diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
index 42605ec1d..5dc24c71a 100644
--- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
@@ -389,7 +389,7 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
         if ( refBases == null ) {
             return  Integer.toString(length)+"D"; // if we do not have reference bases, we can only report something like "5D"
         } else {
-            return "-"+new String(refBases,1,length);
+            return "-"+new String(refBases,1,length).toUpperCase();
         }
     }