diff --git a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
index fe1a386fb..ad6f05563 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
@@ -581,8 +581,8 @@ public class ClippingOp {
         if (cigarElement.getOperator() == CigarOperator.INSERTION)
             return -clippedLength;
 
-            // Deletions should be added to the total hard clip count
-        else if (cigarElement.getOperator() == CigarOperator.DELETION)
+            // Deletions and Ns should be added to the total hard clip count (because we want to maintain the original alignment start)
+        else if (cigarElement.getOperator() == CigarOperator.DELETION || cigarElement.getOperator() == CigarOperator.SKIPPED_REGION)
             return cigarElement.getLength();
 
         // There is no shift if we are not clipping an indel
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 95e0d55f3..c84e4245d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -524,7 +524,7 @@ public class ReadUtils {
                 // If we reached our goal inside a deletion, but the deletion is the next cigar element then we need
                 // to add the shift of the current cigar element but go back to it's last element to return the last
                 // base before the deletion (see warning in function contracts)
-                else if (fallsInsideDeletion && !endsWithinCigar)
+                else if (fallsInsideDeletion && !endsWithinCigar && cigarElement.getOperator().consumesReadBases())
                     readBases += shift - 1;
 
                 // If we reached our goal inside a deletion then we must backtrack to the last base before the deletion
diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
index baad67d53..331121c55 100644
--- a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
@@ -25,13 +25,19 @@
 
 package org.broadinstitute.sting.utils.sam;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.io.File;
+import java.io.FileNotFoundException;
 import java.util.*;
 
 
@@ -179,4 +185,20 @@ public class ReadUtilsUnitTest extends BaseTest {
         final List<GATKSAMRecord> reads = new LinkedList<GATKSAMRecord>();
         Assert.assertEquals(ReadUtils.getMaxReadLength(reads), 0, "Empty list should have max length of zero");
     }
+
+    @Test (enabled = true)
+    public void testReadWithNs() throws FileNotFoundException {
+
+        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
+        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
+        final int readLength = 76;
+
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
+        read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
+        read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
+        read.setCigarString("3M414N1D73M");
+
+        final int result = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, 9392, ReadUtils.ClippingTail.LEFT_TAIL);
+        Assert.assertEquals(result, 3);
+    }
 }