diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
index 964c6b401..d5aa8f944 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
@@ -1033,7 +1033,7 @@ public class SlidingWindow {
     protected void actuallyUpdateHeaderForRead(final LinkedList<HeaderElement> header, final GATKSAMRecord read, final boolean removeRead, final int startIndex) {
 
         final Iterator<HeaderElement> headerElementIterator = header.listIterator(startIndex);
-        final byte mappingQuality = (byte) read.getMappingQuality();
+        final int mappingQuality = read.getMappingQuality();
         final boolean isNegativeStrand = read.getReadNegativeStrandFlag();
 
         // iterator variables
@@ -1062,14 +1062,15 @@ public class SlidingWindow {
 
                     break;
                 case D:
-                    // deletions are added to the baseCounts with the read mapping quality as it's quality score
+                    // deletions are added to the baseCounts with the read mapping quality as its quality score
                     final int nDeletionBases = cigarElement.getLength();
+                    final byte MQbyte = mappingQuality > Byte.MAX_VALUE ? Byte.MAX_VALUE : (byte)mappingQuality;
                     for ( int i = 0; i < nDeletionBases; i++ ) {
                         headerElement = headerElementIterator.next();
                         if (removeRead)
-                            headerElement.removeBase(BaseUtils.Base.D.base, mappingQuality, mappingQuality, mappingQuality, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
+                            headerElement.removeBase(BaseUtils.Base.D.base, MQbyte, MQbyte, MQbyte, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
                         else
-                            headerElement.addBase(BaseUtils.Base.D.base, mappingQuality, mappingQuality, mappingQuality, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
+                            headerElement.addBase(BaseUtils.Base.D.base, MQbyte, MQbyte, MQbyte, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
                     }
                     locationIndex += nDeletionBases;
                     break;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
index 720f00f98..c49a671e2 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
@@ -860,6 +860,29 @@ public class SlidingWindowUnitTest extends BaseTest {
             Assert.assertEquals(windowHeader.get(i).getBaseCounts(SlidingWindow.ConsensusType.POSITIVE_CONSENSUS).countOfBase(BaseUtils.Base.A.base), 0);
     }
 
+    @Test
+    public void testUpdateHeaderForReadWithHighMQ() {
+
+        // set up the window header
+        final int currentHeaderStart = 100;
+        final LinkedList<HeaderElement> windowHeader = new LinkedList<>();
+        for ( int i = 0; i < readLength; i++ )
+            windowHeader.add(new HeaderElement(currentHeaderStart + i));
+
+        // set up the read
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, currentHeaderStart, readLength);
+        read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
+        read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
+        read.setMappingQuality(180);
+        read.setReadNegativeStrandFlag(false);
+
+        // add the read and make sure it's not filtered because of low MQ (byte vs. int)
+        final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 0.05, 20, 20, 10, ReduceReads.DownsampleStrategy.Normal, false);
+        slidingWindow.actuallyUpdateHeaderForRead(windowHeader, read, false, 0);
+        for ( int i = 0; i < readLength; i++ )
+            Assert.assertEquals(windowHeader.get(i).getBaseCounts(SlidingWindow.ConsensusType.POSITIVE_CONSENSUS).countOfBase(BaseUtils.Base.A.base), 1);
+    }
+
     //////////////////////////////////////////////////////////////////////////////////
     //// This section tests functionality related to polyploid consensus creation ////
     //////////////////////////////////////////////////////////////////////////////////