diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
index 8a255391f..cc60ac010 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
@@ -58,6 +58,7 @@ public class RecalDataManager {
     private final HashMap<BaseRecalibrationType, NestedHashMap> dataCollapsedQualityScore;              // Table where everything except read group and quality score has been collapsed
     private final HashMap<BaseRecalibrationType, ArrayList<NestedHashMap>> dataCollapsedByCovariate;    // Tables where everything except read group, quality score, and given covariate has been collapsed
 
+    public final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ"; // The tag that holds the original quality scores
     public final static String COLOR_SPACE_QUAL_ATTRIBUTE_TAG = "CQ";   // The tag that holds the color space quality scores for SOLID bams
     public final static String COLOR_SPACE_ATTRIBUTE_TAG = "CS";        // The tag that holds the color space for SOLID bams
     public final static String COLOR_SPACE_INCONSISTENCY_TAG = "ZC";    // A new tag made up for the recalibrator which will hold an array of ints which say if this base is inconsistent with its color
diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
index df682f215..e10a810fd 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
@@ -109,6 +109,10 @@ public class Haplotype {
         return isReference;
     }
 
+    public byte[] insertAllele( final Allele a ) {
+        return getBases();
+    }
+
     public static LinkedHashMap<Allele,Haplotype> makeHaplotypeListFromAlleles(List<Allele> alleleList, int startPos, ReferenceContext ref,
                                                                final int haplotypeSize, final int numPrefBases) {
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
index b08365a78..4a366bc02 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
@@ -30,7 +30,6 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.text.XReadLines;
@@ -189,13 +188,12 @@ public class BaseRecalibration {
             for( int offset = 0; offset < read.getReadLength(); offset++ ) {
         
                 final Object[] fullCovariateKeyWithErrorMode = covariateKeySet.getKeySet(offset, errorModel);
-
                 final Object[] fullCovariateKey = Arrays.copyOfRange(fullCovariateKeyWithErrorMode, 0, fullCovariateKeyWithErrorMode.length-1); // need to strip off the error mode which was appended to the list of covariates
 
-                Byte qualityScore = (Byte) qualityScoreByFullCovariateKey.get(fullCovariateKey);
+                Byte qualityScore = (Byte) qualityScoreByFullCovariateKey.get(fullCovariateKeyWithErrorMode);
                 if( qualityScore == null ) {
                     qualityScore = performSequentialQualityCalculation( errorModel, fullCovariateKey );
-                    qualityScoreByFullCovariateKey.put(qualityScore, fullCovariateKey);
+                    qualityScoreByFullCovariateKey.put(qualityScore, fullCovariateKeyWithErrorMode);
                 }
         
                 recalQuals[offset] = qualityScore;
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index 2172cfb94..f5a9b2f45 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -171,10 +171,10 @@ public class GATKSAMRecord extends BAMRecord {
                 setBaseQualities(quals);
                 break;
             case BASE_INSERTION:
-                setAttribute( GATKSAMRecord.BQSR_BASE_INSERTION_QUALITIES, quals );
+                setAttribute( GATKSAMRecord.BQSR_BASE_INSERTION_QUALITIES, SAMUtils.phredToFastq(quals) );
                 break;
             case BASE_DELETION:
-                setAttribute( GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES, quals );
+                setAttribute( GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES, SAMUtils.phredToFastq(quals) );
                 break;
             default:
                 throw new ReviewedStingException("Unrecognized Base Recalibration type: " + errorModel );
@@ -195,23 +195,23 @@ public class GATKSAMRecord extends BAMRecord {
     }
 
     public byte[] getBaseInsertionQualities() {
-        byte[] quals = getByteArrayAttribute( BQSR_BASE_INSERTION_QUALITIES );
+        byte[] quals = SAMUtils.fastqToPhred( getStringAttribute( BQSR_BASE_INSERTION_QUALITIES ) );
         if( quals == null ) {
             quals = new byte[getBaseQualities().length];
             Arrays.fill(quals, (byte) 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will
             // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45
-            setAttribute( BQSR_BASE_INSERTION_QUALITIES, quals );
+            setBaseQualities(quals, RecalDataManager.BaseRecalibrationType.BASE_INSERTION);
         }
         return quals;
     }
 
     public byte[] getBaseDeletionQualities() {
-        byte[] quals = getByteArrayAttribute( BQSR_BASE_DELETION_QUALITIES );
+        byte[] quals = SAMUtils.fastqToPhred( getStringAttribute( BQSR_BASE_DELETION_QUALITIES ) );
         if( quals == null ) {
             quals = new byte[getBaseQualities().length];
             Arrays.fill(quals, (byte) 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will
             // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45
-            setAttribute( BQSR_BASE_DELETION_QUALITIES, quals );
+            setBaseQualities(quals, RecalDataManager.BaseRecalibrationType.BASE_DELETION);
         }
         return quals;
     }
@@ -259,12 +259,10 @@ public class GATKSAMRecord extends BAMRecord {
         return (i==0) ? firstCount : (byte) Math.min(firstCount + offsetCount, Byte.MAX_VALUE);
     }
 
-
     ///////////////////////////////////////////////////////////////////////////////
     // *** GATKSAMRecord specific methods                                     ***//
     ///////////////////////////////////////////////////////////////////////////////
 
-
     /**
      * Checks whether an attribute has been set for the given key.
      *