diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
index 78174c096..f80d784d7 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
@@ -101,6 +101,8 @@ public class BQSRIntegrationTest extends WalkerTest {
 
     private static final String HiSeqBam = privateTestDir + "HiSeq.1mb.1RG.bam";
     private static final String HiSeqInterval = "chr1:10,000,000-10,100,000";
+    private static final String SimpleCigarMatchMismatchBam = privateTestDir + "simpleCigarMatchMismatch.bam";
+    private static final String SimpleCigarMatchMismatchInterval = "1:1-60";
 
     @DataProvider(name = "BQSRTest")
     public Object[][] createBQSRTestData() {
@@ -112,6 +114,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                 {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "b74e75f3c5aa90bd21af1e20f2ac8c40")},
                 {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "e564505aea11464de8ed72890d9ea89a")},
                 {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "380d8be121ffaddd3461ee0ac3d1a76f")},
+                {new BQSRTest(b36KGReference, SimpleCigarMatchMismatchBam, SimpleCigarMatchMismatchInterval, "", "56dfb2918a4cdae3ef9d705a43e85194")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "0b5a8e259e997e4c7b5836d4c28e6f4d")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "281682124584ab384f23359934df0c3b")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "0a92fdff5fd26227c29d34eda5a32f49")},
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java
index d6e2bbe0b..23ea65b9d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java
@@ -109,11 +109,13 @@ public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClipping
                     info.nClippingEvents++;
                     info.nClippedBases += elt.getLength();
                     break;
-                case M :
+                case EQ : // sequence match
+                case M : // alignment match
                 case D : // deletion w.r.t. the reference
                 case P : // ignore pads
                 case I : // insertion w.r.t. the reference
                 case N : // reference skip (looks and gets processed just like a "deletion", just different logical meaning)
+                case X : // sequence mismatch
                     break;
                 default : throw new IllegalStateException("Case statement didn't deal with cigar op: " + elt.getOperator());
             }
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java
index da8d00e73..f40ef1c51 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java
@@ -625,7 +625,7 @@ public class BAQ {
                     readI += l;
                     break;
                 case D : refI += l; break;
-                case M :
+                case M : case EQ: case X:
                     for (int i = readI; i < readI + l; i++) {
                         int expectedPos = refI - refOffset + (i - readI);
                         baqResult.bq[i] = capBaseByBAQ( baqResult.rawQuals[i], baqResult.bq[i], baqResult.state[i], expectedPos );
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java
index 7ea26ee07..be9621e76 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java
@@ -141,7 +141,7 @@ public class BAQUnitTest extends BaseTest {
                                 "A?>>@>AA?@@>A?>A@?>@>>?=>?'>?=>7=?A9"));
 
         // raw base qualities are low -- but they shouldn't be capped
-        params.add(new BAQTest(-3, 9999993l, "36M",
+        params.add(new BAQTest(-3, 9999993l, "4=13X2=3X1=4X2=4X1=2X",
                                 "CCACCACGCCTGGCCAATTTTTTTGTATTTTTAGTAGAGATA",
                                 "CCACGCTTGGCAAAGTTTTCCGTACGTTTAGCCGAG",
                                 "33'/(7+270&4),(&&-)$&,%7$',-/61(,6?8",