diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
index 3da2a32c3..94f3c2b6b 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
@@ -214,7 +214,7 @@ import java.util.Map;
             if (entry.getValue() > sumQuals.get(maxI))
                 maxI = entry.getKey();
         }
-        return maxI;
+        return (sumQuals.get(maxI) > 0L ? maxI : baseIndexWithMostCounts());
     }
 
     @Ensures("result != null")
@@ -224,7 +224,7 @@ import java.util.Map;
             if (entry.getKey().isNucleotide() && entry.getValue() > sumQuals.get(maxI))
                 maxI = entry.getKey();
         }
-        return maxI;
+        return (sumQuals.get(maxI) > 0L ? maxI : baseIndexWithMostCountsWithoutIndels());
     }
 
     @Ensures("result >=0")
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
index 00e4d12c6..e938ccba0 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
@@ -472,7 +472,7 @@ public class SlidingWindow {
      * @param rms           the rms mapping quality in the header element
      */
     private void genericAddBaseToConsensus(SyntheticRead syntheticRead, BaseAndQualsCounts baseCounts, double rms) {
-        BaseIndex base = baseCounts.baseIndexWithMostProbability();
+        final BaseIndex base = baseCounts.baseIndexWithMostProbability();
         byte count = (byte) Math.min(baseCounts.countOfBase(base), Byte.MAX_VALUE);
         byte qual = baseCounts.averageQualsOfBase(base);
         byte insQual = baseCounts.averageInsertionQualsOfBase(base);