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 711ed9e04..59ef3d992 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
@@ -99,6 +99,7 @@ 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.
+        // Protect against case when vc only as no-calls too - can happen if we strafity by sample and sample as a single no-call.
        if ( !vc1.isVariant() || (vc1.hasGenotypes() &&  vc1.getHomRefCount() + vc1.getNoCallCount() == vc1.getNSamples()) ) {
             nRefLoci++;
         } else {