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 8a87c9957..9d5495351 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
@@ -299,7 +299,7 @@ public class ConcordanceMetrics {
                 return EVAL_ONLY;
 
             boolean evalSubsetTruth = VariantContextUtils.allelesAreSubset(eval,truth);
-            boolean truthSubsetEval = VariantContextUtils.allelesAreSubset(eval,truth);
+            boolean truthSubsetEval = VariantContextUtils.allelesAreSubset(truth,eval);
 
             if ( evalSubsetTruth && truthSubsetEval )
                 return ALLELES_MATCH;
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 e8965dfc8..6902f864e 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
@@ -168,8 +168,9 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
      * Eval: 20   4000     A     C
      * Eval: 20   4000     A    AC
      * Comp: 20   4000     A     C
-     * So for each eval, loop through the comps. If the eval alleles (non-emptily) intersect the comp alleles, pair them up and remove
-     * that comp records. Continue until we're out of evals or comps. This is n^2, but should rarely actually happen.
+     * So for each eval, loop through the comps. If the types match, or for mixed types if eval alleles (non-emptily)
+     * intersect the comp alleles, pair them up and remove that comp records.
+     * Continue until we're out of evals or comps. This is n^2, but should rarely actually happen.
      *
      * The remaining unpaired records get paird with an empty contexts. So in the example above we'd get a list of:
      *  1 - (20,4000,A/C  |  20,4000,A/C)
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
index 6db44efd5..0fff41d52 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
@@ -190,7 +190,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
     }
 
     @Test(enabled=true)
-    public void testMismatchingAllele() {
+    public void testMismatchingAlleleInAlleleSubset() {
         Pair<VariantContext,VariantContext> data = getData2();
         VariantContext eval = data.getFirst();
         VariantContext truth = data.getSecond();
@@ -709,8 +709,13 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
 
         List<Pair<VariantContext,VariantContext>> data = getData7();
 
+        int idx = 0;
+        int[] expecNotMatch = new int[]{0,0,0,0,0,1,1};
         for ( Pair<VariantContext,VariantContext> varPair : data ) {
             metrics.update(varPair.getFirst(),varPair.getSecond());
+            Assert.assertEquals(metrics.getOverallSiteConcordance().get(ConcordanceMetrics.SiteConcordanceType.ALLELES_DO_NOT_MATCH),expecNotMatch[idx]);
+            logger.info(idx);
+            idx++;
         }
 
         Assert.assertEquals(metrics.getOverallSiteConcordance().get(ConcordanceMetrics.SiteConcordanceType.ALLELES_DO_NOT_MATCH),1);