diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
index 648df327d..ac6752277 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
@@ -173,23 +173,33 @@ public class ConcordanceMetrics {
             return nMismatchingAlt;
         }
 
-        public int getnEvalGenotypes() {
+        public int getnEvalGenotypes(GenotypeType type) {
+            int nGeno = 0;
+            for ( GenotypeType comptype : GenotypeType.values() )
+                nGeno += genotypeCounts[type.ordinal()][comptype.ordinal()];
+            return nGeno;
+        }
+
+        public int getnCalledEvalGenotypes() {
             int nGeno = 0;
             for ( GenotypeType evalType : Arrays.asList(GenotypeType.HOM_REF,GenotypeType.HOM_VAR,GenotypeType.HET) ) {
-                for ( GenotypeType compType : GenotypeType.values() ) {
-                    nGeno += genotypeCounts[evalType.ordinal()][compType.ordinal()];
-                }
+                nGeno += getnEvalGenotypes(evalType);
             }
 
             return nGeno + nMismatchingAlt;
         }
 
-        public int getnCompGenotypes() {
+        public int getnCompGenotypes(GenotypeType type) {
+            int nGeno = 0;
+            for ( GenotypeType evaltype : GenotypeType.values() )
+                nGeno += genotypeCounts[evaltype.ordinal()][type.ordinal()];
+            return nGeno;
+        }
+
+        public int getnCalledCompGenotypes() {
             int nGeno = 0;
             for ( GenotypeType compType : Arrays.asList(GenotypeType.HOM_REF,GenotypeType.HOM_VAR,GenotypeType.HET) ) {
-                for ( GenotypeType evalType : GenotypeType.values() ) {
-                    nGeno += genotypeCounts[evalType.ordinal()][compType.ordinal()];
-                }
+                nGeno += getnCompGenotypes(compType);
             }
             return nGeno;
         }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
index 10d9a79ea..7991e3432 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
@@ -114,21 +114,19 @@ public class GenotypeConcordance extends RodWalker<Pair<VariantContext,VariantCo
             concordanceEvalProportions.set(entry.getKey(),"Sample",entry.getKey());
             concordanceCompProportions.set(entry.getKey(),"Sample",entry.getKey());
             concordanceCounts.set(entry.getKey(),"Sample",entry.getKey());
-            int nEval = table.getnEvalGenotypes();
-            int nComp = table.getnCompGenotypes();
             for ( GenotypeType evalType : GenotypeType.values() ) {
                 for ( GenotypeType compType : GenotypeType.values() ) {
                     String colKey = String.format("%s_%s",evalType.toString(),compType.toString());
                     int count = table.get(evalType, compType);
                     concordanceCounts.set(entry.getKey(),colKey,count);
                     if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
-                        concordanceEvalProportions.set(entry.getKey(),colKey,( (double) count)/nEval);
+                        concordanceEvalProportions.set(entry.getKey(),colKey,( (double) count)/table.getnEvalGenotypes(evalType));
                     if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
-                        concordanceCompProportions.set(entry.getKey(),colKey,( (double) count)/nComp);
+                        concordanceCompProportions.set(entry.getKey(),colKey,( (double) count)/table.getnCompGenotypes(compType));
                 }
             }
-            concordanceEvalProportions.set(entry.getKey(),"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/nEval);
-            concordanceCompProportions.set(entry.getKey(),"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/nComp);
+            concordanceEvalProportions.set(entry.getKey(),"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes());
+            concordanceCompProportions.set(entry.getKey(),"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes());
             concordanceCounts.set(entry.getKey(),"Mismatching_Alleles",table.getnMismatchingAlt());
         }
 
@@ -137,21 +135,19 @@ public class GenotypeConcordance extends RodWalker<Pair<VariantContext,VariantCo
         concordanceEvalProportions.set(rowKey,"Sample",rowKey);
         concordanceCounts.set(rowKey,"Sample",rowKey);
         ConcordanceMetrics.GenotypeConcordanceTable table = metrics.getOverallGenotypeConcordance();
-        int nEval = table.getnEvalGenotypes();
-        int nComp = table.getnCompGenotypes();
         for ( GenotypeType evalType : GenotypeType.values() ) {
             for ( GenotypeType compType : GenotypeType.values() ) {
                 String colKey = String.format("%s_%s",evalType.toString(),compType.toString());
                 int count = table.get(evalType,compType);
                 concordanceCounts.set(rowKey,colKey,count);
                 if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
-                    concordanceEvalProportions.set(rowKey,colKey,( (double) count)/nEval);
+                    concordanceEvalProportions.set(rowKey,colKey,( (double) count)/table.getnEvalGenotypes(evalType));
                 if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
-                    concordanceCompProportions.set(rowKey,colKey,( (double) count)/nComp);
+                    concordanceCompProportions.set(rowKey,colKey,( (double) count)/table.getnCompGenotypes(compType));
             }
         }
-        concordanceEvalProportions.set(rowKey,"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/nEval);
-        concordanceCompProportions.set(rowKey,"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/nComp);
+        concordanceEvalProportions.set(rowKey,"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes());
+        concordanceCompProportions.set(rowKey,"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes());
         concordanceCounts.set(rowKey,"Mismatching_Alleles",table.getnMismatchingAlt());
 
         for ( Map.Entry<String,Double> nrsEntry : metrics.getPerSampleNRS().entrySet() ) {