diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
index 225628292..74956feef 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.BaseUtils;
 import net.sf.samtools.SAMRecord;
 
 /*
@@ -36,9 +37,9 @@ import net.sf.samtools.SAMRecord;
  *
  * The Cycle covariate.
  *  For Solexa the cycle is simply the position in the read (counting backwards if it is a negative strand read)
- *  For 454 the cycle is the number of discontinuous nucleotides seen during the length of the read
- *     For example, for the read: AAACCCCGAAATTTTTTT
- *             the cycle would be 111222234445555555
+ *  For 454 the cycle is the TACG flow cycle, that is, each flow grabs all the TACG's in order in a single cycle
+ *     For example, for the read: AAACCCCGAAATTTTTACT
+ *             the cycle would be 1111111122233333334
  *  For SOLiD the cycle is a more complicated mixture of ligation cycle and primer round
  */
 
@@ -78,23 +79,34 @@ public class CycleCovariate implements StandardCovariate {
         else if( read.getReadGroup().getPlatform().contains( "454" ) ) { // Some bams have "LS454" and others have just "454"
             int cycle = 0;
             byte[] bases = read.getReadBases();
+
+            // BUGBUG: Consider looking at degradation of base quality scores in homopolymer runs to detect when the cycle incremented even though the nucleotide didn't change
+            // For example, AAAAAAA was probably read in two flow cycles but here we count it as one
             if( !read.getReadNegativeStrandFlag() ) { // forward direction
-                byte prevBase = bases[0];
-                for( int iii = 1; iii <= offset; iii++ ) {
-                    if( bases[iii] != prevBase ) { // This base doesn't match the previous one so it is a new cycle
-                        cycle++;
-                        prevBase = bases[iii];
-                    }
+                int iii = 0;
+                while( iii <= offset )
+                {
+                    while( iii <= offset && bases[iii] == (byte)'T' ) { iii++; }
+                    while( iii <= offset && bases[iii] == (byte)'A' ) { iii++; }
+                    while( iii <= offset && bases[iii] == (byte)'C' ) { iii++; }
+                    while( iii <= offset && bases[iii] == (byte)'G' ) { iii++; }
+                    if( iii <= offset ) { cycle++; }
+                    if( iii <= offset && !BaseUtils.isRegularBase(bases[iii]) ) { iii++; }
+
                 }
             } else { // negative direction
-                byte prevBase = bases[bases.length-1];
-                for( int iii = bases.length-2; iii >= offset; iii-- ) {
-                    if( bases[iii] != prevBase ) { // This base doesn't match the previous one so it is a new cycle
-                        cycle++;
-                        prevBase = bases[iii];
-                    }
+                int iii = bases.length-1;
+                while( iii >= offset )
+                {
+                    while( iii >= offset && bases[iii] == (byte)'T' ) { iii--; }
+                    while( iii >= offset && bases[iii] == (byte)'A' ) { iii--; }
+                    while( iii >= offset && bases[iii] == (byte)'C' ) { iii--; }
+                    while( iii >= offset && bases[iii] == (byte)'G' ) { iii--; }
+                    if( iii >= offset ) { cycle++; }
+                    if( iii >= offset && !BaseUtils.isRegularBase(bases[iii]) ) { iii--; }
                 }
             }
+
             return cycle;
         }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
index 780330210..ed355404d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
@@ -59,7 +59,7 @@ public class RecalibrationArgumentCollection {
     public int WINDOW_SIZE = 5;
     @Argument(fullName = "homopolymer_nback", shortName="nback", doc="The number of previous bases to look at in HomopolymerCovariate", required=false)
     public int HOMOPOLYMER_NBACK = 7;
-
+    
     public boolean checkSolidRecalMode() {
         return ( SOLID_RECAL_MODE.equalsIgnoreCase("DO_NOTHING") || SOLID_RECAL_MODE.equalsIgnoreCase("SET_Q_ZERO") ||
                  SOLID_RECAL_MODE.equalsIgnoreCase("SET_Q_ZERO_BASE_N") || SOLID_RECAL_MODE.equalsIgnoreCase("REMOVE_REF_BIAS") );
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 76567bd35..3436a075e 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -18,8 +18,8 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "16f87c9644b27c3c3fe7a963eed45d2d" );
         e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "5a4873064e602e1f945f3881c6b4a3e5");
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "b039f405580ad844cd1dfd4d8ba25913" );
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "dbbb9c49f2e0b1f117b88eb386fb6d0f" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "42f78368cc85eb3963329ad48c244e80" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "f97ec61e98db1a580900d9f4985080d0" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -51,8 +51,8 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "d7f3e0db5ed9fefc917144a0f937d50d" );
         e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "1f1770363f381d06e8db9fead03ad7bb");
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "3fe6ee95cfa6155f8cc8e3e0a6330ad2" );
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "732267e9cd02a72b8c85238f47487509" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "563cdb25b5a963121299ad319d5ec2ae" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "dd8b61060914b75199ca5babc60248fa" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();