;Kaviar_AC=1134;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.077476;snp138=rs11264442;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.1469;dpsi_zscore=0.609;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:119,90:209:99:2423,0,3262:59:99:0.431 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 156104392 rs11264443 C T 2269.8 PASS BaseQRankSum=-1.78;Dels=0;FS=9.808;HRun=0;HaplotypeScore=15.6868;MQ=59;MQ0=0;MQRankSum=0.444;QD=11.58;ReadPosRankSum=-0.938;SB=-912.19;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Silent,Silent,Silent;DP=196;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=LMNA;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1\x3bCCDS58038.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q22;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.18;Kaviar_AF=0.007018;Kaviar_AC=1085;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0750799;snp138=rs11264443;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0468;dpsi_zscore=-0.250;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:112,84:196:99:2300,0,3212:59:99:0.429 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 156104965 rs80356809 T A 2720.59 PASS BaseQRankSum=2.051;Dels=0;FS=2.297;HRun=0;HaplotypeScore=9.2291;MQ=57;MQ0=0;MQRankSum=-0.128;QD=12.04;ReadPosRankSum=2.129;SB=-1523.71;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Silent,Silent,Silent;DP=226;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR5;Gene.knownGene=LMNA;GeneDetail.knownGene=uc009wrp.3:c.-20T>A;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1\x3bCCDS58038.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q22;CLINSIG=other|not_provided|Likely_benign|Likely_benign|Likely_benign|Likely_benign|Likely_benign|Likely_benign|Likely_benign|Likely_benign|Likely_benign|Likely_benign;CLNDBN=not_specified|not_provided|Lethal_tight_skin_contracture_syndrome|Lipoatrophy_with_Diabetes,_Hepatic_Steatosis,_Hypertrophic_Cardiomyopathy,_and_Leukomelanodermic_Papules|Charcot-Marie-Tooth,_Type_2|Hutchinson-Gilford_syndrome|Mandibuloacral_dysplasia|Limb-Girdle_Muscular_Dystrophy,_Recessive|Congenital_muscular_dystrophy,_LMNA-related|Emery-Dreifuss_muscular_dystrophy|Dilated_Cardiomyopathy,_Dominant|Familial_partial_lipodystrophy;CLNACC=RCV000041372.3|RCV000057470.1|RCV000268196.1|RCV000271656.1|RCV000294723.1|RCV000300601.1|RCV000301904.1|RCV000325561.1|RCV000335689.1|RCV000361342.1|RCV000406731.1|RCV000406740.1;CLNDSDB=MedGen|MedGen|MedGen:OMIM:Orphanet:SNOMED_CT|MedGen|MedGen|MedGen:OMIM:Orphanet:SNOMED_CT|MedGen|MedGen|MedGen:OMIM:Orphanet|MedGen:Orphanet:SNOMED_CT|MedGen|MedGen:Orphanet:SNOMED_CT;CLNDSDBID=CN169374|CN221809|C0406585:275210:ORPHA1662:400128006|CN239184|CN239171|C0033300:176670:ORPHA740:238870004|CN118835|CN239352|C2750785:613205:ORPHA157973|C0410189:ORPHA261:111508004|CN239310|C0271694:ORPHA98306:49292002;PopFreqMax=0.0086;Kaviar_AF=0.0026261;Kaviar_AC=406;Kaviar_AN=154602;ExAC_ALL=0.0023;ExAC_AFR=0.0007;ExAC_AMR=0.0018;ExAC_EAS=0;ExAC_FIN=0.0008;ExAC_NFE=0.0037;ExAC_OTH=0.0011;ExAC_SAS=6.056e-05;1000g2014oct_all=0.00219649;snp138=rs80356809;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-1.8572;dpsi_zscore=-1.853;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:119,106:226:99:2751,0,3102:57:99:0.471 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 156105028 rs538089 T C 4129.29 PASS BaseQRankSum=1.548;Dels=0;FS=2.772;HRun=1;HaplotypeScore=13.3466;MQ=57;MQ0=0;MQRankSum=1.11;QD=11.22;ReadPosRankSum=-0.938;SB=-2637.52;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Synonymous_A287A,Synonymous_A287A,Synonymous_A287A;EXON;DP=933;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=LMNA:NM_001257374:exon5:c.T525C:p.A175A\x3bLMNA:NM_001282626:exon5:c.T861C:p.A287A\x3bLMNA:NM_005572:exon5:c.T861C:p.A287A\x3bLMNA:NM_170707:exon5:c.T861C:p.A287A\x3bLMNA:NM_170708:exon5:c.T861C:p.A287A\x3bLMNA:NM_001282624:exon6:c.T618C:p.A206A\x3bLMNA:NM_001282625:exon8:c.T861C:p.A287A;Func.knownGene=exonic;Gene.knownGene=LMNA;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=LMNA:uc009wrp.3:exon1:c.T44C:p.L15P;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1\x3bCCDS58038.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS1129.1:CCDS1129.1:exon5:c.T861C:p.A287A\x3bCCDS1131.1:CCDS1131.1:exon5:c.T861C:p.A287A\x3bCCDS58038.1:CCDS58038.1:exon5:c.T525C:p.A175A;cytoBand=1q22;CLINSIG=other|not_provided|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign;CLNDBN=not_specified|not_provided|Cardiovascular_phenotype|Lethal_tight_skin_contracture_syndrome|Hutchinson-Gilford_syndrome|Dilated_Cardiomyopathy,_Dominant|Congenital_muscular_dystrophy,_LMNA-related|Emery-Dreifuss_muscular_dystrophy|Lipoatrophy_with_Diabetes,_Hepatic_Steatosis,_Hypertrophic_Cardiomyopathy,_and_Leukomelanodermic_Papules|Mandibuloacral_dysplasia|Limb-Girdle_Muscular_Dystrophy,_Recessive|Familial_partial_lipodystrophy|Charcot-Marie-Tooth,_Type_2;CLNACC=RCV000041374.11|RCV000057475.3|RCV000249986.1|RCV000278366.1|RCV000281700.1|RCV000303946.1|RCV000332471.1|RCV000335802.1|RCV000339029.1|RCV000374142.1|RCV000385848.1|RCV000389150.1|RCV000408212.1;CLNDSDB=MedGen|MedGen|MedGen|MedGen:OMIM:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet:SNOMED_CT|MedGen|MedGen:OMIM:Orphanet|MedGen:Orphanet:SNOMED_CT|MedGen|MedGen|MedGen|MedGen:Orphanet:SNOMED_CT|MedGen;CLNDSDBID=CN169374|CN221809|CN230736|C0406585:275210:ORPHA1662:400128006|C0033300:176670:ORPHA740:238870004|CN239310|C2750785:613205:ORPHA157973|C0410189:ORPHA261:111508004|CN239184|CN118835|CN239352|C0271694:ORPHA98306:49292002|CN239171;PopFreqMax=0.52;Kaviar_AF=0.106389;Kaviar_AC=16448;Kaviar_AN=154602;ExAC_ALL=0.1094;ExAC_AFR=0.4522;ExAC_AMR=0.0621;ExAC_EAS=0.0200;ExAC_FIN=0.0560;ExAC_NFE=0.0745;ExAC_OTH=0.0982;ExAC_SAS=0.1360;1000g2014oct_all=0.193091;snp138=rs538089;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.8358;dpsi_zscore=1.413;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:188,179:368:99:4129,0,4534:57:99:0.488 ./.:.:.:.:.:.:.:. 0/1:195,140:337:99:3530,0,4877:57:99:0.418 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:97,131:228:99:3200,0,2442:57:99:0.575
chr1 156105609 rs646840 G T 4506.44 PASS BaseQRankSum=2.936;Dels=0;FS=0;HRun=1;HaplotypeScore=13.8551;MQ=58;MQ0=0;MQRankSum=1.71;QD=12.99;ReadPosRankSum=-0.917;SB=-2742.31;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Silent,Silent,Silent;DP=898;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR5;Gene.knownGene=LMNA;GeneDetail.knownGene=uc010pha.1:c.-179G>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1\x3bCCDS58038.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q22;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.52;Kaviar_AF=0.0191459;Kaviar_AC=2960;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.192891;snp138=rs646840;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0494;dpsi_zscore=-0.262;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:157,173:330:99:4288,0,3682:58:99:0.524 ./.:.:.:.:.:.:.:. 0/1:143,186:329:99:4506,0,3520:57:99:0.565 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:112,126:239:99:3059,0,2842:57:99:0.529
chr1 156105928 rs534807 G A 4405.5 PASS BaseQRankSum=0.925;Dels=0;FS=4.023;HRun=0;HaplotypeScore=17.1617;MQ=57;MQ0=0;MQRankSum=3.78;QD=12.17;ReadPosRankSum=0.504;SB=-2822.95;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Silent,Silent,Silent;DP=954;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=LMNA;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1\x3bCCDS58038.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q22;CLINSIG=Benign|other|not_provided;CLNDBN=Primary_dilated_cardiomyopathy|not_specified|not_provided;CLNACC=RCV000030146.1|RCV000041310.8|RCV000057241.1;CLNDSDB=MedGen:Orphanet:SNOMED_CT|MedGen|MedGen;CLNDSDBID=C0007193:ORPHA217604:195021004|CN169374|CN221809;PopFreqMax=0.52;Kaviar_AF=0.10364;Kaviar_AC=16023;Kaviar_AN=154602;ExAC_ALL=0.1077;ExAC_AFR=0.4537;ExAC_AMR=0.0614;ExAC_EAS=0.0202;ExAC_FIN=0.0542;ExAC_NFE=0.0733;ExAC_OTH=0.0959;ExAC_SAS=0.1303;1000g2014oct_all=0.192292;snp138=rs534807;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2885;dpsi_zscore=0.874;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:187,175:362:99:4405,0,4523:57:99:0.483 ./.:.:.:.:.:.:.:. 0/1:185,159:345:99:3908,0,4844:57:99:0.462 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:130,117:247:99:3045,0,3263:57:99:0.474
chr1 156106185 rs505058 T C 5790.35 PASS BaseQRankSum=0.346;Dels=0;FS=0.697;HRun=0;HaplotypeScore=21.1363;MQ=57;MQ0=0;MQRankSum=1.967;QD=11.09;ReadPosRankSum=-0.145;SB=-3444.76;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Synonymous_D446D,Synonymous_D446D,Synonymous_D446D;EXON;DP=1231;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=LMNA:NM_001257374:exon7:c.T1002C:p.D334D\x3bLMNA:NM_001282626:exon7:c.T1338C:p.D446D\x3bLMNA:NM_005572:exon7:c.T1338C:p.D446D\x3bLMNA:NM_170707:exon7:c.T1338C:p.D446D\x3bLMNA:NM_170708:exon7:c.T1338C:p.D446D\x3bLMNA:NM_001282624:exon8:c.T1095C:p.D365D\x3bLMNA:NM_001282625:exon10:c.T1338C:p.D446D;Func.knownGene=exonic;Gene.knownGene=LMNA;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=LMNA:uc009wrp.3:exon3:c.T521C:p.M174T;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1\x3bCCDS58038.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS1129.1:CCDS1129.1:exon7:c.T1338C:p.D446D\x3bCCDS1131.1:CCDS1131.1:exon7:c.T1338C:p.D446D\x3bCCDS58038.1:CCDS58038.1:exon7:c.T1002C:p.D334D;cytoBand=1q22;CLINSIG=other|not_provided|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign;CLNDBN=not_specified|not_provided|Cardiovascular_phenotype|Familial_partial_lipodystrophy|Congenital_muscular_dystrophy,_LMNA-related|Lipoatrophy_with_Diabetes,_Hepatic_Steatosis,_Hypertrophic_Cardiomyopathy,_and_Leukomelanodermic_Papules|Hutchinson-Gilford_syndrome|Dilated_Cardiomyopathy,_Dominant|Emery-Dreifuss_muscular_dystrophy|Charcot-Marie-Tooth,_Type_2|Mandibuloacral_dysplasia|Lethal_tight_skin_contracture_syndrome|Limb-Girdle_Muscular_Dystrophy,_Recessive;CLNACC=RCV000041315.11|RCV000057270.3|RCV000252403.1|RCV000268754.1|RCV000278595.1|RCV000300868.1|RCV000304015.1|RCV000326241.1|RCV000351015.1|RCV000357954.1|RCV000360967.1|RCV000392971.1|RCV000402362.1;CLNDSDB=MedGen|MedGen|MedGen|MedGen:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet|MedGen|MedGen:OMIM:Orphanet:SNOMED_CT|MedGen|MedGen:Orphanet:SNOMED_CT|MedGen|MedGen|MedGen:OMIM:Orphanet:SNOMED_CT|MedGen;CLNDSDBID=CN169374|CN221809|CN230736|C0271694:ORPHA98306:49292002|C2750785:613205:ORPHA157973|CN239184|C0033300:176670:ORPHA740:238870004|CN239310|C0410189:ORPHA261:111508004|CN239171|CN118835|C0406585:275210:ORPHA1662:400128006|CN239352;PopFreqMax=0.72;Kaviar_AF=0.120911;Kaviar_AC=18693;Kaviar_AN=154602;ExAC_ALL=0.1611;ExAC_AFR=0.6488;ExAC_AMR=0.1012;ExAC_EAS=0.0307;ExAC_FIN=0.0810;ExAC_NFE=0.0978;ExAC_OTH=0.1407;ExAC_SAS=0.1609;1000g2014oct_all=0.249201;snp138=rs505058;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2650;dpsi_zscore=0.838;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:249,214:466:99:5166,0,6109:57:99:0.462 ./.:.:.:.:.:.:.:. 0/1:243,251:494:99:5790,0,6038:57:99:0.508 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:134,136:271:99:3410,0,3344:56:99:0.504
chr1 156106863 rs553016 C T 6064.87 PASS BaseQRankSum=-1.425;Dels=0;FS=2.552;HRun=0;HaplotypeScore=14.6446;MQ=58;MQ0=0;MQRankSum=0.714;QD=14.37;ReadPosRankSum=-0.565;SB=-3509.86;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Silent,Silent,Silent;DP=1184;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=UTR3;Gene.knownGene=LMNA;GeneDetail.knownGene=uc009wrp.3:c.*632C>T;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1\x3bCCDS58038.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q22;CLINSIG=not_provided|Benign;CLNDBN=not_provided|not_specified;CLNACC=RCV000057308.1|RCV000243967.1;CLNDSDB=MedGen|MedGen;CLNDSDBID=CN221809|CN169374;PopFreqMax=0.49;Kaviar_AF=0.102677;Kaviar_AC=15874;Kaviar_AN=154602;ExAC_ALL=0.1064;ExAC_AFR=0.4201;ExAC_AMR=0.0602;ExAC_EAS=0.0205;ExAC_FIN=0.0589;ExAC_NFE=0.0738;ExAC_OTH=0.0955;ExAC_SAS=0.1354;1000g2014oct_all=0.182308;snp138=rs553016;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2779;dpsi_zscore=0.858;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:197,224:422:99:6065,0,5115:58:99:0.532 ./.:.:.:.:.:.:.:. 0/1:225,232:457:99:6026,0,5575:57:99:0.508 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:169,135:305:99:3508,0,4207:55:99:0.444
chr1 156107534 rs4641 C T 3161.9 PASS BaseQRankSum=-1.917;Dels=0;FS=3.61;HRun=0;HaplotypeScore=9.9263;MQ=56;MQ0=0;MQRankSum=0.641;QD=10.47;ReadPosRankSum=-0.542;SB=-1833.88;TI=NM_005572,NM_170707,NM_170708;GI=LMNA,LMNA,LMNA;FC=Synonymous_H566H,Synonymous_H566H,Silent;EXON;DP=1362;AN=12;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=LMNA;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=LMNA:NM_001257374:exon10:c.C1362T:p.H454H\x3bLMNA:NM_001282626:exon10:c.C1698T:p.H566H\x3bLMNA:NM_005572:exon10:c.C1698T:p.H566H\x3bLMNA:NM_170707:exon10:c.C1698T:p.H566H\x3bLMNA:NM_001282624:exon11:c.C1455T:p.H485H\x3bLMNA:NM_001282625:exon13:c.C1698T:p.H566H;Func.knownGene=exonic;Gene.knownGene=LMNA;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=LMNA:uc010pha.1:exon5:c.C666T:p.H222H\x3bLMNA:uc001fng.2:exon10:c.C1698T:p.H566H\x3bLMNA:uc001fni.3:exon10:c.C1698T:p.H566H\x3bLMNA:uc009wro.2:exon10:c.C1698T:p.H566H\x3bLMNA:uc010pgz.2:exon10:c.C1362T:p.H454H\x3bLMNA:uc001fnj.3:exon11:c.C1455T:p.H485H\x3bLMNA:uc001fnk.3:exon11:c.C1401T:p.H467H\x3bLMNA:uc001fnf.1:exon13:c.C1698T:p.H566H;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1129.1\x3bCCDS1131.1\x3bCCDS58038.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS1129.1:CCDS1129.1:exon10:c.C1698T:p.H566H\x3bCCDS1131.1:CCDS1131.1:exon10:c.C1698T:p.H566H\x3bCCDS58038.1:CCDS58038.1:exon10:c.C1362T:p.H454H;cytoBand=1q22;CLINSIG=other|not_provided|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign|Benign;CLNDBN=not_specified|not_provided|Mandibuloacral_dysplasia_with_type_A_lipodystrophy|Cardiovascular_phenotype|Familial_partial_lipodystrophy|Emery-Dreifuss_muscular_dystrophy|Mandibuloacral_dysplasia|Congenital_muscular_dystrophy,_LMNA-related|Hutchinson-Gilford_syndrome|Lethal_tight_skin_contracture_syndrome|Limb-Girdle_Muscular_Dystrophy,_Recessive|Dilated_Cardiomyopathy,_Dominant|Charcot-Marie-Tooth,_Type_2|Lipoatrophy_with_Diabetes,_Hepatic_Steatosis,_Hypertrophic_Cardiomyopathy,_and_Leukomelanodermic_Papules;CLNACC=RCV000041327.8|RCV000057348.2|RCV000225004.1|RCV000252567.1|RCV000280696.1|RCV000307278.1|RCV000310337.1|RCV000313972.1|RCV000335127.1|RCV000339153.1|RCV000350197.1|RCV000375103.1|RCV000393593.1|RCV000398387.1;CLNDSDB=MedGen|MedGen|MedGen|MedGen|MedGen:Orphanet:SNOMED_CT|MedGen:Orphanet:SNOMED_CT|MedGen|MedGen:OMIM:Orphanet|MedGen:OMIM:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet:SNOMED_CT|MedGen|MedGen|MedGen|MedGen;CLNDSDBID=CN169374|CN221809|CN236772|CN230736|C0271694:ORPHA98306:49292002|C0410189:ORPHA261:111508004|CN118835|C2750785:613205:ORPHA157973|C0033300:176670:ORPHA740:238870004|C0406585:275210:ORPHA1662:400128006|CN239352|CN239310|CN239171|CN239184;PopFreqMax=0.37;Kaviar_AF=0.116195;Kaviar_AC=17964;Kaviar_AN=154602;ExAC_ALL=0.2655;ExAC_AFR=0.0998;ExAC_AMR=0.3660;ExAC_EAS=0.3081;ExAC_FIN=0.25;ExAC_NFE=0.2817;ExAC_OTH=0.3297;ExAC_SAS=0.2943;1000g2014oct_all=0.220248;snp138=rs4641;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=1.8285;dpsi_zscore=1.912;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:125,117:242:99:2565,0,2867:56:99:0.483 0/1:87,62:149:99:1458,0,2262:56:99:0.416 ./.:.:.:.:.:.:.:. 0/1:97,113:210:99:2864,0,2424:57:99:0.538 0/1:106,119:225:99:2731,0,2775:56:99:0.529 0/1:143,137:280:99:3176,0,3442:55:99:0.489 ./.:.:.:.:.:.:.:. 0/1:132,124:256:99:3192,0,3264:59:99:0.484 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201008582 rs35360610 T TG 10283.5 PASS BaseQRankSum=0.58;FS=7.03;HRun=4;HaplotypeScore=192.706;MQ=58;MQ0=0;MQRankSum=2.188;QD=15.25;ReadPosRankSum=-3.247;SB=-1323.97;DP=2489;AN=22;AC=14;ANNOVAR_DATE=2016-05-11;Func.refGene=downstream;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=downstream;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=downstream;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.83;Kaviar_AF=0.0003074;Kaviar_AC=8;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.50639;snp138=rs35360610;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:137,120:257:99:3920,0,4118:58:99:0.467 0/1:112,99:211:99:3084,0,3620:58:99:0.469 1/1:4,174:178:99:6577,531,0:60:99:0.978 1/1:3,217:220:99:8124,656,0:60:99:0.986 0/1:129,94:224:99:2851,0,4244:58:99:0.422 0/1:107,104:211:99:3296,0,3361:58:99:0.493 1/1:4,272:277:99:10283,828,0:60:99:0.986 0/1:82,132:215:99:4354,0,2330:59:99:0.617 0/1:140,148:290:99:4665,0,4442:58:99:0.514 0/1:104,109:213:99:3439,0,3268:58:99:0.512 ./.:.:.:.:.:.:.:. 0/1:106,87:193:99:2677,0,3420:58:99:0.451
chr1 201009182 rs12139527 A G 4946.41 PASS BaseQRankSum=0.87;Dels=0;FS=3.839;HRun=0;HaplotypeScore=8.5671;MQ=55;MQ0=0;MQRankSum=3.985;QD=13.11;ReadPosRankSum=0.253;SB=-2654.74;TI=NM_000069;GI=CACNA1S;FC=Missense_L1800S;EXON;DP=1234;AN=8;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=CACNA1S:NM_000069:exon44:c.T5399C:p.L1800S;Func.knownGene=exonic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=CACNA1S:uc001gvv.3:exon44:c.T5399C:p.L1800S;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS1407.1:CCDS1407.1:exon44:c.T5399C:p.L1800S;cytoBand=1q32.1;CLINSIG=Benign|Benign|Benign;CLNDBN=not_specified|Hypokalemic_periodic_paralysis|Malignant_hyperthermia_susceptibility;CLNACC=RCV000242685.1|RCV000311084.1|RCV000368150.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0238358:ORPHA681|C0024591:ORPHA423;PopFreqMax=0.61;Kaviar_AF=0.152825;Kaviar_AC=23627;Kaviar_AN=154602;ExAC_ALL=0.1549;ExAC_AFR=0.5567;ExAC_AMR=0.0832;ExAC_EAS=0.1262;ExAC_FIN=0.1403;ExAC_NFE=0.1312;ExAC_OTH=0.1344;ExAC_SAS=0.0698;1000g2014oct_all=0.229233;snp138=rs12139527;SIFT_score=0.001;SIFT_converted_rankscore=0.784;SIFT_pred=D;Polyphen2_HDIV_score=0.999;Polyphen2_HDIV_rankscore=0.764;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.994;Polyphen2_HVAR_rankscore=0.807;Polyphen2_HVAR_pred=D;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=0.128;MutationTaster_converted_rankscore=0.356;MutationTaster_pred=P;MutationAssessor_score=2.085;MutationAssessor_score_rankscore=0.579;MutationAssessor_pred=M;FATHMM_score=0.56;FATHMM_converted_rankscore=0.546;FATHMM_pred=T;PROVEAN_score=-1.75;PROVEAN_converted_rankscore=0.414;PROVEAN_pred=N;VEST3_score=0.11;VEST3_rankscore=0.118;MetaSVM_score=-0.869;MetaSVM_rankscore=0.506;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.000;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=5.977;CADD_raw_rankscore=0.821;CADD_phred=27.7;DANN_score=0.999;DANN_rankscore=0.942;fathmm-MKL_coding_score=0.966;fathmm-MKL_coding_rankscore=0.698;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.602;Eigen-PC-raw=0.569;GenoCanyon_score=0.901;GenoCanyon_score_rankscore=0.261;integrated_fitCons_score=0.487;integrated_fitCons_score_rankscore=0.133;integrated_confidence_value=0;GERP++_RS=4.93;GERP++_RS_rankscore=0.643;phyloP100way_vertebrate=3.816;phyloP100way_vertebrate_rankscore=0.551;phyloP20way_mammalian=0.990;phyloP20way_mammalian_rankscore=0.601;phastCons100way_vertebrate=0.968;phastCons100way_vertebrate_rankscore=0.339;phastCons20way_mammalian=0.346;phastCons20way_mammalian_rankscore=0.245;SiPhy_29way_logOdds=8.908;SiPhy_29way_logOdds_rankscore=0.345;Interpro_domain=.;GTEx_V6_gene=ENSG00000234132.1|ENSG00000234132.1|ENSG00000229191.1|ENSG00000229191.1;GTEx_V6_tissue=Muscle_Skeletal|Testis|Testis|Whole_Blood;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 0/1:136,165:301:99:3945,0,3326:55:99:0.548 0/1:114,119:233:99:3166,0,2916:57:99:0.511 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:200,203:405:99:4946,0,4944:57:99:0.504 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:151,144:295:99:3801,0,3817:56:99:0.488
chr1 201009556 rs1546416 A G 10535.5 PASS BaseQRankSum=3.052;Dels=0;FS=0.393;HRun=0;HaplotypeScore=14.3786;MQ=57;MQ0=0;MQRankSum=1.805;QD=12.1;ReadPosRankSum=1.025;SB=-2408.22;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=2987;AN=20;AC=12;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.42;Kaviar_AF=0.0677546;Kaviar_AC=10475;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.332468;snp138=rs1546416;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.7115;dpsi_zscore=-1.279;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:186,162:349:99:4222,0,4689:57:99:0.466 0/1:134,159:293:99:3672,0,3204:57:99:0.543 0/1:93,93:186:99:2393,0,2500:57:99:0.5 1/1:0,285:285:99:8582,623,0:58:99:1 0/1:129,147:276:99:3551,0,3025:56:99:0.533 0/1:160,153:313:99:4001,0,3773:56:99:0.489 1/1:1,361:362:99:10535,758,0:57:99:0.997 0/1:136,109:246:99:2844,0,3694:57:99:0.445 0/1:180,174:354:99:4639,0,4459:58:99:0.492 0/1:171,152:323:99:3760,0,3952:56:99:0.471 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201009897 rs6427875 T C 5440.74 PASS Dels=0;FS=0;HRun=3;HaplotypeScore=5.4936;MQ=57;MQ0=0;QD=29.26;SB=-2079.21;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=1799;AN=24;AC=24;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=1.;Kaviar_AF=0.0001921;Kaviar_AC=5;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.997005;snp138=rs6427875;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2396;dpsi_zscore=0.796;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,150:150:99:4389,319,0:57:99:1 1/1:0,155:156:99:4151,295,0:55:99:1 1/1:0,115:115:99:3097,220,0:56:99:1 1/1:0,142:142:99:4136,301,0:58:99:1 1/1:0,164:164:99:4561,331,0:54:99:1 1/1:0,157:157:99:4422,322,0:56:99:1 1/1:0,178:178:99:5134,376,0:59:99:1 1/1:0,132:132:99:3899,286,0:58:99:1 1/1:0,187:188:99:5441,394,0:57:99:1 1/1:0,146:146:99:3999,286,0:56:99:1 1/1:0,142:143:99:3709,262,0:54:99:1 1/1:0,125:126:99:3545,256,0:58:99:1
chr1 201012484 rs13374149 C T 5584.24 PASS BaseQRankSum=1.853;Dels=0;FS=0.338;HRun=0;HaplotypeScore=22.8277;MQ=54;MQ0=0;MQRankSum=4.608;QD=11.28;ReadPosRankSum=0.476;SB=-3474.29;TI=NM_000069;GI=CACNA1S;FC=Missense_R1658H;EXON;DP=1755;AN=8;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=CACNA1S:NM_000069:exon40:c.G4973A:p.R1658H;Func.knownGene=exonic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=CACNA1S:uc001gvv.3:exon40:c.G4973A:p.R1658H;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS1407.1:CCDS1407.1:exon40:c.G4973A:p.R1658H;cytoBand=1q32.1;CLINSIG=Benign|Benign|Benign;CLNDBN=not_specified|Hypokalemic_periodic_paralysis|Malignant_hyperthermia_susceptibility;CLNACC=RCV000246117.1|RCV000328056.1|RCV000384790.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0238358:ORPHA681|C0024591:ORPHA423;PopFreqMax=0.29;Kaviar_AF=0.0642553;Kaviar_AC=9934;Kaviar_AN=154602;ExAC_ALL=0.0656;ExAC_AFR=0.2669;ExAC_AMR=0.0327;ExAC_EAS=0.0020;ExAC_FIN=0.0614;ExAC_NFE=0.0560;ExAC_OTH=0.0452;ExAC_SAS=0.0369;1000g2014oct_all=0.0996406;snp138=rs13374149;SIFT_score=0.31;SIFT_converted_rankscore=0.174;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_rankscore=0.026;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.0;Polyphen2_HVAR_rankscore=0.013;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.002;LRT_pred=U;MutationTaster_score=1;MutationTaster_converted_rankscore=0.090;MutationTaster_pred=P;MutationAssessor_score=1.955;MutationAssessor_score_rankscore=0.530;MutationAssessor_pred=M;FATHMM_score=-3.88;FATHMM_converted_rankscore=0.962;FATHMM_pred=D;PROVEAN_score=1.25;PROVEAN_converted_rankscore=0.011;PROVEAN_pred=N;VEST3_score=0.068;VEST3_rankscore=0.055;MetaSVM_score=-0.887;MetaSVM_rankscore=0.492;MetaSVM_pred=T;MetaLR_score=0.000;MetaLR_rankscore=0.002;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=3.607;CADD_raw_rankscore=0.491;CADD_phred=23.2;DANN_score=0.968;DANN_rankscore=0.305;fathmm-MKL_coding_score=0.211;fathmm-MKL_coding_rankscore=0.211;fathmm-MKL_coding_pred=N;Eigen_coding_or_noncoding=c;Eigen-raw=-0.622;Eigen-PC-raw=-0.571;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.517;integrated_fitCons_score=0.556;integrated_fitCons_score_rankscore=0.300;integrated_confidence_value=0;GERP++_RS=1.62;GERP++_RS_rankscore=0.227;phyloP100way_vertebrate=-0.253;phyloP100way_vertebrate_rankscore=0.087;phyloP20way_mammalian=0.911;phyloP20way_mammalian_rankscore=0.421;phastCons100way_vertebrate=0.009;phastCons100way_vertebrate_rankscore=0.180;phastCons20way_mammalian=0.990;phastCons20way_mammalian_rankscore=0.544;SiPhy_29way_logOdds=6.677;SiPhy_29way_logOdds_rankscore=0.221;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.9789;dpsi_zscore=-1.459;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:245,219:464:99:5232,0,5645:54:99:0.472 0/1:171,229:400:99:5326,0,3803:53:99:0.573 ./.:.:.:.:.:.:.:. 0/1:206,210:416:99:5239,0,4957:57:99:0.505 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:244,231:475:99:5584,0,5964:57:99:0.486 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201012597 rs41267497 G A 3645.84 PASS BaseQRankSum=1.053;Dels=0;FS=4.74;HRun=0;HaplotypeScore=11.332;MQ=55;MQ0=0;MQRankSum=0.45;QD=13.82;ReadPosRankSum=1.971;SB=-982.35;TI=NM_000069;GI=CACNA1S;FC=Synonymous_P1620P;EXON;DP=1523;AN=12;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=CACNA1S:NM_000069:exon40:c.C4860T:p.P1620P;Func.knownGene=exonic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=CACNA1S:uc001gvv.3:exon40:c.C4860T:p.P1620P;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS1407.1:CCDS1407.1:exon40:c.C4860T:p.P1620P;cytoBand=1q32.1;CLINSIG=Benign|Benign|Benign;CLNDBN=not_specified|Hypokalemic_periodic_paralysis|Malignant_hyperthermia_susceptibility;CLNACC=RCV000254312.1|RCV000335360.1|RCV000373693.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0238358:ORPHA681|C0024591:ORPHA423;PopFreqMax=0.16;Kaviar_AF=0.108996;Kaviar_AC=16851;Kaviar_AN=154602;ExAC_ALL=0.1065;ExAC_AFR=0.0287;ExAC_AMR=0.0594;ExAC_EAS=0.0015;ExAC_FIN=0.1228;ExAC_NFE=0.1588;ExAC_OTH=0.0872;ExAC_SAS=0.0271;1000g2014oct_all=0.0461262;snp138=rs41267497;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.4428;dpsi_zscore=-1.031;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:79,91:172:99:2408,0,1946:55:99:0.535 0/1:150,141:291:99:3558,0,3590:57:99:0.485 0/1:129,123:252:99:3107,0,3143:55:99:0.488 0/1:131,133:264:99:3327,0,3220:55:99:0.504 0/1:124,133:257:99:3573,0,3241:57:99:0.518 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:136,150:286:99:3646,0,3222:54:99:0.524 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201016296 rs3850625 G A 6203.69 PASS BaseQRankSum=4.188;Dels=0;FS=1.039;HRun=0;HaplotypeScore=26.6944;MQ=57;MQ0=0;MQRankSum=3.524;QD=12.33;ReadPosRankSum=0.631;SB=-3850.37;TI=NM_000069;GI=CACNA1S;FC=Missense_R1539C;EXON;DP=503;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=CACNA1S:NM_000069:exon38:c.C4615T:p.R1539C;Func.knownGene=exonic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=CACNA1S:uc001gvv.3:exon38:c.C4615T:p.R1539C;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS1407.1:CCDS1407.1:exon38:c.C4615T:p.R1539C;cytoBand=1q32.1;CLINSIG=Benign|Benign|Benign;CLNDBN=not_specified|Hypokalemic_periodic_paralysis|Malignant_hyperthermia_susceptibility;CLNACC=RCV000177926.2|RCV000261312.1|RCV000358880.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0238358:ORPHA681|C0024591:ORPHA423;PopFreqMax=0.21;Kaviar_AF=0.114487;Kaviar_AC=17700;Kaviar_AN=154602;ExAC_ALL=0.1172;ExAC_AFR=0.0207;ExAC_AMR=0.1005;ExAC_EAS=0.0362;ExAC_FIN=0.1495;ExAC_NFE=0.1185;ExAC_OTH=0.1413;ExAC_SAS=0.2129;1000g2014oct_all=0.0840655;snp138=rs3850625;SIFT_score=0.008;SIFT_converted_rankscore=0.586;SIFT_pred=D;Polyphen2_HDIV_score=0.736;Polyphen2_HDIV_rankscore=0.409;Polyphen2_HDIV_pred=P;Polyphen2_HVAR_score=0.299;Polyphen2_HVAR_rankscore=0.393;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_converted_rankscore=0.843;LRT_pred=D;MutationTaster_score=0.000;MutationTaster_converted_rankscore=0.588;MutationTaster_pred=P;MutationAssessor_score=2.02;MutationAssessor_score_rankscore=0.555;MutationAssessor_pred=M;FATHMM_score=-0.47;FATHMM_converted_rankscore=0.701;FATHMM_pred=T;PROVEAN_score=-7.11;PROVEAN_converted_rankscore=0.940;PROVEAN_pred=D;VEST3_score=0.226;VEST3_rankscore=0.277;MetaSVM_score=-0.915;MetaSVM_rankscore=0.462;MetaSVM_pred=T;MetaLR_score=0.006;MetaLR_rankscore=0.021;MetaLR_pred=T;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=7.420;CADD_raw_rankscore=0.951;CADD_phred=34;DANN_score=0.999;DANN_rankscore=0.977;fathmm-MKL_coding_score=0.960;fathmm-MKL_coding_rankscore=0.666;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.412;Eigen-PC-raw=0.501;GenoCanyon_score=0.033;GenoCanyon_score_rankscore=0.141;integrated_fitCons_score=0.497;integrated_fitCons_score_rankscore=0.185;integrated_confidence_value=0;GERP++_RS=5.17;GERP++_RS_rankscore=0.707;phyloP100way_vertebrate=7.708;phyloP100way_vertebrate_rankscore=0.835;phyloP20way_mammalian=1.048;phyloP20way_mammalian_rankscore=0.713;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=1.000;phastCons20way_mammalian_rankscore=0.888;SiPhy_29way_logOdds=19.012;SiPhy_29way_logOdds_rankscore=0.928;Interpro_domain=Voltage-dependent_calcium_channel,_alpha-1_subunit,_IQ_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3036;dpsi_zscore=-0.859;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:259,244:503:99:6204,0,6463:57:99:0.485 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201016646 rs2297905 C T 3441.36 PASS BaseQRankSum=2.312;Dels=0;FS=0.501;HRun=0;HaplotypeScore=8.3615;MQ=55;MQ0=0;MQRankSum=-0.303;QD=11.44;ReadPosRankSum=-0.452;SB=-1556.89;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=543;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=Benign|Benign|Benign;CLNDBN=not_specified|Malignant_hyperthermia_susceptibility|Hypokalemic_periodic_paralysis;CLNACC=RCV000248202.1|RCV000267150.1|RCV000322159.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0024591:ORPHA423|C0238358:ORPHA681;PopFreqMax=0.4;Kaviar_AF=0.132152;Kaviar_AC=20431;Kaviar_AN=154602;ExAC_ALL=0.1345;ExAC_AFR=0.3691;ExAC_AMR=0.0708;ExAC_EAS=0.1348;ExAC_FIN=0.1413;ExAC_NFE=0.1258;ExAC_OTH=0.1261;ExAC_SAS=0.0634;1000g2014oct_all=0.171925;snp138=rs2297905;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.3305;dpsi_zscore=0.934;dbscSNV_ADA_SCORE=0;dbscSNV_RF_SCORE=0;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:115,99:214:99:2477,0,2782:55:99:0.463 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:191,138:329:99:3441,0,4626:56:99:0.419
chr1 201017687 rs35713982 C CT 4190.99 PASS BaseQRankSum=-1.104;FS=3.713;HRun=1;HaplotypeScore=121.071;MQ=58;MQ0=0;MQRankSum=2.047;QD=14.85;ReadPosRankSum=-0.299;SB=-1434.45;TI=NM_000069;GI=CACNA1S;FC=Noncoding;DP=478;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.31;Kaviar_AF=0.003758;Kaviar_AC=581;Kaviar_AN=154602;ExAC_ALL=0.1285;ExAC_AFR=0.2910;ExAC_AMR=0.0684;ExAC_EAS=0.1410;ExAC_FIN=0.1405;ExAC_NFE=0.1258;ExAC_OTH=0.1239;ExAC_SAS=0.0688;1000g2014oct_all=0.149561;snp138=rs35713982;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=.;dpsi_zscore=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:136,98:234:99:3474,0,4926:58:99:0.419 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:128,116:244:99:4191,0,4654:57:99:0.475
chr1 201019652 rs373675720 A G 3415.72 PASS BaseQRankSum=5.506;Dels=0;FS=1.494;HRun=1;HaplotypeScore=8.2153;MQ=57;MQ0=0;MQRankSum=0.457;QD=12.42;ReadPosRankSum=0.347;SB=-1913.63;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=275;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.0013;Kaviar_AF=0.0004981;Kaviar_AC=77;Kaviar_AN=154602;ExAC_ALL=0.0004;ExAC_AFR=0.0002;ExAC_AMR=0;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0007;ExAC_OTH=0;ExAC_SAS=0;1000g2014oct_all=.;snp138=rs373675720;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.9897;dpsi_zscore=-1.465;dbscSNV_ADA_SCORE=0.0001;dbscSNV_RF_SCORE=0.002;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:134,141:275:99:3416,0,3016:57:99:0.513 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201020105 rs6702590 A G 8188.48 PASS BaseQRankSum=0.544;Dels=0;FS=4.842;HRun=0;HaplotypeScore=12.9032;MQ=56;MQ0=0;MQRankSum=0.656;QD=12.36;ReadPosRankSum=-1.141;SB=-2500.23;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=3361;AN=24;AC=16;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=Benign|Benign|Benign;CLNDBN=not_specified|Malignant_hyperthermia_susceptibility|Hypokalemic_periodic_paralysis;CLNACC=RCV000181033.2|RCV000305099.1|RCV000390372.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0024591:ORPHA423|C0238358:ORPHA681;PopFreqMax=0.99;Kaviar_AF=0.752002;Kaviar_AC=116261;Kaviar_AN=154602;ExAC_ALL=0.7705;ExAC_AFR=0.9334;ExAC_AMR=0.8842;ExAC_EAS=0.9947;ExAC_FIN=0.7691;ExAC_NFE=0.6727;ExAC_OTH=0.7852;ExAC_SAS=0.8657;1000g2014oct_all=0.880391;snp138=rs6702590;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0436;dpsi_zscore=-0.236;dbscSNV_ADA_SCORE=0;dbscSNV_RF_SCORE=0;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:171,174:345:99:4263,0,3939:56:99:0.504 1/1:0,297:300:99:8188,587,0:54:99:1 0/1:99,88:187:99:2225,0,2604:56:99:0.471 0/1:168,153:321:99:3787,0,4022:57:99:0.477 0/1:161,138:299:99:3271,0,4019:55:99:0.462 0/1:134,133:267:99:3276,0,3332:55:99:0.498 0/1:155,175:331:99:4161,0,3899:56:99:0.53 1/1:0,235:236:99:6983,509,0:57:99:1 0/1:162,154:317:99:3797,0,4082:56:99:0.487 0/1:153,125:278:99:2814,0,3761:53:99:0.45 1/1:0,243:243:99:6078,424,0:53:99:1 1/1:1,235:237:99:7164,494,0:56:99:0.996
chr1 201020360 rs12138260 G A 2299.36 PASS BaseQRankSum=1.043;Dels=0;FS=14.175;HRun=1;HaplotypeScore=1.7882;MQ=57;MQ0=0;MQRankSum=2.743;QD=13.33;ReadPosRankSum=-0.943;SB=-657.5;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=857;AN=12;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.15;Kaviar_AF=0.0250514;Kaviar_AC=3873;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.0459265;snp138=rs12138260;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1534;dpsi_zscore=-0.589;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:44,49:93:99:1270,0,1291:57:99:0.527 0/1:67,71:138:99:1991,0,1748:58:99:0.514 0/1:75,77:152:99:1971,0,1960:58:99:0.507 0/1:70,70:140:99:1805,0,1944:57:99:0.5 0/1:101,89:191:99:2329,0,2607:58:99:0.468 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:53,90:143:99:2265,0,1383:55:99:0.629 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201021619 rs12029212 C G 2485.22 PASS BaseQRankSum=0.217;Dels=0;FS=3.706;HRun=0;HaplotypeScore=35.6672;MQ=56;MQ0=0;MQRankSum=0.859;QD=10.15;ReadPosRankSum=-1.004;SB=-257.13;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=874;AN=12;AC=6;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.69;Kaviar_AF=0.0384471;Kaviar_AC=5944;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.27516;snp138=rs12029212;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.5073;dpsi_zscore=1.139;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:80,52:135:99:1401,0,2374:56:99:0.394 0/1:68,79:149:99:2195,0,1783:53:99:0.537 0/1:60,52:114:99:1432,0,1707:53:99:0.464 0/1:69,85:155:99:2340,0,1904:55:99:0.552 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:98,94:194:99:2515,0,2725:55:99:0.49 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:53,73:127:99:2071,0,1458:55:99:0.579
chr1 201022762 . A G 22.21 LowVariantFreq;SB BaseQRankSum=-5.137;Dels=0;FS=17.118;HRun=4;HaplotypeScore=37.6587;MQ=51;MQ0=0;MQRankSum=-0.972;QD=0.24;ReadPosRankSum=2.123;SB=-0.01;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=92;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.2183;dpsi_zscore=0.757;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:74,17:92:52.17:52,0,1913:51:22:0.187 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201028466 rs73075033 G A 2859.9 PASS BaseQRankSum=1.095;Dels=0;FS=0.504;HRun=0;HaplotypeScore=16.4951;MQ=58;MQ0=0;MQRankSum=1.416;QD=12.6;ReadPosRankSum=0.438;SB=-1504.51;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=227;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.26;Kaviar_AF=0.0278716;Kaviar_AC=4309;Kaviar_AN=154602;ExAC_ALL=0.0300;ExAC_AFR=0.2399;ExAC_AMR=0.0156;ExAC_EAS=0.0004;ExAC_FIN=0.0309;ExAC_NFE=0.0093;ExAC_OTH=0.0171;ExAC_SAS=0.0044;1000g2014oct_all=0.0732827;snp138=rs73075033;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0111;dpsi_zscore=-0.045;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:111,116:227:99:2890,0,2641:58:99:0.511 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201029939 rs34515088 T C 4203.11 PASS BaseQRankSum=2.236;Dels=0;FS=0.393;HRun=0;HaplotypeScore=14.6122;MQ=56;MQ0=0;MQRankSum=2.827;QD=12.36;ReadPosRankSum=0.158;SB=-2769.1;TI=NM_000069;GI=CACNA1S;FC=Synonymous_Q1087Q;EXON;DP=340;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=CACNA1S:NM_000069:exon26:c.A3261G:p.Q1087Q;Func.knownGene=exonic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=CACNA1S:uc001gvv.3:exon26:c.A3261G:p.Q1087Q;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS1407.1:CCDS1407.1:exon26:c.A3261G:p.Q1087Q;cytoBand=1q32.1;CLINSIG=Benign|Likely_benign|Likely_benign;CLNDBN=not_specified|Hypokalemic_periodic_paralysis|Malignant_hyperthermia_susceptibility;CLNACC=RCV000249689.1|RCV000308056.1|RCV000395292.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0238358:ORPHA681|C0024591:ORPHA423;PopFreqMax=0.02;Kaviar_AF=0.008952;Kaviar_AC=1384;Kaviar_AN=154602;ExAC_ALL=0.0088;ExAC_AFR=0.0024;ExAC_AMR=0.0053;ExAC_EAS=0;ExAC_FIN=0.0057;ExAC_NFE=0.0135;ExAC_OTH=0.0033;ExAC_SAS=0.0022;1000g2014oct_all=0.00459265;snp138=rs34515088;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.7632;dpsi_zscore=-1.318;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:170,169:340:99:4203,0,4304:56:99:0.499 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201030668 rs2297904 G A 1968.56 PASS BaseQRankSum=-1.089;Dels=0;FS=1.522;HRun=0;HaplotypeScore=2.8805;MQ=58;MQ0=0;MQRankSum=-0.477;QD=14.58;ReadPosRankSum=1.298;SB=-714.68;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=528;AN=8;AC=4;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.43;Kaviar_AF=0.0271665;Kaviar_AC=4200;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.265775;snp138=rs2297904;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.2323;dpsi_zscore=-0.746;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:59,76:135:99:1999,0,1507:58:99:0.563 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:67,57:124:99:1447,0,1792:58:99:0.46 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:52,59:111:99:1624,0,1261:58:99:0.532 0/1:93,65:158:99:1695,0,2563:59:99:0.411 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201031059 rs41267501 A G 3873.16 PASS BaseQRankSum=1.359;Dels=0;FS=1.952;HRun=1;HaplotypeScore=6.5753;MQ=58;MQ0=0;MQRankSum=2.045;QD=12.91;ReadPosRankSum=-2.066;SB=-1985.63;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=300;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=Benign|Likely_benign|Likely_benign;CLNDBN=not_specified|Hypokalemic_periodic_paralysis|Malignant_hyperthermia_susceptibility;CLNACC=RCV000244931.1|RCV000263066.1|RCV000299531.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0238358:ORPHA681|C0024591:ORPHA423;PopFreqMax=0.035;Kaviar_AF=0.0170114;Kaviar_AC=2630;Kaviar_AN=154602;ExAC_ALL=0.0179;ExAC_AFR=0.0024;ExAC_AMR=0.0076;ExAC_EAS=0.0003;ExAC_FIN=0.0232;ExAC_NFE=0.0196;ExAC_OTH=0.0233;ExAC_SAS=0.0350;1000g2014oct_all=0.0115815;snp138=rs41267501;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.3259;dpsi_zscore=-0.891;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:149,151:300:99:3873,0,3668:58:99:0.503 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201031307 rs2297903 A C 4112.42 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=3.6546;MQ=58;MQ0=0;QD=28.61;SB=-1604.35;TI=NM_000069;GI=CACNA1S;FC=Silent;BaseQRankSum=0.336;MQRankSum=1.947;ReadPosRankSum=0.162;DP=1069;AN=16;AC=11;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.76;Kaviar_AF=0.537997;Kaviar_AC=14003;Kaviar_AN=26028;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.61242;snp138=rs2297903;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-1.4842;dpsi_zscore=-1.709;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. 1/1:0,129:129:99:3691,268,0:58:99:1 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:70,55:126:99:1368,0,1959:58:99:0.44 0/1:65,86:152:99:2274,0,1711:58:99:0.57 ./.:.:.:.:.:.:.:. 1/1:0,127:127:99:4112,304,0:57:99:1 0/1:77,76:153:99:2075,0,2261:59:99:0.497 0/1:77,61:138:99:1518,0,2149:56:99:0.442 1/1:0,110:111:99:3053,217,0:55:99:1 0/1:62,69:132:99:1902,0,1732:59:99:0.527
chr1 201035087 rs113792034 G A 3395.95 PASS BaseQRankSum=-0.727;Dels=0;FS=0;HRun=0;HaplotypeScore=16.5583;MQ=57;MQ0=0;MQRankSum=0.855;QD=12.58;ReadPosRankSum=-1.081;SB=-2199.66;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=472;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=Benign|Likely_benign|Likely_benign;CLNDBN=not_specified|Malignant_hyperthermia_susceptibility|Hypokalemic_periodic_paralysis;CLNACC=RCV000243661.1|RCV000268269.1|RCV000353533.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0024591:ORPHA423|C0238358:ORPHA681;PopFreqMax=0.082;Kaviar_AF=0.0360151;Kaviar_AC=5568;Kaviar_AN=154602;ExAC_ALL=0.0462;ExAC_AFR=0.0362;ExAC_AMR=0.0255;ExAC_EAS=0.0017;ExAC_FIN=0.0815;ExAC_NFE=0.0563;ExAC_OTH=0.0344;ExAC_SAS=0.0350;1000g2014oct_all=0.0265575;snp138=rs113792034;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1818;dpsi_zscore=-0.650;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:131,139:270:99:3396,0,3146:57:99:0.515 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:101,101:202:99:2420,0,2497:57:99:0.5 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201035488 rs41267503 A T 2125.8 PASS BaseQRankSum=1.371;Dels=0;FS=1.337;HRun=0;HaplotypeScore=12.8503;MQ=55;MQ0=0;MQRankSum=1.995;QD=13.37;ReadPosRankSum=-1.667;SB=-893.09;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=320;AN=4;AC=2;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.091;Kaviar_AF=0.0340552;Kaviar_AC=5265;Kaviar_AN=154602;ExAC_ALL=0.0354;ExAC_AFR=0.0326;ExAC_AMR=0.0190;ExAC_EAS=0.0002;ExAC_FIN=0.0906;ExAC_NFE=0.0449;ExAC_OTH=0.0444;ExAC_SAS=0.0077;1000g2014oct_all=0.0217652;snp138=rs41267503;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.0754;dpsi_zscore=0.401;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:74,84:159:99:2156,0,1882:55:99:0.532 0/1:77,84:161:99:2119,0,1954:57:99:0.522 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201038643 . A C 4740.53 PASS BaseQRankSum=2.428;Dels=0;FS=0.783;HRun=2;HaplotypeScore=11.2001;MQ=57;MQ0=0;MQRankSum=-1.186;QD=12.64;ReadPosRankSum=-0.742;SB=-3221.5;TI=NM_000069;GI=CACNA1S;FC=Missense_L816R;EXON;DP=375;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=CACNA1S:NM_000069:exon18:c.T2447G:p.L816R;Func.knownGene=exonic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=CACNA1S:uc001gvv.3:exon18:c.T2447G:p.L816R;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS1407.1:CCDS1407.1:exon18:c.T2447G:p.L816R;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=.;Kaviar_AF=.;Kaviar_AC=.;Kaviar_AN=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=.;snp138=.;SIFT_score=0.0;SIFT_converted_rankscore=0.912;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_rankscore=0.899;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.999;Polyphen2_HVAR_rankscore=0.916;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_converted_rankscore=0.629;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_converted_rankscore=0.588;MutationTaster_pred=D;MutationAssessor_score=3.635;MutationAssessor_score_rankscore=0.942;MutationAssessor_pred=H;FATHMM_score=-4.6;FATHMM_converted_rankscore=0.979;FATHMM_pred=D;PROVEAN_score=-5.61;PROVEAN_converted_rankscore=0.867;PROVEAN_pred=D;VEST3_score=0.934;VEST3_rankscore=0.927;MetaSVM_score=1.088;MetaSVM_rankscore=0.992;MetaSVM_pred=D;MetaLR_score=0.967;MetaLR_rankscore=0.990;MetaLR_pred=D;M-CAP_score=0.212;M-CAP_rankscore=0.874;M-CAP_pred=D;CADD_raw=5.186;CADD_raw_rankscore=0.700;CADD_phred=25.5;DANN_score=0.998;DANN_rankscore=0.849;fathmm-MKL_coding_score=0.987;fathmm-MKL_coding_rankscore=0.853;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.706;Eigen-PC-raw=0.522;GenoCanyon_score=1.000;GenoCanyon_score_rankscore=0.480;integrated_fitCons_score=0.447;integrated_fitCons_score_rankscore=0.083;integrated_confidence_value=0;GERP++_RS=3.91;GERP++_RS_rankscore=0.442;phyloP100way_vertebrate=9.114;phyloP100way_vertebrate_rankscore=0.936;phyloP20way_mammalian=1.187;phyloP20way_mammalian_rankscore=0.908;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.393;phastCons20way_mammalian_rankscore=0.253;SiPhy_29way_logOdds=13.039;SiPhy_29way_logOdds_rankscore=0.581;Interpro_domain=Ion_transport_domain;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1103;dpsi_zscore=-0.479;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=0.211746141449;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:181,194:375:99:4741,0,4528:57:99:0.517 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201038687 rs7415038 A G 9734 PASS BaseQRankSum=2.718;Dels=0;FS=0.805;HRun=0;HaplotypeScore=7.2583;MQ=56;MQ0=0;MQRankSum=1.584;QD=12.1;ReadPosRankSum=1.698;SB=-2599.94;TI=NM_000069;GI=CACNA1S;FC=Synonymous_F801F;EXON;DP=2688;AN=18;AC=13;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=CACNA1S:NM_000069:exon18:c.T2403C:p.F801F;Func.knownGene=exonic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=CACNA1S:uc001gvv.3:exon18:c.T2403C:p.F801F;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS1407.1:CCDS1407.1:exon18:c.T2403C:p.F801F;cytoBand=1q32.1;CLINSIG=Benign|Benign|Benign;CLNDBN=not_specified|Malignant_hyperthermia_susceptibility|Hypokalemic_periodic_paralysis;CLNACC=RCV000252908.1|RCV000276522.1|RCV000333904.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0024591:ORPHA423|C0238358:ORPHA681;PopFreqMax=0.55;Kaviar_AF=0.283839;Kaviar_AC=43882;Kaviar_AN=154602;ExAC_ALL=0.4034;ExAC_AFR=0.5478;ExAC_AMR=0.2963;ExAC_EAS=0.0181;ExAC_FIN=0.4183;ExAC_NFE=0.4924;ExAC_OTH=0.3448;ExAC_SAS=0.1984;1000g2014oct_all=0.294129;snp138=rs7415038;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1435;dpsi_zscore=-0.566;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:184,170:355:99:4297,0,4648:56:99:0.48 ./.:.:.:.:.:.:.:. 1/1:2,260:262:99:7018,461,0:54:99:0.992 0/1:181,146:328:99:3617,0,4644:57:99:0.446 0/1:148,161:309:99:3977,0,3460:55:99:0.521 0/1:138,151:289:99:3809,0,3302:56:99:0.522 1/1:0,338:339:99:9734,701,0:56:99:1 1/1:0,254:254:99:7418,542,0:57:99:1 ./.:.:.:.:.:.:.:. 1/1:0,301:301:99:8371,599,0:55:99:1 ./.:.:.:.:.:.:.:. 0/1:136,115:251:99:2736,0,3338:55:99:0.458
chr1 201039476 . C G 2634.29 PASS BaseQRankSum=1.279;Dels=0;FS=8.118;HRun=1;HaplotypeScore=10.1349;MQ=56;MQ0=0;MQRankSum=1.235;QD=13.3;ReadPosRankSum=-0.242;SB=-1609.05;TI=NM_000069;GI=CACNA1S;FC=Missense_A762P;EXON;DP=198;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=CACNA1S:NM_000069:exon17:c.G2284C:p.A762P;Func.knownGene=exonic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=nonsynonymous_SNV;AAChange.knownGene=CACNA1S:uc001gvv.3:exon17:c.G2284C:p.A762P;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=nonsynonymous_SNV;AAChange.ccdsGene=CCDS1407.1:CCDS1407.1:exon17:c.G2284C:p.A762P;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.0001;Kaviar_AF=6.5e-06;Kaviar_AC=1;Kaviar_AN=154602;ExAC_ALL=8.242e-06;ExAC_AFR=0;ExAC_AMR=0;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0;ExAC_OTH=0;ExAC_SAS=6.056e-05;1000g2014oct_all=.;snp138=.;SIFT_score=0.003;SIFT_converted_rankscore=0.682;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_rankscore=0.899;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.999;Polyphen2_HVAR_rankscore=0.916;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_converted_rankscore=0.843;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_converted_rankscore=0.499;MutationTaster_pred=D;MutationAssessor_score=2.32;MutationAssessor_score_rankscore=0.666;MutationAssessor_pred=M;FATHMM_score=-3.86;FATHMM_converted_rankscore=0.962;FATHMM_pred=D;PROVEAN_score=-2.49;PROVEAN_converted_rankscore=0.553;PROVEAN_pred=N;VEST3_score=0.733;VEST3_rankscore=0.731;MetaSVM_score=1.052;MetaSVM_rankscore=0.982;MetaSVM_pred=D;MetaLR_score=0.929;MetaLR_rankscore=0.976;MetaLR_pred=D;M-CAP_score=0.173;M-CAP_rankscore=0.850;M-CAP_pred=D;CADD_raw=5.408;CADD_raw_rankscore=0.733;CADD_phred=26.0;DANN_score=0.998;DANN_rankscore=0.842;fathmm-MKL_coding_score=0.920;fathmm-MKL_coding_rankscore=0.544;fathmm-MKL_coding_pred=D;Eigen_coding_or_noncoding=c;Eigen-raw=0.556;Eigen-PC-raw=0.430;GenoCanyon_score=0.314;GenoCanyon_score_rankscore=0.193;integrated_fitCons_score=0.447;integrated_fitCons_score_rankscore=0.083;integrated_confidence_value=0;GERP++_RS=4.18;GERP++_RS_rankscore=0.483;phyloP100way_vertebrate=2.558;phyloP100way_vertebrate_rankscore=0.453;phyloP20way_mammalian=0.843;phyloP20way_mammalian_rankscore=0.344;phastCons100way_vertebrate=1.000;phastCons100way_vertebrate_rankscore=0.715;phastCons20way_mammalian=0.905;phastCons20way_mammalian_rankscore=0.384;SiPhy_29way_logOdds=12.048;SiPhy_29way_logOdds_rankscore=0.526;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.1046;dpsi_zscore=-0.463;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=0.172599277469;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:96,102:198:99:2664,0,2545:56:99:0.515
chr1 201042618 rs9333652 G A 3788.86 PASS BaseQRankSum=-0.24;Dels=0;FS=0.439;HRun=2;HaplotypeScore=22.0819;MQ=56;MQ0=0;MQRankSum=0.369;QD=10.61;ReadPosRankSum=-0.656;SB=-1724.14;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=2249;AN=16;AC=8;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.96;Kaviar_AF=0.0795527;Kaviar_AC=12299;Kaviar_AN=154602;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;1000g2014oct_all=0.591254;snp138=rs9333652;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0289;dpsi_zscore=-0.158;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:170,124:297:99:3181,0,4110:56:99:0.422 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:144,125:271:99:3090,0,3567:57:99:0.465 0/1:143,133:276:99:3155,0,3640:55:99:0.482 0/1:129,134:265:99:3268,0,3251:57:99:0.51 0/1:157,149:306:99:3789,0,3826:57:99:0.487 ./.:.:.:.:.:.:.:. 0/1:178,150:328:99:3635,0,4276:57:99:0.457 ./.:.:.:.:.:.:.:. 0/1:149,133:283:99:2945,0,3198:51:99:0.472 0/1:121,102:223:99:2476,0,2997:55:99:0.457
chr1 201043627 rs79984703 C A 4017.97 PASS BaseQRankSum=1.804;Dels=0;FS=1.824;HRun=1;HaplotypeScore=7.1979;MQ=51;MQ0=0;MQRankSum=0.613;QD=12.07;ReadPosRankSum=-0.195;SB=-2987.71;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=333;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=Benign|Likely_benign|Likely_benign;CLNDBN=not_specified|Malignant_hyperthermia_susceptibility|Hypokalemic_periodic_paralysis;CLNACC=RCV000246825.1|RCV000286777.1|RCV000378785.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0024591:ORPHA423|C0238358:ORPHA681;PopFreqMax=0.077;Kaviar_AF=0.0251679;Kaviar_AC=3891;Kaviar_AN=154602;ExAC_ALL=0.0302;ExAC_AFR=0.0070;ExAC_AMR=0.0107;ExAC_EAS=0.0009;ExAC_FIN=0.0768;ExAC_NFE=0.0369;ExAC_OTH=0.0276;ExAC_SAS=0.0290;1000g2014oct_all=0.0147764;snp138=rs79984703;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.6874;dpsi_zscore=-1.259;dbscSNV_ADA_SCORE=0.0004;dbscSNV_RF_SCORE=0.032;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:153,179:333:99:4018,0,3325:51:99:0.539 ./.:.:.:.:.:.:.:.
chr1 201043702 rs16847664 G A 6413.62 PASS BaseQRankSum=3.324;Dels=0;FS=0.645;HRun=0;HaplotypeScore=26.6663;MQ=58;MQ0=0;MQRankSum=1.262;QD=11.97;ReadPosRankSum=-1.801;SB=-4279.72;TI=NM_000069;GI=CACNA1S;FC=Synonymous_A665A;EXON;DP=536;AN=2;AC=1;ANNOVAR_DATE=2016-05-11;Func.refGene=exonic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=synonymous_SNV;AAChange.refGene=CACNA1S:NM_000069:exon14:c.C1995T:p.A665A;Func.knownGene=exonic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=synonymous_SNV;AAChange.knownGene=CACNA1S:uc001gvv.3:exon14:c.C1995T:p.A665A;Func.ccdsGene=exonic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=synonymous_SNV;AAChange.ccdsGene=CCDS1407.1:CCDS1407.1:exon14:c.C1995T:p.A665A;cytoBand=1q32.1;CLINSIG=Benign|Likely_benign|Likely_benign;CLNDBN=not_specified|Malignant_hyperthermia_susceptibility|Hypokalemic_periodic_paralysis;CLNACC=RCV000249871.1|RCV000290309.1|RCV000347584.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0024591:ORPHA423|C0238358:ORPHA681;PopFreqMax=0.066;Kaviar_AF=0.0067464;Kaviar_AC=1043;Kaviar_AN=154602;ExAC_ALL=0.0072;ExAC_AFR=0.0609;ExAC_AMR=0.0032;ExAC_EAS=0;ExAC_FIN=0.0002;ExAC_NFE=0.0031;ExAC_OTH=0.0023;ExAC_SAS=0;1000g2014oct_all=0.0181709;snp138=rs16847664;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-3.4800;dpsi_zscore=-2.254;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:274,262:536:99:6414,0,6329:58:99:0.489 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.
chr1 201044583 . T C 608.15 SB;LowVariantFreq;LowGQX BaseQRankSum=-7.186;Dels=0;FS=238.386;HRun=5;HaplotypeScore=160.884;MQ=42;MQ0=0;MQRankSum=-5.447;QD=1.46;ReadPosRankSum=-5.295;SB=-0.01;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=1792;AN=18;AC=9;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.06;Kaviar_AF=6.5e-06;Kaviar_AC=1;Kaviar_AN=154602;ExAC_ALL=0.0346;ExAC_AFR=0.0034;ExAC_AMR=0.0008;ExAC_EAS=0.0054;ExAC_FIN=0.0150;ExAC_NFE=0.0603;ExAC_OTH=0.0246;ExAC_SAS=0.0006;1000g2014oct_all=.;snp138=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=0.5628;dpsi_zscore=1.194;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:163,50:219:99:351,0,4474:42:99:0.235 0/1:170,35:209:99:214,0,4979:41:99:0.171 0/1:124,47:172:99:638,0,3289:40:99:0.275 ./.:.:.:.:.:.:.:. 0/1:159,35:198:48.02:48,0,4305:43:18:0.18 0/1:116,31:153:37.07:37,0,3090:45:8:0.211 0/1:191,37:235:99:133,0,5385:43:99:0.162 0/1:147,37:188:99:134,0,4140:44:99:0.201 0/1:184,51:240:99:237,0,5190:41:99:0.217 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:129,42:173:99:196,0,3488:43:99:0.246
chr1 201044748 rs1998721 A G 13354.7 PASS Dels=0;FS=0;HRun=0;HaplotypeScore=19.9239;MQ=54;MQ0=0;QD=27.33;SB=-8862.08;TI=NM_000069;GI=CACNA1S;FC=Silent;BaseQRankSum=1.718;MQRankSum=-0.497;ReadPosRankSum=0.27;DP=4231;AN=22;AC=18;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=Benign|Benign|Benign;CLNDBN=not_specified|Hypokalemic_periodic_paralysis|Malignant_hyperthermia_susceptibility;CLNACC=RCV000254042.1|RCV000345729.1|RCV000388676.1;CLNDSDB=MedGen|MedGen:Orphanet|MedGen:Orphanet;CLNDSDBID=CN169374|C0238358:ORPHA681|C0024591:ORPHA423;PopFreqMax=0.96;Kaviar_AF=0.772034;Kaviar_AC=119358;Kaviar_AN=154602;ExAC_ALL=0.7814;ExAC_AFR=0.5465;ExAC_AMR=0.7180;ExAC_EAS=0.9570;ExAC_FIN=0.7842;ExAC_NFE=0.7783;ExAC_OTH=0.7815;ExAC_SAS=0.8930;1000g2014oct_all=0.759585;snp138=rs1998721;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=2.2871;dpsi_zscore=2.055;dbscSNV_ADA_SCORE=0.0001;dbscSNV_RF_SCORE=0.002;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,470:470:99:12846,939,0:54:99:1 ./.:.:.:.:.:.:.:. 1/1:1,243:244:99:6823,515,0:50:99:0.996 1/1:0,368:368:99:9997,731,0:55:99:1 0/1:190,205:396:99:4945,0,4562:53:99:0.519 0/1:180,172:354:99:4068,0,4103:54:99:0.489 1/1:0,486:486:99:13355,981,0:54:99:1 1/1:1,315:316:99:9050,641,0:53:99:0.997 0/1:256,262:519:99:6137,0,6019:54:99:0.506 1/1:0,369:369:99:9609,686,0:53:99:1 0/1:182,186:368:99:3808,0,3886:49:99:0.505 1/1:2,338:341:99:9104,626,0:52:99:0.994
chr1 201046025 rs7549030 G T 4384.73 PASS BaseQRankSum=1.44;Dels=0;FS=0;HRun=0;HaplotypeScore=11.0354;MQ=55;MQ0=0;MQRankSum=3.432;QD=12.66;ReadPosRankSum=-0.608;SB=-2627.01;TI=NM_000069;GI=CACNA1S;FC=Silent;DP=1003;AN=6;AC=3;ANNOVAR_DATE=2016-05-11;Func.refGene=intronic;Gene.refGene=CACNA1S;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.knownGene=intronic;Gene.knownGene=CACNA1S;GeneDetail.knownGene=.;ExonicFunc.knownGene=.;AAChange.knownGene=.;Func.ccdsGene=intronic;Gene.ccdsGene=CCDS1407.1;GeneDetail.ccdsGene=.;ExonicFunc.ccdsGene=.;AAChange.ccdsGene=.;cytoBand=1q32.1;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;PopFreqMax=0.08;Kaviar_AF=0.0583628;Kaviar_AC=9023;Kaviar_AN=154602;ExAC_ALL=0.0602;ExAC_AFR=0.0756;ExAC_AMR=0.0366;ExAC_EAS=0.0002;ExAC_FIN=0.0797;ExAC_NFE=0.0765;ExAC_OTH=0.0705;ExAC_SAS=0.0245;1000g2014oct_all=0.0457268;snp138=rs7549030;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dpsi_max_tissue=-0.0207;dpsi_zscore=-0.109;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;MCAP=.;ALLELE_END GT:AD:DP:GQ:PL:MQ:GQX:VF ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. 0/1:144,167:312:99:3951,0,3298:55:99:0.537 0/1:199,128:329:99:3032,0,4893:56:99:0.391 0/1:181,180:362:99:4385,0,4417:56:99:0.499 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.