diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
index e3910ef11..89e20dad1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -143,7 +143,7 @@ public class DiffEngine {
      * Not that only pairs of the same length are considered as potentially equivalent
      *
      * @param params determines how we display the items
-     * @param diffs
+     * @param diffs the list of differences to summarize
      */
     public void reportSummarizedDifferences(List<Difference> diffs, SummaryReportParams params ) {
         printSummaryReport(summarizeDifferences(diffs), params );
@@ -207,14 +207,7 @@ public class DiffEngine {
     }
 
     protected void printSummaryReport(List<Difference> sortedSummaries, SummaryReportParams params ) {
-        GATKReport report = new GATKReport();
-        final String tableName = "diffences";
-        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information");
-        GATKReportTable table = report.getTable(tableName);
-        table.addPrimaryKey("Difference", true);
-        table.addColumn("NumberOfOccurrences", 0);
-        table.addColumn("SpecificDifference", 0);
-
+        List<Difference> toShow = new ArrayList<Difference>();
         int count = 0, count1 = 0;
         for ( Difference diff : sortedSummaries ) {
             if ( diff.getCount() < params.minSumDiffToShow )
@@ -230,10 +223,26 @@ public class DiffEngine {
                     break;
             }
 
-            table.set(diff.getPath(), "NumberOfOccurrences", diff.getCount());
-            table.set(diff.getPath(), "SpecificDifference", diff.valueDiffString());
+            toShow.add(diff);
         }
 
+        // if we want it in descending order, reverse the list
+        if ( ! params.descending ) {
+            Collections.reverse(toShow);
+        }
+
+        // now that we have a specific list of values we want to show, display them
+        GATKReport report = new GATKReport();
+        final String tableName = "diffences";
+        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", false);
+        GATKReportTable table = report.getTable(tableName);
+        table.addPrimaryKey("Difference", true);
+        table.addColumn("NumberOfOccurrences", 0);
+        table.addColumn("ExampleDifference", 0);
+        for ( Difference diff : toShow ) {
+            table.set(diff.getPath(), "NumberOfOccurrences", diff.getCount());
+            table.set(diff.getPath(), "ExampleDifference", diff.valueDiffString());
+        }
         table.write(params.out);
     }
 
@@ -252,7 +261,7 @@ public class DiffEngine {
      * commonPostfixLength: how many parts are shared at the end, suppose its 2
      * We want to create a string *.*.C.D
      *
-     * @param parts
+     * @param parts the separated path values [above without .]
      * @param commonPostfixLength
      * @return
      */
@@ -351,6 +360,7 @@ public class DiffEngine {
         int maxItemsToDisplay = 0;
         int maxCountOneItems = 0;
         int minSumDiffToShow = 0;
+        boolean descending = true;
 
         public SummaryReportParams(PrintStream out, int maxItemsToDisplay, int maxCountOneItems, int minSumDiffToShow) {
             this.out = out;
@@ -358,5 +368,9 @@ public class DiffEngine {
             this.maxCountOneItems = maxCountOneItems;
             this.minSumDiffToShow = minSumDiffToShow;
         }
+
+        public void setDescending(boolean descending) {
+            this.descending = descending;
+        }
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
index 8e362dcc4..fba6549fb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -112,6 +112,7 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
         }
 
         DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff);
+        params.setDescending(false);
         diffEngine.reportSummarizedDifferences(diffs, params);
     }
 }
\ No newline at end of file