diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index 8b9674353..c71373cd1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -451,12 +451,12 @@ public class LocusIteratorByState extends LocusIterator {
                 nextAlignmentContext = new AlignmentContext(loc, new ReadBackedExtendedEventPileupImpl(loc, fullExtendedEventPileup), hasBeenSampled);
             }
             else {                                                                      // this is a regular event pileup (not extended)
-                GenomeLoc location = getLocation();
-                Map<String, ReadBackedPileupImpl> fullPileup = new HashMap<String, ReadBackedPileupImpl>();
+                final GenomeLoc location = getLocation();
+                final Map<String, ReadBackedPileupImpl> fullPileup = new HashMap<String, ReadBackedPileupImpl>();
                 boolean hasBeenSampled = false;
                 for (final String sample : samples) {
-                    Iterator<SAMRecordState> iterator = readStates.iterator(sample);
-                    List<PileupElement> pile = new ArrayList<PileupElement>(readStates.size(sample));
+                    final Iterator<SAMRecordState> iterator = readStates.iterator(sample);
+                    final List<PileupElement> pile = new ArrayList<PileupElement>(readStates.size(sample));
                     hasBeenSampled |= location.getStart() <= readStates.getDownsamplingExtent(sample);
 
                     size = 0;                                                           // number of elements in this sample's pileup
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 51b834bd2..44a0498d4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -86,8 +86,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
                 continue;
 
             for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : alleleBins.entrySet() ) {
-                if ( !alleleBin.getKey().equals(Allele.NO_CALL) )
-                    depth += alleleBin.getValue().size();
+                depth += alleleBin.getValue().size();
             }
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
index 858f7a2ae..fcab47618 100644
--- a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
@@ -166,6 +166,9 @@ public class FragmentUtils {
             if( firstReadQuals[iii] > MIN_QUAL_BAD_OVERLAP && secondReadQuals[iii-firstReadStop] > MIN_QUAL_BAD_OVERLAP && firstReadBases[iii] != secondReadBases[iii-firstReadStop] ) {
                 return overlappingPair;// high qual bases don't match exactly, probably indel in only one of the fragments, so don't merge them
             }
+            if( firstReadQuals[iii] < MIN_QUAL_BAD_OVERLAP && secondReadQuals[iii-firstReadStop] < MIN_QUAL_BAD_OVERLAP ) {
+                return overlappingPair; // both reads have low qual bases in the overlap region so don't merge them because don't know what is going on
+            }
             bases[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadBases[iii] : secondReadBases[iii-firstReadStop] );
             quals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadQuals[iii] : secondReadQuals[iii-firstReadStop] );
         }