diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
index a2efa626c..6af6723f2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
@@ -40,7 +40,6 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.BaseUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -314,13 +313,14 @@ public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, Ca
             // count up the depths of all and QC+ bases
             int rawDepth = 0, QCDepth = 0, lowMAPQDepth = 0;
             for (PileupElement e : context.getBasePileup()) {
-                rawDepth++;
+                final int depth = e.getRepresentativeCount();
+                rawDepth += depth;
 
                 if (e.getMappingQual() <= maxLowMAPQ)
-                    lowMAPQDepth++;
+                    lowMAPQDepth += depth;
 
                 if (e.getMappingQual() >= minMappingQuality && (e.getQual() >= minBaseQuality || e.isDeletion())) {
-                    QCDepth++;
+                    QCDepth += depth;
                 }
             }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociIntegrationTest.java
similarity index 77%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
rename to public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociIntegrationTest.java
index 859f6c4c7..6472a10bb 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociIntegrationTest.java
@@ -30,8 +30,9 @@ import org.testng.annotations.Test;
 
 import java.util.Arrays;
 
-public class CallableLociWalkerIntegrationTest extends WalkerTest {
-    final static String commonArgs = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s";
+public class CallableLociIntegrationTest extends WalkerTest {
+    final static String commonArgs     = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s";
+    final static String reduceReadArgs = "-R " + b37KGReference + " -T CallableLoci -I " + " private/testdata/NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s";
 
     final static String SUMMARY_MD5 = "ffdbd9cdcb4169ebed5ae4bec797260f";
 
@@ -66,4 +67,13 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
                 Arrays.asList("46a53379aaaf9803276a0a34b234f6ab", "da431d393f7c2b2b3e27556b86c1dbc7"));
         executeTest("formatBed lots of arguments", spec);
     }
+
+    @Test(enabled=true)
+    public void testWithReducedRead() {
+        String gatk_args = reduceReadArgs + " -L 20:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s";
+        WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1,
+                Arrays.asList("684069ffe94a1175051066ed53f0fd9d", "ebc310cf734d98e26d2d83e16b1144d1"));
+        executeTest("CallableLoci with ReducedRead", spec);
+    }
+
 }