diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index b356a68dc..711ed9e04 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -99,22 +99,24 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
         // This is really not correct.  What we really want here is a polymorphic vs. monomorphic count (i.e. on the Genotypes).
         // So in order to maintain consistency with the previous implementation (and the intention of the original author), I've
         // added in a proxy check for monomorphic status here.
-        if ( !vc1.isVariant() || (vc1.hasGenotypes() && vc1.getHomRefCount() == vc1.getNSamples()) ) {
+       if ( !vc1.isVariant() || (vc1.hasGenotypes() &&  vc1.getHomRefCount() + vc1.getNoCallCount() == vc1.getNSamples()) ) {
             nRefLoci++;
         } else {
-            nVariantLoci++;
-            switch (vc1.getType()) {
+             switch (vc1.getType()) {
                 case NO_VARIATION:
                     break;
                 case SNP:
+                    nVariantLoci++;
                     nSNPs++;
                     if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
                     break;
                 case MNP:
+                    nVariantLoci++;
                     nMNPs++;
                     if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
                     break;
                 case INDEL:
+                    nVariantLoci++;
                     if (vc1.isSimpleInsertion())
                         nInsertions++;
                     else if (vc1.isSimpleDeletion())
@@ -123,6 +125,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                         nComplex++;
                     break;
                 case MIXED:
+                    nVariantLoci++;
                     nMixed++;
                     break;
                 default:
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 7903be507..19db58e0c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -206,28 +206,12 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
             }
 
             if (field.equals("AF") || field.equals("AC")) {
-                     String afo = val;
-
-                     double af=0;
-                     if (afo.contains(",")) {
-                         String[] afs = afo.split(",");
-                         afs[0] = afs[0].substring(1,afs[0].length());
-                         afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
-
-                         double[] afd = new double[afs.length];
-
-                         for (int k=0; k < afd.length; k++)
-                             afd[k] = Double.valueOf(afs[k]);
-
-                         af = MathUtils.arrayMax(afd);
-                         //af = Double.valueOf(afs[0]);
-
-                     }
-                     else
-                         if (!afo.equals("NA"))
-                             af = Double.valueOf(afo);
-
-                val = Double.toString(af);
+                      if (val.contains(",")) {
+                         // strip [,] and spaces
+                         val = val.replace("[","");
+                         val = val.replace("]","");
+                         val = val.replace(" ","");
+                        }
 
             }
             vals.add(val);