diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index fdfe56528..b00e03af2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -285,6 +285,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
                                     table.addColumn(columnName, "unknown");
                                 }
 
+                                table.addColumn("row", "unknown");
+
                                 for ( Object o : t.getColumnKeys() ) {
                                     String c;
 
@@ -319,6 +321,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
 
                                     String newStateKey = stateKey.toString() + r;
                                     table.set(newStateKey, c, t.getCell(row, col));
+
+                                    table.set(newStateKey, "row", r);
                                 }
                             }
                         } else {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
index 66204e24b..2d3103e3b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
@@ -85,7 +85,7 @@ public class GenotypeConcordance extends VariantEvaluator {
         public Object[] getRowKeys() {
             String rows[] = new String[foundMissedByAC.size()];
             int index = 0;
-            for (int i : foundMissedByAC.keySet()) rows[index++] = "Allele Count " + i;
+            for (int i : foundMissedByAC.keySet()) rows[index++] = "AlleleCount_" + i;
             return rows;
         }
 
@@ -471,11 +471,11 @@ class SampleStats implements TableType {
 //                            "n_het/ref","n_het/het","n_het/hom",
 //                            "total_true_hom","%_hom/hom","n_hom/no-call",
 //                            "n_hom/ref","n_hom/het","n_hom/hom"};
-        return new String[]{"total_true_ref","pct_ref_vs_ref","n_ref_vs_no-call",
+        return new String[]{"total_true_ref","pct_ref_vs_ref","n_ref_vs_no_call",
                 "n_ref_vs_ref","n_ref_vs_het","n_ref_vs_hom",
-                "total_true_het","pct_het_vs_het","n_het_vs_no-call",
+                "total_true_het","pct_het_vs_het","n_het_vs_no_call",
                 "n_het_vs_ref","n_het_vs_het","n_het_vs_hom",
-                "total_true_hom","pct_hom_vs_hom","n_hom_vs_no-call",
+                "total_true_hom","pct_hom_vs_hom","n_hom_vs_no_call",
                 "n_hom_vs_ref","n_hom_vs_het","n_hom_vs_hom"};
     }
 
@@ -560,9 +560,9 @@ class SampleSummaryStats implements TableType {
             "percent_comp_het_called_var",
             "percent_comp_hom_called_hom",
             "percent_comp_hom_called_var",
-            "percent_non-reference_sensitivity",
+            "percent_non_reference_sensitivity",
             "percent_overall_genotype_concordance",
-            "percent_non-reference_discrepancy_rate"};
+            "percent_non_reference_discrepancy_rate"};
 
     // sample to concordance stats object
     protected final HashMap<String, double[]> concordanceSummary = new HashMap<String, double[]>();
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index adb1b56b1..9bbd69432 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -342,12 +342,13 @@ public class VariantEvalUtils {
      * @param allowableTypes a set of allowable variation types
      * @param byFilter       if false, only accept PASSing VariantContexts.  Otherwise, accept both PASSing and filtered
      *                       sites
+     * @param subsetBySample if false, do not separate the track into per-sample VCs
      * @param trackPerSample if false, don't stratify per sample (and don't cut up the VariantContext like we would need
      *                       to do this)
      * @param allowNoCalls   if false, don't accept no-call loci from a variant track
      * @return a mapping of track names to a list of VariantContext objects
      */
-    public HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter, boolean trackPerSample, boolean allowNoCalls) {
+    public HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter, boolean subsetBySample, boolean trackPerSample, boolean allowNoCalls) {
         HashMap<String, HashMap<String, VariantContext>> bindings = new HashMap<String, HashMap<String, VariantContext>>();
 
         for (String trackName : trackNames) {
@@ -360,7 +361,7 @@ public class VariantEvalUtils {
             if (vc != null) {
                 VariantContext vcsub = vc;
 
-                if (vc.hasGenotypes() && vc.hasGenotypes(variantEvalWalker.getSampleNamesForEvaluation())) {
+                if (subsetBySample && vc.hasGenotypes() && vc.hasGenotypes(variantEvalWalker.getSampleNamesForEvaluation())) {
                     vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation());
                 }
 
@@ -411,8 +412,8 @@ public class VariantEvalUtils {
             }
         }
 
-        HashMap<String, HashMap<String, VariantContext>> evalBindings = bindVariantContexts(tracker, ref, evalNames, allowableTypes, byFilter, perSampleIsEnabled, true);
-        HashMap<String, HashMap<String, VariantContext>> compBindings = bindVariantContexts(tracker, ref, compNames, allowableTypes, byFilter, false, false);
+        HashMap<String, HashMap<String, VariantContext>> evalBindings = bindVariantContexts(tracker, ref, evalNames, allowableTypes, byFilter, true, perSampleIsEnabled, true);
+        HashMap<String, HashMap<String, VariantContext>> compBindings = bindVariantContexts(tracker, ref, compNames, allowableTypes, byFilter, false, false, false);
 
         vcs.putAll(compBindings);
         vcs.putAll(evalBindings);