diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
index db3dc5abf..9dd056388 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
@@ -222,7 +222,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
     }
 
     public boolean baseIsUsable ( RefMetaDataTracker tracker, ReferenceContext ref, ReadBackedPileup pileup, AlignmentContext context ) {
-        return pileupBelowMismatchThreshold(ref,pileup) && baseIsConfidentRef(tracker,ref,context) && pileupContainsNoNs(pileup);
+        return  pileupContainsNoNs(pileup) && baseIsConfidentRef(tracker,ref,context) && pileupBelowMismatchThreshold(ref,pileup);
     }
 
     public boolean pileupBelowMismatchThreshold( ReferenceContext ref, ReadBackedPileup pileup ) {