diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
index eef73c190..97aebc376 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
@@ -91,25 +91,31 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
     //@DataPoint(description = "Multi-allelic Indel Novelty Rate")
     public String indelNoveltyRate = "NA";
 
-    @DataPoint(description="Histogram of allele frequencies for most common alternate allele")
-    AFHistogram AFhistogramMax = new AFHistogram();
+    @DataPoint(description="Histogram of allele frequencies for most common SNP alternate allele")
+    AFHistogram AFhistogramMaxSnp = new AFHistogram();
 
-    @DataPoint(description="Histogram of allele frequencies for less common alternate alleles")
-    AFHistogram AFhistogramMin = new AFHistogram();
+    @DataPoint(description="Histogram of allele frequencies for less common SNP alternate alleles")
+    AFHistogram AFhistogramMinSnp = new AFHistogram();
+
+    @DataPoint(description="Histogram of allele frequencies for most common Indel alternate allele")
+    AFHistogram AFhistogramMaxIndel = new AFHistogram();
+
+    @DataPoint(description="Histogram of allele frequencies for less common Indel alternate alleles")
+    AFHistogram AFhistogramMinIndel = new AFHistogram();
 
     /*
      * AF histogram table object
      */
     static class AFHistogram implements TableType {
-        private Object[] colKeys, rowKeys = {"pairwise_AF"};
+        private Object[] rowKeys, colKeys = {"count"};
         private int[] AFhistogram;
 
         private static final double AFincrement = 0.01;
         private static final int numBins = (int)(1.00 / AFincrement);
 
         public AFHistogram() {
-            colKeys = initColKeys();
-            AFhistogram = new int[colKeys.length];
+            rowKeys = initRowKeys();
+            AFhistogram = new int[rowKeys.length];
         }
 
         public Object[] getColumnKeys() {
@@ -121,10 +127,10 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
         }
 
         public Object getCell(int row, int col) {
-            return AFhistogram[col];
+            return AFhistogram[row];
         }
 
-        private static Object[] initColKeys() {
+        private static Object[] initRowKeys() {
             ArrayList<String> keyList = new ArrayList<String>(numBins + 1);
             for ( double a = 0.00; a <= 1.01; a += AFincrement ) {
                 keyList.add(String.format("%.2f", a));
@@ -164,6 +170,7 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
                     nMultiSNPs++;
                     calculatePairwiseTiTv(eval);
                     calculateSNPPairwiseNovelty(eval, comp);
+                    updateAFhistogram(eval, AFhistogramMaxSnp, AFhistogramMinSnp);
                 }
                 break;
             case INDEL:
@@ -171,13 +178,13 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
                 if ( !eval.isBiallelic() ) {
                     nMultiIndels++;
                     calculateIndelPairwiseNovelty(eval, comp);
+                    updateAFhistogram(eval, AFhistogramMaxIndel, AFhistogramMinIndel);
                 }
                 break;
             default:
                 throw new UserException.BadInput("Unexpected variant context type: " + eval);
         }
-        updateAFhistogram(eval);
-        
+
         return null; // we don't capture any interesting sites
     }
 
@@ -209,7 +216,7 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
     private void calculateIndelPairwiseNovelty(VariantContext eval, VariantContext comp) {
     }
 
-    private void updateAFhistogram(VariantContext vc) {
+    private void updateAFhistogram(VariantContext vc, AFHistogram max, AFHistogram min) {
 
         final Object obj = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY, null);
         if ( obj == null || !(obj instanceof List) )
@@ -222,9 +229,9 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
         }
 
         Collections.sort(AFs);
-        AFhistogramMax.update(AFs.get(AFs.size()-1));
+        max.update(AFs.get(AFs.size()-1));
         for ( int i = 0; i < AFs.size() - 1; i++ )
-            AFhistogramMin.update(AFs.get(i));
+            min.update(AFs.get(i));
     }
     
     private final String noveltyRate(final int all, final int known) {