diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 0a06e2203..60fa75f41 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -316,6 +316,7 @@ public class UnifiedGenotyperEngine {
             // if in GENOTYPE_GIVEN_ALLELES mode, we still want to allow the use of a poor allele
             else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
                 myAlleles.add(alternateAllele);
+                alleleCountsofMLE.add(AFresult.getAlleleCountsOfMLE()[indexOfAllele-1]);
             }
         }
 
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 7c3991cf0..616503cff 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
@@ -44,7 +44,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithAllelesPassedIn2() {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("42c4e37e0f130dc796231003638a197c"));
+                Arrays.asList("055012eca193a1f12421ea79bef1f4e0"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
 
@@ -327,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("c9b468fe75e7215a6d6d5a050af07918"));
+                Arrays.asList("ebba1c06555c469cfb01d87f34aa6783"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
     }