diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java
index ab24b85cf..91d838604 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java
@@ -3,23 +3,23 @@ package org.broadinstitute.sting.playground.gatk.walkers.secondaryBases;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Reference;
+import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.walkers.genotyper.*;
 import org.broadinstitute.sting.playground.utils.NamedTable;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.genotype.Genotype;
+
 import java.util.HashMap;
 
 /**
- * Created By User: Michael Melgar
- * Date: Nov 2, 2009
- * Time: 8:45:32 PM
  * Given a secondary base annotated .bam file and a reference, this walker generates a table of secondary base counts
  * for all called loci in the .bam. Each base call made is an instance included in the table. Specifically, the walker
  * maps the following vector to a count of secondary bases:
- * <Called Genotype, Reference Base, Primary Base, Previous Genome Base, Read Group, Secondary Base>.
+ * <HomRef/Het/HomVar, Read Group, Called Genotype, AlleleBalance, Reference Base, Primary Base, Previous Read Base, Secondary Base>.
  */
 
 @Reference(window=@Window(start=-1,stop=1))
@@ -41,6 +41,9 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         char refBase = Character.toUpperCase(ref.getBase());
         ReadBackedPileup pileup = context.getBasePileup();
+        int[] baseCounts = pileup.getBaseCounts();
+        int length = 0;
+        for (int i : baseCounts) {length += i;}
         char[] contextBases = ref.getBases();
         char prevBase = Character.toUpperCase(contextBases[0]);
         char nextBase = Character.toUpperCase(contextBases[contextBases.length - 1]);
@@ -51,11 +54,22 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
                 Genotype res = ugResult.genotypes.get(0);
                 String call = res.getBases();
                 String type;
-                if (!res.isVariant(refBase)) {type = "homref";}
+                String alleleBalance = "N/A";
+                if (!res.isVariant(refBase)) {
+                    type = "homref";
+                }
                 else if (!res.isHet()) {type = "homvar";}
-                else if (call.contains(Character.toString(refBase))) {type = "het";}
+                else if (call.contains(Character.toString(refBase))) {
+                    type = "het";
+                    char alt;
+                    if (call.charAt(0) == refBase) {alt = call.charAt(1);}
+                    else {alt = call.charAt(0);}
+                    double refCount = baseCounts[BaseUtils.simpleBaseToBaseIndex(refBase)];
+                    double altCount = baseCounts[BaseUtils.simpleBaseToBaseIndex(alt)];
+                    alleleBalance = Double.toString(Math.round(100.0*refCount/(refCount + altCount))/100.0);
+                }
                 else {type = "bad";}
-                if (type != "bad") {
+                if (!type.equals("bad")) {
                     for (PileupElement element : pileup) {
                         char primaryBase = Character.toUpperCase((char)element.getBase());
                         char secondaryBase = Character.toUpperCase((char)element.getSecondBase());
@@ -65,20 +79,23 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
                             String strandPrimary;
                             String strandPrev;
                             String strandSecondary;
+                            String strandCall;
                             if (!element.getRead().getReadNegativeStrandFlag()) {
                                 strandRef = Character.toString(refBase);
                                 strandPrimary = Character.toString(primaryBase);
                                 strandPrev = Character.toString(prevBase);
                                 strandSecondary = Character.toString(secondaryBase);
+                                strandCall = call;
                             }
                             else {
                                 strandRef = Character.toString(BaseUtils.simpleComplement(refBase));
                                 strandPrimary = Character.toString(BaseUtils.simpleComplement(primaryBase));
                                 strandPrev = Character.toString(BaseUtils.simpleComplement(nextBase));
                                 strandSecondary = Character.toString(BaseUtils.simpleComplement(secondaryBase));
+                                strandCall = BaseUtils.simpleReverseComplement(call);
                             }
                             if (strandPrev.charAt(0) != 'N') {
-                                String key = RG+' '+type+' '+call+' '+strandRef+' '+strandPrimary+' '+strandPrev+' '+strandSecondary;
+                                String key = type+' '+RG+' '+strandCall+' '+alleleBalance+' '+strandRef+' '+strandPrimary+' '+strandPrev+' '+strandSecondary;
                                 if (counts.containsKey(key)) {
                                     counts.put(key, counts.get(key) + Long.valueOf(1));
                                 }
@@ -100,10 +117,10 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
 
     public void onTraversalDone(Integer result) {
         out.println(">>>");
-        out.println("ReadGroup CallType CalledGenotype ReferenceBase PrimaryBase PreviousBase SecondaryBase Count");
+        out.println("Type ReadGroup CalledGenotype AlleleBalance ReferenceBase PrimaryBase PreviousBase SecondaryBase Count");
         for (String key : counts.keySet()) {
             out.println(key + ' ' + counts.get(key).toString());
         }
         out.println("Processed " + result.toString() + " loci.");
     }
-}
+}
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