diff --git a/tests/test_sgkit.py b/tests/test_sgkit.py
index 0940e8b6..b930263a 100644
--- a/tests/test_sgkit.py
+++ b/tests/test_sgkit.py
@@ -527,6 +527,7 @@ def test_ancestral_missingness(tmp_path):
     ancestral_allele = ds.variant_ancestral_allele.values
     ancestral_allele[0] = "N"
     ancestral_allele[11] = "-"
+    ancestral_allele[12] = "💩"
     ancestral_allele[15] = "💩"
     ds = ds.drop_vars(["variant_ancestral_allele"])
     sgkit.save_dataset(ds, str(zarr_path) + ".tmp")
@@ -538,19 +539,16 @@ def test_ancestral_missingness(tmp_path):
     )
     ds = sgkit.load_dataset(str(zarr_path) + ".tmp")
     sd = tsinfer.SgkitSampleData(str(zarr_path) + ".tmp")
-    with pytest.warns(UserWarning, match="The following alleles were not found"):
+    with pytest.warns(
+        UserWarning,
+        match=r"not found in the variant_allele array for the 4 [\s\S]*'💩': 2",
+    ):
         inf_ts = tsinfer.infer(sd)
-    for i, (
-        inf_var,
-        var,
-    ) in enumerate(zip(inf_ts.variants(), ts.variants())):
-        assert inf_var.site.ancestral_state == var.site.ancestral_state or i in [
-            0,
-            11,
-            15,
-        ]
-        if i in [0, 11, 15]:
+    for i, (inf_var, var) in enumerate(zip(inf_ts.variants(), ts.variants())):
+        if i in [0, 11, 12, 15]:
             assert inf_var.site.metadata == {"inference_type": "parsimony"}
+        else:
+            assert inf_var.site.ancestral_state == var.site.ancestral_state
 
 
 @pytest.mark.skipif(sys.platform == "win32", reason="File permission errors on Windows")
diff --git a/tsinfer/formats.py b/tsinfer/formats.py
index ee2125a9..5ae575b7 100644
--- a/tsinfer/formats.py
+++ b/tsinfer/formats.py
@@ -2405,11 +2405,20 @@ def sites_ancestral_allele(self):
             except IndexError:
                 unknown_alleles[allele] += 1
             ret[i] = allele_index
-        if sum(unknown_alleles.values()) > 0:
+        tot = sum(unknown_alleles.values())
+        if tot > 0:
+            num_sites = len(string_allele)
+            frac_bad = tot / num_sites
+            frac_bad_per_type = [v / num_sites for v in unknown_alleles.values()]
+            summarise_unknown = [
+                f"'{k}': {v} ({frac * 100:.2f}% of sites)"  # Summarise per allele type
+                for (k, v), frac in zip(unknown_alleles.items(), frac_bad_per_type)
+            ]
             warnings.warn(
-                "The following alleles were not found in the variant_allele array "
-                "and will be treated as unknown:\n"
-                f"{unknown_alleles}"
+                "An ancestral allele was not found in the variant_allele array for "
+                + f"the {tot} sites ({frac_bad * 100 :.2f}%) listed below. "
+                + "They will be treated as of unknown ancestral state:\n "
+                + "\n ".join(summarise_unknown)
             )
         return ret