diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 4b56ce309..2c388a1e0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -476,7 +476,6 @@ public class AlignmentUtils {
                     }
                     break;
                 case D:
-                case N:
                     if (!isDeletion) {
                         alignmentPos += elementLength;
                     } else {
@@ -498,6 +497,7 @@ public class AlignmentUtils {
                     break;
                 case H:
                 case P:
+                case N:
                     break;
                 default:
                     throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
@@ -516,16 +516,13 @@ public class AlignmentUtils {
             final int elementLength = ce.getLength();
 
             switch (ce.getOperator()) {
-                case I:
-                case S:
-                    break;
                 case D:
                 case N:
-                    alignmentLength += elementLength;
-                    break;
                 case M:
                     alignmentLength += elementLength;
                     break;
+                case I:
+                case S:
                 case H:
                 case P:
                     break;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index f35eb4404..f26486a71 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -373,13 +373,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     // --------------------------------------------------------------------------------------------------------------
     //
-    // testing SnpEff
+    // testing MinIndelFraction
     //
     // --------------------------------------------------------------------------------------------------------------
 
     final static String assessMinIndelFraction = baseCommandIndelsb37 + " -I " + validationDataLocation
             + "978604.bam -L 1:978,586-978,626 -o %s --sites_only -rf Sample -goodSM 7377 -goodSM 22-0022 -goodSM 134 -goodSM 344029-53 -goodSM 14030";
-    
+
     @Test
     public void testMinIndelFraction0() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -403,4 +403,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 Arrays.asList("3f07efb768e08650a7ce333edd4f9a52"));
         executeTest("test minIndelFraction 1.0", spec);
     }
+
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // testing Ns in CIGAR
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
+    @Test
+    public void testNsInCigar() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                baseCommand + " -I " + validationDataLocation + "testWithNs.bam", 1,
+                Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29"));
+        executeTest("test calling on reads with Ns in CIGAR", spec);
+    }
 }