diff --git a/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java b/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
index dad7c907f..9d37dd359 100644
--- a/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
@@ -25,7 +25,7 @@ public class AlignmentUtils {
      * @return
      */
     public static int numMismatches(SAMRecord r, ReferenceSequence ref) {
-        return numMismatches(r, ref.getBases().toString());
+        return numMismatches(r, new String(ref.getBases()));
     }
 
     public static int numMismatches(SAMRecord r, String ref) {