Index: src/jalview/datamodel/ResidueCount.java
===================================================================
diff -u -N -rd43c7d9caca02859542914401ec945744c026bf1 -r227c9c583a110b1581ab1036be289b1f838cf8ea
--- src/jalview/datamodel/ResidueCount.java	(.../ResidueCount.java)	(revision d43c7d9caca02859542914401ec945744c026bf1)
+++ src/jalview/datamodel/ResidueCount.java	(.../ResidueCount.java)	(revision 227c9c583a110b1581ab1036be289b1f838cf8ea)
@@ -212,7 +212,12 @@
         counts[offset] = (short) ++newValue;
       }
     }
-    maxCount = Math.max(maxCount, newValue);
+
+    if (offset!=GAP_COUNT)
+    {
+      // update modal residue count
+      maxCount = Math.max(maxCount, newValue);
+    }
     return newValue;
   }