diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 93921b6ad..e52fd81c4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -550,17 +550,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                     } catch (Exception e) {}
                 }
 
-                // We need to update the mapping quality score of the cleaned reads;
-                // however we don't have enough info to use the proper MAQ scoring system.
-                // For now, we'll use a heuristic:
-                // the mapping quality score is improved by the LOD difference in mismatching
-                // bases between the reference and alternate consensus (divided by 10)
-
                 // finish cleaning the appropriate reads
                 for ( Pair<Integer, Integer> indexPair : bestConsensus.readIndexes ) {
                     final AlignedRead aRead = altReads.get(indexPair.first);
                     if ( aRead.finalizeUpdate() ) {
-                        aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + (int)(improvement/10.0), 255));
+                        // We need to update the mapping quality score of the cleaned reads;
+                        // however we don't have enough info to use the proper MAQ scoring system.
+                        // For now, we will just arbitrarily add 10 to the mapping quality. [EB, 6/7/2010].
+                        // TODO -- we need a better solution here
+                        aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
                         aRead.getRead().setAttribute("NM", AlignmentUtils.numMismatches(aRead.getRead(), reference, aRead.getRead().getAlignmentStart()-(int)leftmostIndex));
                     }
                 }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index 14a74d341..958004e84 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerLod5() {
-        String[] md5s = {"56f1fb75cae706a5a6278257ea2f2598", "18fca887d1eb7dc300e717ae03b9da62"};
+        String[] md5s = {"726c629a382e4da0dffd4de2e439aa91", "18fca887d1eb7dc300e717ae03b9da62"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
@@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerLod50() {
-        String[] md5s = {"56f1fb75cae706a5a6278257ea2f2598", "9537e4f195ce5840136f60fb61201369"};
+        String[] md5s = {"726c629a382e4da0dffd4de2e439aa91", "9537e4f195ce5840136f60fb61201369"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
@@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerKnownsOnly() {
-        String[] md5s = {"54621fe4a53a559908ff20f6f0d0e758", "1091436c40d5ba557d85662999cc0c1d"};
+        String[] md5s = {"d609430ffbc0fd8b68f383b9eec17e8b", "1091436c40d5ba557d85662999cc0c1d"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 1.0 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
                  2,