diff --git a/build.xml b/build.xml
index 1a9c72bd8..34dcc05fb 100644
--- a/build.xml
+++ b/build.xml
@@ -403,7 +403,11 @@
 
     <target name="sting-utils.jar" depends="gatk.compile, init.jar">
         <jar jarfile="${dist.dir}/StingUtils.jar">
-            <fileset dir="${java.classes}" includes="**/utils/**/*.class"/>
+            <fileset dir="${java.classes}">
+              <include name="**/utils/**/*.class"/>
+              <exclude name="**/utils/codecs/**/*.class"/>
+              <exclude name="**/utils/variantcontext/**/*.class"/>
+            </fileset>
             <fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/datasources/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
@@ -415,6 +419,15 @@
         </jar>
     </target>
 
+    <target name="vcf.jar" depends="gatk.compile,init.jar">
+        <jar jarfile="${dist.dir}/vcf.jar">
+            <fileset dir="${java.classes}">
+              <include name="**/utils/codecs/**/*.class"/>
+              <include name="**/utils/variantcontext/**/*.class"/>
+            </fileset>
+        </jar>
+    </target>
+
     <target name="gatk.jar" depends="gatk.compile, init.jar"
             description="generate the GATK distribution">
         <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
@@ -497,7 +510,7 @@
         </jar>
     </target>
 
-    <target name="sting.jar" depends="sting-utils.jar, gatk.jar, gatk.oneoffs.jar, queue.jar" />
+    <target name="sting.jar" depends="sting-utils.jar, vcf.jar, gatk.jar, gatk.oneoffs.jar, queue.jar" />
 
     <target name="init.manifests" depends="sting.jar">
         <pathconvert property="jar.classpath" pathsep=" ">
diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index af355ab03..f8527c33b 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -30,7 +30,7 @@ import net.sf.samtools.*;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.commandline.ArgumentException;
 import org.broadinstitute.sting.commandline.ArgumentSource;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.CommandLineUtils;
 import org.broadinstitute.sting.commandline.ParsingEngine;
 import org.broadinstitute.sting.commandline.Tags;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
index e85ef80be..0a5981a1b 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
@@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.datasources.sample;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
index fdac507f7..74176ec35 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
@@ -2,8 +2,8 @@ package org.broadinstitute.sting.gatk.io.storage;
 
 import org.apache.log4j.Logger;
 import org.broad.tribble.source.BasicFeatureSource;
-import org.broad.tribble.vcf.*;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
index 888f8b36e..7521e754d 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
index a31a16d50..1a79d2785 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
@@ -30,10 +30,10 @@ import java.io.PrintStream;
 import java.io.OutputStream;
 import java.util.Collection;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
index 239877ccf..43bf6f8e0 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index d2595a39e..7d7a9d32c 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -3,21 +3,19 @@ package org.broadinstitute.sting.gatk.refdata;
 import org.broad.tribble.Feature;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broad.tribble.gelitext.GeliTextFeature;
-import org.broad.tribble.hapmap.HapMapFeature;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.MutableGenotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.MutableGenotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import javax.xml.stream.events.Attribute;
 import java.util.*;
-import java.util.jar.Attributes;
 
 /**
  * A terrible but temporary approach to converting objects to VariantContexts.  If you want to add a converter,
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
index dd946287d..c7bf86569 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
@@ -31,7 +31,7 @@ import java.util.ArrayList;
 import java.util.Map;
 
 import net.sf.samtools.util.StringUtil;
-import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 public class BeagleFeature implements Feature {
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java b/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
index d2a5d17ed..75e7c1a32 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.refdata.utils.helpers;
 import net.sf.samtools.util.SequenceUtil;
 import org.broad.tribble.annotation.Strand;
 import org.broad.tribble.dbsnp.DbSNPFeature;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.util.ArrayList;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
index 8ffc7d957..54fd0a20c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
index 726b659e3..2c06b30d6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index e9f324363..b02dcd8e2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -25,10 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
index b853ed5f3..0be737897 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
@@ -1,12 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.vcf.VCFFormatHeaderLine;
-import org.broad.tribble.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.gatk.contexts.*;
-import org.broad.tribble.util.variantcontext.*;
+import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.*;
 
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
index 9b1ee4b4f..51b5381dc 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import java.util.Map;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
index 9d441918f..244627154 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
@@ -31,9 +31,9 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
index 588a86087..ff916bedd 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
index 9c5ba40aa..143722d7c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index bc6f71cbf..e56825dbe 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index 2e033a865..754d28dfd 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFCompoundHeaderLine;
-import org.broad.tribble.vcf.VCFFormatHeaderLine;
-import org.broad.tribble.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index 66d927e1c..2115526a6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -32,10 +32,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
-import org.broad.tribble.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import cern.jet.math.Arithmetic;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
index 8dc7b294c..5eaa30bf3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
index 081d43498..3a5db2884 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index cb7bcbeed..bd8c51a41 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -24,11 +24,11 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
index 05f7fa2e6..ecebfbbd2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
index 16287491c..099780fa7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
index 2a0ae0290..ee8b01d7d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index b3e3a742c..33069f1f5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index 0f874ed7f..11f86b972 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
index 665f5c0a4..25a7b286d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
index de64741dd..00cc30309 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
@@ -31,11 +31,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.vcf.VCFConstants;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 
 import java.util.Map;
 import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
index 46beed71d..dc4934ade 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
@@ -1,9 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
index 760f68b9e..ba3e2cc8b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 2ef9947e2..720984835 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index 4ac4880d3..6e80c7555 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index e5e08472a..1a967293f 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
index 3f0105376..f287549bb 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
@@ -27,19 +27,18 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.vcf.VCFFormatHeaderLine;
-import org.broad.tribble.vcf.VCFCompoundHeaderLine;
-import org.broad.tribble.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 
 import java.util.Map;
 import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
index 9d5f2ec1a..2a17cd436 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
index 5e38fd5b2..fc769ac54 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
index 3c1c87170..82f16be42 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
@@ -25,16 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
index fb34b56ae..0b6cbcc2e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 0d9ccf738..cd5b6694b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
@@ -42,7 +42,7 @@ import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index 3eb60a54f..54c8be73a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -37,9 +37,9 @@ import java.util.Map;
 import java.util.Set;
 import java.util.Map.Entry;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
index caa32fef3..e02c62baf 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
@@ -28,10 +28,10 @@ package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 import java.util.*;
 import java.util.Map.Entry;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
index f10101328..69a35a584 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
@@ -31,10 +31,10 @@ import java.io.IOException;
 import java.util.*;
 import java.util.Map.Entry;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -47,7 +47,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 /**
  * Annotates variant calls with information from user-specified tabular files.
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
index ee0038ee8..29b256479 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
index c82da908f..5b33395b5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
index 3f5dd1396..aa23abc67 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -41,8 +41,8 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 
 import java.util.*;
 import static java.lang.Math.log10;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
index 98ec7f3d7..93ee0b085 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
@@ -25,10 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Input;
@@ -36,7 +36,7 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
@@ -46,13 +46,10 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.File;
 import java.io.PrintStream;
-import java.text.DecimalFormat;
-import java.text.MessageFormat;
 import java.util.*;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
index 9a9aff457..18aa3e257 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
@@ -25,17 +25,17 @@
 
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
@@ -43,7 +43,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
index 6c8eef9a6..828d39717 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
index a5a74ffa4..b31526987 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
index 4ef007e05..c3849e240 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
index 61536e758..884d0ac24 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -39,7 +39,7 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
index 07e8fc2ce..47be7e6fe 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
@@ -26,11 +26,11 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broad.tribble.util.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java
index 2220dd6bc..fbd9c1dbf 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 public class BiallelicGenotypeLikelihoods {
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 7f4185229..89504b371 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -26,9 +26,9 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
index 5b8a2c761..3902a0b7f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
index ca162c749..c4e315f68 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
@@ -26,9 +26,9 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.collections.Pair;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 1ee658f5c..1f430548b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
@@ -44,7 +44,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
index a983036f3..2cf149fd0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 
 import java.util.ArrayList;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 9800ea5c7..9f4d4182f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.utils.*;
@@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
index 4bfb93e80..cf1c57a05 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.DownsampleType;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
index 4a6ab0eaf..1533e8777 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
@@ -24,14 +24,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 0a2b6f503..7a765c602 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -37,7 +37,7 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 import java.io.PrintStream;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 69c616584..4c9080884 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -26,10 +26,10 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.GenotypeLikelihoods;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.pileup.*;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import com.google.java.contract.*;
 
 import java.io.PrintStream;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
index 8153d9b11..5896e784e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
index 5de01392c..7617aa9de 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
@@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.AlignmentBlock;
 import net.sf.samtools.SAMRecord;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index c0b170d25..28b88f9f2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -30,7 +30,7 @@ import net.sf.samtools.util.RuntimeIOException;
 import net.sf.samtools.util.StringUtil;
 import net.sf.samtools.util.SequenceUtil;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 56e2ab6b3..89bdd53c8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -29,7 +29,7 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
-import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 /*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate;
 import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index b536a0cb5..048dbd8cb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.BadCigarFilter;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
index 0d9edcde1..c2953d1d7 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
@@ -25,11 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.*;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
@@ -58,6 +57,8 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.Hidden;
 
+import net.sf.samtools.*;
+
 import java.io.*;
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
index f7e763d8c..869edf784 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
@@ -23,8 +23,8 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
index fac4b5dc1..7989f52db 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
@@ -24,14 +24,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature;
@@ -43,11 +43,11 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
-import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods;
+import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods;
 
 
 /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
index 5122e10c3..709bc44ce 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
@@ -24,11 +24,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -36,11 +35,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
-import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods;
+import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods;
 
 
 /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
index 8acece2ed..abced442e 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
@@ -27,12 +27,12 @@ package org.broadinstitute.sting.gatk.walkers.phasing;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFWriter;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
index 0c1bc7180..ec6f5c648 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
@@ -24,24 +24,24 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
-import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods;
+import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods;
 
 /**
  * Walks along all variant ROD loci, and merges consecutive sites if some sample has segregating alt alleles in the ROD.
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 7e2476f8d..e59b29502 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -23,14 +23,14 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -40,15 +40,15 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broad.tribble.vcf.SortingVCFWriter;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.io.*;
 import java.util.*;
 
-import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods;
+import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods;
 
 
 /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java
index af3960b1a..55da1c152 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java
@@ -24,7 +24,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
index 55a877c57..db1f888a1 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
@@ -23,8 +23,8 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
index ddeadee37..f82e48abd 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
@@ -24,9 +24,9 @@
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 
 public class WriteVCF {
     public static void writeVCF(VariantContext vc, VCFWriter writer, Logger logger) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ProfileRodSystem.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ProfileRodSystem.java
index 142c383e3..67879a442 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ProfileRodSystem.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ProfileRodSystem.java
@@ -24,10 +24,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broad.tribble.util.ParsingUtils;
-import org.broad.tribble.vcf.VCFConstants;
-import org.broad.tribble.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
index 5bf7738ca..ee504b6e7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@@ -27,9 +27,8 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import org.broad.tribble.bed.BEDCodec;
 import org.broad.tribble.dbsnp.DbSNPCodec;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCF3Codec;
-import org.broad.tribble.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.commandline.Gather;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
index 19c272bbf..c1c17bda5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.sequenom;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
index 466184da6..f350e7531 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
@@ -28,8 +28,8 @@ package org.broadinstitute.sting.gatk.walkers.sequenom;
 import net.sf.samtools.util.CloseableIterator;
 import org.broad.tribble.bed.BEDCodec;
 import org.broad.tribble.dbsnp.DbSNPCodec;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 2a21bfe41..15d808ebe 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -2,13 +2,13 @@ package org.broadinstitute.sting.gatk.walkers.varianteval;
 
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
@@ -29,11 +29,9 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import net.sf.picard.reference.FastaSequenceFile;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.gatk.walkers.fasta.FastaSequence;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import net.sf.picard.reference.ReferenceSequence;
 import java.io.FileNotFoundException;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
index 00c997a67..787dbe9af 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 class NewCompEvalGenotypes {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
index 37172617a..76db330ed 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index db4a11960..c4277adc9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
index ad8bfbbe4..4b56cf130 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
index be0b96d3c..3d14dd0e5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
index 6c8ac3dc6..5daf33a9f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
index c6133acdf..eca6c5193 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
index 410e5da9c..48b06d532 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
index 6f2f89fcf..85e0b5889 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
index 3085e358c..7d54d0df8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
@@ -24,7 +24,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
index c1ba8cccb..5f3e6b0fa 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
index 6be2786d2..deed05508 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
index 0d4f4df77..89c67cfe9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
index 99b4daec8..8811dc001 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
index 8bf317b25..405f35635 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
@@ -1,18 +1,15 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
-import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
index 2180bb732..6017ecca3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
index bc8f9a8f8..4af14810b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
@@ -25,11 +25,11 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
index 19f207df1..ff59c9e29 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
index 0daad99dc..48b4ffa91 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
index e4d95c514..9942ba8d6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
index 0ce74f518..1a9d31085 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
index 65608f6b7..15b1d41c1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
index 7c41ea58e..65af6090c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
index 6400d612c..7bd15a974 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
index 10e628520..8d8782ab7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
index ed9d4d266..fd724d6d1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
index 9fa0eca61..a7ccd3182 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
index ab0fa7f4a..39d2e6b4d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
index 940352246..f909de4f3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
index 96603edaf..218cb23ca 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
index 44248e169..3208c26bb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
index dce08da45..0281653af 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
 import org.apache.commons.jexl2.*;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable<SortableJexlVCMatchExp> {
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index 32996a0bc..b8e45e462 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 48deabc14..9877781d1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
index 4ebe9807b..2914385a4 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantQualityScore;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 1d6d9a1e4..2fd1326fe 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import cern.jet.random.Normal;
 import org.apache.log4j.Logger;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 4eb3f7639..e651b62e0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 4cee70def..597a54dc1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -25,13 +25,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import com.sun.tools.internal.xjc.reader.gbind.ElementSets;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Requires;
@@ -42,7 +41,7 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index 298a7e38c..ba6f5e513 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -24,16 +24,16 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.commandline.Output;
-import org.broad.tribble.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index bb39e2765..d9dd85f0c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -28,13 +28,13 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.SortingVCFWriter;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -42,7 +42,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 56c5d8db3..7eda54387 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -24,18 +24,18 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
index 1c9155045..0c41a9728 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
@@ -24,11 +24,11 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.StandardVCFWriter;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -40,7 +40,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.File;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 0f1d5221c..963aa0ce5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -24,26 +24,25 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.MendelianViolation;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.File;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 19932ca2b..ec7395f85 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broad.tribble.TribbleException;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
index c3de49a83..482679593 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
@@ -25,18 +25,17 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 4aa854946..71dd5df3f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -24,12 +24,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index 56fb4c75c..7eb49da34 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -28,14 +28,14 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 import net.sf.samtools.util.CloseableIterator;
 import org.broad.tribble.dbsnp.DbSNPCodec;
 import org.broad.tribble.dbsnp.DbSNPFeature;
-import org.broad.tribble.hapmap.HapMapFeature;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.commandline.Argument;
@@ -45,7 +45,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AffectedConsistencyWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AffectedConsistencyWalker.java
index 044c12cf7..4100b500d 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AffectedConsistencyWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AffectedConsistencyWalker.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
@@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java
index a8c374d63..509d65441 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotateTruthROD.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotateTruthROD.java
index 901a85fd1..3fac966ea 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotateTruthROD.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotateTruthROD.java
@@ -25,21 +25,21 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.MutableVariantContext;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.MutableVariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotationByAlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotationByAlleleFrequencyWalker.java
index 926842b7f..40bec19f6 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotationByAlleleFrequencyWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotationByAlleleFrequencyWalker.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessLikelihoodsAtTruth.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessLikelihoodsAtTruth.java
index 8fa4a3ed1..57d143127 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessLikelihoodsAtTruth.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessLikelihoodsAtTruth.java
@@ -25,9 +25,9 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.GenotypeLikelihoods;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java
index 3b134849d..4478bd501 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java
@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSimulatedPerformance.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSimulatedPerformance.java
index 844a16c3b..47bd82d2f 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSimulatedPerformance.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSimulatedPerformance.java
@@ -24,12 +24,12 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSnpsNearIndels.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSnpsNearIndels.java
index f3baf24f7..b7aa1defe 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSnpsNearIndels.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSnpsNearIndels.java
@@ -25,27 +25,17 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.iterators.DownsampleIterator;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.io.PrintStream;
-import java.io.Writer;
-import java.security.PrivilegedActionException;
 import java.util.*;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
index 5242125db..64e2633da 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
@@ -25,11 +25,10 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
-import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/CNVstatsWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/CNVstatsWalker.java
index 0cdb07e4b..b29917f48 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/CNVstatsWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/CNVstatsWalker.java
@@ -24,9 +24,9 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers.CNV;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CalibrateGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CalibrateGenotypeLikelihoods.java
index ff0a9696c..d454dec7e 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CalibrateGenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CalibrateGenotypeLikelihoods.java
@@ -26,9 +26,9 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import net.sf.samtools.SAMReadGroupRecord;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.GenotypeLikelihoods;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CreateTiTvTrack.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CreateTiTvTrack.java
index 60078cbfb..63b17bda3 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CreateTiTvTrack.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CreateTiTvTrack.java
@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.wiggle.WiggleHeader;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeConcordanceTable.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeConcordanceTable.java
index cfe7fb9a3..d4b73cb59 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeConcordanceTable.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeConcordanceTable.java
@@ -24,8 +24,8 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
index 13499214e..399a3e6df 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
@@ -1,8 +1,7 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.FeatureSource;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -12,12 +11,11 @@ import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.File;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
index fb22c7577..1c7a2d8e4 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java
index a6166be53..a6fcce290 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java
@@ -27,8 +27,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates;
 
 import org.broad.tribble.bed.BEDCodec;
 import org.broad.tribble.dbsnp.DbSNPCodec;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.commandline.Gather;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
index b90a152dc..189db5206 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
@@ -1,15 +1,15 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.StandardVCFWriter;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.walkers.Reference;
@@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java
index 109fa6b40..54bdfdf3f 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java
@@ -38,7 +38,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.List;
 import java.util.Collection;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
index 4ae95f265..65e09f0db 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
@@ -1,18 +1,18 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.StandardVCFWriter;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
@@ -21,7 +21,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 
 import java.io.PrintStream;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimulateReadsForVariants.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimulateReadsForVariants.java
index bb058a6f1..914a9d745 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimulateReadsForVariants.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimulateReadsForVariants.java
@@ -24,37 +24,35 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.vcf.VCFWriter;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.filters.ReadGroupBlackListFilter;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
-import java.io.PrintStream;
 import java.io.PrintWriter;
 import java.util.*;
 
 import net.sf.samtools.*;
+
 import cern.jet.math.Arithmetic;
 import cern.jet.random.Poisson;
 import cern.jet.random.engine.MersenneTwister;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
index 0bd969874..a23b064f1 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
@@ -25,9 +25,8 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.StandardVCFWriter;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.*;
@@ -38,7 +37,6 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.walkers.Window;
 
 import java.util.EnumSet;
-import java.io.File;
 import java.io.PrintStream;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
index 2c476442a..1519aa02e 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -12,7 +12,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.File;
 import java.io.FileInputStream;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/HammingDistance.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/HammingDistance.java
index 95a980a8a..62490b66f 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/HammingDistance.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/HammingDistance.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/InsertSizeDistribution.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/InsertSizeDistribution.java
index d1618697e..95d4b6bf5 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/InsertSizeDistribution.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/InsertSizeDistribution.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java
index 51ebfb2db..1af1fa491 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java
@@ -25,9 +25,9 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/QualByDepthV2.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/QualByDepthV2.java
index 72079733e..416b7e8c2 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/QualByDepthV2.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/QualByDepthV2.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CalcFullHaplotypesWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CalcFullHaplotypesWalker.java
index 4f8d84965..c0dce0d46 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CalcFullHaplotypesWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CalcFullHaplotypesWalker.java
@@ -24,9 +24,9 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -40,7 +40,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import java.io.PrintStream;
 import java.util.*;
 
-import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods;
+import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods;
 
 /**
  * Walks along all variant ROD loci and verifies the phasing from the reads for user-defined pairs of sites.
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java
index f10062185..a385f870d 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java
@@ -24,12 +24,12 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -46,12 +46,12 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.PrintStream;
 import java.util.*;
 
-import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods;
+import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods;
 
 /**
  * Walks along all variant ROD loci and verifies the phasing from the reads for user-defined pairs of sites.
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CountHetPhasingInIntervalWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CountHetPhasingInIntervalWalker.java
index 00f34c03e..5c0af0e41 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CountHetPhasingInIntervalWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CountHetPhasingInIntervalWalker.java
@@ -24,8 +24,8 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhaseByTransmission.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhaseByTransmission.java
index 27d583b4a..ed5406b8b 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhaseByTransmission.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhaseByTransmission.java
@@ -1,23 +1,20 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.report.GATKReport;
-import org.broadinstitute.sting.gatk.report.GATKReportTable;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhasingEval.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhasingEval.java
index 58d007cc2..4a1b51d4c 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhasingEval.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhasingEval.java
@@ -24,8 +24,8 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -36,7 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/PickSequenomProbes2.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/PickSequenomProbes2.java
index 627b5d59b..045d442a9 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/PickSequenomProbes2.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/PickSequenomProbes2.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.validation;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/PrivatePermutations.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/PrivatePermutations.java
index 0b0b87981..b6af87637 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/PrivatePermutations.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/PrivatePermutations.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BootstrapCallsMerger.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BootstrapCallsMerger.java
index 4d9de6eda..b8937d5dd 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BootstrapCallsMerger.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BootstrapCallsMerger.java
@@ -1,22 +1,19 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.vcftools;
 
 import com.google.common.collect.ArrayListMultimap;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
-import javax.management.NotificationBroadcaster;
 import java.util.*;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java
index f0c4bbf10..933fc629d 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java
@@ -1,24 +1,23 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.vcftools;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.exceptions.*;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java b/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java
index e66f1c2b0..49d9713dd 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java
@@ -26,10 +26,10 @@
 package org.broadinstitute.sting.playground.gatk.features.maf;
 
 import org.broad.tribble.Feature;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.utils.exceptions.StingException;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java
index 9e768d166..437fed843 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java
@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.playground.gatk.walkers;
 
-import org.broad.tribble.util.variantcontext.MutableVariantContext;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.MutableVariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -44,7 +44,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
index 1a2025d0d..96d3d175a 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.playground.gatk.walkers;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
index 12a5f372c..272e9ad26 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
@@ -26,8 +26,8 @@
 package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java
index 08a74a431..94df8c69b 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.playground.gatk.walkers;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
index 06632766c..37745c003 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/PrintReferenceVariantsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/PrintReferenceVariantsWalker.java
index 725bf140a..eeaa3ff41 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/PrintReferenceVariantsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/PrintReferenceVariantsWalker.java
@@ -23,10 +23,10 @@
  */
 package org.broadinstitute.sting.playground.gatk.walkers.phasing;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -34,7 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.phasing.WriteVCF;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
index 698dceee8..b3136b54f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
@@ -25,9 +25,9 @@
 package org.broadinstitute.sting.playground.gatk.walkers.phasing;
 
 import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java
index 489cfca8f..661f746f6 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.playground.gatk.walkers.replication_validation;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java
index 1ebdac489..95266d2e9 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java
@@ -24,38 +24,18 @@
 
 package org.broadinstitute.sting.playground.gatk.walkers.validation;
 
-import com.sun.tools.corba.se.idl.constExpr.Not;
-import com.sun.tools.internal.xjc.reader.xmlschema.bindinfo.BIConversion;
-import org.broad.tribble.Feature;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.bed.BedParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
-import javax.activation.*;
-import java.beans.VetoableChangeSupport;
-import java.io.PrintStream;
-import java.io.Writer;
-import java.security.KeyStore;
 import java.util.*;
 
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
index ce73dfd8c..9e832fde6 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.playground.gatk.walkers.validation;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantutils/CGVarToVCF.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantutils/CGVarToVCF.java
index 0263937c8..51951e56c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantutils/CGVarToVCF.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantutils/CGVarToVCF.java
@@ -25,10 +25,10 @@
 
 package org.broadinstitute.sting.playground.gatk.walkers.variantutils;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
diff --git a/java/src/org/broadinstitute/sting/playground/tools/SortROD.java b/java/src/org/broadinstitute/sting/playground/tools/SortROD.java
index 6acb98dab..0a659c010 100644
--- a/java/src/org/broadinstitute/sting/playground/tools/SortROD.java
+++ b/java/src/org/broadinstitute/sting/playground/tools/SortROD.java
@@ -28,15 +28,14 @@ package org.broadinstitute.sting.playground.tools;
 import org.apache.log4j.BasicConfigurator;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.Feature;
-import org.broad.tribble.completegenomics.CGVarCodec;
+import org.broadinstitute.sting.utils.codecs.completegenomics.CGVarCodec;
 import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.soapsnp.SoapSNPCodec;
+import org.broadinstitute.sting.utils.codecs.soapsnp.SoapSNPCodec;
 import org.broad.tribble.gelitext.GeliTextCodec;
 import org.broad.tribble.dbsnp.DbSNPCodec;
 import org.broad.tribble.bed.BEDCodec;
-import org.broad.tribble.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.playground.gatk.features.maf.MafCodec;
diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
index 0ac08b7f7..fe6758e76 100644
--- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.queue.extensions.gatk;
 import net.sf.samtools.BAMIndex;
 import net.sf.samtools.SAMFileWriter;
 import org.broad.tribble.Tribble;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
 
diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
index f035892ce..2da427d44 100644
--- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
+++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
@@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileWriter;
 import org.apache.commons.lang.StringEscapeUtils;
 import org.apache.commons.lang.StringUtils;
 import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
-import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 
 import java.io.File;
 import java.io.InputStream;
diff --git a/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/java/src/org/broadinstitute/sting/utils/IndelUtils.java
index 86363cba0..30e1a3f5b 100755
--- a/java/src/org/broadinstitute/sting/utils/IndelUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/IndelUtils.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/java/src/org/broadinstitute/sting/utils/MendelianViolation.java b/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
index dab1f51fd..a8089ffe8 100755
--- a/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
+++ b/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.utils;
 
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/java/src/org/broadinstitute/sting/utils/SampleUtils.java
index d15eb8e86..c0370064d 100755
--- a/java/src/org/broadinstitute/sting/utils/SampleUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -27,12 +27,12 @@ package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
-import org.broad.tribble.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
new file mode 100755
index 000000000..a286ce789
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
@@ -0,0 +1,160 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.completegenomics;
+
+import org.broad.tribble.Feature;
+import org.broad.tribble.FeatureCodec;
+import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * a codec for the VAR file types produced by the Complete Genomics Institute
+ */
+public class CGVarCodec implements FeatureCodec {
+
+    private static final String REF_TYPE = "ref";
+    private static final String SNP_TYPE = "snp";
+    private static final String DELETION_TYPE = "del";
+    private static final String INSERTION_TYPE = "ins";
+    private static final String SUBSTITUTION_TYPE = "sub";
+
+    // the minimum number of features in the CG file line
+    private static final int minimumFeatureCount = 8;
+
+    /**
+     * decode the location only
+     * @param line the input line to decode
+     * @return a HapMapFeature
+     */
+    public Feature decodeLoc(String line) {
+        return decode(line);
+    }
+
+    /**
+     * decode the CG record
+     * @param line the input line to decode
+     * @return a VariantContext
+     */
+    public Feature decode(String line) {
+        String[] array = line.split("\\s+");
+
+        // make sure the split was successful - that we got an appropriate number of fields
+        if ( array.length < minimumFeatureCount )
+            return null;
+
+        String type = array[6];
+
+        long start = Long.valueOf(array[4]);
+        long end;
+        Allele ref, alt = null;
+
+        //System.out.println(line);
+
+        if ( type.equals(SNP_TYPE) ) {
+            ref = Allele.create(array[7], true);
+            alt = Allele.create(array[8], false);
+            end = start;
+        } else if ( type.equals(INSERTION_TYPE) ) {
+            ref = Allele.create(Allele.NULL_ALLELE_STRING, true);
+            alt = Allele.create(array[7], false);
+            end = start;
+        } else if ( type.equals(DELETION_TYPE) ) {
+            ref = Allele.create(array[7], true);
+            alt = Allele.create(Allele.NULL_ALLELE_STRING, false);
+            end = start + ref.length();
+        //} else if ( type.equals(REF_TYPE) ) {
+        //    ref = Allele.create("N", true); // ref bases aren't accurate
+        //    start++;
+        //    end = start;
+        //} else if ( type.equals(SUBSTITUTION_TYPE) ) {
+        //    ref = Allele.create(array[7], true);
+        //    alt = Allele.create(array[8], false);
+        //    end = start + Math.max(ref.length(), alt.length());
+        } else {
+            return null; // we don't handle other types
+        }
+
+        HashSet<Allele> alleles = new HashSet<Allele>();
+        alleles.add(ref);
+        if ( alt != null )
+            alleles.add(alt);
+
+        HashMap<String, Object> attrs = new HashMap<String, Object>();
+        String id = array[array.length - 1];
+        if ( id.indexOf("dbsnp") != -1 ) {
+            attrs.put(VariantContext.ID_KEY, parseID(id));
+        }
+
+        // create a new feature given the array
+        return new VariantContext("CGI", array[3], start, end, alleles, VariantContext.NO_NEG_LOG_10PERROR, null, attrs);
+    }
+
+    public Class getFeatureType() {
+        return VariantContext.class;
+    }
+
+    // There's no spec and no character to distinguish header lines...
+    private final static int NUM_HEADER_LINES = 12;
+    public Object readHeader(LineReader reader) {
+        return null;
+
+        //String headerLine = null;
+        //try {
+        //    for (int i = 0; i < NUM_HEADER_LINES; i++)
+        //        headerLine = reader.readLine();
+        //} catch (IOException e) {
+        //    throw new IllegalArgumentException("Unable to read a line from the line reader");
+        //}
+        //return headerLine;
+    }
+
+    private static final Pattern DBSNP_PATTERN = Pattern.compile("^dbsnp\\.\\d+:(.*)");
+    private String parseID(String raw) {
+        StringBuilder sb = null;
+
+        String[] ids = raw.split(";");
+        for ( String id : ids ) {
+            Matcher matcher = DBSNP_PATTERN.matcher(id);
+            if ( matcher.matches() ) {
+                String rsID = matcher.group(1);
+                if ( sb == null ) {
+                    sb = new StringBuilder(rsID);
+                } else {
+                    sb.append(";");
+                    sb.append(rsID);
+                }
+            }
+        }
+
+        return sb == null ? null : sb.toString();
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapCodec.java
new file mode 100644
index 000000000..bd95e0f3d
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapCodec.java
@@ -0,0 +1,97 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.hapmap;
+
+import org.broad.tribble.Feature;
+import org.broad.tribble.FeatureCodec;
+import org.broad.tribble.annotation.Strand;
+import org.broad.tribble.readers.LineReader;
+
+import java.io.IOException;
+import java.util.Arrays;
+
+/**
+ * a codec for the file types produced by the HapMap consortium, available on their website:
+ * http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/
+ *
+ * The format includes eleven standard fields, plus genotypes for each of the samples included
+ * in the file
+ * 
+ */
+public class HapMapCodec implements FeatureCodec {
+    // the minimum number of features in the HapMap file line
+    private static final int minimumFeatureCount = 11;
+
+    private String headerLine;
+    /**
+     * decode the location only
+     * @param line the input line to decode
+     * @return a HapMapFeature
+     */
+    public Feature decodeLoc(String line) {
+        return decode(line);
+    }
+
+    /**
+     * decode the hapmap record
+     * @param line the input line to decode
+     * @return a HapMapFeature, with the given fields 
+     */
+    public Feature decode(String line) {
+        String[] array = line.split("\\s+");
+
+        // make sure the split was successful - that we got an appropriate number of fields
+        if (array.length < minimumFeatureCount)
+            throw new IllegalArgumentException("Unable to parse line " + line + ", the length of split features is less than the minimum of " + minimumFeatureCount);
+
+        // create a new feature given the array
+        return new HapMapFeature(array[0],
+                array[1].split("/"),
+                array[2],
+                Long.valueOf(array[3]),
+                Strand.toStrand(array[4]),
+                array[5],
+                array[6],
+                array[7],
+                array[8],
+                array[9],
+                array[10],
+                Arrays.copyOfRange(array,11,array.length),
+                headerLine);
+    }
+
+    public Class getFeatureType() {
+        return HapMapFeature.class;
+    }
+
+    public Object readHeader(LineReader reader) {
+        try {
+            headerLine = reader.readLine();
+        } catch (IOException e) {
+            throw new IllegalArgumentException("Unable to read a line from the line reader");
+        }
+        return headerLine;
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapFeature.java b/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapFeature.java
new file mode 100755
index 000000000..7a47a4b8d
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapFeature.java
@@ -0,0 +1,194 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.hapmap;
+
+import org.broad.tribble.Feature;
+import org.broad.tribble.annotation.Strand;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * a feature returned by the HapMap Codec - it represents contig, position, name,
+ * alleles, other hapmap information, and genotypes for specified samples
+ */
+public class HapMapFeature implements Feature {
+
+    public static final String INSERTION = "I";
+    public static final String DELETION = "D";
+
+    // the variables we store internally in the class
+    private final String name;
+    private final String[] alleles;
+    private Map<String, Allele> actualAlleles = null;
+    private final String contig ;
+    private long position;
+    private final Strand strand;
+    private final String assembly;
+    private final String center;
+    private final String protLSID;
+    private final String assayLSID;
+    private final String panelLSID;
+    private final String qccode;
+    private final String[] genotypes;
+
+    // we store the header line, if they'd like to get the samples
+    private final String headerLine;
+
+    /**
+     * create a HapMap Feature, based on all the records available in the hapmap file
+     * @param contig the contig name
+     * @param position the position
+     * @param strand the strand enum
+     * @param assembly what assembly this feature is from
+     * @param center the center that provided this SNP
+     * @param protLSID ??
+     * @param assayLSID ??
+     * @param panelLSID ??
+     * @param qccode ??
+     * @param genotypes a list of strings, representing the genotypes for the list of samples
+     */
+    public HapMapFeature(String name,
+                         String[] alleles,
+                         String contig,
+                         Long position,
+                         Strand strand,
+                         String assembly,
+                         String center,
+                         String protLSID,
+                         String assayLSID,
+                         String panelLSID,
+                         String qccode,
+                         String[] genotypes,
+                         String headerLine) {
+        this.name = name;
+        this.alleles = alleles;
+        this.contig = contig;
+        this.position = position;
+        this.strand = strand;
+        this.assembly =  assembly;
+        this.center =  center;
+        this.protLSID = protLSID ;
+        this.assayLSID = assayLSID ;
+        this.panelLSID = panelLSID ;
+        this.qccode = qccode;
+        this.genotypes = genotypes;
+        this.headerLine = headerLine;
+    }
+
+    /**
+     * get the contig value
+     * @return a string representing the contig
+     */
+    public String getChr() {
+        return contig;
+    }
+
+    /**
+     * get the start position, as an integer
+     * @return an int, representing the start position
+     */
+    public int getStart() {
+        return (int)position;
+    }
+
+    /**
+     * get the end position
+     * @return get the end position as an int
+     */
+    public int getEnd() {
+        return (int)position;
+    }
+
+    /**
+     * Getter methods
+     */
+
+    public Strand getStrand() {
+        return strand;
+    }
+
+    public String getAssembly() {
+        return assembly;
+    }
+
+    public String getCenter() {
+        return center;
+    }
+
+    public String getProtLSID() {
+        return protLSID;
+    }
+
+    public String getAssayLSID() {
+        return assayLSID;
+    }
+
+    public String getPanelLSID() {
+        return panelLSID;
+    }
+
+    public String getQCCode() {
+        return qccode;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public String[] getAlleles() {
+        return alleles;
+    }
+
+    public String[] getGenotypes() {
+        return genotypes;
+    }
+
+    // This is necessary because HapMap places insertions in the incorrect position
+    public void updatePosition(long position) {
+        this.position = position;
+    }
+
+    public void setActualAlleles(Map<String, Allele> alleleMap) {
+        actualAlleles = new HashMap<String, Allele>(alleleMap);
+    }
+
+    public Map<String, Allele> getActualAlleles() {
+        return actualAlleles;
+    }
+    
+    /**
+     * get a list of the samples from the header (in order)
+     * @return a string array of sample names
+     */
+    public String[] getSampleIDs() {
+		String[] header = headerLine.split("\\s+");
+		String[] sample_ids = new String[header.length-11];
+		for (int i = 11; i < header.length; i++)
+			sample_ids[i-11] = header[i];
+		return sample_ids;
+	}
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
new file mode 100755
index 000000000..618d9ce79
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
@@ -0,0 +1,209 @@
+package org.broadinstitute.sting.utils.codecs.soapsnp;
+
+import org.broad.tribble.Feature;
+import org.broad.tribble.FeatureCodec;
+import org.broad.tribble.NameAwareCodec;
+import org.broad.tribble.TribbleException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broad.tribble.exception.CodecLineParsingException;
+import org.broad.tribble.readers.LineReader;
+
+import java.util.*;
+
+/**
+ * @author depristo
+ *         <p/>
+ *         a codec for parsing soapsnp files (see http://soap.genomics.org.cn/soapsnp.html#usage2)
+ *         <p/>
+ *
+ * A simple text file format with the following whitespace separated fields:
+ *
+1)  Chromosome ID
+2)  Coordinate on chromosome, start from 1
+3)  Reference genotype
+4)  Consensus genotype
+5)  Quality score of consensus genotype
+6)  Best base
+7)  Average quality score of best base
+8)  Count of uniquely mapped best base
+9)  Count of all mapped best base
+10) Second best bases
+11) Average quality score of second best base
+12) Count of uniquely mapped second best base
+13) Count of all mapped second best base
+14) Sequencing depth of the site
+15) Rank sum test p_value
+16) Average copy number of nearby region
+17) Whether the site is a dbSNP.
+ */
+public class SoapSNPCodec implements FeatureCodec, NameAwareCodec {
+    private String[] parts;
+
+    // we store a name to give to each of the variant contexts we emit
+    private String name = "Unknown";
+
+    public Feature decodeLoc(String line) {
+        return decode(line);
+    }
+
+    /**
+     * Decode a line as a Feature.
+     *
+     * @param line
+     *
+     * @return Return the Feature encoded by the line,  or null if the line does not represent a feature (e.g. is
+     *         a comment)
+     */
+    public Feature decode(String line) {
+        try {
+            // parse into lines
+            parts = line.trim().split("\\s+");
+
+            // check that we got the correct number of tokens in the split
+            if (parts.length != 18)
+                throw new CodecLineParsingException("Invalid SoapSNP row found -- incorrect element count.  Expected 18, got " + parts.length + " line = " + line);
+
+            String contig = parts[0];
+            long start = Long.valueOf(parts[1]);
+            AlleleAndGenotype allelesAndGenotype = parseAlleles(parts[2], parts[3], line);
+
+            double negLog10PError = Integer.valueOf(parts[4]) / 10.0;
+
+            Map<String, Object> attributes = new HashMap<String, Object>();
+            attributes.put("BestBaseQ", parts[6]);
+            attributes.put("SecondBestBaseQ", parts[10]);
+            attributes.put("RankSumP", parts[15]);
+            // add info to keys
+
+            //System.out.printf("Alleles  = " + allelesAndGenotype.alleles);
+            //System.out.printf("genotype = " + allelesAndGenotype.genotype);
+            
+            VariantContext vc = new VariantContext(name, contig, start, start, allelesAndGenotype.alleles, allelesAndGenotype.genotype, negLog10PError, VariantContext.PASSES_FILTERS, attributes);
+
+            //System.out.printf("line  = %s%n", line);
+            //System.out.printf("vc    = %s%n", vc);
+
+            return vc;
+        } catch (CodecLineParsingException e) {
+            throw new TribbleException("Unable to parse line " + line,e);
+        } catch (NumberFormatException e) {
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+            throw new TribbleException("Unable to parse line " + line,e);
+        }
+    }
+
+    private static class AlleleAndGenotype {
+        Collection<Allele> alleles;
+        Collection<Genotype> genotype;
+
+        public AlleleAndGenotype(Collection<Allele> alleles, Genotype genotype) {
+            this.alleles = alleles;
+            this.genotype = new HashSet<Genotype>();
+            this.genotype.add(genotype);
+        }
+    }
+
+    private AlleleAndGenotype parseAlleles(String ref, String consensusGenotype, String line) {
+        /* A	Adenine
+    C	Cytosine
+    G	Guanine
+    T (or U)	Thymine (or Uracil)
+    R	A or G
+    Y	C or T
+    S	G or C
+    W	A or T
+    K	G or T
+    M	A or C
+    B	C or G or T
+    D	A or G or T
+    H	A or C or T
+    V	A or C or G
+    N	any base
+    . or -	gap
+    */
+        if ( ref.equals(consensusGenotype) )
+            throw new TribbleException.InternalCodecException("Ref base and consensus genotype are the same " + ref);
+
+        Allele refAllele = Allele.create(ref, true);
+        List<Allele> genotypeAlleles = null;
+
+        char base = consensusGenotype.charAt(0);
+
+        switch ( base ) {
+            case 'A': case 'C': case 'G': case 'T':
+                Allele a = Allele.create(consensusGenotype);
+                genotypeAlleles = Arrays.asList(a, a);
+                break;
+            case 'R': case 'Y': case 'S': case 'W': case 'K': case 'M':
+                genotypeAlleles = determineAlt(refAllele, ref.charAt(0), base);
+                break;
+            default:
+                throw new TribbleException("Unexpected consensus genotype " + consensusGenotype + " at line = " + line);
+        }
+
+
+        Collection<Allele> alleles = new HashSet<Allele>(genotypeAlleles);
+        alleles.add(refAllele);
+        Genotype genotype = new Genotype("unknown", genotypeAlleles); // todo -- probably should include genotype quality
+
+        return new AlleleAndGenotype( alleles, genotype );
+    }
+
+    private static final Map<Character, String> IUPAC_SNPS = new HashMap<Character, String>();
+    static {
+        IUPAC_SNPS.put('R', "AG");
+        IUPAC_SNPS.put('Y', "CT");
+        IUPAC_SNPS.put('S', "GC");
+        IUPAC_SNPS.put('W', "AT");
+        IUPAC_SNPS.put('K', "GT");
+        IUPAC_SNPS.put('M', "AC");
+    }
+
+    private List<Allele> determineAlt(Allele ref, char refbase, char alt) {
+        String alts = IUPAC_SNPS.get(alt);
+        if ( alts == null )
+            throw new IllegalStateException("BUG: unexpected consensus genotype " + alt);
+            
+        Allele a1 = alts.charAt(0) == refbase ? ref : Allele.create((byte)alts.charAt(0));
+        Allele a2 = alts.charAt(1) == refbase ? ref : Allele.create((byte)alts.charAt(1));
+
+        //if ( a1 != ref && a2 != ref )
+        //    throw new IllegalStateException("BUG: unexpected consensus genotype " + alt + " does not contain the reference base " + ref);
+
+        return Arrays.asList(a1, a2);
+    }
+
+    /**
+     * @return VariantContext
+     */
+    public Class getFeatureType() {
+        return VariantContext.class;
+    }
+
+    public Object readHeader(LineReader reader)  {
+        
+        return null;  // we don't have a meaningful header
+    }
+
+    /**
+     * get the name of this codec
+     * @return our set name
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * set the name of this codec
+     * @param name new name
+     */
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public static void main(String[] args) {
+        System.out.printf("Testing " + args[0]);
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
new file mode 100755
index 000000000..cd0f52c68
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -0,0 +1,617 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.apache.log4j.Logger;
+import org.broad.tribble.Feature;
+import org.broad.tribble.FeatureCodec;
+import org.broad.tribble.NameAwareCodec;
+import org.broad.tribble.TribbleException;
+import org.broad.tribble.readers.LineReader;
+import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.*;
+
+
+public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser {
+
+    protected final static Logger log = Logger.getLogger(VCFCodec.class);
+    protected final static int NUM_STANDARD_FIELDS = 8;  // INFO is the 8th column
+
+    protected VCFHeaderVersion version;
+
+    // we have to store the list of strings that make up the header until they're needed
+    protected VCFHeader header = null;
+
+    // a mapping of the allele
+    protected Map<String, List<Allele>> alleleMap = new HashMap<String, List<Allele>>(3);
+
+    // for ParsingUtils.split
+    protected String[] GTValueArray = new String[100];
+    protected String[] genotypeKeyArray = new String[100];
+    protected String[] infoValueArray = new String[1000];
+
+    // for performance testing purposes
+    public static boolean validate = true;
+
+    // a key optimization -- we need a per thread string parts array, so we don't allocate a big array over and over
+    // todo: make this thread safe?
+    protected String[] parts = null;
+    protected String[] genotypeParts = null;
+
+    // for performance we cache the hashmap of filter encodings for quick lookup
+    protected HashMap<String,LinkedHashSet<String>> filterHash = new HashMap<String,LinkedHashSet<String>>();
+
+    // a mapping of the VCF fields to their type, filter fields, and format fields, for quick lookup to validate against
+    TreeMap<String, VCFHeaderLineType> infoFields = new TreeMap<String, VCFHeaderLineType>();
+    TreeMap<String, VCFHeaderLineType> formatFields = new TreeMap<String, VCFHeaderLineType>();
+    Set<String> filterFields = new HashSet<String>();
+
+    // we store a name to give to each of the variant contexts we emit
+    protected String name = "Unknown";
+
+    protected int lineNo = 0;
+
+    protected Map<String, String> stringCache = new HashMap<String, String>();
+
+
+    /**
+     * @param reader the line reader to take header lines from
+     * @return the number of header lines
+     */
+    public abstract Object readHeader(LineReader reader);
+
+    /**
+     * create a genotype map
+     * @param str the string
+     * @param alleles the list of alleles
+     * @param chr chrom
+     * @param pos position
+     * @return a mapping of sample name to genotype object
+     */
+    public abstract Map<String, Genotype> createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
+
+
+    /**
+     * parse the filter string, first checking to see if we already have parsed it in a previous attempt
+     * @param filterString the string to parse
+     * @return a set of the filters applied
+     */
+    protected abstract Set<String> parseFilters(String filterString);
+
+    /**
+     * create a VCF header
+     * @param headerStrings a list of strings that represent all the ## entries
+     * @param line the single # line (column names)
+     * @return the count of header lines
+     */
+    protected Object createHeader(List<String> headerStrings, String line) {
+
+        headerStrings.add(line);
+
+        Set<VCFHeaderLine> metaData = new TreeSet<VCFHeaderLine>();
+        Set<String> auxTags = new LinkedHashSet<String>();
+        // iterate over all the passed in strings
+        for ( String str : headerStrings ) {
+            if ( !str.startsWith(VCFHeader.METADATA_INDICATOR) ) {
+                String[] strings = str.substring(1).split(VCFConstants.FIELD_SEPARATOR);
+                int arrayIndex = 0;
+                for (VCFHeader.HEADER_FIELDS field : VCFHeader.HEADER_FIELDS.values()) {
+                    try {
+                        if (field != VCFHeader.HEADER_FIELDS.valueOf(strings[arrayIndex]))
+                            throw new TribbleException.InvalidHeader("we were expecting column name '" + field + "' but we saw '" + strings[arrayIndex] + "'");
+                    } catch (IllegalArgumentException e) {
+                        throw new TribbleException.InvalidHeader("unknown column name '" + strings[arrayIndex] + "'; it does not match a legal column header name.");
+                    }
+                    arrayIndex++;
+                }
+                if ( arrayIndex < strings.length ) {
+                    if ( !strings[arrayIndex].equals("FORMAT") )
+                        throw new TribbleException.InvalidHeader("we were expecting column name 'FORMAT' but we saw '" + strings[arrayIndex] + "'");
+                    arrayIndex++;
+                }
+
+                while (arrayIndex < strings.length)
+                    auxTags.add(strings[arrayIndex++]);
+
+            } else {
+                if ( str.startsWith("##INFO=") ) {
+                    VCFInfoHeaderLine info = new VCFInfoHeaderLine(str.substring(7),version);
+                    metaData.add(info);
+                    infoFields.put(info.getName(), info.getType());
+                } else if ( str.startsWith("##FILTER=") ) {
+                    VCFFilterHeaderLine filter = new VCFFilterHeaderLine(str.substring(9),version);
+                    metaData.add(filter);
+                    filterFields.add(filter.getName());
+                } else if ( str.startsWith("##FORMAT=") ) {
+                    VCFFormatHeaderLine format = new VCFFormatHeaderLine(str.substring(9),version);
+                    metaData.add(format);
+                    formatFields.put(format.getName(), format.getType());
+                } else {
+                    int equals = str.indexOf("=");
+                    if ( equals != -1 )
+                        metaData.add(new VCFHeaderLine(str.substring(2, equals), str.substring(equals+1)));
+                }
+            }
+        }
+
+        header = new VCFHeader(metaData, auxTags);
+        return header;
+    }
+
+    /**
+     * the fast decode function
+     * @param line the line of text for the record
+     * @return a feature, (not guaranteed complete) that has the correct start and stop
+     */
+    public Feature decodeLoc(String line) {
+        return reallyDecode(line);
+    }
+
+    /**
+     * decode the line into a feature (VariantContext)
+     * @param line the line
+     * @return a VariantContext
+     */
+    public Feature decode(String line) {
+        return reallyDecode(line);
+    }
+
+    private Feature reallyDecode(String line) {
+        try {
+            // the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
+            if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
+
+            // our header cannot be null, we need the genotype sample names and counts
+            if (header == null) throw new IllegalStateException("VCF Header cannot be null when decoding a record");
+
+            if (parts == null)
+                parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)];
+
+            int nParts = ParsingUtils.split(line, parts, VCFConstants.FIELD_SEPARATOR_CHAR, true);
+
+            // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns.  Otherwise check that we have nine (normal colummns + genotyping data)
+            if (( (header == null || (header != null && !header.hasGenotypingData())) && nParts != NUM_STANDARD_FIELDS) ||
+                 (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
+                throw new IllegalArgumentException("There aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
+                        " tokens, and saw " + nParts + " )");
+
+            return parseVCFLine(parts);
+        } catch (TribbleException e) {
+            throw new TribbleException.InvalidDecodeLine(e.getMessage(), line);
+        }
+    }
+
+    protected void generateException(String message) {
+        throw new TribbleException.InvalidDecodeLine(message, lineNo);
+    }
+
+    /**
+     * parse out the VCF line
+     *
+     * @param parts the parts split up
+     * @return a variant context object
+     */
+    private VariantContext parseVCFLine(String[] parts) {
+        // increment the line count
+        lineNo++;
+
+        // parse out the required fields
+        String contig = getCachedString(parts[0]);
+        long pos = Long.valueOf(parts[1]);
+        String id = null;
+        if ( parts[2].length() == 0 )
+            generateException("The VCF specification requires a valid ID field");
+        else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) )
+            id = VCFConstants.EMPTY_ID_FIELD;
+        else
+            id = new String(parts[2]);
+        String ref = getCachedString(parts[3].toUpperCase());
+        String alts = getCachedString(parts[4].toUpperCase());
+        Double qual = parseQual(parts[5]);
+        String filter = getCachedString(parts[6]);
+        String info = new String(parts[7]);
+
+        // get our alleles, filters, and setup an attribute map
+        List<Allele> alleles = parseAlleles(ref, alts, lineNo);
+        Set<String> filters = parseFilters(filter);
+        Map<String, Object> attributes = parseInfo(info, id);
+
+        // find out our current location, and clip the alleles down to their minimum length
+        long loc = pos;
+        // ref alleles don't need to be single bases for monomorphic sites
+        if ( alleles.size() == 1 ) {
+            loc = pos + alleles.get(0).length() - 1;
+        } else if ( !isSingleNucleotideEvent(alleles) ) {
+            ArrayList<Allele> newAlleles = new ArrayList<Allele>();
+            loc = clipAlleles(pos, ref, alleles, newAlleles);
+            alleles = newAlleles;
+        }
+
+        // do we have genotyping data
+        if (parts.length > NUM_STANDARD_FIELDS) {
+            attributes.put(VariantContext.UNPARSED_GENOTYPE_MAP_KEY, new String(parts[8]));
+            attributes.put(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY, this);
+        }
+
+        VariantContext vc = null;
+        try {
+            vc =  new VariantContext(name, contig, pos, loc, alleles, qual, filters, attributes);
+        } catch (Exception e) {
+            generateException(e.getMessage());
+        }
+
+        // did we resort the sample names?  If so, we need to load the genotype data
+        if ( !header.samplesWereAlreadySorted() )
+            vc.getGenotypes();
+
+        // Trim bases of all alleles if necessary
+        return createVariantContextWithTrimmedAlleles(vc);
+    }
+
+    /**
+     *
+     * @return the type of record
+     */
+    public Class getFeatureType() {
+        return VariantContext.class;
+    }
+
+    /**
+     * get the name of this codec
+     * @return our set name
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * set the name of this codec
+     * @param name new name
+     */
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    /**
+     * Return a cached copy of the supplied string.
+     *
+     * @param str string
+     * @return interned string
+     */
+    protected String getCachedString(String str) {
+        String internedString = stringCache.get(str);
+        if ( internedString == null ) {
+            internedString = new String(str);
+            stringCache.put(internedString, internedString);
+        }
+        return internedString;
+    }
+
+    /**
+     * parse out the info fields
+     * @param infoField the fields
+     * @param id the indentifier
+     * @return a mapping of keys to objects
+     */
+    private Map<String, Object> parseInfo(String infoField, String id) {
+        Map<String, Object> attributes = new HashMap<String, Object>();
+
+        if ( infoField.length() == 0 )
+            generateException("The VCF specification requires a valid info field");
+
+        if ( !infoField.equals(VCFConstants.EMPTY_INFO_FIELD) ) {
+            int infoValueSplitSize = ParsingUtils.split(infoField, infoValueArray, VCFConstants.INFO_FIELD_SEPARATOR_CHAR);
+            for (int i = 0; i < infoValueSplitSize; i++) {
+                String key;
+                Object value;
+
+                int eqI = infoValueArray[i].indexOf("=");
+                if ( eqI != -1 ) {
+                    key = infoValueArray[i].substring(0, eqI);
+                    String str = infoValueArray[i].substring(eqI+1, infoValueArray[i].length());
+
+                    // lets see if the string contains a , separator
+                    if ( str.contains(",") )
+                        value = Arrays.asList(str.split(","));
+                    else
+                        value = str;
+                } else {
+                    key = infoValueArray[i];
+                    value = true;
+                }
+
+                attributes.put(key, value);
+            }
+        }
+
+        attributes.put(VariantContext.ID_KEY, id);
+        return attributes;
+    }
+
+    /**
+     * create a an allele from an index and an array of alleles
+     * @param index the index
+     * @param alleles the alleles
+     * @return an Allele
+     */
+    protected static Allele oneAllele(String index, List<Allele> alleles) {
+        if ( index.equals(VCFConstants.EMPTY_ALLELE) )
+            return Allele.NO_CALL;
+        int i = Integer.valueOf(index);
+        if ( i >= alleles.size() )
+            throw new TribbleException.InternalCodecException("The allele with index " + index + " is not defined in the REF/ALT columns in the record");
+        return alleles.get(i);
+    }
+
+
+    /**
+     * parse genotype alleles from the genotype string
+     * @param GT         GT string
+     * @param alleles    list of possible alleles
+     * @param cache      cache of alleles for GT
+     * @return the allele list for the GT string
+     */
+    protected static List<Allele> parseGenotypeAlleles(String GT, List<Allele> alleles, Map<String, List<Allele>> cache) {
+        // cache results [since they are immutable] and return a single object for each genotype
+        List<Allele> GTAlleles = cache.get(GT);
+
+        if ( GTAlleles == null ) {
+            StringTokenizer st = new StringTokenizer(GT, VCFConstants.PHASING_TOKENS);
+            GTAlleles = new ArrayList<Allele>(st.countTokens());
+            while ( st.hasMoreTokens() ) {
+                String genotype = st.nextToken();
+                GTAlleles.add(oneAllele(genotype, alleles));
+            }
+            cache.put(GT, GTAlleles);
+        }
+
+        return GTAlleles;
+    }
+
+    /**
+     * parse out the qual value
+     * @param qualString the quality string
+     * @return return a double
+     */
+    protected static Double parseQual(String qualString) {
+        // if we're the VCF 4 missing char, return immediately
+        if ( qualString.equals(VCFConstants.MISSING_VALUE_v4))
+            return VariantContext.NO_NEG_LOG_10PERROR;
+
+        Double val = Double.valueOf(qualString);
+
+        // check to see if they encoded the missing qual score in VCF 3 style, with either the -1 or -1.0.  check for val < 0 to save some CPU cycles
+        if ((val < 0) && (Math.abs(val - VCFConstants.MISSING_QUALITY_v3_DOUBLE) < VCFConstants.VCF_ENCODING_EPSILON))
+            return VariantContext.NO_NEG_LOG_10PERROR;
+
+        // scale and return the value
+        return val / 10.0;
+    }
+
+    /**
+     * parse out the alleles
+     * @param ref the reference base
+     * @param alts a string of alternates to break into alleles
+     * @param lineNo  the line number for this record
+     * @return a list of alleles, and a pair of the shortest and longest sequence
+     */
+    protected static List<Allele> parseAlleles(String ref, String alts, int lineNo) {
+        List<Allele> alleles = new ArrayList<Allele>(2); // we are almost always biallelic
+        // ref
+        checkAllele(ref, true, lineNo);
+        Allele refAllele = Allele.create(ref, true);
+        alleles.add(refAllele);
+
+        if ( alts.indexOf(",") == -1 ) // only 1 alternatives, don't call string split
+            parseSingleAltAllele(alleles, alts, lineNo);
+        else
+            for ( String alt : alts.split(",") )
+                parseSingleAltAllele(alleles, alt, lineNo);
+
+        return alleles;
+    }
+
+    /**
+     * check to make sure the allele is an acceptable allele
+     * @param allele the allele to check
+     * @param isRef are we the reference allele?
+     * @param lineNo  the line number for this record
+     */
+    private static void checkAllele(String allele, boolean isRef, int lineNo) {
+	if ( allele == null || allele.length() == 0 )
+	    generateException("Empty alleles are not permitted in VCF records", lineNo);
+
+        if ( isSymbolicAllele(allele) ) {
+            if ( isRef ) {
+                generateException("Symbolic alleles not allowed as reference allele: " + allele, lineNo);
+            }
+        } else {
+            // check for VCF3 insertions or deletions
+            if ( (allele.charAt(0) == VCFConstants.DELETION_ALLELE_v3) || (allele.charAt(0) == VCFConstants.INSERTION_ALLELE_v3) )
+                generateException("Insertions/Deletions are not supported when reading 3.x VCF's. Please" +
+                        " convert your file to VCF4 using VCFTools, available at http://vcftools.sourceforge.net/index.html", lineNo);
+
+            if (!Allele.acceptableAlleleBases(allele))
+                generateException("Unparsable vcf record with allele " + allele, lineNo);
+
+            if ( isRef && allele.equals(VCFConstants.EMPTY_ALLELE) )
+                generateException("The reference allele cannot be missing", lineNo);
+        }
+    }
+
+    /**
+     * return true if this is a symbolic allele (e.g. <SOMETAG>) otherwise false
+     * @param allele the allele to check
+     * @return true if the allele is a symbolic allele, otherwise false
+     */
+    private static boolean isSymbolicAllele(String allele) {
+        return (allele != null && allele.startsWith("<") && allele.endsWith(">") && allele.length() > 2);
+    }
+
+    /**
+     * parse a single allele, given the allele list
+     * @param alleles the alleles available
+     * @param alt the allele to parse
+     * @param lineNo  the line number for this record
+     */
+    private static void parseSingleAltAllele(List<Allele> alleles, String alt, int lineNo) {
+        checkAllele(alt, false, lineNo);
+
+        Allele allele = Allele.create(alt, false);
+        if ( ! allele.isNoCall() )
+            alleles.add(allele);
+    }
+
+    protected static boolean isSingleNucleotideEvent(List<Allele> alleles) {
+        for ( Allele a : alleles ) {
+            if ( a.length() != 1 )
+                return false;
+        }
+        return true;
+    }
+
+    private static void generateException(String message, int lineNo) {
+        throw new TribbleException.InvalidDecodeLine(message, lineNo);
+    }
+
+    private static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
+        boolean clipping = true;
+        // Note that the computation of forward clipping here is meant only to see whether there is a common
+        // base to all alleles, and to correctly compute reverse clipping,
+        // but it is not used for actually changing alleles - this is done in function
+        // createVariantContextWithTrimmedAlleles() below.
+
+        for (Allele a : unclippedAlleles) {
+            if (a.isSymbolic()) {
+                continue;
+            }
+            if (a.length() < 1 || (a.getBases()[0] != ref.getBytes()[0])) {
+                clipping = false;
+            }
+        }
+        return (clipping) ? 1 : 0;
+
+    }
+
+    /**
+     * clip the alleles, based on the reference
+     *
+     * @param position the unadjusted start position (pre-clipping)
+     * @param ref the reference string
+     * @param unclippedAlleles the list of unclipped alleles
+     * @param clippedAlleles output list of clipped alleles
+     * @return a list of alleles, clipped to the reference
+     */
+    protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles) {
+
+        // Note that the computation of forward clipping here is meant only to see whether there is a common
+        // base to all alleles, and to correctly compute reverse clipping,
+        // but it is not used for actually changing alleles - this is done in function
+        // createVariantContextWithTrimmedAlleles() below.
+
+        int forwardClipping = computeForwardClipping(unclippedAlleles, ref);
+
+        int reverseClipped = 0;
+        boolean clipping = true;
+        while (clipping) {
+            for (Allele a : unclippedAlleles) {
+                if (a.isSymbolic()) {
+                    continue;
+                }
+                if (a.length() - reverseClipped <= forwardClipping || a.length() - forwardClipping == 0)
+                    clipping = false;
+                else if (a.getBases()[a.length()-reverseClipped-1] != ref.getBytes()[ref.length()-reverseClipped-1])
+                    clipping = false;
+            }
+            if (clipping) reverseClipped++;
+        }
+
+        for (Allele a : unclippedAlleles) {
+            if (a.isSymbolic()) {
+                clippedAlleles.add(a);
+            } else {
+                clippedAlleles.add(Allele.create(Arrays.copyOfRange(a.getBases(),0,a.getBases().length-reverseClipped),a.isReference()));
+            }
+        }
+
+        // the new reference length
+        int refLength = ref.length() - reverseClipped;
+
+        return position+Math.max(refLength - 1,0);
+    }
+
+    public static VariantContext createVariantContextWithTrimmedAlleles(VariantContext inputVC) {
+        // see if we need to trim common reference base from all alleles
+        boolean trimVC;
+
+        // We need to trim common reference base from all alleles in all genotypes if a ref base is common to all alleles
+        Allele refAllele = inputVC.getReference();
+        if (!inputVC.isVariant())
+            trimVC = false;
+        else if (refAllele.isNull())
+            trimVC = false;
+        else {
+            trimVC = (computeForwardClipping(new ArrayList<Allele>(inputVC.getAlternateAlleles()),
+                    inputVC.getReference().getDisplayString()) > 0);
+         }
+
+        // nothing to do if we don't need to trim bases
+        if (trimVC) {
+            List<Allele> alleles = new ArrayList<Allele>();
+            Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();
+
+            // set the reference base for indels in the attributes
+            Map<String,Object> attributes = new TreeMap<String,Object>(inputVC.getAttributes());
+            attributes.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, new Byte(inputVC.getReference().getBases()[0]));
+
+            Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>();
+
+            for (Allele a : inputVC.getAlleles()) {
+                if (a.isSymbolic()) {
+                    alleles.add(a);
+                    originalToTrimmedAlleleMap.put(a, a);
+                } else {
+                    // get bases for current allele and create a new one with trimmed bases
+                    byte[] newBases = Arrays.copyOfRange(a.getBases(), 1, a.length());
+                    Allele trimmedAllele = Allele.create(newBases, a.isReference());
+                    alleles.add(trimmedAllele);
+                    originalToTrimmedAlleleMap.put(a, trimmedAllele);
+                }
+            }
+
+            // detect case where we're trimming bases but resulting vc doesn't have any null allele. In that case, we keep original representation
+            // example: mixed records such as {TA*,TGA,TG}
+            boolean hasNullAlleles = false;
+
+            for (Allele a: originalToTrimmedAlleleMap.values()) {
+                if (a.isNull())
+                    hasNullAlleles = true;
+                if (a.isReference())
+                    refAllele = a;
+             }
+
+             if (!hasNullAlleles)
+               return inputVC;
+           // now we can recreate new genotypes with trimmed alleles
+            for ( Map.Entry<String, Genotype> sample : inputVC.getGenotypes().entrySet() ) {
+
+                List<Allele> originalAlleles = sample.getValue().getAlleles();
+                List<Allele> trimmedAlleles = new ArrayList<Allele>();
+                for ( Allele a : originalAlleles ) {
+                    if ( a.isCalled() )
+                        trimmedAlleles.add(originalToTrimmedAlleleMap.get(a));
+                    else
+                        trimmedAlleles.add(Allele.NO_CALL);
+                }
+                genotypes.put(sample.getKey(), Genotype.modifyAlleles(sample.getValue(), trimmedAlleles));
+
+            }
+            return new VariantContext(inputVC.getSource(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(), inputVC.filtersWereApplied() ? inputVC.getFilters() : null, attributes);
+
+        }
+
+        return inputVC;
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java
new file mode 100755
index 000000000..7dcdab924
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java
@@ -0,0 +1,52 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+/**
+ * this class writes VCF files, allowing records to be passed in unsorted.
+ */
+public class ManualSortingVCFWriter extends SortingVCFWriterBase {
+
+    /**
+     * create a local-sorting VCF writer, given an inner VCF writer to write to
+     *
+     * @param innerWriter        the VCFWriter to write to
+     * @param takeOwnershipOfInner Should this Writer close innerWriter when it's done with it
+     */
+    public ManualSortingVCFWriter(VCFWriter innerWriter, boolean takeOwnershipOfInner) {
+        super(innerWriter, takeOwnershipOfInner);
+    }
+
+    public ManualSortingVCFWriter(VCFWriter innerWriter) {
+        super(innerWriter);
+    }
+
+    // Note that if mostUpstreamWritableLoc = null, then ALL records will be emitted (since not currently waiting for anything)
+    public void setmostUpstreamWritableLocus(Integer mostUpstreamWritableLoc) {
+        this.mostUpstreamWritableLoc = mostUpstreamWritableLoc;
+        emitSafeRecords();
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java
new file mode 100755
index 000000000..7ece5edf8
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java
@@ -0,0 +1,61 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+/**
+ * this class writes VCF files, allowing records to be passed in unsorted (up to a certain genomic distance away)
+ */
+public class SortingVCFWriter extends SortingVCFWriterBase {
+
+    // the maximum START distance between records that we'll cache
+    private int maxCachingStartDistance;
+
+    /**
+     * create a local-sorting VCF writer, given an inner VCF writer to write to
+     *
+     * @param innerWriter        the VCFWriter to write to
+     * @param maxCachingStartDistance the maximum start distance between records that we'll cache
+     * @param takeOwnershipOfInner Should this Writer close innerWriter when it's done with it
+     */
+    public SortingVCFWriter(VCFWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner) {
+        super(innerWriter, takeOwnershipOfInner);
+        this.maxCachingStartDistance = maxCachingStartDistance;
+    }
+
+    public SortingVCFWriter(VCFWriter innerWriter, int maxCachingStartDistance) {
+        this(innerWriter, maxCachingStartDistance, false); // by default, don't own inner
+    }
+
+    protected void noteCurrentRecord(VariantContext vc) {
+        super.noteCurrentRecord(vc); // first, check for errors
+
+        // then, update mostUpstreamWritableLoc:
+        int mostUpstreamWritableIndex = vc.getStart() - maxCachingStartDistance;
+        this.mostUpstreamWritableLoc = Math.max(BEFORE_MOST_UPSTREAM_LOC, mostUpstreamWritableIndex);
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java
new file mode 100755
index 000000000..311aaecf7
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java
@@ -0,0 +1,168 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.Comparator;
+import java.util.PriorityQueue;
+import java.util.Set;
+import java.util.TreeSet;
+
+/**
+ * This class writes VCF files, allowing records to be passed in unsorted.
+ * It also enforces that it is never passed records of the same chromosome with any other chromosome in between them.
+ */
+public abstract class SortingVCFWriterBase implements VCFWriter {
+
+    // The VCFWriter to which to actually write the sorted VCF records
+    private VCFWriter innerWriter = null;
+
+    // the current queue of un-emitted records
+    private PriorityQueue<VCFRecord> queue = null;
+
+    // The locus until which we are permitted to write out (inclusive)
+    protected Integer mostUpstreamWritableLoc;
+    protected static final int BEFORE_MOST_UPSTREAM_LOC = 0; // No real locus index is <= 0
+
+    // The set of chromosomes already passed over and to which it is forbidden to return
+    private Set<String> finishedChromosomes = null;
+
+    // Should we call innerWriter.close() in close()
+    private boolean takeOwnershipOfInner;
+
+    /**
+     * create a local-sorting VCF writer, given an inner VCF writer to write to
+     *
+     * @param innerWriter        the VCFWriter to write to
+     * @param takeOwnershipOfInner Should this Writer close innerWriter when it's done with it
+     */
+    public SortingVCFWriterBase(VCFWriter innerWriter, boolean takeOwnershipOfInner) {
+        this.innerWriter = innerWriter;
+        this.queue = new PriorityQueue<VCFRecord>(50, new VariantContextComparator());
+        this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC;
+        this.finishedChromosomes = new TreeSet<String>();
+        this.takeOwnershipOfInner = takeOwnershipOfInner;
+    }
+
+    public SortingVCFWriterBase(VCFWriter innerWriter) {
+        this(innerWriter, false); // by default, don't own inner
+    }
+
+    public void writeHeader(VCFHeader header) {
+        innerWriter.writeHeader(header);
+    }
+
+    /**
+     * attempt to close the VCF file; we need to flush the queue first
+     */
+    public void close() {
+        stopWaitingToSort();
+
+        if (takeOwnershipOfInner)
+            innerWriter.close();
+    }
+
+    private void stopWaitingToSort() {
+        emitRecords(true);
+        mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC;
+    }
+
+    protected void emitSafeRecords() {
+        emitRecords(false);
+    }
+
+    protected void noteCurrentRecord(VariantContext vc) {
+        // did the user break the contract by giving a record too late?
+        if (mostUpstreamWritableLoc != null && vc.getStart() < mostUpstreamWritableLoc) // went too far back, since may have already written anything that is <= mostUpstreamWritableLoc
+            throw new IllegalArgumentException("Permitted to write any record upstream of position " + mostUpstreamWritableLoc + ", but a record at " + vc.getChr() + ":" + vc.getStart() + " was just added.");
+    }
+
+    /**
+     * add a record to the file
+     *
+     * @param vc      the Variant Context object
+     * @param refBase the ref base
+     */
+    public void add(VariantContext vc, byte refBase) {
+        /* Note that the code below does not prevent the successive add()-ing of: (chr1, 10), (chr20, 200), (chr15, 100)
+           since there is no implicit ordering of chromosomes:
+         */
+        VCFRecord firstRec = queue.peek();
+        if (firstRec != null && !vc.getChr().equals(firstRec.vc.getChr())) { // if we hit a new contig, flush the queue
+            if (finishedChromosomes.contains(vc.getChr()))
+                throw new IllegalArgumentException("Added a record at " + vc.getChr() + ":" + vc.getStart() + ", but already finished with chromosome" + vc.getChr());
+
+            finishedChromosomes.add(firstRec.vc.getChr());
+            stopWaitingToSort();
+        }
+
+        noteCurrentRecord(vc); // possibly overwritten
+
+        queue.add(new VCFRecord(vc, refBase));
+        emitSafeRecords();
+    }
+
+    private void emitRecords(boolean emitUnsafe) {
+        while (!queue.isEmpty()) {
+            VCFRecord firstRec = queue.peek();
+
+            // No need to wait, waiting for nothing, or before what we're waiting for:
+            if (emitUnsafe || mostUpstreamWritableLoc == null || firstRec.vc.getStart() <= mostUpstreamWritableLoc) {
+                queue.poll();
+                innerWriter.add(firstRec.vc, firstRec.refBase);
+            }
+            else {
+                break;
+            }
+        }
+    }
+
+    /**
+     * Gets a string representation of this object.
+     * @return
+     */
+    @Override
+    public String toString() {
+        return getClass().getName();
+    }
+
+    private static class VariantContextComparator implements Comparator<VCFRecord> {
+        public int compare(VCFRecord r1, VCFRecord r2) {
+            return r1.vc.getStart() - r2.vc.getStart();
+        }
+    }
+
+    private static class VCFRecord {
+        public VariantContext vc;
+        public byte refBase;
+
+        public VCFRecord(VariantContext vc, byte refBase) {
+            this.vc = vc;
+            this.refBase = refBase;
+        }
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
new file mode 100755
index 000000000..31251c089
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
@@ -0,0 +1,529 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broad.tribble.Tribble;
+import org.broad.tribble.TribbleException;
+import org.broad.tribble.index.DynamicIndexCreator;
+import org.broad.tribble.index.Index;
+import org.broad.tribble.index.IndexFactory;
+import org.broad.tribble.util.LittleEndianOutputStream;
+import org.broad.tribble.util.ParsingUtils;
+import org.broad.tribble.util.PositionalStream;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+
+import java.io.*;
+import java.util.*;
+import java.lang.reflect.Array;
+
+/**
+ * this class writes VCF files
+ */
+public class StandardVCFWriter implements VCFWriter {
+
+    // the VCF header we're storing
+    protected VCFHeader mHeader = null;
+
+    // the print stream we're writing to
+    protected BufferedWriter mWriter;
+    protected PositionalStream positionalStream = null;
+
+    // were filters applied?
+    protected boolean filtersWereAppliedToContext = false;
+
+    // should we write genotypes or just sites?
+    protected boolean doNotWriteGenotypes = false;
+
+    protected DynamicIndexCreator indexer = null;
+    protected File indexFile = null;
+    LittleEndianOutputStream idxStream = null;
+    File location = null;
+
+    /**         
+     * create a VCF writer, given a file to write to
+     *
+     * @param location the file location to write to
+     */
+    public StandardVCFWriter(File location) {
+        this(location, openOutputStream(location), true, false);
+    }
+
+    public StandardVCFWriter(File location, boolean enableOnTheFlyIndexing) {
+        this(location, openOutputStream(location), enableOnTheFlyIndexing, false);
+    }
+
+    /**
+     * create a VCF writer, given a stream to write to
+     *
+     * @param output   the file location to write to
+     */
+    public StandardVCFWriter(OutputStream output) {
+        this(output, false);
+    }
+
+    /**
+     * create a VCF writer, given a stream to write to
+     *
+     * @param output   the file location to write to
+     * @param doNotWriteGenotypes   do not write genotypes
+     */
+    public StandardVCFWriter(OutputStream output, boolean doNotWriteGenotypes) {
+        mWriter = new BufferedWriter(new OutputStreamWriter(output));
+        this.doNotWriteGenotypes = doNotWriteGenotypes;
+    }
+
+    public StandardVCFWriter(File location, OutputStream output, boolean enableOnTheFlyIndexing, boolean doNotWriteGenotypes) {
+        this.location = location;
+
+        if ( enableOnTheFlyIndexing ) {
+            indexFile = Tribble.indexFile(location);
+            try {
+                idxStream = new LittleEndianOutputStream(new FileOutputStream(indexFile));
+                //System.out.println("Creating index on the fly for " + location);
+                indexer = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
+                indexer.initialize(location, indexer.defaultBinSize());
+                positionalStream = new PositionalStream(output);
+                output = positionalStream;
+            } catch ( IOException ex ) {
+                // No matter what we keep going, since we don't care if we can't create the index file
+            }
+        }
+
+        //mWriter = new BufferedWriter(new OutputStreamWriter(new PositionalStream(output)));
+        mWriter = new BufferedWriter(new OutputStreamWriter(output));
+        this.doNotWriteGenotypes = doNotWriteGenotypes;
+    }
+
+    public void writeHeader(VCFHeader header) {
+        mHeader = doNotWriteGenotypes ? new VCFHeader(header.getMetaData()) : header;
+        
+        try {
+            // the file format field needs to be written first
+            mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_0.getFormatString() + "=" + VCFHeaderVersion.VCF4_0.getVersionString() + "\n");
+
+            for ( VCFHeaderLine line : mHeader.getMetaData() ) {
+                if ( line.getKey().equals(VCFHeaderVersion.VCF4_0.getFormatString()) ||
+                        line.getKey().equals(VCFHeaderVersion.VCF3_3.getFormatString()) ||
+                        line.getKey().equals(VCFHeaderVersion.VCF3_2.getFormatString()) )
+                    continue;
+
+                // are the records filtered (so we know what to put in the FILTER column of passing records) ?
+                if ( line instanceof VCFFilterHeaderLine)
+                    filtersWereAppliedToContext = true;
+
+                mWriter.write(VCFHeader.METADATA_INDICATOR);
+                mWriter.write(line.toString());
+                mWriter.write("\n");
+            }
+
+            // write out the column line
+            mWriter.write(VCFHeader.HEADER_INDICATOR);
+            for ( VCFHeader.HEADER_FIELDS field : mHeader.getHeaderFields() ) {
+                mWriter.write(field.toString());
+                mWriter.write(VCFConstants.FIELD_SEPARATOR);
+            }
+
+            if ( mHeader.hasGenotypingData() ) {
+                mWriter.write("FORMAT");
+                for ( String sample : mHeader.getGenotypeSamples() ) {
+                    mWriter.write(VCFConstants.FIELD_SEPARATOR);
+                    mWriter.write(sample);
+                }
+            }
+
+            mWriter.write("\n");
+            mWriter.flush();  // necessary so that writing to an output stream will work
+        }
+        catch (IOException e) {
+            throw new TribbleException("IOException writing the VCF header to " + locationString(), e);
+        }
+    }
+
+    private String locationString() {
+        return location == null ? mWriter.toString() : location.getAbsolutePath();
+    }
+
+    /**
+     * attempt to close the VCF file
+     */
+    public void close() {
+        // try to close the vcf stream
+        try {
+            mWriter.flush();
+            mWriter.close();
+        } catch (IOException e) {
+            throw new TribbleException("Unable to close " + locationString() + " because of " + e.getMessage());
+        }
+
+        // try to close the index stream (keep it separate to help debugging efforts)
+        if ( indexer != null ) {
+            try {
+                Index index = indexer.finalizeIndex(positionalStream.getPosition());
+                index.write(idxStream);
+                idxStream.close();
+            } catch (IOException e) {
+                throw new TribbleException("Unable to close index for " + locationString() + " because of " + e.getMessage());
+            }
+        }
+    }
+
+    protected static OutputStream openOutputStream(File location) {
+        try {
+            return new FileOutputStream(location);
+        } catch (FileNotFoundException e) {
+            throw new TribbleException("Unable to create VCF file at location: " + location);
+        }
+    }
+
+    /**
+     * add a record to the file
+     *
+     * @param vc      the Variant Context object
+     * @param refBase the ref base used for indels
+     */
+    public void add(VariantContext vc, byte refBase) {
+        add(vc, refBase, false);
+    }
+
+    /**
+     * add a record to the file
+     *
+     * @param vc      the Variant Context object
+     * @param refBase the ref base used for indels
+     * @param refBaseShouldBeAppliedToEndOfAlleles *** THIS SHOULD BE FALSE EXCEPT FOR AN INDEL AT THE EXTREME BEGINNING OF A CONTIG (WHERE THERE IS NO PREVIOUS BASE, SO WE USE THE BASE AFTER THE EVENT INSTEAD)
+     */
+    public void add(VariantContext vc, byte refBase, boolean refBaseShouldBeAppliedToEndOfAlleles) {
+        if ( mHeader == null )
+            throw new IllegalStateException("The VCF Header must be written before records can be added: " + locationString());
+
+        if ( doNotWriteGenotypes )
+            vc = VariantContext.modifyGenotypes(vc, null);
+
+        try {
+            vc = VariantContext.createVariantContextWithPaddedAlleles(vc, refBase, refBaseShouldBeAppliedToEndOfAlleles);
+
+            // if we are doing on the fly indexing, add the record ***before*** we write any bytes 
+            if ( indexer != null ) indexer.addFeature(vc, positionalStream.getPosition());
+
+            Map<Allele, String> alleleMap = new HashMap<Allele, String>(vc.getAlleles().size());
+            alleleMap.put(Allele.NO_CALL, VCFConstants.EMPTY_ALLELE); // convenience for lookup
+
+            // CHROM
+            mWriter.write(vc.getChr());
+            mWriter.write(VCFConstants.FIELD_SEPARATOR);
+
+            // POS
+            mWriter.write(String.valueOf(vc.getStart()));
+            mWriter.write(VCFConstants.FIELD_SEPARATOR);
+
+            // ID
+            String ID = vc.hasID() ? vc.getID() : VCFConstants.EMPTY_ID_FIELD;
+            mWriter.write(ID);
+            mWriter.write(VCFConstants.FIELD_SEPARATOR);
+
+            // REF
+            alleleMap.put(vc.getReference(), "0");
+            String refString = vc.getReference().getDisplayString();
+            mWriter.write(refString);
+            mWriter.write(VCFConstants.FIELD_SEPARATOR);
+
+            // ALT
+            if ( vc.isVariant() ) {
+                Allele altAllele = vc.getAlternateAllele(0);
+                alleleMap.put(altAllele, "1");
+                String alt = altAllele.getDisplayString();
+                mWriter.write(alt);
+
+                for (int i = 1; i < vc.getAlternateAlleles().size(); i++) {
+                    altAllele = vc.getAlternateAllele(i);
+                    alleleMap.put(altAllele, String.valueOf(i+1));
+                    alt = altAllele.getDisplayString();
+                    mWriter.write(",");
+                    mWriter.write(alt);
+                }
+            } else {
+                mWriter.write(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD);
+            }
+            mWriter.write(VCFConstants.FIELD_SEPARATOR);
+
+            // QUAL
+            if ( !vc.hasNegLog10PError() )
+                mWriter.write(VCFConstants.MISSING_VALUE_v4);
+            else
+                mWriter.write(getQualValue(vc.getPhredScaledQual()));
+            mWriter.write(VCFConstants.FIELD_SEPARATOR);
+
+            // FILTER
+            String filters = vc.isFiltered() ? ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters())) : (filtersWereAppliedToContext || vc.filtersWereApplied() ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.UNFILTERED);
+            mWriter.write(filters);
+            mWriter.write(VCFConstants.FIELD_SEPARATOR);
+
+            // INFO
+            Map<String, String> infoFields = new TreeMap<String, String>();
+            for ( Map.Entry<String, Object> field : vc.getAttributes().entrySet() ) {
+                String key = field.getKey();
+                if ( key.equals(VariantContext.ID_KEY) || key.equals(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY) )
+                    continue;
+
+                String outputValue = formatVCFField(field.getValue());
+                if ( outputValue != null )
+                    infoFields.put(key, outputValue);
+            }
+            writeInfoString(infoFields);
+
+            // FORMAT
+            if ( vc.hasAttribute(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) ) {
+                mWriter.write(VCFConstants.FIELD_SEPARATOR);
+                mWriter.write(vc.getAttributeAsString(VariantContext.UNPARSED_GENOTYPE_MAP_KEY, ""));
+            } else {
+                List<String> genotypeAttributeKeys = new ArrayList<String>();
+                if ( vc.hasGenotypes() ) {
+                    genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
+                    for ( String key : calcVCFGenotypeKeys(vc) ) {
+                        genotypeAttributeKeys.add(key);
+                    }
+                } else if ( mHeader.hasGenotypingData() ) {
+                    // this needs to be done in case all samples are no-calls
+                    genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
+                }
+
+                if ( genotypeAttributeKeys.size() > 0 ) {
+                    String genotypeFormatString = ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
+                    mWriter.write(VCFConstants.FIELD_SEPARATOR);
+                    mWriter.write(genotypeFormatString);
+
+                    addGenotypeData(vc, alleleMap, genotypeAttributeKeys);
+                }
+            }
+            
+            mWriter.write("\n");
+            mWriter.flush();  // necessary so that writing to an output stream will work
+        } catch (IOException e) {
+            throw new RuntimeException("Unable to write the VCF object to " + locationString());
+        }
+
+    }
+
+    private String getQualValue(double qual) {
+        String s = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, qual);
+        if ( s.endsWith(VCFConstants.DOUBLE_PRECISION_INT_SUFFIX) )
+            s = s.substring(0, s.length() - VCFConstants.DOUBLE_PRECISION_INT_SUFFIX.length());
+        return s;
+    }
+
+    /**
+     * create the info string; assumes that no values are null
+     *
+     * @param infoFields a map of info fields
+     * @throws IOException for writer
+     */
+    private void writeInfoString(Map<String, String> infoFields) throws IOException {
+        if ( infoFields.isEmpty() ) {
+            mWriter.write(VCFConstants.EMPTY_INFO_FIELD);
+            return;
+        }
+
+        boolean isFirst = true;
+        for ( Map.Entry<String, String> entry : infoFields.entrySet() ) {
+            if ( isFirst )
+                isFirst = false;
+            else
+                mWriter.write(VCFConstants.INFO_FIELD_SEPARATOR);
+
+            String key = entry.getKey();
+            mWriter.write(key);
+
+            if ( !entry.getValue().equals("") ) {
+                int numVals = 1;
+                VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key);
+                if ( metaData != null )
+                    numVals = metaData.getCount();
+
+                // take care of unbounded encoding
+                if ( numVals == VCFInfoHeaderLine.UNBOUNDED )
+                    numVals = 1;
+
+                if ( numVals > 0 ) {
+                    mWriter.write("=");
+                    mWriter.write(entry.getValue());
+                }
+            }
+        }
+    }
+
+    /**
+     * add the genotype data
+     *
+     * @param vc                     the variant context
+     * @param genotypeFormatKeys  Genotype formatting string
+     * @param alleleMap              alleles for this context
+     * @throws IOException for writer
+     */
+    private void addGenotypeData(VariantContext vc, Map<Allele, String> alleleMap, List<String> genotypeFormatKeys)
+    throws IOException {
+
+        for ( String sample : mHeader.getGenotypeSamples() ) {
+            mWriter.write(VCFConstants.FIELD_SEPARATOR);
+
+            Genotype g = vc.getGenotype(sample);
+            if ( g == null ) {
+                // TODO -- The VariantContext needs to know what the general ploidy is of the samples
+                // TODO -- We shouldn't be assuming diploid genotypes here!
+                mWriter.write(VCFConstants.EMPTY_GENOTYPE);
+                continue;
+            }
+
+            writeAllele(g.getAllele(0), alleleMap);
+            for (int i = 1; i < g.getPloidy(); i++) {
+                mWriter.write(g.isPhased() ? VCFConstants.PHASED : VCFConstants.UNPHASED);
+                writeAllele(g.getAllele(i), alleleMap);
+            }
+
+            List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
+            for ( String key : genotypeFormatKeys ) {
+                if ( key.equals(VCFConstants.GENOTYPE_KEY) )
+                    continue;
+
+                Object val = g.hasAttribute(key) ? g.getAttribute(key) : VCFConstants.MISSING_VALUE_v4;
+
+                // some exceptions
+                if ( key.equals(VCFConstants.GENOTYPE_QUALITY_KEY) ) {
+                    if ( Math.abs(g.getNegLog10PError() - Genotype.NO_NEG_LOG_10PERROR) < 1e-6)
+                        val = VCFConstants.MISSING_VALUE_v4;
+                    else {
+                        val = getQualValue(Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL));
+                    }
+                } else if ( key.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
+                    val = g.isFiltered() ? ParsingUtils.join(";", ParsingUtils.sortList(g.getFilters())) : (g.filtersWereApplied() ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.UNFILTERED);
+                }
+
+                VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(key);
+                if ( metaData != null ) {
+                    int numInFormatField = metaData.getCount();
+                    if ( numInFormatField > 1 && val.equals(VCFConstants.MISSING_VALUE_v4) ) {
+                        // If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
+                        // For example, if Number=2, the string has to be ".,."
+                        StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
+                        for ( int i = 1; i < numInFormatField; i++ ) {
+                            sb.append(",");
+                            sb.append(VCFConstants.MISSING_VALUE_v4);
+                        }
+                        val = sb.toString();
+                    }
+                }
+
+                // assume that if key is absent, then the given string encoding suffices
+                String outputValue = formatVCFField(val);
+                if ( outputValue != null )
+                    attrs.add(outputValue);
+            }
+
+            // strip off trailing missing values
+            for (int i = attrs.size()-1; i >= 0; i--) {
+                if ( isMissingValue(attrs.get(i)) )
+                    attrs.remove(i);
+                else
+                    break;
+            }
+
+            for (String s : attrs ) {
+                mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
+                mWriter.write(s);
+            }
+        }
+    }
+
+    private boolean isMissingValue(String s) {
+        // we need to deal with the case that it's a list of missing values
+        return (countOccurrences(VCFConstants.MISSING_VALUE_v4.charAt(0), s) + countOccurrences(',', s) == s.length());
+    }
+
+    private void writeAllele(Allele allele, Map<Allele, String> alleleMap) throws IOException {
+        String encoding = alleleMap.get(allele);
+        if ( encoding == null )
+            throw new TribbleException.InternalCodecException("Allele " + allele + " is not an allele in the variant context");
+        mWriter.write(encoding);
+    }
+
+    private static String formatVCFField(Object val) {
+        String result;
+        if ( val == null )
+            result = VCFConstants.MISSING_VALUE_v4;
+        else if ( val instanceof Double )
+            result = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, (Double)val);
+        else if ( val instanceof Boolean )
+            result = (Boolean)val ? "" : null; // empty string for true, null for false
+        else if ( val instanceof List ) {
+            result = formatVCFField(((List)val).toArray());
+        } else if ( val.getClass().isArray() ) {
+            int length = Array.getLength(val);
+            if ( length == 0 )
+                return formatVCFField(null);
+            StringBuffer sb = new StringBuffer(formatVCFField(Array.get(val, 0)));
+            for ( int i = 1; i < length; i++) {
+                sb.append(",");
+                sb.append(formatVCFField(Array.get(val, i)));
+            }
+            result = sb.toString();
+        } else
+            result = val.toString();
+
+        return result;
+    }
+
+    private static List<String> calcVCFGenotypeKeys(VariantContext vc) {
+        Set<String> keys = new HashSet<String>();
+
+        boolean sawGoodQual = false;
+        boolean sawGenotypeFilter = false;
+        for ( Genotype g : vc.getGenotypes().values() ) {
+            keys.addAll(g.getAttributes().keySet());
+            if ( g.hasNegLog10PError() )
+                sawGoodQual = true;
+            if (g.isFiltered() && g.isCalled())
+                sawGenotypeFilter = true;
+        }
+
+        if ( sawGoodQual )
+            keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
+
+        if (sawGenotypeFilter)
+            keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
+
+        return ParsingUtils.sortList(new ArrayList<String>(keys));
+    }
+
+
+    public static int countOccurrences(char c, String s) {
+           int count = 0;
+           for (int i = 0; i < s.length(); i++) {
+               count += s.charAt(i) == c ? 1 : 0;
+           }
+           return count;
+    }
+
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
new file mode 100755
index 000000000..f3c99e963
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
@@ -0,0 +1,182 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broad.tribble.TribbleException;
+import org.broad.tribble.readers.LineReader;
+import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.IOException;
+import java.util.*;
+
+
+/**
+ * a feature codec for the VCF 3 specification.  Our aim is to read in the records and convert to VariantContext as
+ * quickly as possible, relying on VariantContext to do the validation of any contradictory (or malformed) record parameters.
+ */
+public class VCF3Codec extends AbstractVCFCodec {
+
+    /**
+     * @param reader the line reader to take header lines from
+     * @return the number of header lines
+     */
+    public Object readHeader(LineReader reader) {
+        List<String> headerStrings = new ArrayList<String>();
+
+        String line;
+        try {
+            boolean foundHeaderVersion = false;
+            while ((line = reader.readLine()) != null) {
+                lineNo++;
+                if (line.startsWith(VCFHeader.METADATA_INDICATOR)) {
+                    String[] lineFields = line.substring(2).split("=");
+                    if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) {
+                        if ( !VCFHeaderVersion.isVersionString(lineFields[1]) )
+                            throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
+                        foundHeaderVersion = true;
+                        version = VCFHeaderVersion.toHeaderVersion(lineFields[1]);
+                        if ( version != VCFHeaderVersion.VCF3_3 && version != VCFHeaderVersion.VCF3_2 )
+                            throw new TribbleException.InvalidHeader("This codec is strictly for VCFv3 and does not support " + lineFields[1]);
+                    }
+                    headerStrings.add(line);
+                }
+                else if (line.startsWith(VCFHeader.HEADER_INDICATOR)) {
+                    if (!foundHeaderVersion) {
+                        throw new TribbleException.InvalidHeader("We never saw a header line specifying VCF version");
+                    }
+                    return createHeader(headerStrings, line);
+                }
+                else {
+                    throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");
+                }
+
+            }
+        } catch (IOException e) {
+            throw new RuntimeException("IO Exception ", e);
+        }
+        throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");
+    }
+
+
+    /**
+     * parse the filter string, first checking to see if we already have parsed it in a previous attempt
+     * @param filterString the string to parse
+     * @return a set of the filters applied
+     */
+    protected Set<String> parseFilters(String filterString) {
+
+        // null for unfiltered
+        if ( filterString.equals(VCFConstants.UNFILTERED) )
+            return null;
+
+        // empty set for passes filters
+        LinkedHashSet<String> fFields = new LinkedHashSet<String>();
+
+        if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) )
+            return fFields;
+
+        if ( filterString.length() == 0 )
+            generateException("The VCF specification requires a valid filter status");
+
+        // do we have the filter string cached?
+        if ( filterHash.containsKey(filterString) )
+            return filterHash.get(filterString);
+
+        // otherwise we have to parse and cache the value
+        if ( filterString.indexOf(VCFConstants.FILTER_CODE_SEPARATOR) == -1 )
+            fFields.add(filterString);
+        else
+            fFields.addAll(Arrays.asList(filterString.split(VCFConstants.FILTER_CODE_SEPARATOR)));
+
+        filterHash.put(filterString, fFields);
+
+        return fFields;
+    }
+
+    /**
+     * create a genotype map
+     * @param str the string
+     * @param alleles the list of alleles
+     * @param chr chrom
+     * @param pos position
+     * @return a mapping of sample name to genotype object
+     */
+    public Map<String, Genotype> createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
+        if (genotypeParts == null)
+            genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
+
+        int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
+
+        Map<String, Genotype> genotypes = new LinkedHashMap<String, Genotype>(nParts);
+
+        // get the format keys
+        int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
+
+        // cycle through the sample names
+        Iterator<String> sampleNameIterator = header.getGenotypeSamples().iterator();
+
+        // clear out our allele mapping
+        alleleMap.clear();
+
+        // cycle through the genotype strings
+        for (int genotypeOffset = 1; genotypeOffset < nParts; genotypeOffset++) {
+            int GTValueSplitSize = ParsingUtils.split(genotypeParts[genotypeOffset], GTValueArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
+
+            double GTQual = VariantContext.NO_NEG_LOG_10PERROR;
+            Set<String> genotypeFilters = null;
+            Map<String, String> gtAttributes = null;
+            String sampleName = sampleNameIterator.next();
+
+            // check to see if the value list is longer than the key list, which is a problem
+            if (nGTKeys < GTValueSplitSize)
+                generateException("There are too many keys for the sample " + sampleName + ", keys = " + parts[8] + ", values = " + parts[genotypeOffset]);
+
+            int genotypeAlleleLocation = -1;
+            if (nGTKeys >= 1) {
+                gtAttributes = new HashMap<String, String>(nGTKeys - 1);
+
+                for (int i = 0; i < nGTKeys; i++) {
+                    final String gtKey = new String(genotypeKeyArray[i]);
+                    boolean missing = i >= GTValueSplitSize;
+
+                    if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) {
+                        if (i != 0)
+                            generateException("Saw GT at position " + i + ", but it must be at the first position for genotypes");
+                        genotypeAlleleLocation = i;
+                    } else if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) {
+                        GTQual = missing ? parseQual(VCFConstants.MISSING_VALUE_v4) : parseQual(GTValueArray[i]);
+                    } else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) {
+                        genotypeFilters = missing ? parseFilters(VCFConstants.MISSING_VALUE_v4) : parseFilters(getCachedString(GTValueArray[i]));
+                    } else if ( missing || GTValueArray[i].equals(VCFConstants.MISSING_GENOTYPE_QUALITY_v3) ) {
+                        gtAttributes.put(gtKey, VCFConstants.MISSING_VALUE_v4);
+                    } else {
+                        gtAttributes.put(gtKey, new String(GTValueArray[i]));
+                    }
+                }
+            }
+
+            // check to make sure we found a gentoype field
+            if (genotypeAlleleLocation < 0) generateException("Unable to find required field GT for the record; we don't yet support a missing GT field");
+
+            // todo -- assuming allele list length in the single digits is bad.  Fix me.
+            // Check for > 1 for haploid genotypes
+            boolean phased = GTValueArray[genotypeAlleleLocation].length() > 1 && GTValueArray[genotypeAlleleLocation].charAt(1) == '|';
+
+            // add it to the list
+            try {
+                genotypes.put(sampleName, new Genotype(sampleName,
+                        parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap),
+                        GTQual,
+                        genotypeFilters,
+                        gtAttributes,
+                        phased));
+            } catch (TribbleException e) {
+                throw new TribbleException.InternalCodecException(e.getMessage() + ", at position " + chr+":"+pos);
+            }
+        }
+
+        return genotypes;
+    }
+
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
new file mode 100755
index 000000000..0fb2940bb
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
@@ -0,0 +1,188 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broad.tribble.TribbleException;
+import org.broad.tribble.readers.LineReader;
+import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.IOException;
+import java.util.*;
+
+
+/**
+ * a feature codec for the VCF 4 specification.  Our aim is to read in the records and convert to VariantContext as
+ * quickly as possible, relying on VariantContext to do the validation of any contradictory (or malformed) record parameters.
+ */
+public class VCFCodec extends AbstractVCFCodec {
+
+    /**
+     * @param reader the line reader to take header lines from
+     * @return the number of header lines
+     */
+    public Object readHeader(LineReader reader) {
+        List<String> headerStrings = new ArrayList<String>();
+
+        String line;
+        try {
+            boolean foundHeaderVersion = false;
+            while ((line = reader.readLine()) != null) {
+                lineNo++;
+                if (line.startsWith(VCFHeader.METADATA_INDICATOR)) {
+                    String[] lineFields = line.substring(2).split("=");
+                    if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) {
+                        if ( !VCFHeaderVersion.isVersionString(lineFields[1]) )
+                            throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
+                        foundHeaderVersion = true;
+                        version = VCFHeaderVersion.toHeaderVersion(lineFields[1]);
+                        if ( version == VCFHeaderVersion.VCF3_3 || version == VCFHeaderVersion.VCF3_2 )
+                            throw new TribbleException.InvalidHeader("This codec is strictly for VCFv4; please use the VCF3 codec for " + lineFields[1]);
+                        if ( version != VCFHeaderVersion.VCF4_0 && version != VCFHeaderVersion.VCF4_1 )
+                            throw new TribbleException.InvalidHeader("This codec is strictly for VCFv4 and does not support " + lineFields[1]);
+                    }
+                    headerStrings.add(line);
+                }
+                else if (line.startsWith(VCFHeader.HEADER_INDICATOR)) {
+                    if (!foundHeaderVersion) {
+                        throw new TribbleException.InvalidHeader("We never saw a header line specifying VCF version");
+                    }
+                    return createHeader(headerStrings, line);
+                }
+                else {
+                    throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");
+                }
+
+            }
+        } catch (IOException e) {
+            throw new RuntimeException("IO Exception ", e);
+        }
+        throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");
+    }
+
+
+    /**
+     * parse the filter string, first checking to see if we already have parsed it in a previous attempt
+     *
+     * @param filterString the string to parse
+     * @return a set of the filters applied or null if filters were not applied to the record (e.g. as per the missing value in a VCF)
+     */
+    protected Set<String> parseFilters(String filterString) {
+
+        // null for unfiltered
+        if ( filterString.equals(VCFConstants.UNFILTERED) )
+            return null;
+
+        // empty set for passes filters
+        LinkedHashSet<String> fFields = new LinkedHashSet<String>();
+
+        if ( filterString.equals(VCFConstants.PASSES_FILTERS_v4) )
+            return fFields;
+        if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) )
+            generateException(VCFConstants.PASSES_FILTERS_v3 + " is an invalid filter name in vcf4");
+        if ( filterString.length() == 0 )
+            generateException("The VCF specification requires a valid filter status");
+
+        // do we have the filter string cached?
+        if ( filterHash.containsKey(filterString) )
+            return filterHash.get(filterString);
+
+        // otherwise we have to parse and cache the value
+        if ( filterString.indexOf(VCFConstants.FILTER_CODE_SEPARATOR) == -1 )
+            fFields.add(filterString);
+        else
+            fFields.addAll(Arrays.asList(filterString.split(VCFConstants.FILTER_CODE_SEPARATOR)));
+
+        filterHash.put(filterString, fFields);
+
+        return fFields;
+    }
+
+
+    /**
+     * create a genotype map
+     * @param str the string
+     * @param alleles the list of alleles
+     * @return a mapping of sample name to genotype object
+     */
+    public Map<String, Genotype> createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
+        if (genotypeParts == null)
+            genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
+
+        int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
+
+        Map<String, Genotype> genotypes = new LinkedHashMap<String, Genotype>(nParts);
+
+        // get the format keys
+        int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
+
+        // cycle through the sample names
+        Iterator<String> sampleNameIterator = header.getGenotypeSamples().iterator();
+
+        // clear out our allele mapping
+        alleleMap.clear();
+
+        // cycle through the genotype strings
+        for (int genotypeOffset = 1; genotypeOffset < nParts; genotypeOffset++) {
+            int GTValueSplitSize = ParsingUtils.split(genotypeParts[genotypeOffset], GTValueArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
+
+            double GTQual = VariantContext.NO_NEG_LOG_10PERROR;
+            Set<String> genotypeFilters = null;
+            Map<String, String> gtAttributes = null;
+            String sampleName = sampleNameIterator.next();
+
+            // check to see if the value list is longer than the key list, which is a problem
+            if (nGTKeys < GTValueSplitSize)
+                generateException("There are too many keys for the sample " + sampleName + ", keys = " + parts[8] + ", values = " + parts[genotypeOffset]);
+
+            int genotypeAlleleLocation = -1;
+            if (nGTKeys >= 1) {
+                gtAttributes = new HashMap<String, String>(nGTKeys - 1);
+
+                for (int i = 0; i < nGTKeys; i++) {
+                    final String gtKey = new String(genotypeKeyArray[i]);
+                    boolean missing = i >= GTValueSplitSize;
+
+                    // todo -- all of these on the fly parsing of the missing value should be static constants
+                    if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) {
+                        if (i != 0)
+                            generateException("Saw GT at position " + i + ", but it must be at the first position for genotypes");
+                        genotypeAlleleLocation = i;
+                    } else if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) {
+                        GTQual = missing ? parseQual(VCFConstants.MISSING_VALUE_v4) : parseQual(GTValueArray[i]);
+                    } else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) {
+                        genotypeFilters = missing ? parseFilters(VCFConstants.MISSING_VALUE_v4) : parseFilters(getCachedString(GTValueArray[i]));
+                    } else if ( missing ) {
+                        gtAttributes.put(gtKey, VCFConstants.MISSING_VALUE_v4);
+                    } else {
+                        gtAttributes.put(gtKey, new String(GTValueArray[i]));
+                    }
+                }
+            }
+
+            // check to make sure we found a gentoype field
+            // TODO -- This is no longer required in v4.1
+            if (genotypeAlleleLocation < 0) generateException("Unable to find required field GT for the record; we don't yet support a missing GT field");
+
+            // todo -- assuming allele list length in the single digits is bad.  Fix me.
+            // Check for > 1 for haploid genotypes
+            boolean phased = GTValueArray[genotypeAlleleLocation].length() > 1 && GTValueArray[genotypeAlleleLocation].charAt(1) == '|';
+
+            // add it to the list
+            try {
+                genotypes.put(sampleName, new Genotype(sampleName,
+                        parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap),
+                        GTQual,
+                        genotypeFilters,
+                        gtAttributes,
+                        phased));
+            } catch (TribbleException e) {
+                throw new TribbleException.InternalCodecException(e.getMessage() + ", at position " + chr+":"+pos);
+            }
+        }
+
+        return genotypes;
+    }
+
+
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
new file mode 100755
index 000000000..a799161ad
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
@@ -0,0 +1,164 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+/**
+ * a base class for compound header lines, which include info lines and format lines (so far)
+ */
+public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine {
+    public enum SupportedHeaderLineType {
+        INFO(true), FORMAT(false);
+
+        public final boolean allowFlagValues;
+        SupportedHeaderLineType(boolean flagValues) {
+            allowFlagValues = flagValues;
+        }
+    }
+
+    // the field types
+    private String name;
+    private int count;
+    private String description;
+    private VCFHeaderLineType type;
+
+    // access methods
+    public String getName() { return name; }
+    public int getCount() { return count; }
+    public String getDescription() { return description; }
+    public VCFHeaderLineType getType() { return type; }
+
+    //
+    public void setNumberToUnbounded() { this.count = UNBOUNDED; }
+
+    // our type of line, i.e. format, info, etc
+    private final SupportedHeaderLineType lineType;
+
+    // line numerical values are allowed to be unbounded (or unknown), which is
+    // marked with a dot (.)
+    public static final int UNBOUNDED = -1;    // the value we store internally for unbounded types
+
+    /**
+     * create a VCF format header line
+     *
+     * @param name         the name for this header line
+     * @param count        the count for this header line
+     * @param type         the type for this header line
+     * @param description  the description for this header line
+     */
+    protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        this.name = name;
+        this.count = count;
+        this.type = type;
+        this.description = description;
+        this.lineType = lineType;
+        validate();
+    }
+
+    /**
+     * create a VCF format header line
+     *
+     * @param line   the header line
+     * @param version      the VCF header version
+     *
+     */
+    protected VCFCompoundHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Number","Type","Description"));
+        name = mapping.get("ID");
+        count = (version == VCFHeaderVersion.VCF4_0 || version == VCFHeaderVersion.VCF4_1) ?
+                        mapping.get("Number").equals(VCFConstants.UNBOUNDED_ENCODING_v4) ? UNBOUNDED : Integer.valueOf(mapping.get("Number")) :
+                        mapping.get("Number").equals(VCFConstants.UNBOUNDED_ENCODING_v3) ? UNBOUNDED : Integer.valueOf(mapping.get("Number"));
+        type = VCFHeaderLineType.valueOf(mapping.get("Type"));
+        if (type == VCFHeaderLineType.Flag && !allowFlagValues())
+            throw new IllegalArgumentException("Flag is an unsupported type for this kind of field");
+
+        description = mapping.get("Description");
+        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided
+            description = UNBOUND_DESCRIPTION;
+        
+        this.lineType = lineType;
+
+        validate();
+    }
+
+    private void validate() {
+        if ( name == null || type == null || description == null || lineType == null )
+            throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s type=%s desc=%s lineType=%s", 
+                    super.getKey(), name, type, description, lineType ));
+    }
+
+    /**
+     * make a string representation of this header line
+     * @return a string representation
+     */
+    protected String toStringEncoding() {
+        Map<String,Object> map = new LinkedHashMap<String,Object>();
+        map.put("ID", name);
+        map.put("Number", count == UNBOUNDED ? VCFConstants.UNBOUNDED_ENCODING_v4 : count);
+        map.put("Type", type);
+        map.put("Description", description);
+        return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map);
+    }
+
+    /**
+     * returns true if we're equal to another compounder header line
+     * @param o a compound header line
+     * @return true if equal
+     */
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFCompoundHeaderLine) )
+            return false;
+        VCFCompoundHeaderLine other = (VCFCompoundHeaderLine)o;
+        return name.equals(other.name) &&
+                count == other.count &&
+                description.equals(other.description) &&
+                type == other.type &&
+                lineType == other.lineType;
+    }
+
+    public boolean equalsExcludingDescription(VCFCompoundHeaderLine other) {
+        return count == other.count &&
+                type == other.type &&
+                lineType == other.lineType &&
+                name.equals(other.name);
+    }
+
+    public boolean sameLineTypeAndName(VCFCompoundHeaderLine other) {
+        return  lineType == other.lineType &&
+                name.equals(other.name);
+    }
+
+    /**
+     * do we allow flag (boolean) values? (i.e. booleans where you don't have specify the value, AQ means AQ=true)
+     * @return true if we do, false otherwise
+     */
+    abstract boolean allowFlagValues();
+
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
new file mode 100755
index 000000000..695c46c27
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
@@ -0,0 +1,109 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import java.util.Locale;
+
+public final class VCFConstants {
+    public static final Locale VCF_LOCALE = Locale.US;
+
+    // reserved INFO/FORMAT field keys
+    public static final String ANCESTRAL_ALLELE_KEY = "AA";
+    public static final String ALLELE_COUNT_KEY = "AC";
+    public static final String ALLELE_FREQUENCY_KEY = "AF";
+    public static final String ALLELE_NUMBER_KEY = "AN";
+    public static final String RMS_BASE_QUALITY_KEY = "BQ";
+    public static final String CIGAR_KEY = "CIGAR";
+    public static final String DBSNP_KEY = "DB";
+    public static final String DEPTH_KEY = "DP";
+    public static final String DOWNSAMPLED_KEY = "DS";
+    public static final String EXPECTED_ALLELE_COUNT_KEY = "EC";
+    public static final String END_KEY = "END";
+    public static final String GENOTYPE_FILTER_KEY = "FT";
+    public static final String GENOTYPE_KEY = "GT";
+    @Deprecated
+    public static final String GENOTYPE_LIKELIHOODS_KEY = "GL";         // log10 scaled genotype likelihoods
+    public static final String GENOTYPE_POSTERIORS_KEY = "GP";
+    public static final String GENOTYPE_QUALITY_KEY = "GQ";
+    public static final String HAPMAP2_KEY = "H2";
+    public static final String HAPMAP3_KEY = "H3";
+    public static final String HAPLOTYPE_QUALITY_KEY = "HQ";
+    public static final String RMS_MAPPING_QUALITY_KEY = "MQ";
+    public static final String MAPPING_QUALITY_ZERO_KEY = "MQ0";
+    public static final String SAMPLE_NUMBER_KEY = "NS";
+    public static final String PHRED_GENOTYPE_LIKELIHOODS_KEY = "PL";   // phred-scaled genotype likelihoods
+    public static final String PHASE_QUALITY_KEY = "PQ";
+    public static final String PHASE_SET_KEY = "PS";
+    public static final String OLD_DEPTH_KEY = "RD";
+    public static final String STRAND_BIAS_KEY = "SB";
+    public static final String SOMATIC_KEY = "SOMATIC";
+    public static final String VALIDATED_KEY = "VALIDATED";
+    public static final String THOUSAND_GENOMES_KEY = "1000G";
+
+    // separators
+    public static final String FORMAT_FIELD_SEPARATOR = ":";
+    public static final String GENOTYPE_FIELD_SEPARATOR = ":";
+    public static final char   GENOTYPE_FIELD_SEPARATOR_CHAR = ':';
+    public static final String FIELD_SEPARATOR = "\t";
+    public static final char   FIELD_SEPARATOR_CHAR = '\t';
+    public static final String FILTER_CODE_SEPARATOR = ";";
+    public static final String INFO_FIELD_ARRAY_SEPARATOR = ",";
+    public static final String ID_FIELD_SEPARATOR = ";";
+    public static final String INFO_FIELD_SEPARATOR = ";";
+    public static final char INFO_FIELD_SEPARATOR_CHAR = ';';
+    public static final String UNPHASED = "/";
+    public static final String PHASED = "|";
+    public static final String PHASED_SWITCH_PROB_v3 = "\\";
+    public static final String PHASING_TOKENS = "/|\\";
+
+    // old indel alleles
+    public static final char DELETION_ALLELE_v3 = 'D';
+    public static final char INSERTION_ALLELE_v3 = 'I';
+
+    // missing/default values
+    public static final String UNFILTERED = ".";
+    public static final String PASSES_FILTERS_v3 = "0";
+    public static final String PASSES_FILTERS_v4 = "PASS";
+    public static final String EMPTY_ID_FIELD = ".";
+    public static final String EMPTY_INFO_FIELD = ".";
+    public static final String EMPTY_ALTERNATE_ALLELE_FIELD = ".";
+    public static final String MISSING_VALUE_v4 = ".";
+    public static final String MISSING_QUALITY_v3 = "-1";
+    public static final Double MISSING_QUALITY_v3_DOUBLE = Double.valueOf(MISSING_QUALITY_v3);
+
+    public static final String MISSING_GENOTYPE_QUALITY_v3 = "-1";
+    public static final String MISSING_HAPLOTYPE_QUALITY_v3 = "-1";
+    public static final String MISSING_DEPTH_v3 = "-1";
+    public static final String UNBOUNDED_ENCODING_v4 = ".";
+    public static final String UNBOUNDED_ENCODING_v3 = "-1";
+    public static final String EMPTY_ALLELE = ".";
+    public static final String EMPTY_GENOTYPE = "./.";
+    public static final double MAX_GENOTYPE_QUAL = 99.0;
+
+    public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
+    public static final String DOUBLE_PRECISION_INT_SUFFIX = ".00";
+    public static final Double VCF_ENCODING_EPSILON = 0.00005; // when we consider fields equal(), used in the Qual compare
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
new file mode 100755
index 000000000..9176fc16e
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
@@ -0,0 +1,70 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+
+/**
+ * @author ebanks
+ * A class representing a key=value entry for FILTER fields in the VCF header
+ */
+public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine  {
+
+    private String name;
+    private String description;
+
+
+    /**
+     * create a VCF filter header line
+     *
+     * @param name         the name for this header line
+     * @param description  the description for this header line
+     */
+    public VCFFilterHeaderLine(String name, String description) {
+        super("FILTER", "");
+        this.name = name;
+        this.description = description;
+
+        if ( name == null || description == null )
+            throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
+    }
+
+    /**
+     * create a VCF info header line
+     *
+     * @param line      the header line
+     * @param version   the vcf header version
+     */
+    protected VCFFilterHeaderLine(String line, VCFHeaderVersion version) {
+        super("FILTER", "");
+        Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
+        name = mapping.get("ID");
+        description = mapping.get("Description");
+        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided 
+            description = UNBOUND_DESCRIPTION;
+    }
+
+    protected String toStringEncoding() {
+        Map<String,Object> map = new LinkedHashMap<String,Object>();
+        map.put("ID", name);
+        map.put("Description", description);
+        return "FILTER=" + VCFHeaderLine.toStringEncoding(map);
+    }
+
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFFilterHeaderLine) )
+            return false;
+        VCFFilterHeaderLine other = (VCFFilterHeaderLine)o;
+        return name.equals(other.name) &&
+               description.equals(other.description);
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
new file mode 100755
index 000000000..352be3e97
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
@@ -0,0 +1,28 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class VCFFormatHeaderLine
+ *         <p/>
+ *         A class representing a key=value entry for genotype FORMAT fields in the VCF header
+ */
+public class VCFFormatHeaderLine extends VCFCompoundHeaderLine {
+
+    public VCFFormatHeaderLine(String name, int count, VCFHeaderLineType type, String description) {
+        super(name, count, type, description, SupportedHeaderLineType.FORMAT);
+        if (type == VCFHeaderLineType.Flag)
+            throw new IllegalArgumentException("Flag is an unsupported type for format fields");
+    }
+
+    protected VCFFormatHeaderLine(String line, VCFHeaderVersion version) {
+        super(line, version, SupportedHeaderLineType.FORMAT);
+    }
+
+    // format fields do not allow flag values (that wouldn't make much sense, how would you encode this in the genotype).
+    @Override
+    boolean allowFlagValues() {
+        return false;
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
new file mode 100755
index 000000000..eb01e5dca
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
@@ -0,0 +1,191 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+
+import org.broad.tribble.util.ParsingUtils;
+
+import java.util.*;
+
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Class VCFHeader
+ *         <p/>
+ *         A class representing the VCF header
+ */
+public class VCFHeader {
+
+    // the mandatory header fields
+    public enum HEADER_FIELDS {
+        CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO
+    }
+
+    // the associated meta data
+    private final Set<VCFHeaderLine> mMetaData;
+    private final Map<String, VCFInfoHeaderLine> mInfoMetaData = new HashMap<String, VCFInfoHeaderLine>();
+    private final Map<String, VCFFormatHeaderLine> mFormatMetaData = new HashMap<String, VCFFormatHeaderLine>();
+
+    // the list of auxillary tags
+    private final Set<String> mGenotypeSampleNames = new LinkedHashSet<String>();
+
+    // the character string that indicates meta data
+    public static final String METADATA_INDICATOR = "##";
+
+    // the header string indicator
+    public static final String HEADER_INDICATOR = "#";
+
+    /** do we have genotying data? */
+    private boolean hasGenotypingData = false;
+
+    // were the input samples sorted originally (or are we sorting them)?
+    private boolean samplesWereAlreadySorted = true;
+
+
+    /**
+     * create a VCF header, given a list of meta data and auxillary tags
+     *
+     * @param metaData     the meta data associated with this header
+     */
+    public VCFHeader(Set<VCFHeaderLine> metaData) {
+        mMetaData = new TreeSet<VCFHeaderLine>(metaData);
+        loadVCFVersion();
+        loadMetaDataMaps();
+    }
+
+    /**
+     * create a VCF header, given a list of meta data and auxillary tags
+     *
+     * @param metaData            the meta data associated with this header
+     * @param genotypeSampleNames the genotype format field, and the sample names
+     */
+    public VCFHeader(Set<VCFHeaderLine> metaData, Set<String> genotypeSampleNames) {
+        mMetaData = new TreeSet<VCFHeaderLine>();
+        if ( metaData != null )
+            mMetaData.addAll(metaData);
+        for (String col : genotypeSampleNames) {
+            if (!col.equals("FORMAT"))
+                mGenotypeSampleNames.add(col);
+        }
+        if (genotypeSampleNames.size() > 0) hasGenotypingData = true;
+        loadVCFVersion();
+        loadMetaDataMaps();
+
+        samplesWereAlreadySorted = ParsingUtils.isSorted(genotypeSampleNames);
+    }
+
+    /**
+     * Adds a header line to the header metadata.
+     *
+     * @param headerLine Line to add to the existing metadata component.
+     */
+    public void addMetaDataLine(VCFHeaderLine headerLine) {
+        mMetaData.add(headerLine);    
+    }
+
+    /**
+     * check our metadata for a VCF version tag, and throw an exception if the version is out of date
+     * or the version is not present
+     */
+    public void loadVCFVersion() {
+        List<VCFHeaderLine> toRemove = new ArrayList<VCFHeaderLine>();
+        for ( VCFHeaderLine line : mMetaData )
+            if ( VCFHeaderVersion.isFormatString(line.getKey())) {
+                toRemove.add(line);
+            }
+        // remove old header lines for now,
+        mMetaData.removeAll(toRemove);
+
+    }
+
+    /**
+     * load the format/info meta data maps (these are used for quick lookup by key name)
+     */
+    private void loadMetaDataMaps() {
+        for ( VCFHeaderLine line : mMetaData ) {
+            if ( line instanceof VCFInfoHeaderLine )  {
+                VCFInfoHeaderLine infoLine = (VCFInfoHeaderLine)line;
+                mInfoMetaData.put(infoLine.getName(), infoLine);
+            }
+            else if ( line instanceof VCFFormatHeaderLine ) {
+                VCFFormatHeaderLine formatLine = (VCFFormatHeaderLine)line;
+                mFormatMetaData.put(formatLine.getName(), formatLine);
+            }
+        }
+    }
+
+    /**
+     * get the header fields in order they're presented in the input file (which is now required to be
+     * the order presented in the spec).
+     *
+     * @return a set of the header fields, in order
+     */
+    public Set<HEADER_FIELDS> getHeaderFields() {
+        Set<HEADER_FIELDS> fields = new LinkedHashSet<HEADER_FIELDS>();
+        for (HEADER_FIELDS field : HEADER_FIELDS.values())
+            fields.add(field);
+        return fields;
+    }
+
+    /**
+     * get the meta data, associated with this header
+     *
+     * @return a set of the meta data
+     */
+    public Set<VCFHeaderLine> getMetaData() {
+        Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>();
+        lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_0.getFormatString(), VCFHeaderVersion.VCF4_0.getVersionString()));
+        lines.addAll(mMetaData);
+        return Collections.unmodifiableSet(lines);
+    }
+
+    /**
+     * get the genotyping sample names
+     *
+     * @return a list of the genotype column names, which may be empty if hasGenotypingData() returns false
+     */
+    public Set<String> getGenotypeSamples() {
+        return mGenotypeSampleNames;
+    }
+
+    /**
+     * do we have genotyping data?
+     *
+     * @return true if we have genotyping columns, false otherwise
+     */
+    public boolean hasGenotypingData() {
+        return hasGenotypingData;
+    }
+
+    /**
+     * were the input samples sorted originally?
+     *
+     * @return true if the input samples were sorted originally, false otherwise
+     */
+    public boolean samplesWereAlreadySorted() {
+        return samplesWereAlreadySorted;
+    }
+
+    /** @return the column count */
+    public int getColumnCount() {
+        return HEADER_FIELDS.values().length + ((hasGenotypingData) ? mGenotypeSampleNames.size() + 1 : 0);
+    }
+
+    /**
+     * @param key    the header key name
+     * @return the meta data line, or null if there is none
+     */
+    public VCFInfoHeaderLine getInfoHeaderLine(String key) {
+        return mInfoMetaData.get(key);
+    }
+
+    /**
+     * @param key    the header key name
+     * @return the meta data line, or null if there is none
+     */
+    public VCFFormatHeaderLine getFormatHeaderLine(String key) {
+        return mFormatMetaData.get(key);
+    }
+}
+
+
+
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java
new file mode 100755
index 000000000..162c34d80
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java
@@ -0,0 +1,134 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broad.tribble.TribbleException;
+
+import java.util.Map;
+
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class VCFHeaderLine
+ *         <p/>
+ *         A class representing a key=value entry in the VCF header
+ */
+public class VCFHeaderLine implements Comparable {
+    protected static boolean ALLOW_UNBOUND_DESCRIPTIONS = true;
+    protected static String UNBOUND_DESCRIPTION = "Not provided in original VCF header";
+
+    private String mKey = null;
+    private String mValue = null;
+
+
+    /**
+     * create a VCF header line
+     *
+     * @param key     the key for this header line
+     * @param value   the value for this header line
+     */
+    public VCFHeaderLine(String key, String value) {
+        if ( key == null )
+            throw new IllegalArgumentException("VCFHeaderLine: key cannot be null: key = " + key);
+        mKey = key;
+        mValue = value;
+    }
+
+    /**
+     * Get the key
+     *
+     * @return the key
+     */
+    public String getKey() {
+        return mKey;
+    }
+
+    /**
+     * Get the value
+     *
+     * @return the value
+     */
+    public String getValue() {
+        return mValue;
+    }
+
+    public String toString() {
+        return toStringEncoding();
+    }
+
+    /**
+     * Should be overloaded in sub classes to do subclass specific
+     *
+     * @return the string encoding
+     */
+    protected String toStringEncoding() {
+        return mKey + "=" + mValue;
+    }
+
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFHeaderLine) )
+            return false;
+        return mKey.equals(((VCFHeaderLine)o).getKey()) && mValue.equals(((VCFHeaderLine)o).getValue());
+    }
+
+    public int compareTo(Object other) {
+        return toString().compareTo(other.toString());
+    }
+
+    /**
+     * @param line    the line
+     * @return true if the line is a VCF meta data line, or false if it is not
+     */
+    public static boolean isHeaderLine(String line) {
+        return line != null && line.length() > 0 && VCFHeader.HEADER_INDICATOR.equals(line.substring(0,1));
+    }
+
+    /**
+     * create a string of a mapping pair for the target VCF version
+     * @param keyValues a mapping of the key->value pairs to output
+     * @return a string, correctly formatted
+     */
+    public static String toStringEncoding(Map<String, ? extends Object> keyValues) {
+        StringBuilder builder = new StringBuilder();
+        builder.append("<");
+        boolean start = true;
+        for (Map.Entry<String,?> entry : keyValues.entrySet()) {
+            if (start) start = false;
+            else builder.append(",");
+
+            if ( entry.getValue() == null ) throw new TribbleException.InternalCodecException("Header problem: unbound value at " + entry + " from " + keyValues);
+
+            builder.append(entry.getKey());
+            builder.append("=");
+            builder.append(entry.getValue().toString().contains(",") ||
+                           entry.getValue().toString().contains(" ") ||
+                           entry.getKey().equals("Description") ? "\""+ entry.getValue() + "\"" : entry.getValue());
+        }
+        builder.append(">");
+        return builder.toString();
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java
new file mode 100755
index 000000000..16f2a3d5a
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java
@@ -0,0 +1,124 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import java.util.*;
+
+/**
+ * A class for translating between vcf header versions
+ */
+public class VCFHeaderLineTranslator {
+    private static Map<VCFHeaderVersion,VCFLineParser> mapping;
+
+    static {
+        mapping = new HashMap<VCFHeaderVersion,VCFLineParser>();
+        mapping.put(VCFHeaderVersion.VCF4_0,new VCF4Parser());
+        mapping.put(VCFHeaderVersion.VCF4_1,new VCF4Parser());
+        mapping.put(VCFHeaderVersion.VCF3_3,new VCF3Parser());
+        mapping.put(VCFHeaderVersion.VCF3_2,new VCF3Parser());
+    }
+
+    public static Map<String,String> parseLine(VCFHeaderVersion version, String valueLine, List<String> expectedTagOrder) {
+        return mapping.get(version).parseLine(valueLine,expectedTagOrder);
+    }
+}
+
+
+interface VCFLineParser {
+    public Map<String,String> parseLine(String valueLine, List<String> expectedTagOrder);
+}
+
+
+/**
+ * a class that handles the to and from disk for VCF 4 lines
+ */
+class VCF4Parser implements VCFLineParser {
+    Set<String> bracketed = new HashSet<String>();
+
+    /**
+     * parse a VCF4 line
+     * @param valueLine the line
+     * @return a mapping of the tags parsed out
+     */
+    public Map<String, String> parseLine(String valueLine, List<String> expectedTagOrder) {
+        // our return map
+        Map<String, String> ret = new LinkedHashMap<String, String>();
+
+        // a builder to store up characters as we go
+        StringBuilder builder = new StringBuilder();
+
+        // store the key when we're parsing out the values
+        String key = "";
+
+        // where are we in the stream of characters?
+        int index = 0;
+
+        // are we inside a quotation? we don't special case ',' then
+        boolean inQuote = false;
+
+        // a little switch machine to parse out the tags. Regex ended up being really complicated and ugly [yes, but this machine is getting ugly now... MAD]
+        for (char c: valueLine.toCharArray()) {
+            if ( c == '\"' ) {
+                inQuote = ! inQuote;
+            } else if ( inQuote ) {
+                builder.append(c);
+            } else {
+                switch (c) {
+                    case ('<') : if (index == 0) break; // if we see a open bracket at the beginning, ignore it
+                    case ('>') : if (index == valueLine.length()-1) ret.put(key,builder.toString().trim()); break; // if we see a close bracket, and we're at the end, add an entry to our list
+                    case ('=') : key = builder.toString().trim(); builder = new StringBuilder(); break; // at an equals, copy the key and reset the builder
+                    case (',') : ret.put(key,builder.toString().trim()); builder = new StringBuilder(); break; // drop the current key value to the return map
+                    default: builder.append(c); // otherwise simply append to the current string
+                }
+            }
+            
+            index++;
+        }
+
+        // validate the tags against the expected list
+        index = 0;
+        if (ret.size() > expectedTagOrder.size()) throw new IllegalArgumentException("Unexpected tag count " + ret.size() + " in string " + expectedTagOrder.size());
+        for (String str : ret.keySet()) {
+            if (!expectedTagOrder.get(index).equals(str)) throw new IllegalArgumentException("Unexpected tag " + str + " in string " + valueLine);
+            index++;
+        }
+        return ret;
+    }
+}
+
+class VCF3Parser implements VCFLineParser {
+
+    public Map<String, String> parseLine(String valueLine, List<String> expectedTagOrder) {
+        // our return map
+        Map<String, String> ret = new LinkedHashMap<String, String>();
+
+        // a builder to store up characters as we go
+        StringBuilder builder = new StringBuilder();
+
+        // where are we in the stream of characters?
+        int index = 0;
+        // where in the expected tag order are we?
+        int tagIndex = 0;
+
+        // are we inside a quotation? we don't special case ',' then
+        boolean inQuote = false;
+
+        // a little switch machine to parse out the tags. Regex ended up being really complicated and ugly
+        for (char c: valueLine.toCharArray()) {
+            switch (c) {
+                case ('\"') : inQuote = !inQuote; break; // a quote means we ignore ',' in our strings, keep track of it
+                case (',') : if (!inQuote) { ret.put(expectedTagOrder.get(tagIndex++),builder.toString()); builder = new StringBuilder(); break; } // drop the current key value to the return map
+                default: builder.append(c); // otherwise simply append to the current string
+            }
+            index++;
+        }
+        ret.put(expectedTagOrder.get(tagIndex++),builder.toString());
+        
+        // validate the tags against the expected list
+        index = 0;
+        if (tagIndex != expectedTagOrder.size()) throw new IllegalArgumentException("Unexpected tag count " + tagIndex + ", we expected " + expectedTagOrder.size());
+        for (String str : ret.keySet()){
+            if (!expectedTagOrder.get(index).equals(str)) throw new IllegalArgumentException("Unexpected tag " + str + " in string " + valueLine);
+            index++;
+        }
+        return ret;
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java
new file mode 100755
index 000000000..83e272415
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java
@@ -0,0 +1,8 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+/**
+ * the type encodings we use for fields in VCF header lines
+ */
+public enum VCFHeaderLineType {
+    Integer, Float, String, Character, Flag;
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java
new file mode 100755
index 000000000..c65ce17b9
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java
@@ -0,0 +1,91 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broad.tribble.TribbleException;
+
+/**
+ * information that identifies each header version
+ */
+public enum VCFHeaderVersion {
+    VCF3_2("VCRv3.2","format"),
+    VCF3_3("VCFv3.3","fileformat"),
+    VCF4_0("VCFv4.0","fileformat"),
+    VCF4_1("VCFv4.1","fileformat");
+
+    private final String versionString;
+    private final String formatString;
+
+    /**
+     * create the enum, privately, using:
+     * @param vString the version string
+     * @param fString the format string
+     */
+    VCFHeaderVersion(String vString, String fString) {
+        this.versionString = vString;
+        this.formatString = fString;
+    }
+
+    /**
+     * get the header version
+     * @param version the version string
+     * @return a VCFHeaderVersion object
+     */
+    public static VCFHeaderVersion toHeaderVersion(String version) {
+        version = clean(version);
+        for (VCFHeaderVersion hv : VCFHeaderVersion.values())
+            if (hv.versionString.equals(version))
+                    return hv;
+        return null;
+    }
+
+    /**
+     * are we a valid version string of some type
+     * @param version the version string
+     * @return true if we're valid of some type, false otherwise
+     */
+    public static boolean isVersionString(String version){
+        return toHeaderVersion(version) != null;
+    }
+
+    /**
+     * are we a valid format string for some type
+     * @param format the format string
+     * @return true if we're valid of some type, false otherwise
+     */
+    public static boolean isFormatString(String format){
+        format = clean(format);
+        for (VCFHeaderVersion hv : VCFHeaderVersion.values())
+            if (hv.formatString.equals(format))
+                    return true;
+        return false;
+    }
+
+    public static VCFHeaderVersion getHeaderVersion(String versionLine) {
+        String[] lineFields = versionLine.split("=");
+        if ( lineFields.length != 2 || !isFormatString(lineFields[0].substring(2)) )
+            throw new TribbleException.InvalidHeader(versionLine + " is not a valid VCF version line");
+
+        if ( !isVersionString(lineFields[1]) )
+            throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
+
+        return toHeaderVersion(lineFields[1]);
+    }
+
+    /**
+     * Utility function to clean up a VCF header string
+     * 
+     * @param s string
+     * @return  trimmed version of s
+     */
+    private static String clean(String s) {
+        return s.trim();
+    }
+
+
+    public String getVersionString() {
+        return versionString;
+    }
+
+    public String getFormatString() {
+        return formatString;
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
new file mode 100755
index 000000000..135a5c1a1
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
@@ -0,0 +1,25 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class VCFInfoHeaderLine
+ *         <p/>
+ *         A class representing a key=value entry for INFO fields in the VCF header
+ */
+public class VCFInfoHeaderLine extends VCFCompoundHeaderLine {
+    public VCFInfoHeaderLine(String name, int count, VCFHeaderLineType type, String description) {
+        super(name, count, type, description, SupportedHeaderLineType.INFO);
+    }
+
+    protected VCFInfoHeaderLine(String line, VCFHeaderVersion version) {
+        super(line, version, SupportedHeaderLineType.INFO);
+    }
+
+    // info fields allow flag values
+    @Override
+    boolean allowFlagValues() {
+        return true;
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFNamedHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFNamedHeaderLine.java
new file mode 100755
index 000000000..f78e936b2
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFNamedHeaderLine.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+/** an interface for named header lines **/
+public interface VCFNamedHeaderLine {
+    String getName();
+}
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java
new file mode 100755
index 000000000..dac996494
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java
@@ -0,0 +1,23 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import java.util.*;
+
+
+/**
+ * All VCF codecs need to implement this interface so that we can perform lazy loading.
+ */
+public interface VCFParser {
+
+    /**
+     * create a genotype map
+     * @param str the string
+     * @param alleles the list of alleles
+     * @param chr chrom
+     * @param pos position
+     * @return a mapping of sample name to genotype object
+     */
+    public Map<String, Genotype> createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
+
+}
diff --git a/java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java
rename to java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index 08de5bf56..e919d5c25 100755
--- a/java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -23,13 +23,11 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.vcf;
+package org.broadinstitute.sting.utils.codecs.vcf;
 
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.apache.log4j.Logger;
 
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java
new file mode 100755
index 000000000..0d23fe455
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java
@@ -0,0 +1,18 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+/**
+ * this class writes VCF files
+ */
+public interface VCFWriter {
+
+    public void writeHeader(VCFHeader header);
+
+    /**
+     * attempt to close the VCF file
+     */
+    public void close();
+
+    public void add(VariantContext vc, byte refBase);
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 3336eb34f..0be4bec91 100755
--- a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -28,8 +28,8 @@ import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.io.File;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java b/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
index e22adc4a6..cb6557408 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
@@ -24,8 +24,8 @@
 
 package org.broadinstitute.sting.utils.genotype;
 
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
new file mode 100755
index 000000000..a9ba46159
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
@@ -0,0 +1,456 @@
+package org.broadinstitute.sting.utils.variantcontext;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Collection;
+
+/**
+ * Immutable representation of an allele
+ *
+ * Types of alleles:
+ *
+ * Ref: a t C g a // C is the reference base
+ *
+ *    : a t G g a // C base is a G in some individuals
+ *
+ *    : a t - g a // C base is deleted w.r.t. the reference
+ *
+ *    : a t CAg a // A base is inserted w.r.t. the reference sequence
+ *
+ * In these cases, where are the alleles?
+ *
+ * SNP polymorphism of C/G  -> { C , G } -> C is the reference allele
+ * 1 base deletion of C     -> { C , - } -> C is the reference allele
+ * 1 base insertion of A    -> { - ; A } -> Null is the reference allele
+ *
+ * Suppose I see a the following in the population:
+ *
+ * Ref: a t C g a // C is the reference base
+ *    : a t G g a // C base is a G in some individuals
+ *    : a t - g a // C base is deleted w.r.t. the reference
+ *
+ * How do I represent this?  There are three segregating alleles:
+ *
+ *  { C , G , - }
+ *
+ * Now suppose I have this more complex example:
+ *
+ * Ref: a t C g a // C is the reference base
+ *    : a t - g a
+ *    : a t - - a
+ *    : a t CAg a
+ *
+ * There are actually four segregating alleles:
+ *
+ *   { C g , - g, - -, and CAg } over bases 2-4
+ *
+ * However, the molecular equivalence explicitly listed above is usually discarded, so the actual
+ * segregating alleles are:
+ *
+ *   { C g, g, -, C a g }
+ *
+ * Critically, it should be possible to apply an allele to a reference sequence to create the
+ * correct haplotype sequence:
+ *
+ * Allele + reference => haplotype
+ *
+ * For convenience, we are going to create Alleles where the GenomeLoc of the allele is stored outside of the
+ * Allele object itself.  So there's an idea of an A/C polymorphism independent of it's surrounding context.
+ *
+ * Given list of alleles it's possible to determine the "type" of the variation
+ *
+ *      A / C @ loc => SNP with
+ *      - / A => INDEL
+ *
+ * If you know where allele is the reference, you can determine whether the variant is an insertion or deletion.
+ *
+ * Alelle also supports is concept of a NO_CALL allele.  This Allele represents a haplotype that couldn't be
+ * determined. This is usually represented by a '.' allele.
+ *
+ * Note that Alleles store all bases as bytes, in **UPPER CASE**.  So 'atc' == 'ATC' from the perspective of an
+ * Allele.
+
+ * @author ebanks, depristo
+ */
+public class Allele implements Comparable<Allele> {
+    private static final byte[] EMPTY_ALLELE_BASES = new byte[0];
+
+    private boolean isRef = false;
+    private boolean isNull = false;
+    private boolean isNoCall = false;
+    private boolean isSymbolic = false;
+
+    private byte[] bases = null;
+
+    public final static String NULL_ALLELE_STRING = "-";
+    public final static String NO_CALL_STRING = ".";
+    /** A generic static NO_CALL allele for use */
+
+    // no public way to create an allele
+    private Allele(byte[] bases, boolean isRef) {
+        // standardize our representation of null allele and bases
+        if ( wouldBeNullAllele(bases) ) {
+            bases = EMPTY_ALLELE_BASES;
+            isNull = true;
+        } else if ( wouldBeNoCallAllele(bases) ) {
+            bases = EMPTY_ALLELE_BASES;
+            isNoCall = true;
+            if ( isRef ) throw new IllegalArgumentException("Cannot tag a NoCall allele as the reference allele");
+        } else if ( wouldBeSymbolicAllele(bases) ) {
+            isSymbolic = true;
+            if ( isRef ) throw new IllegalArgumentException("Cannot tag a symbolic allele as the reference allele");
+        }
+//        else
+//            bases = new String(bases).toUpperCase().getBytes(); // todo -- slow performance
+
+        this.isRef = isRef;
+        this.bases = bases;
+
+        if ( ! acceptableAlleleBases(bases) )
+            throw new IllegalArgumentException("Unexpected base in allele bases " + new String(bases));
+    }
+
+    private Allele(String bases, boolean isRef) {
+        this(bases.getBytes(), isRef);
+    }
+
+
+    private final static Allele REF_A = new Allele("A", true);
+    private final static Allele ALT_A = new Allele("A", false);
+    private final static Allele REF_C = new Allele("C", true);
+    private final static Allele ALT_C = new Allele("C", false);
+    private final static Allele REF_G = new Allele("G", true);
+    private final static Allele ALT_G = new Allele("G", false);
+    private final static Allele REF_T = new Allele("T", true);
+    private final static Allele ALT_T = new Allele("T", false);
+    private final static Allele REF_N = new Allele("N", true);
+    private final static Allele ALT_N = new Allele("N", false);
+    private final static Allele REF_NULL = new Allele(NULL_ALLELE_STRING, true);
+    private final static Allele ALT_NULL = new Allele(NULL_ALLELE_STRING, false);
+    public final static Allele NO_CALL = new Allele(NO_CALL_STRING, false);
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // creation routines
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    /**
+     * Create a new Allele that includes bases and if tagged as the reference allele if isRef == true.  If bases
+     * == '-', a Null allele is created.  If bases ==  '.', a no call Allele is created.
+     *
+     * @param bases the DNA sequence of this variation, '-', of '.'
+     * @param isRef should we make this a reference allele?
+     * @throws IllegalArgumentException if bases contains illegal characters or is otherwise malformated
+     */
+    public static Allele create(byte[] bases, boolean isRef) {
+        if ( bases == null )
+            throw new IllegalArgumentException("create: the Allele base string cannot be null; use new Allele() or new Allele(\"\") to create a Null allele");
+
+        if ( bases.length == 1 ) {
+            // optimization to return a static constant Allele for each single base object
+            switch (bases[0]) {
+                case '.':
+                    if ( isRef ) throw new IllegalArgumentException("Cannot tag a NoCall allele as the reference allele");
+                    return NO_CALL;
+                case '-': return isRef ? REF_NULL : ALT_NULL;
+                case 'A': case 'a' : return isRef ? REF_A : ALT_A;
+                case 'C': case 'c' : return isRef ? REF_C : ALT_C;
+                case 'G': case 'g' : return isRef ? REF_G : ALT_G;
+                case 'T': case 't' : return isRef ? REF_T : ALT_T;
+                case 'N': case 'n' : return isRef ? REF_N : ALT_N;
+                default: throw new IllegalArgumentException("Illegal base: " + (char)bases[0]);
+            }
+        } else {
+            return new Allele(bases, isRef);
+        }
+    }
+
+    public static Allele create(byte base, boolean isRef) {
+//    public Allele(byte base, boolean isRef) {
+        return create( new byte[]{ base }, isRef);
+    }
+
+    public static Allele create(byte base) {
+        return create( base, false );
+    }
+
+    public static Allele extend(Allele left, byte[] right) {
+        if (left.isSymbolic())
+            throw new IllegalArgumentException("Cannot extend a symbolic allele");
+        byte[] bases = null;
+        if ( left.length() == 0 )
+            bases = right;
+        else {
+            bases = new byte[left.length() + right.length];
+            System.arraycopy(left.getBases(), 0, bases, 0, left.length());
+            System.arraycopy(right, 0, bases, left.length(), right.length);
+        }
+
+        return create(bases, left.isReference());
+    }
+
+    /**
+     * @param bases  bases representing an allele
+     * @return true if the bases represent the null allele
+     */
+    public static boolean wouldBeNullAllele(byte[] bases) {
+        return (bases.length == 1 && bases[0] == '-') || bases.length == 0;
+    }
+
+    /**
+     * @param bases  bases representing an allele
+     * @return true if the bases represent the NO_CALL allele
+     */
+    public static boolean wouldBeNoCallAllele(byte[] bases) {
+        return bases.length == 1 && bases[0] == '.';
+    }
+
+    /**
+     * @param bases  bases representing an allele
+     * @return true if the bases represent a symbolic allele
+     */
+    public static boolean wouldBeSymbolicAllele(byte[] bases) {
+        return bases.length > 2 && bases[0] == '<' && bases[bases.length-1] == '>';
+    }
+
+    /**
+     * @param bases  bases representing an allele
+     * @return true if the bases represent the well formatted allele
+     */
+    public static boolean acceptableAlleleBases(String bases) {
+        return acceptableAlleleBases(bases.getBytes());
+    }
+
+    /**
+     * @param bases  bases representing an allele
+     * @return true if the bases represent the well formatted allele
+     */
+    public static boolean acceptableAlleleBases(byte[] bases) {
+        if ( wouldBeNullAllele(bases) || wouldBeNoCallAllele(bases) || wouldBeSymbolicAllele(bases) )
+            return true;
+
+        for ( int i = 0; i < bases.length; i++ ) {
+            switch (bases[i]) {
+                case 'A': case 'C': case 'G': case 'T': case 'N' : case 'a': case 'c': case 'g': case 't': case 'n' :
+                    break;
+                default:
+                    return false;
+            }
+        }
+
+        return true;
+    }
+
+    /**
+     * @see Allele(byte[], boolean)
+     *
+     * @param bases  bases representing an allele
+     * @param isRef  is this the reference allele?
+     */
+    public static Allele create(String bases, boolean isRef) {
+    //public Allele(String bases, boolean isRef) {
+        return create(bases.getBytes(), isRef);
+    }
+
+
+    /**
+     * Creates a non-Ref allele.  @see Allele(byte[], boolean) for full information
+     *
+     * @param bases  bases representing an allele
+     */
+    public static Allele create(String bases) {
+        return create(bases, false);
+    }
+
+    /**
+     * Creates a non-Ref allele.  @see Allele(byte[], boolean) for full information
+     *
+     * @param bases  bases representing an allele
+     */
+    public static Allele create(byte[] bases) {
+        return create(bases, false);
+        //this(bases, false);
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // accessor routines
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    //Returns true if this is the null allele
+    public boolean isNull()             { return isNull; }
+    // Returns true if this is not the null allele
+    public boolean isNonNull()          { return ! isNull(); }
+
+    // Returns true if this is the NO_CALL allele
+    public boolean isNoCall()           { return isNoCall; }
+    // Returns true if this is not the NO_CALL allele
+    public boolean isCalled()           { return ! isNoCall(); }
+
+    // Returns true if this Allele is the reference allele
+    public boolean isReference()        { return isRef; }
+    // Returns true if this Allele is not the reference allele
+    public boolean isNonReference()     { return ! isReference(); }
+
+    // Returns true if this Allele is symbolic (i.e. no well-defined base sequence)
+    public boolean isSymbolic()         { return isSymbolic; }
+
+    // Returns a nice string representation of this object
+    public String toString() {
+        return (isNull() ? NULL_ALLELE_STRING : ( isNoCall() ? NO_CALL_STRING : getDisplayString() )) + (isReference() ? "*" : "");
+    }
+
+    /**
+     * Return the DNA bases segregating in this allele.  Note this isn't reference polarized,
+     * so the Null allele is represented by a vector of length 0
+     *
+     * @return the segregating bases
+     */
+    public byte[] getBases() { return isSymbolic ? EMPTY_ALLELE_BASES : bases; }
+
+    /**
+     * Return the DNA bases segregating in this allele in String format.
+     * This is useful, because toString() adds a '*' to reference alleles and getBases() returns garbage when you call toString() on it.
+     *
+     * @return the segregating bases
+     */
+    public String getBaseString() { return new String(getBases()); }
+
+    /**
+     * Return the printed representation of this allele.
+     * Same as getBaseString(), except for symbolic alleles.
+     * For symbolic alleles, the base string is empty while the display string contains <TAG>.
+     *
+     * @return the allele string representation
+     */
+    public String getDisplayString() { return new String(bases); }
+
+    /**
+     * @param other  the other allele
+     *
+     * @return true if these alleles are equal
+     */
+    public boolean equals(Object other) {
+        return ( ! (other instanceof Allele) ? false : equals((Allele)other, false) );
+    }
+
+    /**
+     * @return hash code
+     */
+    public int hashCode() {
+        int hash = 1;
+        for (int i = 0; i < bases.length; i++)
+            hash += (i+1) * bases[i];
+        return hash;
+    }
+
+    /**
+     * Returns true if this and other are equal.  If ignoreRefState is true, then doesn't require both alleles has the
+     * same ref tag
+     *
+     * @param other            allele to compare to
+     * @param ignoreRefState   if true, ignore ref state in comparison
+     * @return true if this and other are equal
+     */
+    public boolean equals(Allele other, boolean ignoreRefState) {
+        return this == other || (isRef == other.isRef || ignoreRefState) && isNull == other.isNull && isNoCall == other.isNoCall && (bases == other.bases || Arrays.equals(bases, other.bases));
+    }
+
+    /**
+     * @param test  bases to test against
+     *
+     * @return  true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles
+     */
+    public boolean basesMatch(byte[] test) { return !isSymbolic && (bases == test || Arrays.equals(bases, test)); }
+
+    /**
+     * @param test  bases to test against
+     *
+     * @return  true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles
+     */
+    public boolean basesMatch(String test) { return basesMatch(test.toUpperCase().getBytes()); }
+
+    /**
+     * @param test  allele to test against
+     *
+     * @return  true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles
+     */
+    public boolean basesMatch(Allele test) { return basesMatch(test.getBases()); }
+
+    /**
+     * @return the length of this allele.  Null and NO_CALL alleles have 0 length.
+     */
+    public int length() {
+        return isSymbolic ? 0 : bases.length;
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // useful static functions
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    public static Allele getMatchingAllele(Collection<Allele> allAlleles, String alleleBases) {
+        return getMatchingAllele(allAlleles, alleleBases.getBytes());
+    }
+
+    public static Allele getMatchingAllele(Collection<Allele> allAlleles, byte[] alleleBases) {
+        for ( Allele a : allAlleles ) {
+            if ( a.basesMatch(alleleBases) ) {
+                return a;
+            }
+        }
+
+        if ( wouldBeNoCallAllele(alleleBases) )
+            return NO_CALL;
+        else
+            return null;    // couldn't find anything
+    }
+
+    public static List<Allele> resolveAlleles(List<Allele> possibleAlleles, List<String> alleleStrings) {
+        List<Allele> myAlleles = new ArrayList<Allele>(alleleStrings.size());
+
+        for ( String alleleString : alleleStrings ) {
+            Allele allele = getMatchingAllele(possibleAlleles, alleleString);
+
+            if ( allele == null ) {
+                if ( Allele.wouldBeNoCallAllele(alleleString.getBytes()) ) {
+                    allele = create(alleleString);
+                } else {
+                    throw new IllegalArgumentException("Allele " + alleleString + " not present in the list of alleles " + possibleAlleles);
+                }
+            }
+
+            myAlleles.add(allele);
+        }
+
+        return myAlleles;
+    }
+
+    public int compareTo(Allele other) {
+        if ( isReference() && other.isNonReference() )
+            return -1;
+        else if ( isNonReference() && other.isReference() ) 
+            return 1;
+        else
+            return getBaseString().compareTo(other.getBaseString()); // todo -- potential performance issue
+    }
+
+    public static boolean oneIsPrefixOfOther(Allele a1, Allele a2) {
+        if ( a1.isNull() || a2.isNull() )
+            return true;
+
+        if ( a2.length() >= a1.length() )
+            return firstIsPrefixOfSecond(a1, a2);
+        else
+            return firstIsPrefixOfSecond(a2, a1);
+    }
+
+    private static boolean firstIsPrefixOfSecond(Allele a1, Allele a2) {
+        String a1String = a1.getBaseString();
+        return a2.getBaseString().substring(0, a1String.length()).equals(a1String);
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
new file mode 100755
index 000000000..3a87f1196
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -0,0 +1,279 @@
+package org.broadinstitute.sting.utils.variantcontext;
+
+
+import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+
+import java.util.*;
+
+/**
+ * This class encompasses all the basic information about a genotype.  It is immutable.
+ *
+ * @author Mark DePristo
+ */
+public class Genotype {
+
+    public final static String PHASED_ALLELE_SEPARATOR = "|";
+    public final static String UNPHASED_ALLELE_SEPARATOR = "/";
+
+    protected InferredGeneticContext commonInfo;
+    public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
+    protected List<Allele> alleles = null; // new ArrayList<Allele>();
+
+    protected boolean isPhased = false;
+    private boolean filtersWereAppliedToContext;
+
+    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
+        this.alleles = Collections.unmodifiableList(alleles);
+        commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes);
+        filtersWereAppliedToContext = filters != null;
+        this.isPhased = isPhased;
+        validate();
+    }
+
+    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError) {
+        this(sampleName, alleles, negLog10PError, null, null, false);
+    }
+
+    public Genotype(String sampleName, List<Allele> alleles) {
+        this(sampleName, alleles, NO_NEG_LOG_10PERROR, null, null, false);
+    }
+
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // Partial-cloning routines (because Genotype is immutable).
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    public static Genotype modifyName(Genotype g, String name) {
+        return new Genotype(name, g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, g.getAttributes(), g.isPhased());
+    }
+
+    public static Genotype modifyAttributes(Genotype g, Map<String, Object> attributes) {
+        return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attributes, g.isPhased());
+    }
+
+    public static Genotype modifyAlleles(Genotype g, List<Allele> alleles) {
+        return new Genotype(g.getSampleName(), alleles, g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, g.getAttributes(), g.isPhased());
+    }
+
+    /**
+     * @return the alleles for this genotype
+     */
+    public List<Allele> getAlleles() {
+        return alleles;
+    }
+
+    public List<Allele> getAlleles(Allele allele) {
+        List<Allele> al = new ArrayList<Allele>();
+        for ( Allele a : alleles )
+            if ( a.equals(allele) )
+                al.add(a);
+
+        return Collections.unmodifiableList(al);
+    }
+
+    public Allele getAllele(int i) {
+        return alleles.get(i);
+    }
+
+    public boolean isPhased() { return isPhased; }
+
+    /**
+     * @return the ploidy of this genotype
+     */
+    public int getPloidy() { return alleles.size(); }
+
+    public enum Type {
+        NO_CALL,
+        HOM_REF,
+        HET,
+        HOM_VAR
+    }
+
+    public Type getType() {
+        Allele firstAllele = alleles.get(0);
+
+        if ( firstAllele.isNoCall() ) {
+            return Type.NO_CALL;
+        }
+
+        for (Allele a : alleles) {
+            if ( ! firstAllele.equals(a) )
+                return Type.HET;
+        }
+        return firstAllele.isReference() ? Type.HOM_REF : Type.HOM_VAR;
+    }
+
+    /**
+     * @return true if all observed alleles are the same (regardless of whether they are ref or alt)
+     */
+    public boolean isHom()    { return isHomRef() || isHomVar(); }
+    public boolean isHomRef() { return getType() == Type.HOM_REF; }
+    public boolean isHomVar() { return getType() == Type.HOM_VAR; }
+    
+    /**
+     * @return true if we're het (observed alleles differ)
+     */
+    public boolean isHet() { return getType() == Type.HET; }
+
+    /**
+     * @return true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF)
+     */
+    public boolean isNoCall() { return getType() == Type.NO_CALL; }
+    public boolean isCalled() { return getType() != Type.NO_CALL; }
+
+    //
+    // Useful methods for getting genotype likelihoods for a genotype object, if present
+    //
+    public boolean hasLikelihoods() {
+        return (hasAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) && !getAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4)) ||
+                (hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && !getAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4));
+    }
+    
+    public GenotypeLikelihoods getLikelihoods() {
+        GenotypeLikelihoods x = getLikelihoods(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, true);
+        if ( x != null )
+            return x;
+        else {
+            x = getLikelihoods(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, false);
+            if ( x != null ) return x;
+            else
+                throw new IllegalStateException("BUG: genotype likelihood field in " + this.getSampleName() + " sample are not either a string or a genotype likelihood class!");
+        }
+    }
+
+    private GenotypeLikelihoods getLikelihoods(String key, boolean asPL) {
+        Object x = getAttribute(key);
+        if ( x instanceof String ) {
+            if ( asPL )
+                return GenotypeLikelihoods.fromPLField((String)x);
+            else
+                return GenotypeLikelihoods.fromGLField((String)x);
+        }
+        else if ( x instanceof GenotypeLikelihoods ) return (GenotypeLikelihoods)x;
+        else return null;
+    }
+
+    public void validate() {
+        if ( alleles == null ) throw new IllegalArgumentException("BUG: alleles cannot be null in setAlleles");
+        if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0 in setAlleles");
+
+        int nNoCalls = 0;
+        for ( Allele allele : alleles ) {
+            if ( allele == null )
+                throw new IllegalArgumentException("BUG: allele cannot be null in Genotype");
+            nNoCalls += allele.isNoCall() ? 1 : 0;
+        }
+        if ( nNoCalls > 0 && nNoCalls != alleles.size() )
+            throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
+    }
+
+    public String getGenotypeString() {
+        return getGenotypeString(true);
+    }
+
+    public String getGenotypeString(boolean ignoreRefState) {
+        // Notes:
+        // 1. Make sure to use the appropriate separator depending on whether the genotype is phased
+        // 2. If ignoreRefState is true, then we want just the bases of the Alleles (ignoring the '*' indicating a ref Allele)
+        // 3. So that everything is deterministic with regards to integration tests, we sort Alleles (when the genotype isn't phased, of course)
+        return ParsingUtils.join(isPhased() ? PHASED_ALLELE_SEPARATOR : UNPHASED_ALLELE_SEPARATOR,
+                ignoreRefState ? getAlleleStrings() : (isPhased() ? getAlleles() : ParsingUtils.sortList(getAlleles())));
+    }
+
+    private List<String> getAlleleStrings() {
+        List<String> al = new ArrayList<String>();
+        for ( Allele a : alleles )
+            al.add(a.getBaseString());
+
+        return al;
+    }
+
+    public String toString() {
+        int Q = (int)Math.round(getPhredScaledQual());
+        return String.format("[%s %s Q%s %s]", getSampleName(), getGenotypeString(false),
+                Q == -10 ? "." : String.format("%2d",Q), sortedString(getAttributes()));
+    }
+
+    public String toBriefString() {
+        return String.format("%s:Q%.2f", getGenotypeString(false), getPhredScaledQual());
+    }
+
+    public boolean sameGenotype(Genotype other) {
+        return sameGenotype(other, true);
+    }
+
+    public boolean sameGenotype(Genotype other, boolean ignorePhase) {
+        if (getPloidy() != other.getPloidy())
+            return false; // gotta have the same number of allele to be equal
+
+        // By default, compare the elements in the lists of alleles, element-by-element
+        Collection<Allele> thisAlleles = this.getAlleles();
+        Collection<Allele> otherAlleles = other.getAlleles();
+
+        if (ignorePhase) { // do not care about order, only identity of Alleles
+            thisAlleles = new TreeSet<Allele>(thisAlleles);   //implemented Allele.compareTo()
+            otherAlleles = new TreeSet<Allele>(otherAlleles);
+        }
+
+        return thisAlleles.equals(otherAlleles);
+    }
+
+    /**
+     * a utility method for generating sorted strings from a map key set.
+     * @param c the map
+     * @param <T> the key type
+     * @param <V> the value type
+     * @return a sting, enclosed in {}, with comma seperated key value pairs in order of the keys
+     */
+    public static <T extends Comparable<T>, V> String sortedString(Map<T, V> c) {
+        List<T> t = new ArrayList<T>(c.keySet());
+        Collections.sort(t);
+
+        List<String> pairs = new ArrayList<String>();
+        for (T k : t) {
+            pairs.add(k + "=" + c.get(k));
+        }
+
+        return "{" + ParsingUtils.join(", ", pairs.toArray(new String[pairs.size()])) + "}";
+    }
+
+
+    // ---------------------------------------------------------------------------------------------------------
+    // 
+    // get routines to access context info fields
+    //
+    // ---------------------------------------------------------------------------------------------------------
+    public String getSampleName()       { return commonInfo.getName(); }
+    public Set<String> getFilters()     { return commonInfo.getFilters(); }
+    public boolean isFiltered()         { return commonInfo.isFiltered(); }
+    public boolean isNotFiltered()      { return commonInfo.isNotFiltered(); }
+    public boolean filtersWereApplied() { return filtersWereAppliedToContext; }
+    public boolean hasNegLog10PError()  { return commonInfo.hasNegLog10PError(); }
+    public double getNegLog10PError()   { return commonInfo.getNegLog10PError(); }
+    public double getPhredScaledQual()  { return commonInfo.getPhredScaledQual(); }
+
+    public Map<String, Object> getAttributes()  { return commonInfo.getAttributes(); }
+    public boolean hasAttribute(String key)     { return commonInfo.hasAttribute(key); }
+    public Object getAttribute(String key)      { return commonInfo.getAttribute(key); }
+    
+    public Object getAttribute(String key, Object defaultValue) {
+        return commonInfo.getAttribute(key, defaultValue); 
+    }
+
+    public String getAttributeAsString(String key)                        { return commonInfo.getAttributeAsString(key); }
+    public String getAttributeAsString(String key, String defaultValue)   { return commonInfo.getAttributeAsString(key, defaultValue); }
+    public int getAttributeAsInt(String key)                              { return commonInfo.getAttributeAsInt(key); }
+    public int getAttributeAsInt(String key, int defaultValue)            { return commonInfo.getAttributeAsInt(key, defaultValue); }
+    public double getAttributeAsDouble(String key)                        { return commonInfo.getAttributeAsDouble(key); }
+    public double getAttributeAsDouble(String key, double  defaultValue)  { return commonInfo.getAttributeAsDouble(key, defaultValue); }
+    public boolean getAttributeAsBoolean(String key)                        { return commonInfo.getAttributeAsBoolean(key); }
+    public boolean getAttributeAsBoolean(String key, boolean  defaultValue)  { return commonInfo.getAttributeAsBoolean(key, defaultValue); }
+
+    public Integer getAttributeAsIntegerNoException(String key)  { return commonInfo.getAttributeAsIntegerNoException(key); }
+    public Double getAttributeAsDoubleNoException(String key)    { return commonInfo.getAttributeAsDoubleNoException(key); }
+    public String getAttributeAsStringNoException(String key)    { return commonInfo.getAttributeAsStringNoException(key); }
+    public Boolean getAttributeAsBooleanNoException(String key)  { return commonInfo.getAttributeAsBooleanNoException(key); }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
new file mode 100755
index 000000000..3feaf5e1c
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -0,0 +1,151 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.variantcontext;
+
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broad.tribble.TribbleException;
+
+public class GenotypeLikelihoods {
+    public static final boolean CAP_PLS = false;
+    public static final int PL_CAP = 255;
+
+    //
+    // There are two objects here because we are lazy in creating both representations
+    // for this object: a vector of log10 Probs and the PL phred-scaled string.  Supports
+    // having one set during initializating, and dynamic creation of the other, if needed
+    //
+    private double[] log10Likelihoods = null;
+    private String likelihoodsAsString_PLs = null;
+
+    public final static GenotypeLikelihoods fromPLField(String PLs) {
+        return new GenotypeLikelihoods(PLs);
+    }
+
+    public final static GenotypeLikelihoods fromGLField(String GLs) {
+        return new GenotypeLikelihoods(parseDeprecatedGLString(GLs));
+    }
+
+    public final static GenotypeLikelihoods fromLog10Likelihoods(double[] log10Likelihoods) {
+        return new GenotypeLikelihoods(log10Likelihoods);
+    }
+
+    //
+    // You must use the factory methods now
+    //
+    protected GenotypeLikelihoods(String asString) {
+        likelihoodsAsString_PLs = asString;
+    }
+
+    protected GenotypeLikelihoods(double[] asVector) {
+        log10Likelihoods = asVector;
+    }
+
+    /**
+     * Returns the genotypes likelihoods in negative log10 vector format.  pr{AA} = x, this
+     * vector returns math.log10(x) for each of the genotypes.  Can return null if the
+     * genotype likelihoods are "missing".
+     *
+     * @return
+     */
+    public double[] getAsVector() {
+        // assumes one of the likelihoods vector or the string isn't null
+        if ( log10Likelihoods == null ) {
+            // make sure we create the GL string if it doesn't already exist
+            log10Likelihoods = parsePLsIntoLikelihoods(likelihoodsAsString_PLs);
+        }
+
+        return log10Likelihoods;
+    }
+
+    public String toString() {
+        return getAsString();
+    }
+
+    public String getAsString() {
+        if ( likelihoodsAsString_PLs == null ) {
+            // todo -- should we accept null log10Likelihoods and set PLs as MISSING?
+            if ( log10Likelihoods == null )
+                throw new TribbleException("BUG: Attempted to get likelihoods as strings and neither the vector nor the string is set!");
+            likelihoodsAsString_PLs = convertLikelihoodsToPLString(log10Likelihoods);
+        }
+
+        return likelihoodsAsString_PLs;
+    }
+
+    private final static double[] parsePLsIntoLikelihoods(String likelihoodsAsString_PLs) {
+        if ( !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) {
+            String[] strings = likelihoodsAsString_PLs.split(",");
+            double[] likelihoodsAsVector = new double[strings.length];
+            for ( int i = 0; i < strings.length; i++ ) {
+                likelihoodsAsVector[i] = Integer.parseInt(strings[i]) / -10.0;
+            }
+            return likelihoodsAsVector;
+        } else
+            return null;
+    }
+
+    /**
+     * Back-compatibility function to read old style GL formatted genotype likelihoods in VCF format
+     * @param GLString
+     * @return
+     */
+    private final static double[] parseDeprecatedGLString(String GLString) {
+        if ( !GLString.equals(VCFConstants.MISSING_VALUE_v4) ) {
+            String[] strings = GLString.split(",");
+            double[] likelihoodsAsVector = new double[strings.length];
+            for ( int i = 0; i < strings.length; i++ ) {
+                likelihoodsAsVector[i] = Double.parseDouble(strings[i]);
+            }
+            return likelihoodsAsVector;
+        }
+
+        return null;
+    }
+
+    private final static String convertLikelihoodsToPLString(double[] GLs) {
+        if ( GLs == null )
+            return VCFConstants.MISSING_VALUE_v4;
+
+        StringBuilder s = new StringBuilder();
+
+        double adjust = Double.NEGATIVE_INFINITY;
+        for ( double l : GLs ) adjust = Math.max(adjust, l);
+
+        boolean first = true;
+        for ( double l : GLs ) {
+            if ( ! first )
+                s.append(",");
+            else
+                first = false;
+
+            long PL = Math.round(-10 * (l - adjust));
+            if ( CAP_PLS )
+                PL = Math.min(PL, PL_CAP);
+            s.append(Long.toString(PL));
+        }
+
+        return s.toString();
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java b/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java
new file mode 100755
index 000000000..3d162adb0
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java
@@ -0,0 +1,230 @@
+package org.broadinstitute.sting.utils.variantcontext;
+
+
+import java.util.*;
+
+
+/**
+ * Common utility routines for VariantContext and Genotype
+ *
+ * @author depristo
+ */
+public final class InferredGeneticContext {
+    public static final double NO_NEG_LOG_10PERROR = -1.0;
+
+    private static Set<String> NO_FILTERS = Collections.unmodifiableSet(new HashSet<String>());
+    private static Map<String, Object> NO_ATTRIBUTES = Collections.unmodifiableMap(new HashMap<String, Object>());
+
+    private double negLog10PError = NO_NEG_LOG_10PERROR;
+    private String name = null;
+    private Set<String> filters = NO_FILTERS;
+    private Map<String, Object> attributes = NO_ATTRIBUTES;
+
+//    public InferredGeneticContext(String name) {
+//        this.name = name;
+//    }
+//
+//    public InferredGeneticContext(String name, double negLog10PError) {
+//        this(name);
+//        setNegLog10PError(negLog10PError);
+//    }
+
+    public InferredGeneticContext(String name, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+        this.name = name;
+        setNegLog10PError(negLog10PError);
+        if ( filters != null )
+            setFilters(filters);
+        if ( attributes != null )
+            setAttributes(attributes);
+    }
+
+    /**
+     * @return the name
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Sets the name
+     *
+     * @param name    the name associated with this information
+     */
+    public void setName(String name) {
+        if ( name == null ) throw new IllegalArgumentException("Name cannot be null " + this);
+        this.name = name;
+    }
+
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // Filter
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    public Set<String> getFilters() {
+        return Collections.unmodifiableSet(filters);
+    }
+
+    public boolean isFiltered() {
+        return filters.size() > 0;
+    }
+
+    public boolean isNotFiltered() {
+        return ! isFiltered();
+    }
+
+    public void addFilter(String filter) {
+        if ( filters == NO_FILTERS ) // immutable -> mutable
+            filters = new HashSet<String>(filters);
+
+        if ( filter == null ) throw new IllegalArgumentException("BUG: Attempting to add null filter " + this);
+        if ( getFilters().contains(filter) ) throw new IllegalArgumentException("BUG: Attempting to add duplicate filter " + filter + " at " + this);
+        filters.add(filter);
+    }
+
+    public void addFilters(Collection<String> filters) {
+        if ( filters == null ) throw new IllegalArgumentException("BUG: Attempting to add null filters at" + this);
+        for ( String f : filters )
+            addFilter(f);
+    }
+
+    public void clearFilters() {
+        filters = new HashSet<String>();
+    }
+
+    public void setFilters(Collection<String> filters) {
+        clearFilters();
+        addFilters(filters);
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // Working with log error rates
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    public boolean hasNegLog10PError() {
+        return getNegLog10PError() != NO_NEG_LOG_10PERROR;
+    }
+
+    /**
+     * @return the -1 * log10-based error estimate
+     */
+    public double getNegLog10PError() { return negLog10PError; }
+    public double getPhredScaledQual() { return getNegLog10PError() * 10; }
+
+    public void setNegLog10PError(double negLog10PError) {
+        if ( negLog10PError < 0 && negLog10PError != NO_NEG_LOG_10PERROR ) throw new IllegalArgumentException("BUG: negLog10PError cannot be < than 0 : " + negLog10PError);
+        if ( Double.isInfinite(negLog10PError) ) throw new IllegalArgumentException("BUG: negLog10PError should not be Infinity");
+        if ( Double.isNaN(negLog10PError) ) throw new IllegalArgumentException("BUG: negLog10PError should not be NaN");
+
+        this.negLog10PError = negLog10PError;
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // Working with attributes
+    //
+    // ---------------------------------------------------------------------------------------------------------
+    public void clearAttributes() {
+        attributes = new HashMap<String, Object>();
+    }
+
+    /**
+     * @return the attribute map
+     */
+    public Map<String, Object> getAttributes() {
+        return Collections.unmodifiableMap(attributes);
+    }
+
+    // todo -- define common attributes as enum
+
+    public void setAttributes(Map<String, ?> map) {
+        clearAttributes();
+        putAttributes(map);
+    }
+
+    public void putAttribute(String key, Object value) {
+        putAttribute(key, value, false);
+    }
+
+    public void putAttribute(String key, Object value, boolean allowOverwrites) {
+        if ( ! allowOverwrites && hasAttribute(key) )
+            throw new IllegalStateException("Attempting to overwrite key->value binding: key = " + key + " this = " + this);
+
+        if ( attributes == NO_ATTRIBUTES ) // immutable -> mutable
+            attributes = new HashMap<String, Object>();
+        
+        attributes.put(key, value);
+    }
+
+    public void removeAttribute(String key) {
+        if ( attributes == NO_ATTRIBUTES ) // immutable -> mutable
+            attributes = new HashMap<String, Object>();
+        attributes.remove(key);
+    }
+
+    public void putAttributes(Map<String, ?> map) {
+        if ( map != null ) {
+            // for efficiency, we can skip the validation if the map is empty
+            if ( attributes.size() == 0 ) {
+                if ( attributes == NO_ATTRIBUTES ) // immutable -> mutable
+                    attributes = new HashMap<String, Object>();
+                attributes.putAll(map);
+            } else {
+                for ( Map.Entry<String, ?> elt : map.entrySet() ) {
+                    putAttribute(elt.getKey(), elt.getValue(), false);
+                }
+            }
+        }
+    }
+
+    public boolean hasAttribute(String key) {
+        return attributes.containsKey(key);
+    }
+
+    public int getNumAttributes() {
+        return attributes.size();
+    }
+
+    /**
+     * @param key    the attribute key
+     *
+     * @return the attribute value for the given key (or null if not set)
+     */
+    public Object getAttribute(String key) {
+        return attributes.get(key);
+    }
+
+    public Object getAttribute(String key, Object defaultValue) {
+        if ( hasAttribute(key) )
+            return attributes.get(key);
+        else
+            return defaultValue;
+    }
+
+//    public AttributedObject getAttributes(Collection<Object> keys) {
+//        AttributedObject selected = new AttributedObject();
+//
+//        for ( Object key : keys )
+//            selected.putAttribute(key, this.getAttribute(key));
+//
+//        return selected;
+//    }
+
+    public String getAttributeAsString(String key)      { return (String.valueOf(getAttribute(key))); } // **NOTE**: will turn a null Object into the String "null"
+    public int getAttributeAsInt(String key)            { Object x = getAttribute(key); return x instanceof Integer ? (Integer)x : Integer.valueOf((String)x); }
+    public double getAttributeAsDouble(String key)      { Object x = getAttribute(key); return x instanceof Double ? (Double)x : Double.valueOf((String)x); }
+    public boolean getAttributeAsBoolean(String key)      { Object x = getAttribute(key); return x instanceof Boolean ? (Boolean)x : Boolean.valueOf((String)x); }
+
+    public String getAttributeAsString(String key, String defaultValue)   { return (String)getAttribute(key, defaultValue); }
+    public int getAttributeAsInt(String key, int defaultValue)            { return (Integer)getAttribute(key, defaultValue); }
+    public double getAttributeAsDouble(String key, double defaultValue)   { return (Double)getAttribute(key, defaultValue); }
+    public boolean getAttributeAsBoolean(String key, boolean defaultValue){ return (Boolean)getAttribute(key, defaultValue); }
+
+    public Integer getAttributeAsIntegerNoException(String key)  { try {return getAttributeAsInt(key);} catch (Exception e) {return null;} }
+    public Double getAttributeAsDoubleNoException(String key)    { try {return getAttributeAsDouble(key);} catch (Exception e) {return null;} }
+    public String getAttributeAsStringNoException(String key)    { if (getAttribute(key) == null) return null; return getAttributeAsString(key); }
+    public Boolean getAttributeAsBooleanNoException(String key)  { try {return getAttributeAsBoolean(key);} catch (Exception e) {return null;} }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java b/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java
new file mode 100755
index 000000000..0cd684cb6
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java
@@ -0,0 +1,80 @@
+package org.broadinstitute.sting.utils.variantcontext;
+
+import java.util.*;
+
+/**
+ * This class emcompasses all the basic information about a genotype.  It is immutable.
+ *
+ * @author Mark DePristo
+ */
+public class MutableGenotype extends Genotype {
+    public MutableGenotype(Genotype parent) {
+        super(parent.getSampleName(), parent.getAlleles(), parent.getNegLog10PError(), parent.getFilters(), parent.getAttributes(), parent.isPhased());
+    }
+
+    public MutableGenotype(String sampleName, Genotype parent) {
+        super(sampleName, parent.getAlleles(), parent.getNegLog10PError(), parent.getFilters(), parent.getAttributes(), parent.isPhased());
+    }
+
+
+    public MutableGenotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean genotypesArePhased) {
+        super(sampleName, alleles, negLog10PError, filters, attributes, genotypesArePhased);
+    }
+
+    public MutableGenotype(String sampleName, List<Allele> alleles, double negLog10PError) {
+        super(sampleName, alleles, negLog10PError);
+    }
+
+    public MutableGenotype(String sampleName, List<Allele> alleles) {
+        super(sampleName, alleles);
+    }
+
+    public Genotype unmodifiableGenotype() {
+        return new Genotype(getSampleName(), getAlleles(), getNegLog10PError(), getFilters(), getAttributes(), isPhased());
+    }
+
+
+    /**
+     *
+     * @param alleles list of alleles
+     */
+    public void setAlleles(List<Allele> alleles) {
+        this.alleles = new ArrayList<Allele>(alleles);
+
+        // todo -- add validation checking here
+
+        if ( alleles == null ) throw new IllegalArgumentException("BUG: alleles cannot be null in setAlleles");
+        if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0 in setAlleles");
+
+        int nNoCalls = 0;
+        for ( Allele allele : alleles ) { nNoCalls += allele.isNoCall() ? 1 : 0; }
+        if ( nNoCalls > 0 && nNoCalls != alleles.size() )
+            throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
+
+        for ( Allele allele : alleles )
+            if ( allele == null ) throw new IllegalArgumentException("BUG: Cannot add a null allele to a genotype");
+    }
+
+    public void setPhase(boolean isPhased) {
+        super.isPhased = isPhased;
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // InferredGeneticContext mutation operators
+    //
+    // ---------------------------------------------------------------------------------------------------------
+    public void setName(String name)                    { commonInfo.setName(name); }
+    public void addFilter(String filter)                { commonInfo.addFilter(filter); }
+    public void addFilters(Collection<String> filters)  { commonInfo.addFilters(filters); }
+    public void clearFilters()                          { commonInfo.clearFilters(); }
+    public void setFilters(Collection<String> filters)  { commonInfo.setFilters(filters); }
+    public void setAttributes(Map<String, ?> map)       { commonInfo.setAttributes(map); }
+    public void clearAttributes()                       { commonInfo.clearAttributes(); }
+    public void putAttribute(String key, Object value)  { commonInfo.putAttribute(key, value); }
+    public void removeAttribute(String key)             { commonInfo.removeAttribute(key); }
+    public void putAttributes(Map<String, ?> map)       { commonInfo.putAttributes(map); }
+    public void setNegLog10PError(double negLog10PError) { commonInfo.setNegLog10PError(negLog10PError); }
+    public void putAttribute(String key, Object value, boolean allowOverwrites) { commonInfo.putAttribute(key, value, allowOverwrites); }
+
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java b/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
new file mode 100755
index 000000000..4efba8825
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
@@ -0,0 +1,210 @@
+package org.broadinstitute.sting.utils.variantcontext;
+
+
+import java.util.*;
+
+/**
+ * Mutable version of VariantContext
+ *
+ * @author depristo
+ */
+public class MutableVariantContext extends VariantContext {
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // constructors
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+        super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
+    }
+
+    public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+        super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
+    }
+
+    public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles) {
+        this(source, contig, start, stop, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null);
+    }
+
+    public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes) {
+        this(source, contig, start, stop, alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null);
+    }
+
+    public MutableVariantContext(VariantContext parent) {
+        this(parent.getSource(), parent.contig, parent.start, parent.stop, parent.getAlleles(), parent.getGenotypes(), parent.getNegLog10PError(), parent.getFilters(), parent.getAttributes());
+    }
+
+    /**
+     * Sets the alleles segregating in this context to the collect of alleles.  Each of which must be unique according
+     * to equals() in Allele.  Validate() should be called when you are done modifying the context.
+     *
+     * @param alleles
+     */
+    public void setAlleles(Collection<Allele> alleles) {
+        this.alleles.clear();
+        for ( Allele a : alleles )
+            addAllele(a);
+    }
+
+    /**
+     * Adds allele to the segregating allele list in this context to the collection of alleles.  The new
+     * allele must be be unique according to equals() in Allele.
+     * Validate() should be called when you are done modifying the context.
+     *
+     * @param allele
+     */
+    public void addAllele(Allele allele) {
+        final boolean allowDuplicates = false;  // used to be a parameter
+
+        type = null;
+
+        for ( Allele a : alleles ) {
+            if ( a.basesMatch(allele) && ! allowDuplicates )
+                throw new IllegalArgumentException("Duplicate allele added to VariantContext" + this);
+        }
+
+        // we are a novel allele
+        alleles.add(allele);
+    }
+
+    public void clearGenotypes() {
+        genotypes = new TreeMap<String, Genotype>();
+    }
+
+    /**
+     * Adds this single genotype to the context, not allowing duplicate genotypes to be added
+     * @param genotype
+     */
+    public void addGenotypes(Genotype genotype) {
+        putGenotype(genotype.getSampleName(), genotype, false);
+    }
+
+    /**
+     * Adds these genotypes to the context, not allowing duplicate genotypes to be added
+     * @param genotypes
+     */
+    public void addGenotypes(Collection<Genotype> genotypes) {
+        for ( Genotype g : genotypes ) {
+            addGenotype(g);
+        }
+    }
+
+    /**
+     * Adds these genotype to the context, not allowing duplicate genotypes to be added.
+     * @param genotypes
+     */
+    public void addGenotypes(Map<String, Genotype> genotypes) {
+
+        for ( Map.Entry<String, Genotype> elt : genotypes.entrySet() ) {
+            addGenotype(elt.getValue());
+        }
+    }
+
+    /**
+     * Adds these genotypes to the context.
+     *
+     * @param genotypes
+     */
+    public void putGenotypes(Map<String, Genotype> genotypes) {
+        for ( Map.Entry<String, Genotype> g : genotypes.entrySet() )
+            putGenotype(g.getKey(), g.getValue());
+    }
+
+    /**
+     * Adds these genotypes to the context.
+     *
+     * @param genotypes
+     */
+    public void putGenotypes(Collection<Genotype> genotypes) {
+        for ( Genotype g : genotypes )
+            putGenotype(g);
+    }
+
+    /**
+     * Adds this genotype to the context, throwing an error if it's already bound.
+     *
+     * @param genotype
+     */
+    public void addGenotype(Genotype genotype) {
+        addGenotype(genotype.getSampleName(), genotype);
+    }
+
+    /**
+     * Adds this genotype to the context, throwing an error if it's already bound.
+     *
+     * @param genotype
+     */
+    public void addGenotype(String sampleName, Genotype genotype) {
+        putGenotype(sampleName, genotype, false);
+    }
+
+    /**
+     * Adds this genotype to the context.
+     *
+     * @param genotype
+     */
+    public void putGenotype(Genotype genotype) {
+        putGenotype(genotype.getSampleName(), genotype);
+    }
+
+    /**
+     * Adds this genotype to the context.
+     *
+     * @param genotype
+     */
+    public void putGenotype(String sampleName, Genotype genotype) {
+        putGenotype(sampleName, genotype, true);
+    }
+
+    private void putGenotype(String sampleName, Genotype genotype, boolean allowOverwrites) {
+        if ( hasGenotype(sampleName) && ! allowOverwrites )
+            throw new IllegalStateException("Attempting to overwrite sample->genotype binding: " + sampleName + " this=" + this);
+
+        if ( ! sampleName.equals(genotype.getSampleName()) )
+            throw new IllegalStateException("Sample name doesn't equal genotype.getSample(): " + sampleName + " genotype=" + genotype);
+
+        this.genotypes.put(sampleName, genotype);
+    }
+
+    /**
+     * Removes the binding from sampleName to genotype.  If this doesn't exist, throws an IllegalArgumentException
+     * @param sampleName
+     */
+    public void removeGenotype(String sampleName) {
+        if ( ! this.genotypes.containsKey(sampleName) )
+            throw new IllegalArgumentException("Sample name isn't contained in genotypes " + sampleName + " genotypes =" + genotypes);
+
+        this.genotypes.remove(sampleName);
+    }
+
+    /**
+     * Removes genotype from the context.  If this doesn't exist, throws an IllegalArgumentException
+     * @param genotype
+     */
+    public void removeGenotype(Genotype genotype) {
+        removeGenotype(genotype.getSampleName());
+    }
+
+    // todo -- add replace genotype routine
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // InferredGeneticContext mutation operators
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    public void setSource(String source)                { commonInfo.setName(source); }
+    public void addFilter(String filter)                { commonInfo.addFilter(filter); }
+    public void addFilters(Collection<String> filters)  { commonInfo.addFilters(filters); }
+    public void clearFilters()                          { commonInfo.clearFilters(); }
+    public void setFilters(Collection<String> filters)  { commonInfo.setFilters(filters); }
+    public void setAttributes(Map<String, ?> map)       { commonInfo.setAttributes(map); }
+    public void clearAttributes()                       { commonInfo.clearAttributes(); }
+    public void putAttribute(String key, Object value)  { commonInfo.putAttribute(key, value); }
+    public void removeAttribute(String key)             { commonInfo.removeAttribute(key); }
+    public void putAttributes(Map<String, ?> map)       { commonInfo.putAttributes(map); }
+    public void setNegLog10PError(double negLog10PError) { commonInfo.setNegLog10PError(negLog10PError); }
+    public void putAttribute(String key, Object value, boolean allowOverwrites) { commonInfo.putAttribute(key, value, allowOverwrites); }
+    public void setID(String id) { putAttribute(ID_KEY, id, true); }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
new file mode 100755
index 000000000..87466e21b
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -0,0 +1,1521 @@
+package org.broadinstitute.sting.utils.variantcontext;
+
+import org.broad.tribble.Feature;
+import org.broad.tribble.TribbleException;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFParser;
+
+import java.util.*;
+
+/**
+ * Class VariantContext
+ *
+ * == High-level overview ==
+ *
+ * The VariantContext object is a single general class system for representing genetic variation data composed of:
+ *
+ * * Allele: representing single genetic haplotypes (A, T, ATC, -)
+ * * Genotype: an assignment of alleles for each chromosome of a single named sample at a particular locus
+ * * VariantContext: an abstract class holding all segregating alleles at a locus as well as genotypes
+ *    for multiple individuals containing alleles at that locus
+ *
+ * The class system works by defining segregating alleles, creating a variant context representing the segregating
+ * information at a locus, and potentially creating and associating genotypes with individuals in the context.
+ *
+ * All of the classes are highly validating -- call validate() if you modify them -- so you can rely on the
+ * self-consistency of the data once you have a VariantContext in hand.  The system has a rich set of assessor
+ * and manipulator routines, as well as more complex static support routines in VariantContextUtils.
+ *
+ * The VariantContext (and Genotype) objects are attributed (supporting addition of arbitrary key/value pairs) and
+ * filtered (can represent a variation that is viewed as suspect).
+ *
+ * VariantContexts are dynamically typed, so whether a VariantContext is a SNP, Indel, or NoVariant depends
+ * on the properties of the alleles in the context.  See the detailed documentation on the Type parameter below.
+ *
+ * It's also easy to create subcontexts based on selected genotypes.
+ *
+ * == Working with Variant Contexts ==
+ * By default, VariantContexts are immutable.  In order to access (in the rare circumstances where you need them)
+ * setter routines, you need to create MutableVariantContexts and MutableGenotypes.
+ *
+ * === Some example data ===
+ *
+ * Allele A, Aref, T, Tref;
+ * Allele del, delRef, ATC, ATCref;
+ *
+ * A [ref] / T at 10
+ * GenomeLoc snpLoc = GenomeLocParser.createGenomeLoc("chr1", 10, 10);
+ *
+ * - / ATC [ref] from 20-23
+ * GenomeLoc delLoc = GenomeLocParser.createGenomeLoc("chr1", 20, 22);
+ *
+ *  // - [ref] / ATC immediately after 20
+ * GenomeLoc insLoc = GenomeLocParser.createGenomeLoc("chr1", 20, 20);
+ *
+ * === Alleles ===
+ *
+ * See the documentation in the Allele class itself
+ *
+ * What are they?
+ *
+ * Alleles can be either reference or non-reference
+ *
+ * Example alleles used here:
+ *
+ *   del = new Allele("-");
+ *   A = new Allele("A");
+ *   Aref = new Allele("A", true);
+ *   T = new Allele("T");
+ *   ATC = new Allele("ATC");
+ *
+ * === Creating variant contexts ===
+ *
+ * ==== By hand ====
+ *
+ * Here's an example of a A/T polymorphism with the A being reference:
+ *
+ * <pre>
+ * VariantContext vc = new VariantContext(name, snpLoc, Arrays.asList(Aref, T));
+ * </pre>
+ *
+ * If you want to create a non-variant site, just put in a single reference allele
+ *
+ * <pre>
+ * VariantContext vc = new VariantContext(name, snpLoc, Arrays.asList(Aref));
+ * </pre>
+ *
+ * A deletion is just as easy:
+ *
+ * <pre>
+ * VariantContext vc = new VariantContext(name, delLoc, Arrays.asList(ATCref, del));
+ * </pre>
+ *
+ * The only 2 things that distinguishes between a insertion and deletion are the reference allele
+ * and the location of the variation.  An insertion has a Null reference allele and at least
+ * one non-reference Non-Null allele.  Additionally, the location of the insertion is immediately after
+ * a 1-bp GenomeLoc (at say 20).
+ *
+ * <pre>
+ * VariantContext vc = new VariantContext("name", insLoc, Arrays.asList(delRef, ATC));
+ * </pre>
+ *
+ * ==== Converting rods and other data structures to VCs ====
+ *
+ * You can convert many common types into VariantContexts using the general function:
+ *
+ * <pre>
+ * VariantContextAdaptors.convertToVariantContext(name, myObject)
+ * </pre>
+ *
+ * dbSNP and VCFs, for example, can be passed in as myObject and a VariantContext corresponding to that
+ * object will be returned.  A null return type indicates that the type isn't yet supported.  This is the best
+ * and easiest way to create contexts using RODs.
+ *
+ *
+ * === Working with genotypes ===
+ *
+ * <pre>
+ * List<Allele> alleles = Arrays.asList(Aref, T);
+ * Genotype g1 = new Genotype(Arrays.asList(Aref, Aref), "g1", 10);
+ * Genotype g2 = new Genotype(Arrays.asList(Aref, T), "g2", 10);
+ * Genotype g3 = new Genotype(Arrays.asList(T, T), "g3", 10);
+ * VariantContext vc = new VariantContext(snpLoc, alleles, Arrays.asList(g1, g2, g3));
+ * </pre>
+ *
+ * At this point we have 3 genotypes in our context, g1-g3.
+ *
+ * You can assess a good deal of information about the genotypes through the VariantContext:
+ *
+ * <pre>
+ * vc.hasGenotypes()
+ * vc.isMonomorphic()
+ * vc.isPolymorphic()
+ * vc.getSampleNames().size()
+ *
+ * vc.getGenotypes()
+ * vc.getGenotypes().get("g1")
+ * vc.hasGenotype("g1")
+ *
+ * vc.getChromosomeCount()
+ * vc.getChromosomeCount(Aref)
+ * vc.getChromosomeCount(T)
+ * </pre>
+ *
+ * === NO_CALL alleles ===
+ *
+ * The system allows one to create Genotypes carrying special NO_CALL alleles that aren't present in the
+ * set of context alleles and that represent undetermined alleles in a genotype:
+ *
+ * Genotype g4 = new Genotype(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), "NO_DATA_FOR_SAMPLE", 10);
+ *
+ *
+ * === subcontexts ===
+ * It's also very easy get subcontext based only the data in a subset of the genotypes:
+ *
+ * <pre>
+ * VariantContext vc12 = vc.subContextFromGenotypes(Arrays.asList(g1,g2));
+ * VariantContext vc1 = vc.subContextFromGenotypes(Arrays.asList(g1));
+ * </pre>
+ *
+ * @author depristo
+ */
+public class VariantContext implements Feature { // to enable tribble intergration
+    protected InferredGeneticContext commonInfo = null;
+    public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
+    public final static String REFERENCE_BASE_FOR_INDEL_KEY = "_REFERENCE_BASE_FOR_INDEL_";
+    public final static String UNPARSED_GENOTYPE_MAP_KEY = "_UNPARSED_GENOTYPE_MAP_";
+    public final static String UNPARSED_GENOTYPE_PARSER_KEY = "_UNPARSED_GENOTYPE_PARSER_";
+    public final static String ID_KEY = "ID";
+
+    public final static Set<String> PASSES_FILTERS = Collections.unmodifiableSet(new LinkedHashSet<String>());
+
+    /** The location of this VariantContext */
+    protected String contig;
+    protected long start;
+    protected long stop;
+
+    /** The type (cached for performance reasons) of this context */
+    protected Type type = null;
+
+    /** A set of the alleles segregating in this context */
+    protected LinkedHashSet<Allele> alleles = null;
+
+    /** A mapping from sampleName -> genotype objects for all genotypes associated with this context */
+    protected Map<String, Genotype> genotypes = null;
+
+    /** Counts for each of the possible Genotype types in this context */
+    protected int[] genotypeCounts = null;
+
+    public final static Map<String, Genotype> NO_GENOTYPES = Collections.unmodifiableMap(new HashMap<String, Genotype>());
+
+    // a fast cached access point to the ref / alt alleles for biallelic case
+    private Allele REF = null;
+
+    // set to the alt allele when biallelic, otherwise == null
+    private Allele ALT = null;
+
+    // were filters applied?
+    private boolean filtersWereAppliedToContext;
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // constructors
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+
+    /**
+     * the complete constructor.  Makes a complete VariantContext from its arguments
+     *
+     * @param source          source
+     * @param contig          the contig
+     * @param start           the start base (one based)
+     * @param stop            the stop reference base (one based)
+     * @param alleles         alleles
+     * @param genotypes       genotypes map
+     * @param negLog10PError  qual
+     * @param filters         filters: use null for unfiltered and empty set for passes filters
+     * @param attributes      attributes
+     */
+    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+        this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, false);
+    }
+
+    /**
+     * Makes a VariantContext from its arguments without parsing the genotypes.
+     * Note that this constructor assumes that if there is genotype data, then it's been put into
+     * the attributes with the UNPARSED_GENOTYPE_MAP_KEY and that the codec has been added with the
+     * UNPARSED_GENOTYPE_PARSER_KEY.  It doesn't validate that this is the case because it's possible
+     * that there is no genotype data.
+     *
+     * @param source          source
+     * @param contig          the contig
+     * @param start           the start base (one based)
+     * @param stop            the stop reference base (one based)
+     * @param alleles         alleles
+     * @param negLog10PError  qual
+     * @param filters         filters: use null for unfiltered and empty set for passes filters
+     * @param attributes      attributes
+     */
+    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+        this(source, contig, start, stop, alleles, NO_GENOTYPES, negLog10PError, filters, attributes, true);
+    }
+
+    /**
+     * Create a new VariantContext
+     *
+     * @param source         source
+     * @param contig         the contig
+     * @param start          the start base (one based)
+     * @param stop           the stop reference base (one based)
+     * @param alleles        alleles
+     * @param genotypes      genotypes set
+     * @param negLog10PError qual
+     * @param filters        filters: use null for unfiltered and empty set for passes filters
+     * @param attributes     attributes
+     */
+    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
+        this(source, contig, start, stop, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes, false);
+    }
+
+    /**
+     * Create a new variant context without genotypes and no Perror, no filters, and no attributes
+     *
+     * @param source          source
+     * @param contig          the contig
+     * @param start           the start base (one based)
+     * @param stop            the stop reference base (one based)
+     * @param alleles alleles
+     */
+    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles) {
+        this(source, contig, start, stop, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, false);
+    }
+
+    /**
+     * Create a new variant context without genotypes and no Perror, no filters, and no attributes
+     *
+     * @param source          source
+     * @param contig          the contig
+     * @param start           the start base (one based)
+     * @param stop            the stop reference base (one based)
+     * @param alleles   alleles
+     * @param genotypes genotypes
+     */
+    public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes) {
+        this(source, contig, start, stop, alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null);
+    }
+
+    /**
+     * Copy constructor
+     *
+     * @param other the VariantContext to copy
+     */
+    public VariantContext(VariantContext other) {
+        this(other.getSource(), other.getChr(), other.getStart(), other.getEnd() , other.getAlleles(), other.getGenotypes(), other.getNegLog10PError(), other.filtersWereApplied() ? other.getFilters() : null, other.getAttributes(), false);
+    }
+
+    /**
+     * the actual constructor.  Private access only
+     *
+     * @param source          source
+     * @param contig          the contig
+     * @param start           the start base (one based)
+     * @param stop            the stop reference base (one based)
+     * @param alleles         alleles
+     * @param genotypes       genotypes map
+     * @param negLog10PError  qual
+     * @param filters         filters: use null for unfiltered and empty set for passes filters
+     * @param attributes      attributes
+     */
+    private VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean genotypesAreUnparsed) {
+        if ( contig == null ) { throw new IllegalArgumentException("Contig cannot be null"); }
+        this.contig = contig;
+        this.start = start;
+        this.stop = stop;
+
+        if ( !genotypesAreUnparsed && attributes != null ) {
+            if ( attributes.containsKey(UNPARSED_GENOTYPE_MAP_KEY) )
+                attributes.remove(UNPARSED_GENOTYPE_MAP_KEY);
+            if ( attributes.containsKey(UNPARSED_GENOTYPE_PARSER_KEY) )
+                attributes.remove(UNPARSED_GENOTYPE_PARSER_KEY);
+        }
+
+        this.commonInfo = new InferredGeneticContext(source, negLog10PError, filters, attributes);
+        filtersWereAppliedToContext = filters != null;
+
+        if ( alleles == null ) { throw new IllegalArgumentException("Alleles cannot be null"); }
+
+        // we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles
+        this.alleles = alleleCollectionToSet(new LinkedHashSet<Allele>(), alleles);
+
+
+        if ( genotypes == null ) { genotypes = NO_GENOTYPES; }
+        this.genotypes = Collections.unmodifiableMap(genotypes);
+
+        // cache the REF and ALT alleles
+        int nAlleles = alleles.size();
+        for ( Allele a : alleles ) {
+            if ( a.isReference() ) {
+                REF = a;
+            } else if ( nAlleles == 2 ) { // only cache ALT when biallelic
+                ALT = a;
+            }
+        }
+
+        validate();
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // Partial-cloning routines (because Variant Context is immutable).
+    //    Note that we don't call vc.getGenotypes() because that triggers the lazy loading.
+    //    Also note that we need to create a new attributes map because it's unmodifiable and the constructor may try to modify it.
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    public static VariantContext modifyGenotypes(VariantContext vc, Map<String, Genotype> genotypes) {
+        return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap<String, Object>(vc.getAttributes()), false);
+    }
+
+    public static VariantContext modifyLocation(VariantContext vc, String chr, int start, int end) {
+        return new VariantContext(vc.getSource(), chr, start, end, vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap<String, Object>(vc.getAttributes()), true);
+    }
+
+    public static VariantContext modifyFilters(VariantContext vc, Set<String> filters) {
+        return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd() , vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), filters, new HashMap<String, Object>(vc.getAttributes()), true);
+    }
+
+    public static VariantContext modifyAttributes(VariantContext vc, Map<String, Object> attributes) {
+        return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes, true);
+    }
+
+    public static VariantContext modifyPErrorFiltersAndAttributes(VariantContext vc, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
+        return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, negLog10PError, filters, attributes, true);
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // Selectors
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    /**
+     * Returns a context identical to this (i.e., filter, qual are all the same) but containing only the Genotype
+     * genotype and alleles in genotype.  This is the right way to test if a single genotype is actually
+     * variant or not.
+     *
+     * @param genotype genotype
+     * @return vc subcontext
+     */
+    public VariantContext subContextFromGenotypes(Genotype genotype) {
+        return subContextFromGenotypes(Arrays.asList(genotype));
+    }
+
+
+    /**
+     * Returns a context identical to this (i.e., filter, qual are all the same) but containing only the Genotypes
+     * genotypes and alleles in these genotypes.  This is the right way to test if a single genotype is actually
+     * variant or not.
+     *
+     * @param genotypes genotypes
+     * @return vc subcontext
+     */
+    public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes) {
+        return subContextFromGenotypes(genotypes, allelesOfGenotypes(genotypes)) ;
+    }
+
+    /**
+     * Returns a context identical to this (i.e., filter, qual are all the same) but containing only the Genotypes
+     * genotypes.  Also, the resulting variant context will contain the alleles provided, not only those found in genotypes
+     *
+     * @param genotypes genotypes
+     * @param alleles the set of allele segregating alleles at this site.  Must include those in genotypes, but may be more
+     * @return vc subcontext
+     */
+    public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes, Set<Allele> alleles) {
+        return new VariantContext(getSource(), contig, start, stop, alleles, genotypes, getNegLog10PError(), getFilters(), getAttributes());
+    }
+
+
+    /**
+     * helper routine for subcontext
+     * @param genotypes genotypes
+     * @return allele set
+     */
+    private Set<Allele> allelesOfGenotypes(Collection<Genotype> genotypes) {
+        Set<Allele> alleles = new HashSet<Allele>();
+
+        boolean addedref = false;
+        for ( Genotype g : genotypes ) {
+            for ( Allele a : g.getAlleles() ) {
+                addedref = addedref || a.isReference();
+                if ( a.isCalled() )
+                    alleles.add(a);
+            }
+        }
+        if ( ! addedref ) alleles.add(getReference());
+
+        return alleles;
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // type operations
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    /**
+     * see: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch5&rendertype=table&id=ch5.ch5_t3
+     *
+     * Format:
+     * dbSNP variation class
+     * Rules for assigning allele classes
+     * Sample allele definition
+     *
+     * Single Nucleotide Polymorphisms (SNPs)a
+     *   Strictly defined as single base substitutions involving A, T, C, or G.
+     *   A/T
+     *
+     * Deletion/Insertion Polymorphisms (DIPs)
+     *   Designated using the full sequence of the insertion as one allele, and either a fully
+     *   defined string for the variant allele or a '-' character to specify the deleted allele.
+     *   This class will be assigned to a variation if the variation alleles are of different lengths or
+     *   if one of the alleles is deleted ('-').
+     *   T/-/CCTA/G
+     *
+     * No-variation
+     *   Reports may be submitted for segments of sequence that are assayed and determined to be invariant
+     *   in the sample.
+     *   (NoVariation)
+     *
+     * Mixed
+     *   Mix of other classes
+     *
+     * Also supports NO_VARIATION type, used to indicate that the site isn't polymorphic in the population
+     *
+     *
+     * Not currently supported:
+     *
+     * Heterozygous sequencea
+     * The term heterozygous is used to specify a region detected by certain methods that do not
+     * resolve the polymorphism into a specific sequence motif. In these cases, a unique flanking
+     * sequence must be provided to define a sequence context for the variation.
+     * (heterozygous)
+     *
+     * Microsatellite or short tandem repeat (STR)
+     * Alleles are designated by providing the repeat motif and the copy number for each allele.
+     * Expansion of the allele repeat motif designated in dbSNP into full-length sequence will
+     * be only an approximation of the true genomic sequence because many microsatellite markers are
+     * not fully sequenced and are resolved as size variants only.
+     * (CAC)8/9/10/11
+     *
+     * Named variant
+     * Applies to insertion/deletion polymorphisms of longer sequence features, such as retroposon
+     * dimorphism for Alu or line elements. These variations frequently include a deletion '-' indicator
+     * for the absent allele.
+     * (alu) / -
+     *
+     * Multi-Nucleotide Polymorphism (MNP)
+     *   Assigned to variations that are multi-base variations of a single, common length
+     *   GGA/AGT
+     */
+    public enum Type {
+        NO_VARIATION,
+        SNP,
+        MNP,    // a multi-nucleotide polymorphism
+        INDEL,
+        SYMBOLIC,
+        MIXED,
+    }
+
+    /**
+     * Determines (if necessary) and returns the type of this variation by examining the alleles it contains.
+     *
+     * @return the type of this VariantContext
+     **/
+    public Type getType() {
+        if ( type == null )
+            determineType();
+
+        return type;
+    }
+
+    /**
+     * convenience method for SNPs
+     *
+     * @return true if this is a SNP, false otherwise
+     */
+    public boolean isSNP() { return getType() == Type.SNP; }
+
+
+    /**
+     * convenience method for variants
+     *
+     * @return true if this is a variant allele, false if it's reference
+     */
+    public boolean isVariant() { return getType() != Type.NO_VARIATION; }
+
+    /**
+     * convenience method for point events
+     *
+     * @return true if this is a SNP or ref site, false if it's an indel or mixed event
+     */
+    public boolean isPointEvent() { return isSNP() || !isVariant(); }
+
+    /**
+     * convenience method for indels
+     *
+     * @return true if this is an indel, false otherwise
+     */
+    public boolean isIndel() { return getType() == Type.INDEL; }
+
+    /**
+     * @return true if the alleles indicate a simple insertion (i.e., the reference allele is Null)
+     */
+    public boolean isInsertion() {
+        // can't just call !isDeletion() because of complex indels
+        return getType() == Type.INDEL && getReference().isNull();
+    }
+
+    /**
+     * @return true if the alleles indicate a simple deletion (i.e., a single alt allele that is Null)
+     */
+    public boolean isDeletion() {
+        // can't just call !isInsertion() because of complex indels
+        return getType() == Type.INDEL && getAlternateAllele(0).isNull();
+    }
+
+    public boolean isSymbolic() {
+        return getType() == Type.SYMBOLIC;
+    }
+
+    /**
+     * convenience method for indels
+     *
+     * @return true if this is an mixed variation, false otherwise
+     */
+    public boolean isMixed() { return getType() == Type.MIXED; }
+
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // Generic accessors
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    public boolean hasID() {
+        return commonInfo.hasAttribute(ID_KEY);
+    }
+
+    public String getID() {
+        return (String)commonInfo.getAttribute(ID_KEY);
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // get routines to access context info fields
+    //
+    // ---------------------------------------------------------------------------------------------------------
+    public String getSource()                   { return commonInfo.getName(); }
+    public Set<String> getFilters()             { return commonInfo.getFilters(); }
+    public boolean isFiltered()                 { return commonInfo.isFiltered(); }
+    public boolean isNotFiltered()              { return commonInfo.isNotFiltered(); }
+    public boolean filtersWereApplied()         { return filtersWereAppliedToContext; }
+    public boolean hasNegLog10PError()          { return commonInfo.hasNegLog10PError(); }
+    public double getNegLog10PError()           { return commonInfo.getNegLog10PError(); }
+    public double getPhredScaledQual()          { return commonInfo.getPhredScaledQual(); }
+
+    public Map<String, Object>  getAttributes() { return commonInfo.getAttributes(); }
+    public boolean hasAttribute(String key)     { return commonInfo.hasAttribute(key); }
+    public Object getAttribute(String key)      { return commonInfo.getAttribute(key); }
+
+    public Object getAttribute(String key, Object defaultValue) {
+        return commonInfo.getAttribute(key, defaultValue);
+    }
+
+    public String getAttributeAsString(String key)                        { return commonInfo.getAttributeAsString(key); }
+    public String getAttributeAsString(String key, String defaultValue)   { return commonInfo.getAttributeAsString(key, defaultValue); }
+    public int getAttributeAsInt(String key)                              { return commonInfo.getAttributeAsInt(key); }
+    public int getAttributeAsInt(String key, int defaultValue)            { return commonInfo.getAttributeAsInt(key, defaultValue); }
+    public double getAttributeAsDouble(String key)                        { return commonInfo.getAttributeAsDouble(key); }
+    public double getAttributeAsDouble(String key, double  defaultValue)  { return commonInfo.getAttributeAsDouble(key, defaultValue); }
+    public boolean getAttributeAsBoolean(String key)                        { return commonInfo.getAttributeAsBoolean(key); }
+    public boolean getAttributeAsBoolean(String key, boolean  defaultValue)  { return commonInfo.getAttributeAsBoolean(key, defaultValue); }
+
+    public Integer getAttributeAsIntegerNoException(String key)  { return commonInfo.getAttributeAsIntegerNoException(key); }
+    public Double getAttributeAsDoubleNoException(String key)    { return commonInfo.getAttributeAsDoubleNoException(key); }
+    public String getAttributeAsStringNoException(String key)    { return commonInfo.getAttributeAsStringNoException(key); }
+    public Boolean getAttributeAsBooleanNoException(String key)  { return commonInfo.getAttributeAsBooleanNoException(key); }
+
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // Working with alleles
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    /**
+     * @return the reference allele for this context
+     */
+    public Allele getReference() {
+        Allele ref = REF;
+        if ( ref == null )
+            throw new IllegalStateException("BUG: no reference allele found at " + this);
+        return ref;
+    }
+
+    /** Private helper routine that grabs the reference allele but doesn't throw an error if there's no such allele */
+
+//    private Allele getReferenceWithoutError() {
+//        for ( Allele allele : getAlleles() ) {
+//            if ( allele.isReference() ) {
+//                return allele;
+//            }
+//        }
+//
+//        return null;
+//    }
+
+    /**
+     * @return true if the context is strictly bi-allelic
+     */
+    public boolean isBiallelic() {
+        return getNAlleles() == 2;
+    }
+
+    /**
+     * @return The number of segregating alleles in this context
+     */
+    public int getNAlleles() {
+        return alleles.size();
+    }
+
+    /**
+     * @return The allele sharing the same bases as this String.  A convenience method; better to use byte[]
+     */
+    public Allele getAllele(String allele) {
+        return getAllele(allele.getBytes());
+    }
+
+    /**
+     * @return The allele sharing the same bases as this byte[], or null if no such allele is present.
+     */
+    public Allele getAllele(byte[] allele) {
+        return Allele.getMatchingAllele(getAlleles(), allele);
+    }
+
+    /**
+     * @return True if this context contains Allele allele, or false otherwise
+     */
+    public boolean hasAllele(Allele allele) {
+        return hasAllele(allele, false);
+    }
+
+    public boolean hasAllele(Allele allele, boolean ignoreRefState) {
+        if ( allele == REF || allele == ALT ) // optimization for cached cases
+            return true;
+
+        for ( Allele a : getAlleles() ) {
+            if ( a.equals(allele, ignoreRefState) )
+                return true;
+        }
+
+        return false;
+    }
+
+
+    /**
+     * Gets the alleles.  This method should return all of the alleles present at the location,
+     * including the reference allele.  There are no constraints imposed on the ordering of alleles
+     * in the set. If the reference is not an allele in this context it will not be included.
+     *
+     * @return the set of alleles
+     */
+    public Set<Allele> getAlleles() { return alleles; }
+
+    /**
+     * Gets the alternate alleles.  This method should return all the alleles present at the location,
+     * NOT including the reference allele.  There are no constraints imposed on the ordering of alleles
+     * in the set.
+     *
+     * @return the set of alternate alleles
+     */
+    public Set<Allele> getAlternateAlleles() {
+        LinkedHashSet<Allele> altAlleles = new LinkedHashSet<Allele>();
+        for ( Allele allele : alleles ) {
+            if ( allele.isNonReference() )
+                altAlleles.add(allele);
+        }
+
+        return Collections.unmodifiableSet(altAlleles);
+    }
+
+    /**
+     * Gets the sizes of the alternate alleles if they are insertion/deletion events, and returns a list of their sizes
+     *
+     * @return a list of indel lengths ( null if not of type indel or mixed )
+     */
+    public List<Integer> getIndelLengths() {
+        if ( getType() != Type.INDEL && getType() != Type.MIXED ) {
+            return null;
+        }
+
+        List<Integer> lengths = new ArrayList<Integer>();
+        for ( Allele a : getAlternateAlleles() ) {
+            lengths.add(a.length() - getReference().length());
+        }
+
+        return lengths;
+    }
+
+    /**
+     * @param i -- the ith allele (from 0 to n - 2 for a context with n alleles including a reference allele)
+     * @return the ith non-reference allele in this context
+     * @throws IllegalArgumentException if i is invalid
+     */
+    public Allele getAlternateAllele(int i) {
+        int n = 0;
+
+        for ( Allele allele : alleles ) {
+            if ( allele.isNonReference() && n++ == i )
+                return allele;
+        }
+
+        throw new IllegalArgumentException("Requested " + i + " alternative allele but there are only " + n + " alternative alleles " + this);
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // Working with genotypes
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    private void loadGenotypes() {
+        if ( !hasAttribute(UNPARSED_GENOTYPE_MAP_KEY) )
+            return;
+
+        Object parserObj = getAttribute(UNPARSED_GENOTYPE_PARSER_KEY);
+        if ( parserObj == null || !(parserObj instanceof VCFParser) )
+            throw new IllegalStateException("There is no VCF parser stored to unparse the genotype data");
+        VCFParser parser = (VCFParser)parserObj;
+
+        Object mapObj = getAttribute(UNPARSED_GENOTYPE_MAP_KEY);
+        if ( mapObj == null )
+            throw new IllegalStateException("There is no mapping string stored to unparse the genotype data");
+
+        genotypes = parser.createGenotypeMap(mapObj.toString(), new ArrayList<Allele>(alleles), getChr(), getStart());
+
+        commonInfo.removeAttribute(UNPARSED_GENOTYPE_MAP_KEY);
+        commonInfo.removeAttribute(UNPARSED_GENOTYPE_PARSER_KEY);
+
+        validateGenotypes();
+    }
+
+    /**
+     * @return the number of samples in the context
+     */
+    public int getNSamples() {
+        loadGenotypes();
+        return genotypes.size();
+    }
+
+    /**
+     * @return true if the context has associated genotypes
+     */
+    public boolean hasGenotypes() {
+        loadGenotypes();
+        return genotypes.size() > 0;
+    }
+
+    public boolean hasGenotypes(Collection<String> sampleNames) {
+        loadGenotypes();
+        for ( String name : sampleNames ) {
+            if ( ! genotypes.containsKey(name) )
+                return false;
+        }
+        return true;
+    }
+
+    /**
+     * @return set of all Genotypes associated with this context
+     */
+    public Map<String, Genotype> getGenotypes() {
+        loadGenotypes();
+        return genotypes;
+    }
+
+    public List<Genotype> getGenotypesSortedByName() {
+        loadGenotypes();
+        Collection<Genotype> types = new TreeMap<String,Genotype>(genotypes).values();
+        return new ArrayList<Genotype>(types);
+    }
+
+    /**
+     * Returns a map from sampleName -> Genotype for the genotype associated with sampleName.  Returns a map
+     * for consistency with the multi-get function.
+     *
+     * @param sampleName
+     * @return
+     * @throws IllegalArgumentException if sampleName isn't bound to a genotype
+     */
+    public Map<String, Genotype> getGenotypes(String sampleName) {
+        return getGenotypes(Arrays.asList(sampleName));
+    }
+
+    /**
+     * Returns a map from sampleName -> Genotype for each sampleName in sampleNames.  Returns a map
+     * for consistency with the multi-get function.
+     *
+     * @param sampleNames a unique list of sample names
+     * @return
+     * @throws IllegalArgumentException if sampleName isn't bound to a genotype
+     */
+    public Map<String, Genotype> getGenotypes(Collection<String> sampleNames) {
+        HashMap<String, Genotype> map = new HashMap<String, Genotype>();
+
+        for ( String name : sampleNames ) {
+            if ( map.containsKey(name) ) throw new IllegalArgumentException("Duplicate names detected in requested samples " + sampleNames);
+            map.put(name, getGenotype(name));
+        }
+
+        return map;
+    }
+
+    /**
+     * @return the set of all sample names in this context
+     */
+    public Set<String> getSampleNames() {
+        return getGenotypes().keySet();
+    }
+
+    /**
+     * @param sample  the sample name
+     *
+     * @return the Genotype associated with the given sample in this context or null if the sample is not in this context
+     */
+    public Genotype getGenotype(String sample) {
+        return getGenotypes().get(sample);
+    }
+
+    public boolean hasGenotype(String sample) {
+        return getGenotypes().containsKey(sample);
+    }
+
+    public Genotype getGenotype(int ith) {
+        return getGenotypesSortedByName().get(ith);
+    }
+
+
+    /**
+     * Returns the number of chromosomes carrying any allele in the genotypes (i.e., excluding NO_CALLS
+     *
+     * @return chromosome count
+     */
+    public int getChromosomeCount() {
+        int n = 0;
+
+        for ( Genotype g : getGenotypes().values() ) {
+            n += g.isNoCall() ? 0 : g.getPloidy();
+        }
+
+        return n;
+    }
+
+    /**
+     * Returns the number of chromosomes carrying allele A in the genotypes
+     *
+     * @param a allele
+     * @return chromosome count
+     */
+    public int getChromosomeCount(Allele a) {
+        int n = 0;
+
+        for ( Genotype g : getGenotypes().values() ) {
+            n += g.getAlleles(a).size();
+        }
+
+        return n;
+    }
+
+    /**
+     * Genotype-specific functions -- are the genotypes monomorphic w.r.t. to the alleles segregating at this
+     * site?  That is, is the number of alternate alleles among all fo the genotype == 0?
+     *
+     * @return true if it's monomorphic
+     */
+    public boolean isMonomorphic() {
+        return ! isVariant() || getChromosomeCount(getReference()) == getChromosomeCount();
+    }
+
+    /**
+     * Genotype-specific functions -- are the genotypes polymorphic w.r.t. to the alleles segregating at this
+     * site?  That is, is the number of alternate alleles among all fo the genotype > 0?
+     *
+     * @return true if it's polymorphic
+     */
+    public boolean isPolymorphic() {
+        return ! isMonomorphic();
+    }
+
+    private void calculateGenotypeCounts() {
+        if ( genotypeCounts == null ) {
+            genotypeCounts = new int[Genotype.Type.values().length];
+
+            for ( Genotype g : getGenotypes().values() ) {
+                if ( g.isNoCall() )
+                    genotypeCounts[Genotype.Type.NO_CALL.ordinal()]++;
+                else if ( g.isHomRef() )
+                    genotypeCounts[Genotype.Type.HOM_REF.ordinal()]++;
+                else if ( g.isHet() )
+                    genotypeCounts[Genotype.Type.HET.ordinal()]++;
+                else if ( g.isHomVar() )
+                    genotypeCounts[Genotype.Type.HOM_VAR.ordinal()]++;
+                else
+                    throw new IllegalStateException("Genotype of unknown type: " + g);
+            }
+        }
+    }
+
+    /**
+     * Genotype-specific functions -- how many no-calls are there in the genotypes?
+     *
+     * @return number of no calls
+     */
+    public int getNoCallCount() {
+        calculateGenotypeCounts();
+        return genotypeCounts[Genotype.Type.NO_CALL.ordinal()];
+    }
+
+    /**
+     * Genotype-specific functions -- how many hom ref calls are there in the genotypes?
+     *
+     * @return number of hom ref calls
+     */
+    public int getHomRefCount() {
+        calculateGenotypeCounts();
+        return genotypeCounts[Genotype.Type.HOM_REF.ordinal()];
+    }
+
+    /**
+     * Genotype-specific functions -- how many het calls are there in the genotypes?
+     *
+     * @return number of het calls
+     */
+    public int getHetCount() {
+        calculateGenotypeCounts();
+        return genotypeCounts[Genotype.Type.HET.ordinal()];
+    }
+
+    /**
+     * Genotype-specific functions -- how many hom var calls are there in the genotypes?
+     *
+     * @return number of hom var calls
+     */
+    public int getHomVarCount() {
+        return genotypeCounts[Genotype.Type.HOM_VAR.ordinal()];
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // validation: extra-strict validation routines for paranoid users
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    /**
+     * Run all extra-strict validation tests on a Variant Context object
+     *
+     * @param reference        the true reference allele
+     * @param rsIDs            the true dbSNP IDs
+     */
+    public void extraStrictValidation(Allele reference, Set<String> rsIDs) {
+        // validate the reference
+        validateReferenceBases(reference);
+
+        // validate the RS IDs
+        validateRSIDs(rsIDs);
+
+        // validate the altenate alleles
+        validateAlternateAlleles();
+
+        // validate the AN and AC fields
+        validateChromosomeCounts();
+
+        // TODO: implement me
+        //checkReferenceTrack();
+    }
+
+    public void validateReferenceBases(Allele reference) {
+        // don't validate if we're an insertion
+        if ( !reference.isNull() && !reference.basesMatch(getReference()) ) {
+            throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
+        }
+    }
+
+    public void validateRSIDs(Set<String> rsIDs) {
+        if ( rsIDs != null && hasAttribute(VariantContext.ID_KEY) ) {
+            for ( String id : getID().split(VCFConstants.ID_FIELD_SEPARATOR) ) {
+                if ( id.startsWith("rs") && !rsIDs.contains(id) )
+                    throw new TribbleException.InternalCodecException(String.format("the rsID %s for the record at position %s:%d is not in dbSNP", id, getChr(), getStart()));
+            }
+        }
+    }
+
+    public void validateAlternateAlleles() {
+        if ( !hasGenotypes() )
+            return;
+
+        Set<Allele> reportedAlleles = getAlleles();
+        Set<Allele> observedAlleles = new HashSet<Allele>();
+        observedAlleles.add(getReference());
+        for ( Genotype g : getGenotypes().values() ) {
+            if ( g.isCalled() )
+                observedAlleles.addAll(g.getAlleles());
+        }
+
+        if ( reportedAlleles.size() != observedAlleles.size() )
+            throw new TribbleException.InternalCodecException(String.format("the ALT allele(s) for the record at position %s:%d do not match what is observed in the per-sample genotypes", getChr(), getStart()));
+
+        int originalSize = reportedAlleles.size();
+        // take the intersection and see if things change
+        observedAlleles.retainAll(reportedAlleles);
+        if ( observedAlleles.size() != originalSize )
+            throw new TribbleException.InternalCodecException(String.format("the ALT allele(s) for the record at position %s:%d do not match what is observed in the per-sample genotypes", getChr(), getStart()));
+    }
+
+    public void validateChromosomeCounts() {
+        Map<String, Object> observedAttrs = calculateChromosomeCounts();
+
+        // AN
+        if ( hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) {
+            int reportedAN = Integer.valueOf(getAttribute(VCFConstants.ALLELE_NUMBER_KEY).toString());
+            int observedAN = (Integer)observedAttrs.get(VCFConstants.ALLELE_NUMBER_KEY);
+            if ( reportedAN != observedAN )
+                throw new TribbleException.InternalCodecException(String.format("the Allele Number (AN) tag is incorrect for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedAN, observedAN));
+        }
+
+        // AC
+        if ( hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
+            List<Integer> observedACs = (List<Integer>)observedAttrs.get(VCFConstants.ALLELE_COUNT_KEY);
+            if ( getAttribute(VCFConstants.ALLELE_COUNT_KEY) instanceof List ) {
+                Collections.sort(observedACs);
+                List reportedACs = (List)getAttribute(VCFConstants.ALLELE_COUNT_KEY);
+                Collections.sort(reportedACs);
+                if ( observedACs.size() != reportedACs.size() )
+                    throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag doesn't have the correct number of values for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedACs.size(), observedACs.size()));
+                for (int i = 0; i < observedACs.size(); i++) {
+                    if ( Integer.valueOf(reportedACs.get(i).toString()) != observedACs.get(i) )
+                        throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag is incorrect for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedACs.get(i), observedACs.get(i)));
+                }
+            } else {
+                if ( observedACs.size() != 1 )
+                    throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag doesn't have enough values for the record at position %s:%d", getChr(), getStart()));
+                int reportedAC = Integer.valueOf(getAttribute(VCFConstants.ALLELE_COUNT_KEY).toString());
+                if ( reportedAC != observedACs.get(0) )
+                    throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag is incorrect for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedAC, observedACs.get(0)));
+            }
+        }
+    }
+
+    private Map<String, Object> calculateChromosomeCounts() {
+        Map<String, Object> attributes = new HashMap<String, Object>();
+
+        attributes.put(VCFConstants.ALLELE_NUMBER_KEY, getChromosomeCount());
+        ArrayList<Double> alleleFreqs = new ArrayList<Double>();
+        ArrayList<Integer> alleleCounts = new ArrayList<Integer>();
+
+        // if there are alternate alleles, record the relevant tags
+        if ( getAlternateAlleles().size() > 0 ) {
+            for ( Allele allele : getAlternateAlleles() ) {
+                alleleCounts.add(getChromosomeCount(allele));
+                alleleFreqs.add((double)getChromosomeCount(allele) / (double)getChromosomeCount());
+            }
+        }
+        // otherwise, set them to 0
+        else {
+            alleleCounts.add(0);
+            alleleFreqs.add(0.0);
+        }
+
+        attributes.put(VCFConstants.ALLELE_COUNT_KEY, alleleCounts);
+        attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs);
+        return attributes;
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // validation: the normal validation routines are called automatically upon creation of the VC
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    /**
+     * To be called by any modifying routines
+     */
+    private boolean validate() {
+        return validate(true);
+    }
+
+    private boolean validate(boolean throwException) {
+        try {
+            validateAlleles();
+            validateGenotypes();
+        } catch ( IllegalArgumentException e ) {
+            if ( throwException )
+                throw e;
+            else
+                return false;
+        }
+
+        return true;
+    }
+
+    private void validateAlleles() {
+        // check alleles
+        boolean alreadySeenRef = false, alreadySeenNull = false;
+        for ( Allele allele : alleles ) {
+            // make sure there's only one reference allele
+            if ( allele.isReference() ) {
+                if ( alreadySeenRef ) throw new IllegalArgumentException("BUG: Received two reference tagged alleles in VariantContext " + alleles + " this=" + this);
+                alreadySeenRef = true;
+            }
+
+            if ( allele.isNoCall() ) {
+                throw new IllegalArgumentException("BUG: Cannot add a no call allele to a variant context " + alleles + " this=" + this);
+            }
+
+            // make sure there's only one null allele
+            if ( allele.isNull() ) {
+                if ( alreadySeenNull ) throw new IllegalArgumentException("BUG: Received two null alleles in VariantContext " + alleles + " this=" + this);
+                alreadySeenNull = true;
+            }
+        }
+
+        // make sure there's one reference allele
+        if ( ! alreadySeenRef )
+            throw new IllegalArgumentException("No reference allele found in VariantContext");
+
+//        if ( getType() == Type.INDEL ) {
+//            if ( getReference().length() != (getLocation().size()-1) ) {
+        long length = (stop - start) + 1;
+        if ( (getReference().isNull() && length != 1 ) ||
+                (getReference().isNonNull() && (length - getReference().length()  > 1))) {
+            throw new IllegalStateException("BUG: GenomeLoc " + contig + ":" + start + "-" + stop + " has a size == " + length + " but the variation reference allele has length " + getReference().length() + " this = " + this);
+        }
+    }
+
+    private void validateGenotypes() {
+        if ( this.genotypes == null ) throw new IllegalStateException("Genotypes is null");
+
+        for ( Map.Entry<String, Genotype> elt : this.genotypes.entrySet() ) {
+            String name = elt.getKey();
+            Genotype g = elt.getValue();
+
+            if ( ! name.equals(g.getSampleName()) ) throw new IllegalStateException("Bound sample name " + name + " does not equal the name of the genotype " + g.getSampleName());
+
+            for ( Allele gAllele : g.getAlleles() ) {
+                if ( ! hasAllele(gAllele) && gAllele.isCalled() )
+                    throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles);
+            }
+        }
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // utility routines
+    //
+    // ---------------------------------------------------------------------------------------------------------
+
+    // the indel base that gets stripped off for indels
+    public boolean hasReferenceBaseForIndel() {
+        return hasAttribute(REFERENCE_BASE_FOR_INDEL_KEY);
+    }
+
+    // the indel base that gets stripped off for indels
+    public byte getReferenceBaseForIndel() {
+        return hasReferenceBaseForIndel() ? (Byte)getAttribute(REFERENCE_BASE_FOR_INDEL_KEY) : (byte)'N';
+    }
+
+    private void determineType() {
+        if ( type == null ) {
+            switch ( getNAlleles() ) {
+                case 0:
+                    throw new IllegalStateException("Unexpected error: requested type of VariantContext with no alleles!" + this);
+                case 1:
+                    // note that this doesn't require a reference allele.  You can be monomorphic independent of having a
+                    // reference allele
+                    type = Type.NO_VARIATION;
+                    break;
+                default:
+                    determinePolymorphicType();
+            }
+        }
+    }
+
+    private void determinePolymorphicType() {
+        type = null;
+
+        // do a pairwise comparison of all alleles against the reference allele
+        for ( Allele allele : alleles ) {
+            if ( allele == REF )
+                continue;
+
+            // find the type of this allele relative to the reference
+            Type biallelicType = typeOfBiallelicVariant(REF, allele);
+
+            // for the first alternate allele, set the type to be that one
+            if ( type == null ) {
+                type = biallelicType;
+            }
+            // if the type of this allele is different from that of a previous one, assign it the MIXED type and quit
+            else if ( biallelicType != type ) {
+                type = Type.MIXED;
+                return;
+            }
+        }
+    }
+
+    private static Type typeOfBiallelicVariant(Allele ref, Allele allele) {
+        if ( ref.isSymbolic() )
+            throw new IllegalStateException("Unexpected error: encountered a record with a symbolic reference allele");
+
+        if ( allele.isSymbolic() )
+            return Type.SYMBOLIC;
+
+        if ( ref.length() == allele.length() ) {
+            if ( allele.length() == 1 )
+                return Type.SNP;
+            else
+                return Type.MNP;
+        }
+
+        // Important note: previously we were checking that one allele is the prefix of the other.  However, that's not an
+        // appropriate check as can be seen from the following example:
+        // REF = CTTA and ALT = C,CT,CA
+        // This should be assigned the INDEL type but was being marked as a MIXED type because of the prefix check.
+        // In truth, it should be absolutely impossible to return a MIXED type from this method because it simply
+        // performs a pairwise comparison of a single alternate allele against the reference allele (whereas the MIXED type
+        // is reserved for cases of multiple alternate alleles of different types).  Therefore, if we've reached this point
+        // in the code (so we're not a SNP, MNP, or symbolic allele), we absolutely must be an INDEL.
+        return Type.INDEL;
+
+        // old incorrect logic:
+        // if (oneIsPrefixOfOther(ref, allele))
+        //     return Type.INDEL;
+        // else
+        //     return Type.MIXED;
+    }
+
+    public String toString() {
+        return String.format("[VC %s @ %s of type=%s alleles=%s attr=%s GT=%s",
+                getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop), this.getType(),
+                ParsingUtils.sortList(this.getAlleles()), ParsingUtils.sortedString(this.getAttributes()), this.getGenotypesSortedByName());
+    }
+
+    // protected basic manipulation routines
+    private static LinkedHashSet<Allele> alleleCollectionToSet(LinkedHashSet<Allele> dest, Collection<Allele> alleles) {
+        for ( Allele a : alleles ) {
+            for ( Allele b : dest ) {
+                if ( a.equals(b, true) )
+                    throw new IllegalArgumentException("Duplicate allele added to VariantContext: " + a);
+            }
+
+            dest.add(a);
+        }
+
+        return dest;
+    }
+
+    public static Map<String, Genotype> genotypeCollectionToMap(Map<String, Genotype> dest, Collection<Genotype> genotypes) {
+        for ( Genotype g : genotypes ) {
+            if ( dest.containsKey(g.getSampleName() ) )
+                throw new IllegalArgumentException("Duplicate genotype added to VariantContext: " + g);
+            dest.put(g.getSampleName(), g);
+        }
+
+        return dest;
+    }
+
+    // ---------------------------------------------------------------------------------------------------------
+    //
+    // tribble integration routines -- not for public consumption
+    //
+    // ---------------------------------------------------------------------------------------------------------
+    public String getChr() {
+        return contig;
+    }
+
+    public int getStart() {
+        return (int)start;
+    }
+
+    public int getEnd() {
+        return (int)stop;
+    }
+
+    public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte inputRefBase, boolean refBaseShouldBeAppliedToEndOfAlleles) {
+        Allele refAllele = inputVC.getReference();
+
+        // see if we need to pad common reference base from all alleles
+        boolean padVC;
+
+        // We need to pad a VC with a common base if the length of the reference allele is less than the length of the VariantContext.
+        // This happens because the position of e.g. an indel is always one before the actual event (as per VCF convention).
+        long locLength = (inputVC.getEnd() - inputVC.getStart()) + 1;
+        if (refAllele.length() == locLength)
+            padVC = false;
+        else if (refAllele.length() == locLength-1)
+            padVC = true;
+        else throw new IllegalArgumentException("Badly formed variant context at location " + String.valueOf(inputVC.getStart()) +
+                    " in contig " + inputVC.getChr() + ". Reference length must be at most one base shorter than location size");
+
+
+        // nothing to do if we don't need to pad bases
+        if (padVC) {
+            Byte refByte;
+
+            Map<String,Object> attributes = inputVC.getAttributes();
+
+            // upper-case for consistency; note that we can safely make these casts because the input is constrained to be a byte
+            inputRefBase = (byte)Character.toUpperCase((char)inputRefBase);
+            if (attributes.containsKey(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY))
+                refByte = (Byte)attributes.get(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY);
+            else if (inputRefBase == 'A' || inputRefBase == 'T' || inputRefBase == 'C' || inputRefBase == 'G' || inputRefBase == 'N')
+                refByte = inputRefBase;
+            else
+                throw new IllegalArgumentException("Error when trying to pad Variant Context at location " + String.valueOf(inputVC.getStart())
+                        + " in contig " + inputVC.getChr() +
+                        ". Either input reference base ("+(char)inputRefBase+
+                        ", ascii code="+inputRefBase+") must be a regular base, or input VC must contain reference base key");
+
+            List<Allele> alleles = new ArrayList<Allele>();
+            Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();
+
+            Map<String, Genotype> inputGenotypes = inputVC.getGenotypes();
+
+            for (Allele a : inputVC.getAlleles()) {
+                // get bases for current allele and create a new one with trimmed bases
+                if (a.isSymbolic()) {
+                    alleles.add(a);
+                } else {
+                    String newBases;
+                    if ( refBaseShouldBeAppliedToEndOfAlleles )
+                        newBases = a.getBaseString() + new String(new byte[]{refByte});
+                    else
+                        newBases = new String(new byte[]{refByte}) + a.getBaseString();
+                    alleles.add(Allele.create(newBases,a.isReference()));
+                }
+            }
+
+            // now we can recreate new genotypes with trimmed alleles
+            for (String sample : inputVC.getSampleNames()) {
+                Genotype g = inputGenotypes.get(sample);
+
+                List<Allele> inAlleles = g.getAlleles();
+                List<Allele> newGenotypeAlleles = new ArrayList<Allele>();
+                for (Allele a : inAlleles) {
+                    if (a.isCalled()) {
+                        if (a.isSymbolic()) {
+                            newGenotypeAlleles.add(a);
+                        } else {
+                            String newBases;
+                            if ( refBaseShouldBeAppliedToEndOfAlleles )
+                                newBases = a.getBaseString() + new String(new byte[]{refByte});
+                            else
+                                newBases = new String(new byte[]{refByte}) + a.getBaseString();
+                            newGenotypeAlleles.add(Allele.create(newBases,a.isReference()));
+                        }
+                    }
+                    else {
+                        // add no-call allele
+                        newGenotypeAlleles.add(Allele.NO_CALL);
+                    }
+                }
+                genotypes.put(sample, new Genotype(sample, newGenotypeAlleles, g.getNegLog10PError(),
+                        g.getFilters(),g.getAttributes(),g.isPhased()));
+
+            }
+
+            // Do not change the filter state if filters were not applied to this context
+            Set<String> inputVCFilters = inputVC.filtersWereAppliedToContext ? inputVC.getFilters() : null;
+            return new VariantContext(inputVC.getSource(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(),
+                    inputVCFilters, attributes);
+
+
+
+        }
+        else
+            return inputVC;
+
+    }
+
+    public ArrayList<Allele> getTwoAllelesWithHighestAlleleCounts() {
+        // first idea: get two alleles with highest AC
+        int maxAC1 = 0, maxAC2=0,maxAC1ind =0, maxAC2ind = 0;
+        int i=0;
+        int[] alleleCounts = new int[this.getAlleles().size()];
+        ArrayList<Allele> alleleArray = new ArrayList<Allele>();
+        for (Allele a:this.getAlleles()) {
+            int ac = this.getChromosomeCount(a);
+            if (ac >=maxAC1) {
+                maxAC1 = ac;
+                maxAC1ind = i;
+            }
+            alleleArray.add(a);
+            alleleCounts[i++] = ac;
+        }
+        // now get second best allele
+        for (i=0; i < alleleCounts.length; i++) {
+            if (i == maxAC1ind)
+                continue;
+            if (alleleCounts[i] >= maxAC2) {
+                maxAC2 = alleleCounts[i];
+                maxAC2ind = i;
+            }
+        }
+
+        Allele alleleA, alleleB;
+        if (alleleArray.get(maxAC1ind).isReference()) {
+            alleleA = alleleArray.get(maxAC1ind);
+            alleleB = alleleArray.get(maxAC2ind);
+        }
+        else if  (alleleArray.get(maxAC2ind).isReference()) {
+            alleleA = alleleArray.get(maxAC2ind);
+            alleleB = alleleArray.get(maxAC1ind);
+        } else {
+            alleleA = alleleArray.get(maxAC1ind);
+            alleleB = alleleArray.get(maxAC2ind);
+        }
+        ArrayList<Allele> a = new ArrayList<Allele>();
+        a.add(alleleA);
+        a.add(alleleB);
+        return a;
+    }
+    public Allele getAltAlleleWithHighestAlleleCount() {
+        // first idea: get two alleles with highest AC
+        Allele best = null;
+        int maxAC1 = 0;
+        for (Allele a:this.getAlternateAlleles()) {
+            int ac = this.getChromosomeCount(a);
+            if (ac >=maxAC1) {
+                maxAC1 = ac;
+                best = a;
+            }
+
+        }
+        return best;
+    }
+
+    public int[] getGLIndecesOfAllele(Allele inputAllele) {
+        int[] idxVector = new int[3];
+        int numAlleles =  this.getAlleles().size();
+
+        int idxDiag = numAlleles;
+        int incr = numAlleles - 1;
+        int k=1;
+        for (Allele a: getAlternateAlleles()) {
+            // multi-allelic approximation, part 1: Ideally
+            // for each alt allele compute marginal (suboptimal) posteriors -
+            // compute indices for AA,AB,BB for current allele - genotype likelihoods are a linear vector that can be thought of
+            // as a row-wise upper triangular matrix of likelihoods.
+            // So, for example, with 2 alt alleles, likelihoods have AA,AB,AC,BB,BC,CC.
+            // 3 alt alleles: AA,AB,AC,AD BB BC BD CC CD DD
+
+            int idxAA = 0;
+            int idxAB = k++;
+            // yy is always element on the diagonal.
+            // 2 alleles: BBelement 2
+            // 3 alleles: BB element  3. CC element 5
+            // 4 alleles:
+            int idxBB = idxDiag;
+
+            if (a.equals(inputAllele)) {
+                idxVector[0] = idxAA;
+                idxVector[1] = idxAB;
+                idxVector[2]  = idxBB;
+                break;
+            }
+            idxDiag += incr--;
+        }
+        return idxVector;
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
rename to java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index c848a300b..5d58954aa 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -21,7 +21,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.contexts.variantcontext;
+package org.broadinstitute.sting.utils.variantcontext;
 
 import java.io.Serializable;
 import java.util.*;
@@ -31,11 +31,10 @@ import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.util.StringUtil;
 import org.apache.commons.jexl2.*;
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
-import org.broad.tribble.util.variantcontext.*;
-import org.broad.tribble.vcf.AbstractVCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
 import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
 import org.broadinstitute.sting.utils.*;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java
rename to java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
index e29054893..c5a3b6f2a 100644
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java
+++ b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
@@ -21,14 +21,12 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.contexts.variantcontext;
+package org.broadinstitute.sting.utils.variantcontext;
 
 import org.apache.commons.jexl2.JexlContext;
 import org.apache.commons.jexl2.MapContext;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.Utils;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.*;
diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java
index 822034720..dacaf2738 100755
--- a/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting;
 import org.apache.commons.lang.StringUtils;
 import org.broad.tribble.Tribble;
 import org.broad.tribble.index.IndexFactory;
-import org.broad.tribble.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java
index 8e04fd24e..59405c065 100644
--- a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.datasources.sample;
 
 import net.sf.samtools.SAMFileHeader;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.exceptions.StingException;
diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java
index 218948c52..e475e732d 100644
--- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java
@@ -28,9 +28,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMSequenceDictionary;
 import org.broad.tribble.Tribble;
 import org.broad.tribble.index.Index;
-import org.broad.tribble.vcf.VCF3Codec;
-import org.broad.tribble.vcf.VCFCodec;
-import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
+import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
index 2eef77400..a64d0b5ab 100644
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
@@ -1,18 +1,17 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.vcf.VCFCodec;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.testng.Assert;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderUnitTest;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import org.testng.annotations.Test;
 
 import java.io.StringBufferInputStream;
 import java.util.ArrayList;
-import java.util.List;
 import java.util.Set;
 
 /**
diff --git a/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java b/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
new file mode 100644
index 000000000..2e618d5eb
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
@@ -0,0 +1,162 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.codecs.hapmap;
+
+import org.broad.tribble.annotation.Strand;
+import org.broad.tribble.readers.AsciiLineReader;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+/**
+ * Unit tests for the HapMap codec
+ */
+public class HapMapUnitTest {
+    // our sample hapmap file
+    private final static File hapMapFile = new File("testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap");
+    private final static String knownLine = "rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_r" +
+            "s2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC TC TT CT CC CC CC CC CC CC CC CC CC";
+    /**
+     * test reading the header off of the file.  We take in the file, read off the first line,
+     * close the reader, and then ask the HapMap decoder for the header with a new reader.  These should
+     * be equal (i.e. they return the same object).
+     */
+    @Test
+    public void testReadHeader() {
+        HapMapCodec codec = new HapMapCodec();
+        AsciiLineReader reader = getReader();
+        try {
+            String header = reader.readLine();
+            reader.close();
+            Assert.assertTrue(header.equals((String)codec.readHeader(getReader())));
+        } catch (IOException e) {
+            Assert.fail("Unable to read from file " + hapMapFile);
+        }
+        reader.close();
+    }
+
+    @Test
+    public void testKnownRecordConversion() {
+        HapMapCodec codec = new HapMapCodec();
+        HapMapFeature feature = (HapMapFeature)codec.decode(knownLine);
+
+
+        // check that the alleles are right
+        Assert.assertEquals(feature.getAlleles().length,2);
+        Assert.assertTrue("C".equals(feature.getAlleles()[0]));
+        Assert.assertTrue("T".equals(feature.getAlleles()[1]));
+
+        // check the name
+        Assert.assertTrue("rs2185539".equals(feature.getName()));
+
+        // check the position
+        Assert.assertEquals(feature.getStart(),556738);
+        Assert.assertEquals(feature.getEnd(),556738);
+
+        // check the contig
+        Assert.assertTrue("chr1".equals(feature.getChr()));
+                
+        // check the assembly, center, protLSID, assayLSID, panelLSID, and qccode
+        Assert.assertTrue("ncbi_b36".equals(feature.getAssembly()));
+        Assert.assertTrue("bbs".equals(feature.getCenter()));
+        Assert.assertTrue("urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1".equals(feature.getProtLSID()));
+        Assert.assertTrue("urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2185539:1".equals(feature.getAssayLSID()));
+        Assert.assertTrue("urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4".equals(feature.getPanelLSID()));
+        Assert.assertTrue("QC+".equals(feature.getQCCode()));
+
+        // check the strand
+        Assert.assertEquals(feature.getStrand(),Strand.POSITIVE);
+
+        // check the genotypes
+        int x = 0;
+        for (; x < feature.getGenotypes().length; x++) {
+            switch (x) {
+                case 1: Assert.assertTrue("TC".equals(feature.getGenotypes()[x])); break;
+                case 2: Assert.assertTrue("TT".equals(feature.getGenotypes()[x])); break;
+                case 3: Assert.assertTrue("CT".equals(feature.getGenotypes()[x])); break;
+                default: Assert.assertTrue("CC".equals(feature.getGenotypes()[x])); break;
+            }
+        }
+        // assert that we found the correct number of records
+        Assert.assertEquals(x,13);
+    }
+
+    @Test
+    public void testReadCorrectNumberOfRecords() {
+        // setup the record for reading our 500 line file (499 records, 1 header line)
+        HapMapCodec codec = new HapMapCodec();
+        AsciiLineReader reader = getReader();
+
+        String line = null;
+        int count = 0;
+        try {
+            codec.readHeader(reader);
+            line = reader.readLine();
+            while (line != null) {
+                HapMapFeature feature = (HapMapFeature) codec.decode(line);
+                line = reader.readLine();
+                ++count;
+            }
+        } catch (IOException e) {
+            Assert.fail("IOException " + e.getMessage());
+        }
+        reader.close();
+        Assert.assertEquals(count,499);
+    }
+
+    @Test
+    public void testGetSampleNames() {
+        // setup the record for reading our 500 line file (499 records, 1 header line)
+        HapMapCodec codec = new HapMapCodec();
+        AsciiLineReader reader = getReader();
+
+        String line = null;
+        try {
+            codec.readHeader(reader);
+            line = reader.readLine();
+            HapMapFeature feature = (HapMapFeature) codec.decode(line);
+            Assert.assertEquals(feature.getSampleIDs().length,87);
+
+        } catch (IOException e) {
+            Assert.fail("IOException " + e.getMessage());
+        }
+        reader.close();
+    }
+
+
+    public AsciiLineReader getReader() {
+        try {
+            return new AsciiLineReader(new FileInputStream(hapMapFile));            
+        } catch (FileNotFoundException e) {
+            Assert.fail("Unable to open hapmap file : " + hapMapFile);
+        }
+        return null; // for intellij, it doesn't know that assert.fail is fatal
+    }
+
+}
diff --git a/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java b/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
new file mode 100755
index 000000000..3929ff388
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
@@ -0,0 +1,81 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broad.tribble.Tribble;
+import org.broad.tribble.index.*;
+import org.broad.tribble.iterators.CloseableTribbleIterator;
+import org.broad.tribble.source.BasicFeatureSource;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+
+/**
+ * tests out the various functions in the index factory class
+ */
+public class IndexFactoryUnitTest {
+
+    File inputFile = new File("testdata/HiSeq.10000.vcf");
+    File outputFile = new File("testdata/onTheFlyOutputTest.vcf");
+    File outputFileIndex = Tribble.indexFile(outputFile);
+
+    /**
+     * test out scoring the indexes
+     */
+    @Test
+    public void testScoreIndexes() {
+        /*// make a list of indexes to score
+        Map<Class,IndexCreator> creators = new HashMap<Class,IndexCreator>();
+        // add a linear index with the default bin size
+        LinearIndexCreator linearNormal = new LinearIndexCreator();
+        linearNormal.initialize(inputFile, linearNormal.defaultBinSize());
+        creators.add(LInearIndexlinearNormal);
+
+        // create a tree index with a small index size
+        IntervalIndexCreator treeSmallBin = new IntervalIndexCreator();
+        treeSmallBin.initialize(inputFile, Math.max(200,treeSmallBin.defaultBinSize()/10));
+        creators.add(treeSmallBin);
+
+        List<Index> indexes = new ArrayList<Index>();
+        for (IndexCreator creator : creators)
+            indexes.add(creator.finalizeIndex(0));
+
+        ArrayList<Double> scores = IndexFactory.scoreIndexes(0.5,indexes,100, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
+        System.err.println("scores are : ");
+        for (Double score : scores) {
+            System.err.println(score);
+*/
+    }
+
+    //
+    // test out scoring the indexes
+    //
+    @Test
+    public void testOnTheFlyIndexing1() throws IOException {
+        Index indexFromInputFile = IndexFactory.createIndex(inputFile, new VCFCodec());
+        if ( outputFileIndex.exists() ) {
+            System.err.println("Deleting " + outputFileIndex);
+            outputFileIndex.delete();
+        }
+
+        for ( int maxRecords : Arrays.asList(0, 1, 10, 100, 1000, -1)) {
+            BasicFeatureSource<VariantContext> source = new BasicFeatureSource<VariantContext>(inputFile.getAbsolutePath(), indexFromInputFile, new VCFCodec());
+
+            int counter = 0;
+            VCFWriter writer = new StandardVCFWriter(outputFile);
+            writer.writeHeader((VCFHeader)source.getHeader());
+            CloseableTribbleIterator<VariantContext> it = source.iterator();
+            while (it.hasNext() && (counter++ < maxRecords || maxRecords == -1) ) {
+                VariantContext vc = it.next();
+                writer.add(vc, vc.getReferenceBaseForIndel());
+            }
+            writer.close();
+
+            // test that the input index is the same as the one created from the identical input file
+            // test that the dynamic index is the same as the output index, which is equal to the input index
+            Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(outputFile, outputFileIndex, new VCFCodec()));
+        }
+    }
+}
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java
index 88c1b8294..c4ca6a551 100644
--- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.utils.genotype.vcf;
 
 import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 
@@ -11,8 +11,6 @@ import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.io.StringBufferInputStream;
-import java.util.ArrayList;
-import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
index 3552af037..34a2e616a 100644
--- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
@@ -2,10 +2,10 @@ package org.broadinstitute.sting.utils.genotype.vcf;
 
 import org.broad.tribble.Tribble;
 import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
diff --git a/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java b/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java
new file mode 100755
index 000000000..ed9805d19
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java
@@ -0,0 +1,217 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+// our package
+package org.broadinstitute.sting.utils.variantcontext;
+
+
+// the imports for unit testing.
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+//    public Allele(byte[] bases, boolean isRef) {
+//    public Allele(boolean isRef) {
+//    public Allele(String bases, boolean isRef) {
+//    public boolean isNullAllele()       { return length() == 0; }
+//    public boolean isNonNullAllele()    { return ! isNullAllele(); }
+//    public boolean isReference()        { return isRef; }
+//    public boolean isNonReference()     { return ! isReference(); }
+//    public byte[] getBases() { return bases; }
+//    public boolean equals(Allele other) {
+//    public int length() {
+
+/**
+ * Basic unit test for RecalData
+ */
+public class AlleleUnitTest {
+    Allele ARef, del, delRef, A, T, ATIns, ATCIns, NoCall;
+    
+    @BeforeSuite
+    public void before() {
+        del = Allele.create("-");
+        delRef = Allele.create("-", true);
+
+        A = Allele.create("A");
+        ARef = Allele.create("A", true);
+        T = Allele.create("T");
+
+        ATIns = Allele.create("AT");
+        ATCIns = Allele.create("ATC");
+
+        NoCall = Allele.create(".");
+    }
+
+    @Test
+    public void testCreatingSNPAlleles() {
+        Assert.assertTrue(A.isNonReference());
+        Assert.assertFalse(A.isReference());
+        Assert.assertTrue(A.basesMatch("A"));
+        Assert.assertEquals(A.length(), 1);
+        Assert.assertTrue(A.isNonNull());
+        Assert.assertFalse(A.isNull());
+
+        Assert.assertTrue(ARef.isReference());
+        Assert.assertFalse(ARef.isNonReference());
+        Assert.assertTrue(ARef.basesMatch("A"));
+        Assert.assertFalse(ARef.basesMatch("T"));
+
+        Assert.assertTrue(T.isNonReference());
+        Assert.assertFalse(T.isReference());
+        Assert.assertTrue(T.basesMatch("T"));
+        Assert.assertFalse(T.basesMatch("A"));
+    }
+
+    @Test
+    public void testCreatingNoCallAlleles() {
+        Assert.assertTrue(NoCall.isNonReference());
+        Assert.assertFalse(NoCall.isReference());
+        Assert.assertFalse(NoCall.basesMatch("."));
+        Assert.assertEquals(NoCall.length(), 0);
+        Assert.assertTrue(NoCall.isNonNull());
+        Assert.assertFalse(NoCall.isNull());
+    }
+
+
+    @Test
+    public void testCreatingIndelAlleles() {
+        Assert.assertEquals(ATIns.length(), 2);
+        Assert.assertEquals(ATCIns.length(), 3);
+        Assert.assertEquals(ATIns.getBases(), "AT".getBytes());
+        Assert.assertEquals(ATCIns.getBases(), "ATC".getBytes());
+
+        Assert.assertTrue(del.isNonReference());
+        Assert.assertFalse(delRef.isNonReference());
+        Assert.assertFalse(del.isReference());
+        Assert.assertTrue(delRef.isReference());
+        Assert.assertFalse(del.basesMatch("-"));
+        Assert.assertTrue(del.basesMatch(""));
+        Assert.assertEquals(del.length(), 0);
+        Assert.assertFalse(del.isNonNull());
+        Assert.assertTrue(del.isNull());
+    }
+
+
+    @Test
+    public void testConstructors1() {
+        Allele a1 = Allele.create("A");
+        Allele a2 = Allele.create("A".getBytes());
+        Allele a3 = Allele.create("A");
+        Allele a4 = Allele.create("A", true);
+
+        Assert.assertTrue(a1.equals(a2));
+        Assert.assertTrue(a1.equals(a3));
+        Assert.assertFalse(a1.equals(a4));
+    }
+
+    @Test
+    public void testDelConstructors() {
+        Allele a1 = Allele.create("-");
+        Allele a2 = Allele.create("-".getBytes());
+        Allele a3 = Allele.create("");
+        Allele a4 = Allele.create("", true);
+
+        Assert.assertTrue(a1.equals(a2));
+        Assert.assertTrue(a1.equals(a3));
+        Assert.assertFalse(a1.equals(a4));
+    }
+
+    @Test
+    public void testInsConstructors() {
+        Allele a1 = Allele.create("AC");
+        Allele a2 = Allele.create("AC".getBytes());
+        Allele a3 = Allele.create("AC");
+        Allele a4 = Allele.create("AC", true);
+
+        Assert.assertTrue(a1.equals(a2));
+        Assert.assertTrue(a1.equals(a3));
+        Assert.assertFalse(a1.equals(a4));
+    }
+
+    @Test
+    public void testEquals() {
+        Assert.assertTrue(ARef.basesMatch(A));
+        Assert.assertFalse(ARef.equals(A));
+        Assert.assertFalse(ARef.equals(del));
+        Assert.assertFalse(ARef.equals(ATIns));
+        Assert.assertFalse(ARef.equals(ATCIns));
+
+        Assert.assertTrue(T.basesMatch(T));
+        Assert.assertFalse(T.basesMatch(A));
+        Assert.assertFalse(T.equals(A));
+
+        Assert.assertTrue(del.basesMatch(del));
+        Assert.assertTrue(del.basesMatch(delRef));
+        Assert.assertTrue(del.equals(del));
+        Assert.assertFalse(del.equals(delRef));
+
+        Assert.assertTrue(ATIns.equals(ATIns));
+        Assert.assertFalse(ATIns.equals(ATCIns));
+        Assert.assertTrue(ATIns.basesMatch("AT"));
+        Assert.assertFalse(ATIns.basesMatch("A"));
+        Assert.assertFalse(ATIns.basesMatch("ATC"));
+
+        Assert.assertTrue(ATIns.basesMatch("AT"));
+        Assert.assertFalse(ATIns.basesMatch("ATC"));
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgs1() {
+        byte[] foo = null;
+        Allele.create(foo);
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgs2() {
+        Allele.create("x");
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgs3() {
+        Allele.create("--");
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgs4() {
+        Allele.create("-A");
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgs5() {
+        Allele.create("A A");
+    }
+
+    @Test
+    public void testExtend() {
+        Assert.assertEquals("AT", Allele.extend(Allele.create("A"), "T".getBytes()).toString());
+        Assert.assertEquals("ATA", Allele.extend(Allele.create("A"), "TA".getBytes()).toString());
+        Assert.assertEquals("A", Allele.extend(Allele.create("-"), "A".getBytes()).toString());
+        Assert.assertEquals("A", Allele.extend(Allele.NO_CALL, "A".getBytes()).toString());
+        Assert.assertEquals("ATCGA", Allele.extend(Allele.create("AT"), "CGA".getBytes()).toString());
+        Assert.assertEquals("ATCGA", Allele.extend(Allele.create("ATC"), "GA".getBytes()).toString());
+    }
+}
\ No newline at end of file
diff --git a/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java b/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java
new file mode 100755
index 000000000..9243588ab
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java
@@ -0,0 +1,78 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+// our package
+package org.broadinstitute.sting.utils.variantcontext;
+
+
+// the imports for unit testing.
+
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+
+
+/**
+ * Basic unit test for Genotype likelihoods objects
+ */
+public class GenotypeLikelihoodsUnitTest {
+    double [] v = new double[]{-10.5, -1.25, -5.11};
+    final static String vGLString = "-10.50,-1.25,-5.11";
+    final static String vPLString = "93,0,39";
+
+    @Test
+    public void testFromVector2() {
+        GenotypeLikelihoods gl = new GenotypeLikelihoods(v);
+        assertDoubleArraysAreEqual(gl.getAsVector(), v);
+        Assert.assertEquals(gl.getAsString(), vPLString);
+    }
+
+    @Test
+    public void testFromString1() {
+        GenotypeLikelihoods gl = new GenotypeLikelihoods(vPLString);
+        assertDoubleArraysAreEqual(gl.getAsVector(), new double[]{-9.3, 0, -3.9});
+        Assert.assertEquals(gl.getAsString(), vPLString);
+    }
+
+    @Test
+    public void testFromString2() {
+        GenotypeLikelihoods gl = GenotypeLikelihoods.fromGLField(vGLString);
+        assertDoubleArraysAreEqual(gl.getAsVector(), v);
+        Assert.assertEquals(gl.getAsString(), vPLString);
+    }
+
+    @Test (expectedExceptions = NumberFormatException.class)
+    public void testErrorBadFormat() {
+        GenotypeLikelihoods gl = new GenotypeLikelihoods("adf,b,c");
+        gl.getAsVector();
+    }
+
+    private void assertDoubleArraysAreEqual(double[] v1, double[] v2) {
+        Assert.assertEquals(v1.length, v2.length);
+        for ( int i = 0; i < v1.length; i++ ) {
+            Assert.assertEquals(v1[i], v2[i], 1e-6);
+        }
+    }
+}
\ No newline at end of file
diff --git a/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
new file mode 100755
index 000000000..e82817714
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
@@ -0,0 +1,458 @@
+// our package
+package org.broadinstitute.sting.utils.variantcontext;
+
+
+// the imports for unit testing.
+
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+import java.util.List;
+
+
+/**
+ * Basic unit test for RecalData
+ */
+public class VariantContextUnitTest {
+    Allele A, Aref, T, Tref;
+    Allele del, delRef, ATC, ATCref;
+
+    // A [ref] / T at 10
+    String snpLoc = "chr1";
+    int snpLocStart = 10;
+    int snpLocStop = 10;
+
+    // - / ATC [ref] from 20-23
+    String delLoc = "chr1";
+    int delLocStart = 20;
+    int delLocStop = 23;
+
+    // - [ref] / ATC from 20-20
+    String insLoc = "chr1";
+    int insLocStart = 20;
+    int insLocStop = 20;
+
+    // - / A / T / ATC [ref] from 20-23
+    String mixedLoc = "chr1";
+    int mixedLocStart = 20;
+    int mixedLocStop = 23;
+
+    @BeforeSuite
+    public void before() {
+        del = Allele.create("-");
+        delRef = Allele.create("-", true);
+
+        A = Allele.create("A");
+        Aref = Allele.create("A", true);
+        T = Allele.create("T");
+        Tref = Allele.create("T", true);
+
+        ATC = Allele.create("ATC");
+        ATCref = Allele.create("ATC", true);
+    }
+
+    @Test
+    public void testDetermineTypes() {
+        Allele ACref = Allele.create("AC", true);
+        Allele AC = Allele.create("AC");
+        Allele AT = Allele.create("AT");
+        Allele C = Allele.create("C");
+        Allele CAT = Allele.create("CAT");
+        Allele TAref = Allele.create("TA", true);
+        Allele TA = Allele.create("TA");
+        Allele TC = Allele.create("TC");
+        Allele symbolic = Allele.create("<FOO>");
+
+        // test REF
+        List<Allele> alleles = Arrays.asList(Tref);
+        VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.NO_VARIATION);
+
+        // test SNPs
+        alleles = Arrays.asList(Tref, A);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
+
+        alleles = Arrays.asList(Tref, A, C);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
+
+        // test MNPs
+        alleles = Arrays.asList(ACref, TA);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.MNP);
+
+        alleles = Arrays.asList(ATCref, CAT, Allele.create("GGG"));
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.MNP);
+
+        // test INDELs
+        alleles = Arrays.asList(Aref, ATC);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
+
+        alleles = Arrays.asList(ATCref, A);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
+
+        alleles = Arrays.asList(Tref, TA, TC);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
+
+        alleles = Arrays.asList(ATCref, A, AC);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
+
+        alleles = Arrays.asList(ATCref, A, Allele.create("ATCTC"));
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
+
+        // test MIXED
+        alleles = Arrays.asList(TAref, T, TC);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
+
+        alleles = Arrays.asList(TAref, T, AC);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
+
+        alleles = Arrays.asList(ACref, ATC, AT);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
+
+        alleles = Arrays.asList(Aref, T, symbolic);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
+
+        // test SYMBOLIC
+        alleles = Arrays.asList(Tref, symbolic);
+        vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.SYMBOLIC);
+    }
+
+    @Test
+    public void testCreatingSNPVariantContext() {
+
+        List<Allele> alleles = Arrays.asList(Aref, T);
+        VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
+
+        Assert.assertEquals(vc.getChr(), snpLoc);
+        Assert.assertEquals(vc.getStart(), snpLocStart);
+        Assert.assertEquals(vc.getEnd(), snpLocStop);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
+        Assert.assertTrue(vc.isSNP());
+        Assert.assertFalse(vc.isIndel());
+        Assert.assertFalse(vc.isInsertion());
+        Assert.assertFalse(vc.isDeletion());
+        Assert.assertFalse(vc.isMixed());
+        Assert.assertTrue(vc.isBiallelic());
+        Assert.assertEquals(vc.getNAlleles(), 2);
+
+        Assert.assertEquals(vc.getReference(), Aref);
+        Assert.assertEquals(vc.getAlleles().size(), 2);
+        Assert.assertEquals(vc.getAlternateAlleles().size(), 1);
+        Assert.assertEquals(vc.getAlternateAllele(0), T);
+
+        Assert.assertFalse(vc.hasGenotypes());
+
+        Assert.assertEquals(vc.getSampleNames().size(), 0);
+    }
+
+    @Test
+    public void testCreatingRefVariantContext() {
+         List<Allele> alleles = Arrays.asList(Aref);
+        VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
+
+        Assert.assertEquals(vc.getChr(), snpLoc);
+        Assert.assertEquals(vc.getStart(), snpLocStart);
+        Assert.assertEquals(vc.getEnd(), snpLocStop);
+        Assert.assertEquals(VariantContext.Type.NO_VARIATION, vc.getType());
+        Assert.assertFalse(vc.isSNP());
+        Assert.assertFalse(vc.isIndel());
+        Assert.assertFalse(vc.isInsertion());
+        Assert.assertFalse(vc.isDeletion());
+        Assert.assertFalse(vc.isMixed());
+        Assert.assertFalse(vc.isBiallelic());
+        Assert.assertEquals(vc.getNAlleles(), 1);
+
+        Assert.assertEquals(vc.getReference(), Aref);
+        Assert.assertEquals(vc.getAlleles().size(), 1);
+        Assert.assertEquals(vc.getAlternateAlleles().size(), 0);
+        //Assert.assertEquals(vc.getAlternateAllele(0), T);
+
+        Assert.assertFalse(vc.hasGenotypes());
+        Assert.assertEquals(vc.getSampleNames().size(), 0);
+    }
+
+    @Test
+    public void testCreatingDeletionVariantContext() {
+        List<Allele> alleles = Arrays.asList(ATCref, del);
+        VariantContext vc = new VariantContext("test", delLoc, delLocStart, delLocStop, alleles);
+
+        Assert.assertEquals(vc.getChr(), delLoc);
+        Assert.assertEquals(vc.getStart(), delLocStart);
+        Assert.assertEquals(vc.getEnd(), delLocStop);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
+        Assert.assertFalse(vc.isSNP());
+        Assert.assertTrue(vc.isIndel());
+        Assert.assertFalse(vc.isInsertion());
+        Assert.assertTrue(vc.isDeletion());
+        Assert.assertFalse(vc.isMixed());
+        Assert.assertTrue(vc.isBiallelic());
+        Assert.assertEquals(vc.getNAlleles(), 2);
+
+        Assert.assertEquals(vc.getReference(), ATCref);
+        Assert.assertEquals(vc.getAlleles().size(), 2);
+        Assert.assertEquals(vc.getAlternateAlleles().size(), 1);
+        Assert.assertEquals(vc.getAlternateAllele(0), del);
+
+        Assert.assertFalse(vc.hasGenotypes());
+
+        Assert.assertEquals(vc.getSampleNames().size(), 0);
+    }
+
+    @Test
+    public void testCreatingInsertionVariantContext() {
+        List<Allele> alleles = Arrays.asList(delRef, ATC);
+        VariantContext vc = new VariantContext("test", insLoc, insLocStart, insLocStop, alleles);
+
+        Assert.assertEquals(vc.getChr(), insLoc);
+        Assert.assertEquals(vc.getStart(), insLocStart);
+        Assert.assertEquals(vc.getEnd(), insLocStop);
+        Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
+        Assert.assertFalse(vc.isSNP());
+        Assert.assertTrue(vc.isIndel());
+        Assert.assertTrue(vc.isInsertion());
+        Assert.assertFalse(vc.isDeletion());
+        Assert.assertFalse(vc.isMixed());
+        Assert.assertTrue(vc.isBiallelic());
+        Assert.assertEquals(vc.getNAlleles(), 2);
+
+        Assert.assertEquals(vc.getReference(), delRef);
+        Assert.assertEquals(vc.getAlleles().size(), 2);
+        Assert.assertEquals(vc.getAlternateAlleles().size(), 1);
+        Assert.assertEquals(vc.getAlternateAllele(0), ATC);
+        Assert.assertFalse(vc.hasGenotypes());
+
+        Assert.assertEquals(vc.getSampleNames().size(), 0);
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgs1() {
+        new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref));
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgs2() {
+        new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, del));
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgs3() {
+        new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(del));
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgsDuplicateAlleles1() {
+        new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(Aref, T, T));
+    }
+
+    @Test (expectedExceptions = IllegalArgumentException.class)
+    public void testBadConstructorArgsDuplicateAlleles2() {
+        new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(Aref, A));
+    }
+
+    @Test (expectedExceptions = IllegalStateException.class)
+    public void testBadLoc1() {
+        List<Allele> alleles = Arrays.asList(Aref, T, del);
+        new VariantContext("test", delLoc, delLocStart, delLocStop, alleles);
+    }
+
+    @Test
+    public void testAccessingSimpleSNPGenotypes() {
+        List<Allele> alleles = Arrays.asList(Aref, T);
+
+        Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
+        Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
+        Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
+
+        VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3));
+
+        Assert.assertTrue(vc.hasGenotypes());
+        Assert.assertFalse(vc.isMonomorphic());
+        Assert.assertTrue(vc.isPolymorphic());
+        Assert.assertEquals(vc.getSampleNames().size(), 3);
+
+        Assert.assertEquals(vc.getGenotypes().size(), 3);
+        Assert.assertEquals(vc.getGenotypes().get("AA"), g1);
+        Assert.assertEquals(vc.getGenotype("AA"), g1);
+        Assert.assertEquals(vc.getGenotypes().get("AT"), g2);
+        Assert.assertEquals(vc.getGenotype("AT"), g2);
+        Assert.assertEquals(vc.getGenotypes().get("TT"), g3);
+        Assert.assertEquals(vc.getGenotype("TT"), g3);
+
+        Assert.assertTrue(vc.hasGenotype("AA"));
+        Assert.assertTrue(vc.hasGenotype("AT"));
+        Assert.assertTrue(vc.hasGenotype("TT"));
+        Assert.assertFalse(vc.hasGenotype("foo"));
+        Assert.assertFalse(vc.hasGenotype("TTT"));
+        Assert.assertFalse(vc.hasGenotype("at"));
+        Assert.assertFalse(vc.hasGenotype("tt"));
+
+        Assert.assertEquals(vc.getChromosomeCount(), 6);
+        Assert.assertEquals(vc.getChromosomeCount(Aref), 3);
+        Assert.assertEquals(vc.getChromosomeCount(T), 3);
+    }
+
+    @Test
+    public void testAccessingCompleteGenotypes() {
+        List<Allele> alleles = Arrays.asList(Aref, T, del);
+
+        Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
+        Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
+        Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
+        Genotype g4 = new Genotype("Td", Arrays.asList(T, del), 10);
+        Genotype g5 = new Genotype("dd", Arrays.asList(del, del), 10);
+        Genotype g6 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
+
+        VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3, g4, g5, g6));
+
+        Assert.assertTrue(vc.hasGenotypes());
+        Assert.assertFalse(vc.isMonomorphic());
+        Assert.assertTrue(vc.isPolymorphic());
+        Assert.assertEquals(vc.getGenotypes().size(), 6);
+
+        Assert.assertEquals(3, vc.getGenotypes(Arrays.asList("AA", "Td", "dd")).size());
+
+        Assert.assertEquals(10, vc.getChromosomeCount());
+        Assert.assertEquals(3, vc.getChromosomeCount(Aref));
+        Assert.assertEquals(4, vc.getChromosomeCount(T));
+        Assert.assertEquals(3, vc.getChromosomeCount(del));
+        Assert.assertEquals(2, vc.getChromosomeCount(Allele.NO_CALL));
+    }
+
+    @Test
+    public void testAccessingRefGenotypes() {
+        List<Allele> alleles1 = Arrays.asList(Aref, T);
+        List<Allele> alleles2 = Arrays.asList(Aref);
+        List<Allele> alleles3 = Arrays.asList(Aref, T, del);
+        for ( List<Allele> alleles : Arrays.asList(alleles1, alleles2, alleles3)) {
+            Genotype g1 = new Genotype("AA1", Arrays.asList(Aref, Aref), 10);
+            Genotype g2 = new Genotype("AA2", Arrays.asList(Aref, Aref), 10);
+            Genotype g3 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
+            VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3));
+
+            Assert.assertTrue(vc.hasGenotypes());
+            Assert.assertTrue(vc.isMonomorphic());
+            Assert.assertFalse(vc.isPolymorphic());
+            Assert.assertEquals(vc.getGenotypes().size(), 3);
+
+            Assert.assertEquals(4, vc.getChromosomeCount());
+            Assert.assertEquals(4, vc.getChromosomeCount(Aref));
+            Assert.assertEquals(0, vc.getChromosomeCount(T));
+            Assert.assertEquals(2, vc.getChromosomeCount(Allele.NO_CALL));
+        }
+    }
+
+    @Test
+    public void testFilters() {
+        List<Allele> alleles = Arrays.asList(Aref, T, del);
+        Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
+        Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
+        MutableVariantContext vc = new MutableVariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2));
+
+        Assert.assertTrue(vc.isNotFiltered());
+        Assert.assertFalse(vc.isFiltered());
+        Assert.assertEquals(0, vc.getFilters().size());
+
+        vc.addFilter("BAD_SNP_BAD!");
+
+        Assert.assertFalse(vc.isNotFiltered());
+        Assert.assertTrue(vc.isFiltered());
+        Assert.assertEquals(1, vc.getFilters().size());
+
+        vc.addFilters(Arrays.asList("REALLY_BAD_SNP", "CHRIST_THIS_IS_TERRIBLE"));
+
+        Assert.assertFalse(vc.isNotFiltered());
+        Assert.assertTrue(vc.isFiltered());
+        Assert.assertEquals(3, vc.getFilters().size());
+
+        vc.clearFilters();
+
+        Assert.assertTrue(vc.isNotFiltered());
+        Assert.assertFalse(vc.isFiltered());
+        Assert.assertEquals(0, vc.getFilters().size());
+    }
+
+    @Test
+    public void testVCromGenotypes() {
+        List<Allele> alleles = Arrays.asList(Aref, T, del);
+        Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
+        Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
+        Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
+        Genotype g4 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
+        Genotype g5 = new Genotype("--", Arrays.asList(del, del), 10);
+        VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop , alleles, Arrays.asList(g1,g2,g3,g4,g5));
+
+        VariantContext vc12 = vc.subContextFromGenotypes(Arrays.asList(g1,g2));
+        VariantContext vc1 = vc.subContextFromGenotypes(Arrays.asList(g1));
+        VariantContext vc23 = vc.subContextFromGenotypes(Arrays.asList(g2, g3));
+        VariantContext vc4 = vc.subContextFromGenotypes(Arrays.asList(g4));
+        VariantContext vc14 = vc.subContextFromGenotypes(Arrays.asList(g1, g4));
+        VariantContext vc5 = vc.subContextFromGenotypes(Arrays.asList(g5));
+
+        Assert.assertTrue(vc12.isPolymorphic());
+        Assert.assertTrue(vc23.isPolymorphic());
+        Assert.assertTrue(vc1.isMonomorphic());
+        Assert.assertTrue(vc4.isMonomorphic());
+        Assert.assertTrue(vc14.isMonomorphic());
+        Assert.assertTrue(vc5.isPolymorphic());
+
+        Assert.assertTrue(vc12.isSNP());
+        Assert.assertTrue(vc12.isVariant());
+        Assert.assertTrue(vc12.isBiallelic());
+
+        Assert.assertFalse(vc1.isSNP());
+        Assert.assertFalse(vc1.isVariant());
+        Assert.assertFalse(vc1.isBiallelic());
+
+        Assert.assertTrue(vc23.isSNP());
+        Assert.assertTrue(vc23.isVariant());
+        Assert.assertTrue(vc23.isBiallelic());
+
+        Assert.assertFalse(vc4.isSNP());
+        Assert.assertFalse(vc4.isVariant());
+        Assert.assertFalse(vc4.isBiallelic());
+
+        Assert.assertFalse(vc14.isSNP());
+        Assert.assertFalse(vc14.isVariant());
+        Assert.assertFalse(vc14.isBiallelic());
+
+        Assert.assertTrue(vc5.isIndel());
+        Assert.assertTrue(vc5.isDeletion());
+        Assert.assertTrue(vc5.isVariant());
+        Assert.assertTrue(vc5.isBiallelic());
+
+        Assert.assertEquals(3, vc12.getChromosomeCount(Aref));
+        Assert.assertEquals(1, vc23.getChromosomeCount(Aref));
+        Assert.assertEquals(2, vc1.getChromosomeCount(Aref));
+        Assert.assertEquals(0, vc4.getChromosomeCount(Aref));
+        Assert.assertEquals(2, vc14.getChromosomeCount(Aref));
+        Assert.assertEquals(0, vc5.getChromosomeCount(Aref));
+    }
+
+
+    @Test
+    public void testManipulatingAlleles() {
+        // todo -- add tests that call add/set/remove
+    }
+
+    @Test
+    public void testManipulatingGenotypes() {
+        // todo -- add tests that call add/set/remove
+    }
+}
diff --git a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContextUnitTest.java b/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
similarity index 96%
rename from java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContextUnitTest.java
rename to java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
index 4de413334..b5f6b1b1a 100644
--- a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContextUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
@@ -21,11 +21,9 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.contexts.variantcontext;
+package org.broadinstitute.sting.utils.variantcontext;
 
 import net.sf.samtools.SAMFileHeader;
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
diff --git a/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
index 91b7bd874..f2592e05c 100644
--- a/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
+++ b/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
@@ -5,7 +5,7 @@ import org.apache.commons.io.FilenameUtils
 import scala.io.Source._
 import net.sf.samtools.SAMFileReader
 import org.broad.tribble.source.BasicFeatureSource
-import org.broad.tribble.vcf.{VCFHeader, VCFCodec}
+import org.broadinstitute.sting.utils.codecs.vcf.{VCFHeader, VCFCodec}
 import scala.collection.JavaConversions._
 
 object VCF_BAM_utilities {
@@ -56,4 +56,4 @@ object VCF_BAM_utilities {
     val l: List[File] = Nil
     return l ++ findBAMsForSamplesHelper(samples)
   }
-}
\ No newline at end of file
+}
diff --git a/testdata/HiSeq.10000.vcf b/testdata/HiSeq.10000.vcf
new file mode 100644
index 000000000..ac0107746
--- /dev/null
+++ b/testdata/HiSeq.10000.vcf
@@ -0,0 +1,10000 @@
+##fileformat=VCFv4.0
+##FILTER=<ID=ABFilter,Description="AB  0.75 && DP  40">
+##FILTER=<ID=DPFilter,Description="DP  120 || SB  -0.10">
+##FILTER=<ID=FDRtranche0.00to0.10,Description="FDR tranche level at qual 0.06">
+##FILTER=<ID=FDRtranche0.10to1.00,Description="FDR tranche level at qual 0.03">
+##FILTER=<ID=FDRtranche1.00to2.00,Description="FDR tranche level at qual 0.02">
+##FILTER=<ID=FDRtranche2.00to10.00+,Description="FDR tranche level at qual > 0.06">
+##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 = 4 && ((MQ0 / (1.0 * DP))  0.1)">
+##FILTER=<ID=Indel,Description="Overlaps a user-input mask">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=LowQual,Description="QUAL  50.0">
+##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=OQ,Number=1,Type=Float,Description="The original variant quality score">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-23/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-24/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-5/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-9/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-6/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-19/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-25/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-4/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-14/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-22/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-2/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-3/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-7/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-16/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-1/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-17/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-8/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-10/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-18/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-20/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-11/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-15/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-21/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-12/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-13/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam] read_buffer_size=null read_filter=[] intervals=[chrX] excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod, interval,Intervals,chrX] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod hapmap=null hapmap_chip=null out=null err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=10000 num_threads=1 interval_merging=ALL read_group_black_list=null genotype_model=JOINT_ESTIMATE base_model=EMPIRICAL heterozygosity=7.8E-4 genotype=false output_all_callable_bases=false standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 trigger_min_confidence_threshold_for_calling=30.0 trigger_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=null platform=null min_base_quality_score=20 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 cap_base_quality_by_mapping_quality=false"
+##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=null excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.vcf, mask,Bed,wgs.v9/HiSeq.WGS.cleaned.indels.10.mask] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=2147483647 num_threads=1 interval_merging=ALL read_group_black_list=null filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Indel NO_HEADER=false"
+##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=null excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/HiSeq.WGS.cleaned.ug.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.vcf err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=2147483647 num_threads=1 interval_merging=ALL read_group_black_list=null filterExpression=[QUAL < 50.0, MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1), AB > 0.75 && DP > 40, DP > 120 || SB > -0.10] filterName=[LowQual, HARD_TO_VALIDATE, ABFilter, DPFilter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=10 maskName=Mask NO_HEADER=false"
+##source=VariantOptimizer
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	
+chr1	109	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1019;Dels=0.00;HRun=0;HaplotypeScore=686.65;MQ=19.20;MQ0=288;OQ=2175.54;QD=2.13;SB=-1042.18	GT:AD:DP:GL:GQ	0/1:610,327:308:-316.30,-95.47,-803.03:99
+chr1	147	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=348;Dels=0.01;HRun=2;HaplotypeScore=268.66;MQ=20.23;MQ0=105;OQ=196.24;QD=0.56;SB=-76.48	GT:AD:DP:GL:GQ	0/1:294,49:118:-57.87,-34.96,-338.46:99
+chr1	177	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=432;Dels=0.02;HRun=2;HaplotypeScore=404.17;MQ=17.76;MQ0=153;OQ=697.20;QD=1.61;SB=-140.54	GT:AD:DP:GL:GQ	0/1:283,140:122:-108.58,-35.57,-292.84:99
+chr1	180	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=630;Dels=0.01;HRun=2;HaplotypeScore=495.41;MQ=14.22;MQ0=327;OQ=885.33;QD=1.41;SB=-412.44	GT:AD:DP:GL:GQ	0/1:466,154:104:-122.27,-30.46,-246.17:99
+chr1	234	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=336;Dels=0.00;HRun=1;HaplotypeScore=423.95;MQ=19.45;MQ0=111;OQ=596.60;QD=1.78;SB=-230.12	GT:AD:DP:GL:GQ	0/1:267,67:106:-94.87,-31.93,-297.68:99
+chr1	235	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=326;Dels=0.00;HRun=2;HaplotypeScore=391.04;MQ=19.68;MQ0=106;OQ=580.03;QD=1.78;SB=-219.50	GT:AD:DP:GL:GQ	0/1:274,47:105:-99.60,-38.31,-293.27:99
+chr1	250	.	A	C	22.88	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=182;Dels=0.01;HRun=3;HaplotypeScore=244.83;MQ=21.91;MQ0=52;QD=0.13;SB=-23.67	GT:AD:DP:GL:GQ	0/1:148,33:70:-26.66,-21.09,-215.78:55.69
+chr1	291	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=284.50;MQ=20.72;MQ0=39;OQ=529.94;QD=3.93;SB=-160.31	GT:AD:DP:GL:GQ	0/1:87,43:32:-69.55,-13.28,-54.44:99
+chr1	297	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=214.52;MQ=20.93;MQ0=36;OQ=101.21;QD=0.82;SB=-38.97	GT:AD:DP:GL:GQ	0/1:98,15:30:-33.20,-19.79,-87.91:99
+chr1	309	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=153.70;MQ=21.12;MQ0=35;OQ=53.98;QD=0.46;SB=-50.01	GT:AD:DP:GL:GQ	0/1:103,9:32:-18.33,-9.64,-96.32:86.82
+chr1	321	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=612.30;MQ=19.11;MQ0=29;OQ=136.39;QD=0.67;SB=-61.25	GT:AD:DP:GL:GQ	0/1:171,23:33:-33.14,-16.22,-92.98:99
+chr1	327	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=3;HaplotypeScore=227.75;MQ=19.74;MQ0=24;OQ=143.34;QD=0.69;SB=-63.56	GT:AD:DP:GL:GQ	0/1:183,21:38:-34.61,-16.99,-113.13:99
+chr1	352	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=325;Dels=0.00;HRun=1;HaplotypeScore=437.89;MQ=18.90;MQ0=142;OQ=774.23;QD=2.38;SB=-355.54	GT:AD:DP:GL:GQ	0/1:238,84:81:-104.82,-24.11,-183.81:99
+chr1	354	.	C	A	24.89	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=486;Dels=0.01;HRun=1;HaplotypeScore=281.11;MQ=16.12;MQ0=261;QD=0.05;SB=17.54	GT:AD:DP:GL:GQ	0/1:459,24:90:-32.28,-26.51,-269.47:57.71
+chr1	469	.	C	A	22.04	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=82.51;MQ=26.50;MQ0=12;QD=0.39;SB=-7.00	GT:AD:DP:GL:GQ	0/1:34,21:20:-11.52,-6.03,-45.07:54.85
+chr1	664	.	C	G	30.66	PASS	AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=50.85;QD=25.42;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,2:2:-8.49,-0.60,-0.00:6.02
+chr1	666	.	C	G	10.99	LowQual	AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=10.99;SB=-10.00	GT:AD:DP:GL:GQ	0/1:0,1:1:-4.35,-0.30,-0.00:1.76
+chr1	2646	rs62635284	G	A	0.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=9.27;MQ=6.23;MQ0=107;OQ=89.13;QD=0.70;SB=-10.00	GT:AD:DP:GL:GQ	1/1:53,75:3:-12.40,-0.90,-0.00:9.03
+chr1	2979	rs62635286	T	G	83.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=11.99;MQ0=41;OQ=300.29;QD=4.77;SB=-10.00	GT:AD:DP:GL:GQ	1/1:31,32:9:-33.61,-2.71,-0.00:27.09
+chr1	2981	rs62028691	A	G	14.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=11.89;MQ0=42;OQ=285.31;QD=4.46;SB=-10.00	GT:AD:DP:GL:GQ	1/1:31,33:9:-32.12,-2.71,-0.00:27.08
+chr1	3759	.	C	A	0.19	PASS	AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=9.71;MQ0=116;OQ=458.45;QD=3.14;SB=-211.61	GT:AD:DP:GL:GQ	0/1:106,40:25:-56.66,-7.53,-33.77:99
+chr1	4536	rs11582131	G	C	0.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=9.63;MQ=12.37;MQ0=52;OQ=335.66;QD=4.48;SB=8.06	GT:AD:DP:GL:GQ	0/1:42,33:16:-41.67,-4.82,-26.29:99
+chr1	4540	.	G	A	47.71	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=2;HaplotypeScore=11.12;MQ=11.52;MQ0=49;QD=0.67;SB=8.05	GT:AD:DP:GL:GQ	0/1:66,5:13:-11.97,-3.92,-35.35:80.54
+chr1	4562	rs11490464	C	G	0.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=2.62;MQ=11.28;MQ0=37;OQ=136.40;QD=2.44;SB=-10.00	GT:AD:DP:GL:GQ	0/1:26,30:9:-19.64,-2.72,-14.87:99
+chr1	4770	rs6682375	A	G	0.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=121;Dels=0.00;HRun=1;HaplotypeScore=1.93;MQ=26.23;MQ0=31;OQ=2992.25;QD=24.73;SB=-1410.84	GT:AD:DP:GL:GQ	1/1:9,111:84:-306.27,-28.58,-3.46:99
+chr1	4793	rs6682385	A	G	0.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=8.98;MQ=29.61;MQ0=5;OQ=3517.41;QD=29.56;SB=-1722.01	GT:AD:DP:GL:GQ	1/1:4,115:109:-350.74,-32.88,-0.10:99
+chr1	5074	rs11586607	T	G	0.01	FDRtranche2.00to10.00	AC=2;AF=1.00;AN=2;DB;DP=126;Dels=0.00;HRun=1;HaplotypeScore=24.34;MQ=21.42;MQ0=68;OQ=1230.02;QD=9.76;SB=-234.94	GT:AD:DP:GL:GQ	1/1:29,97:39:-130.41,-11.75,-3.82:79.31
+chr1	5137	rs62636497	A	T	140.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=21.69;MQ0=25;OQ=1453.92;QD=17.73;SB=-222.33	GT:AD:DP:GL:GQ	1/1:0,74:39:-148.99,-11.75,-0.01:99
+chr1	5966	.	T	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=129;Dels=0.18;HRun=5;HaplotypeScore=140.84;MQ=21.40;MQ0=8;OQ=1764.68;QD=13.68;SB=-234.42	GT:AD:DP:GL:GQ	1/1:0,106:53:-180.07,-15.66,-0.02:99
+chr1	6092	.	C	A	11.16	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=9.08;MQ=27.90;MQ0=10;QD=0.08;SB=14.05	GT:AD:DP:GL:GQ	0/1:125,11:94:-32.68,-28.32,-307.61:43.65
+chr1	6120	rs11489794	G	C	0.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=3.83;MQ=27.31;MQ0=11;OQ=181.15;QD=2.01;SB=8.06	GT:AD:DP:GL:GQ	0/1:73,17:66:-41.29,-19.89,-251.91:99
+chr1	6151	rs62028673	C	G	0.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=22.13;MQ0=10;OQ=58.79;QD=1.73;SB=-6.99	GT:AD:DP:GL:GQ	0/1:24,10:14:-13.38,-4.22,-45.26:91.62
+chr1	6241	rs17041382	T	C	5.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=138;Dels=0.00;HRun=0;HaplotypeScore=4.98;MQ=14.62;MQ0=74;OQ=755.36;QD=5.47;SB=-258.37	GT:AD:DP:GL:GQ	0/1:39,99:33:-88.77,-9.95,-20.05:99
+chr1	6358	rs3210724	G	C	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=174;Dels=0.00;HRun=0;HaplotypeScore=19.20;MQ=25.41;MQ0=15;OQ=678.86;QD=3.90;SB=-150.77	GT:AD:DP:GL:GQ	0/1:131,42:113:-105.24,-34.07,-360.44:99
+chr1	6360	rs7359297	A	G	49.26	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.00;HRun=2;HaplotypeScore=19.20;MQ=25.54;MQ0=15;QD=0.29;SB=20.10	GT:AD:DP:GL:GQ	0/1:155,16:111:-41.64,-33.43,-398.12:82.10
+chr1	6397	rs15642	C	T	157.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=21.39;MQ0=24;OQ=850.53;QD=7.88;SB=-122.64	GT:AD:DP:GL:GQ	0/1:45,63:33:-98.28,-9.94,-33.57:99
+chr1	7270	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=0;HaplotypeScore=18.12;MQ=8.37;MQ0=128;OQ=66.01;QD=0.43;SB=-47.55	GT:AD:DP:GL:GQ	0/1:137,16:8:-12.30,-2.42,-14.38:98.84
+chr1	7558	rs7357853	G	A	28.66	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=2.85;MQ=11.88;MQ0=88;QD=0.23;SB=-10.00	GT:AD:DP:GL:GQ	0/1:113,10:21:-12.48,-6.33,-62.63:61.49
+chr1	7609	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=1;HaplotypeScore=4.53;MQ=19.87;MQ0=60;OQ=69.47;QD=0.58;SB=-10.00	GT:AD:DP:GL:GQ	0/1:98,22:48:-24.69,-14.46,-166.38:99
+chr1	7766	.	C	T	24.46	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=9.88;MQ=9.94;MQ0=60;QD=0.35;SB=-10.00	GT:AD:DP:GL:GQ	0/1:66,3:7:-7.84,-2.11,-15.08:57.28
+chr1	9089	rs28609851	T	A	1.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=14.01;MQ0=34;OQ=172.68;QD=2.93;SB=-37.66	GT:AD:DP:GL:GQ	0/1:50,9:19:-26.28,-5.72,-45.27:99
+chr1	9185	rs2974813	C	T	45.14	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=3.92;MQ0=67;QD=0.65;SB=-47.56	GT:AD:DP:GL:GQ	1/1:67,2:2:-7.92,-0.60,-0.00:6.02
+chr1	9721	rs12354145	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=2;HaplotypeScore=26.09;MQ=12.03;MQ0=77;OQ=197.90;QD=1.55;SB=-10.00	GT:AD:DP:GL:GQ	0/1:97,31:18:-28.50,-5.42,-36.05:99
+chr1	9805	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=1;HaplotypeScore=1.10;MQ=10.83;MQ0=134;OQ=142.73;QD=0.73;SB=-10.00	GT:AD:DP:GL:GQ	0/1:171,24:24:-24.81,-7.25,-68.77:99
+chr1	9993	rs7354882	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=155;Dels=0.00;HRun=0;HaplotypeScore=22.48;MQ=21.20;MQ0=19;OQ=727.76;QD=4.70;SB=-285.16	GT:AD:DP:GL:GQ	0/1:126,29:124:-113.46,-37.39,-308.40:99
+chr1	10108	rs6682921	G	A	129.70	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=249;Dels=0.00;HRun=1;HaplotypeScore=98.13;MQ=8.71;MQ0=185;QD=0.52;SB=-64.03	GT:AD:DP:GL:GQ	0/1:175,74:25:-23.78,-7.53,-70.54:99
+chr1	10113	rs11490226	T	C	60.45	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=252;Dels=0.00;HRun=0;HaplotypeScore=99.00;MQ=8.29;MQ0=191;QD=0.24;SB=-6.56	GT:AD:DP:GL:GQ	0/1:200,52:22:-15.96,-6.63,-68.61:93.28
+chr1	10117	.	G	A	27.78	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=251;Dels=0.00;HRun=0;HaplotypeScore=92.18;MQ=8.29;MQ0=191;QD=0.11;SB=-12.58	GT:AD:DP:GL:GQ	0/1:210,41:21:-12.39,-6.33,-58.67:60.61
+chr1	10375	rs6683179	G	T	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=229;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=7.78;MQ0=173;OQ=50.55;QD=0.22;SB=-10.00	GT:AD:DP:GL:GQ	0/1:152,76:16:-13.16,-4.82,-44.89:83.39
+chr1	10410	rs11489908	A	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=236;Dels=0.00;HRun=2;HaplotypeScore=3.67;MQ=7.06;MQ0=196;OQ=84.39;QD=0.36;SB=-10.00	GT:AD:DP:GL:GQ	0/1:188,48:18:-17.15,-5.42,-52.83:99
+chr1	16862	rs376349	A	G	0.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=2;HaplotypeScore=2.47;MQ=20.73;MQ0=3;OQ=399.27;QD=24.95;SB=-188.41	GT:AD:DP:GL:GQ	1/1:2,14:12:-43.52,-3.61,-0.00:36.11
+chr1	18110	rs4413987	G	A	0.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=114;Dels=0.00;HRun=0;HaplotypeScore=6.99;MQ=6.98;MQ0=101;OQ=80.12;QD=0.70;SB=-10.00	GT:AD:DP:GL:GQ	0/1:95,19:5:-12.80,-1.51,-7.39:58.87
+chr1	18357	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=8.76;MQ=5.01;MQ0=96;OQ=60.18;QD=0.60;SB=-6.99	GT:AD:DP:GL:GQ	0/1:80,21:4:-10.51,-1.20,-3.97:27.63
+chr1	18421	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=23.14;MQ=14.44;MQ0=48;OQ=339.38;QD=4.35;SB=-90.89	GT:AD:DP:GL:GQ	0/1:55,23:25:-44.76,-7.53,-46.87:99
+chr1	18426	rs4099234	A	G	0.05	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=22.14;MQ=14.77;MQ0=46;OQ=857.23;QD=11.13;SB=-429.56	GT:AD:DP:GL:GQ	1/1:24,53:25:-89.32,-7.53,-0.01:75.22
+chr1	18451	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=15;HaplotypeScore=19.76;MQ=19.64;MQ0=16;OQ=152.23;QD=2.67;SB=-85.40	GT:AD:DP:GL:GQ	0/1:45,12:33:-28.45,-9.95,-82.12:99
+chr1	18454	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=47.13;MQ=19.20;MQ0=19;OQ=58.45;QD=0.99;SB=-20.71	GT:AD:DP:GL:GQ	0/1:53,6:35:-19.67,-10.55,-115.15:91.28
+chr1	18526	rs2418705	T	A	37.69	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=4.16;MQ0=59;QD=0.62;SB=-10.00	GT:AD:DP:GL:GQ	1/1:52,9:2:-7.18,-0.60,-0.00:6.02
+chr1	18698	rs3871714	A	G	0.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=9.06;MQ0=38;OQ=98.37;QD=2.19;SB=-10.00	GT:AD:DP:GL:GQ	1/1:27,18:4:-13.37,-1.21,-0.00:12.03
+chr1	18726	rs16924801	C	A	45.81	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=3.57;MQ=10.40;MQ0=25;QD=1.27;SB=-10.00	GT:AD:DP:GL:GQ	1/1:31,5:2:-7.99,-0.60,-0.00:6.02
+chr1	20391	rs4248192	C	T	0.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=17.17;MQ0=74;OQ=114.21;QD=1.08;SB=-10.00	GT:AD:DP:GL:GQ	0/1:95,11:32:-24.34,-9.64,-88.28:99
+chr1	20411	rs62028215	T	G	8.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=3.84;MQ=18.51;MQ0=71;OQ=573.84;QD=5.26;SB=-10.00	GT:AD:DP:GL:GQ	0/1:56,53:38:-72.12,-11.45,-46.57:99
+chr1	20723	rs28673882	G	C	0.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=113;Dels=0.00;HRun=0;HaplotypeScore=9.28;MQ=29.99;MQ0=37;OQ=163.32;QD=1.45;SB=40.84	GT:AD:DP:GL:GQ	0/1:100,13:69:-40.42,-20.80,-251.48:99
+chr1	20786	rs806731	G	T	139.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=34.31;MQ0=5;OQ=1407.60;QD=31.99;SB=-624.57	GT:AD:DP:GL:GQ	1/1:0,44:38:-144.35,-11.44,-0.01:99
+chr1	21158	rs806729	A	C	233.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.41;MQ0=5;OQ=71.14;QD=7.90;SB=-10.00	GT:AD:DP:GL:GQ	1/1:6,3:3:-10.60,-0.90,-0.00:9.03
+chr1	30569	rs62101646	G	A	24.23	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=13.59;MQ0=55;QD=0.37;SB=-0.99	GT:AD:DP:GL:GQ	0/1:53,12:8:-8.12,-2.41,-18.79:57.05
+chr1	30757	rs56954914	G	A	38.24	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=7.79;MQ0=81;QD=0.44;SB=-10.00	GT:AD:DP:GL:GQ	0/1:56,30:4:-8.31,-1.20,-6.94:57.33
+chr1	30916	.	C	T	44.25	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=6.25;MQ0=41;QD=1.03;SB=-10.00	GT:AD:DP:GL:GQ	1/1:40,3:2:-7.83,-0.60,-0.00:6.02
+chr1	41536	rs2531251	T	C	28.51	LowQual	AC=1;AF=0.50;AN=2;DB;DP=6;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=19.20;MQ0=3;QD=4.75;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,2:3:-7.04,-0.90,-3.46:25.52
+chr1	41761	.	C	A	0.43	PASS	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=4.86;MQ=27.62;MQ0=8;OQ=172.06;QD=5.55;SB=14.07	GT:AD:DP:GL:GQ	0/1:17,14:19:-26.21,-5.72,-39.58:99
+chr1	41791	.	G	A	3.24	PASS	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.83;MQ=30.13;MQ0=12;OQ=368.88;QD=8.20;SB=14.07	GT:AD:DP:GL:GQ	0/1:28,17:31:-49.51,-9.34,-69.71:99
+chr1	42101	rs2691277	T	G	379.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.14;MQ0=8;OQ=1117.45;QD=27.25;SB=-498.06	GT:AD:DP:GL:GQ	1/1:0,41:32:-115.34,-9.64,-0.01:96.29
+chr1	44243	rs2691279	T	C	13.38	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=44.42;MQ0=2;QD=0.32;SB=29.13	GT:AD:DP:GL:GQ	0/1:35,7:40:-16.65,-12.05,-143.10:46.01
+chr1	44449	.	T	C	10.02	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=30.96;MQ0=0;QD=0.25;SB=38.15	GT:AD:DP:GL:GQ	0/1:31,9:34:-14.48,-10.24,-121.45:42.40
+chr1	44539	rs2462492	C	T	2.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=48.14;MQ0=0;OQ=219.90;QD=4.40;SB=-111.03	GT:AD:DP:GL:GQ	0/1:40,10:50:-40.33,-15.06,-146.68:99
+chr1	44571	.	G	C	349.91	SnpCluster	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=22.88;MQ=46.02;MQ0=0;QD=5.74;SB=-120.67	GT:AD:DP:GL:GQ	0/1:43,18:49:-53.04,-14.77,-155.67:99
+chr1	44573	.	A	T	77.97	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=5;HaplotypeScore=28.86;MQ=46.27;MQ0=0;QD=1.22;SB=18.79	GT:AD:DP:GL:GQ	0/1:55,9:53:-27.05,-15.97,-167.03:99
+chr1	44575	.	T	C	100.77	SnpCluster	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=36.58;MQ=45.60;MQ0=1;QD=1.53;SB=-17.16	GT:AD:DP:GL:GQ	0/1:57,9:54:-29.63,-16.27,-179.47:99
+chr1	44579	.	C	T	185.88	SnpCluster	AC=1;AF=0.50;AN=2;DP=83;Dels=0.04;HRun=5;HaplotypeScore=85.91;MQ=43.82;MQ0=2;QD=2.24;SB=-100.05	GT:AD:DP:GL:GQ	0/1:66,14:58:-39.34,-17.47,-169.22:99
+chr1	44707	.	G	A	14.95	PASS	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=25.67;MQ0=14;OQ=285.82;QD=6.35;SB=-102.92	GT:AD:DP:GL:GQ	0/1:29,16:26:-39.70,-7.83,-56.06:99
+chr1	44948	.	T	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=3.69;MQ=36.35;MQ0=4;OQ=152.52;QD=2.99;SB=0.17	GT:AD:DP:GL:GQ	0/1:39,12:36:-29.38,-10.84,-106.91:99
+chr1	45027	rs3091274	C	A	22.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=21.32;MQ0=9;OQ=324.14;QD=13.51;SB=-88.90	GT:AD:DP:GL:GQ	1/1:0,24:10:-36.00,-3.01,-0.00:30.09
+chr1	45162	rs10399749	C	T	268.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=27.59;MQ0=3;OQ=1749.04;QD=37.21;SB=-889.19	GT:AD:DP:GL:GQ	1/1:1,46:44:-178.50,-13.25,-0.01:99
+chr1	45189	rs3107975	T	C	528.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.64;MQ0=0;OQ=1690.04;QD=36.74;SB=-682.96	GT:AD:DP:GL:GQ	1/1:0,46:46:-172.60,-13.85,-0.01:99
+chr1	45408	rs28396308	C	T	25.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=23.65;MQ0=4;OQ=659.03;QD=19.97;SB=-174.67	GT:AD:DP:GL:GQ	1/1:0,33:17:-69.49,-5.12,-0.00:51.17
+chr1	46501	rs2691308	C	T	1.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=36.83;MQ0=2;OQ=218.70;QD=3.22;SB=47.17	GT:AD:DP:GL:GQ	0/1:55,13:65:-44.73,-19.58,-190.42:99
+chr1	46662	rs2691309	T	C	45.27	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=41.65;MQ0=3;QD=1.29;SB=26.11	GT:AD:DP:GL:GQ	0/1:27,8:32:-17.45,-9.64,-107.04:78.10
+chr1	46896	rs2691311	T	C	94.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=47.00;MQ0=0;OQ=492.79;QD=6.48;SB=-211.35	GT:AD:DP:GL:GQ	0/1:55,21:75:-75.15,-22.59,-219.09:99
+chr1	46927	rs2548884	G	A	0.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=44.33;MQ0=0;OQ=115.48;QD=1.89;SB=-71.32	GT:AD:DP:GL:GQ	0/1:53,8:60:-32.90,-18.07,-195.48:99
+chr1	47021	rs6658003	G	C	0.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=8.74;MQ0=44;OQ=79.96;QD=1.45;SB=-46.90	GT:AD:DP:GL:GQ	0/1:36,19:6:-13.09,-1.81,-12.99:99
+chr1	47109	rs2691313	C	G	35.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=36.99;MQ0=0;OQ=346.71;QD=6.80;SB=47.18	GT:AD:DP:GL:GQ	0/1:38,13:51:-53.32,-15.37,-164.95:99
+chr1	47155	.	C	T	135.45	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=34.92;MQ0=10;OQ=1281.86;QD=17.56;SB=-510.08	GT:AD:DP:GL:GQ	0/1:34,39:60:-149.57,-18.10,-69.03:99
+chr1	47239	rs2854673	C	T	32.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=43.73;MQ0=3;OQ=244.39;QD=4.61;SB=47.16	GT:AD:DP:GL:GQ	0/1:39,14:49:-42.48,-14.76,-140.73:99
+chr1	47719	.	T	A	0.78	PASS	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=2;HaplotypeScore=3.14;MQ=19.08;MQ0=29;OQ=670.79;QD=8.49;SB=-194.63	GT:AD:DP:GL:GQ	0/1:47,32:46:-84.22,-13.86,-89.29:99
+chr1	48074	rs2691335	A	G	2.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.51;MQ0=2;OQ=156.22;QD=22.32;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,7:5:-19.18,-1.51,-0.00:15.05
+chr1	48634	.	T	C	2.39	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=1.66;MQ=33.49;MQ0=8;OQ=733.26;QD=12.22;SB=-133.25	GT:AD:DP:GL:GQ	0/1:32,28:50:-91.67,-15.06,-103.96:99
+chr1	50195	rs62637816	T	C	137.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=17.45;MQ0=31;OQ=544.88;QD=7.46;SB=-273.42	GT:AD:DP:GL:GQ	0/1:46,26:42:-70.43,-12.65,-88.66:99
+chr1	50884	rs3844232	G	A	43.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.69;MQ0=8;OQ=74.12;QD=4.12;SB=-10.00	GT:AD:DP:GL:GQ	0/1:11,7:6:-12.50,-1.81,-9.19:73.80
+chr1	51151	.	T	A	30.50	LowQual	AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.43;MQ0=2;QD=5.08;SB=-37.96	GT:AD:DP:GL:GQ	0/1:4,2:4:-7.54,-1.20,-7.68:63.33
+chr1	51152	.	A	G	76.91	PASS	AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.59;MQ0=2;OQ=62.44;QD=8.92;SB=-39.93	GT:AD:DP:GL:GQ	0/1:4,3:5:-11.03,-1.51,-8.33:68.29
+chr1	51305	rs2531261	A	G	318.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.94;MQ0=3;OQ=1035.37;QD=25.88;SB=-471.86	GT:AD:DP:GL:GQ	1/1:0,40:29:-107.13,-8.73,-0.01:87.27
+chr1	51850	.	A	G	82.68	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=39.81;MQ0=7;OQ=720.99;QD=12.22;SB=-171.50	GT:AD:DP:GL:GQ	0/1:32,27:50:-90.45,-15.06,-94.52:99
+chr1	51852	.	G	C	25.49	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=40.15;MQ0=6;OQ=1021.36;QD=17.61;SB=-245.09	GT:AD:DP:GL:GQ	0/1:31,27:50:-120.48,-15.06,-101.09:99
+chr1	52066	rs28402963	T	C	139.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=39.80;MQ0=3;OQ=684.28;QD=9.50;SB=-320.22	GT:AD:DP:GL:GQ	0/1:42,30:68:-92.19,-20.48,-169.52:99
+chr1	52134	rs28599927	A	G	180.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=31.13;MQ0=5;OQ=314.17;QD=8.73;SB=-124.71	GT:AD:DP:GL:GQ	0/1:23,13:30:-43.74,-9.04,-73.62:99
+chr1	52441	rs2531315	G	A	15.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.89;MQ0=7;OQ=286.62;QD=17.91;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,16:8:-32.24,-2.41,-0.00:24.08
+chr1	52640	rs3844233	A	T	1.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=20.92;MQ0=32;OQ=114.33;QD=2.04;SB=-23.31	GT:AD:DP:GL:GQ	0/1:45,11:17:-19.84,-5.12,-46.79:99
+chr1	53560	.	T	C	39.15	PASS	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=25.49;MQ0=11;OQ=919.76;QD=11.22;SB=-454.58	GT:AD:DP:GL:GQ	0/1:47,35:69:-116.05,-20.79,-145.77:99
+chr1	54476	rs1627939	T	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=2;HaplotypeScore=1.16;MQ=27.48;MQ0=38;OQ=233.94;QD=2.36;SB=-139.05	GT:AD:DP:GL:GQ	0/1:84,15:50:-41.74,-15.06,-148.46:99
+chr1	54790	rs996010	G	T	31.78	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=23.12;MQ0=20;QD=0.47;SB=29.08	GT:AD:DP:GL:GQ	0/1:55,13:40:-18.51,-12.05,-121.17:64.61
+chr1	54839	rs2854687	C	T	10.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=27.08;MQ0=0;OQ=1633.87;QD=34.04;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,48:40:-166.98,-12.05,-0.01:99
+chr1	55660	.	T	C	47.12	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=8.71;MQ0=70;QD=0.52;SB=-10.00	GT:AD:DP:GL:GQ	0/1:73,17:9:-10.71,-2.71,-24.43:79.96
+chr1	55735	.	T	G	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=7.24;MQ0=61;OQ=58.14;QD=0.81;SB=-10.00	GT:AD:DP:GL:GQ	0/1:55,17:5:-10.60,-1.51,-6.69:51.83
+chr1	56025	rs62639105	A	T	0.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=3;HaplotypeScore=1.00;MQ=23.00;MQ0=0;OQ=377.29;QD=31.44;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,11:12:-44.38,-3.61,-3.44:2.23
+chr1	60591	.	C	T	1.69	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=14.15;MQ0=46;OQ=324.67;QD=4.39;SB=-159.64	GT:AD:DP:GL:GQ	0/1:50,24:28:-44.18,-8.43,-61.59:99
+chr1	60624	.	T	C	29.51	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=5.38;MQ0=69;QD=0.40;SB=-6.99	GT:AD:DP:GL:GQ	0/1:53,20:3:-7.14,-0.90,-3.77:28.64
+chr1	63704	rs3020697	C	T	122.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.04;MQ=34.36;MQ0=1;OQ=168.10;QD=12.93;SB=-51.56	GT:AD:DP:GL:GQ	1/1:0,13:6:-20.39,-1.81,-0.01:18.05
+chr1	64418	.	A	G	43.84	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;HRun=1;HaplotypeScore=8.82;MQ=6.47;MQ0=82;QD=0.45;SB=-10.00	GT:AD:DP:GL:GQ	1/1:82,16:2:-7.79,-0.60,-0.00:6.02
+chr1	64433	.	T	A	31.10	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=2.89;MQ=7.92;MQ0=71;QD=0.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:82,12:3:-7.30,-0.90,-3.84:29.36
+chr1	64544	rs13328683	G	T	4.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=1.57;MQ=18.78;MQ0=9;OQ=435.52;QD=13.61;SB=-10.00	GT:AD:DP:GL:GQ	1/1:10,22:12:-47.14,-3.61,-0.00:36.12
+chr1	67325	rs2462497	G	A	48.02	LowQual	AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.51;MQ0=2;QD=12.01;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,4:2:-8.21,-0.60,-0.00:6.02
+chr1	72009	.	A	G	32.65	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=5.60;MQ=18.28;MQ0=7;QD=1.72;SB=-38.67	GT:AD:DP:GL:GQ	0/1:14,5:11:-9.86,-3.31,-31.53:65.48
+chr1	72112	rs1851945	A	G	1.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=25.77;MQ0=4;OQ=504.38;QD=26.55;SB=-10.00	GT:AD:DP:GL:GQ	1/1:4,15:15:-54.03,-4.52,-0.00:45.14
+chr1	72166	rs2907073	T	C	81.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.95;MQ0=1;OQ=468.64;QD=33.47;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,14:13:-50.45,-3.91,-0.00:39.13
+chr1	72179	rs2260604	A	C	22.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.51;MQ0=4;OQ=244.12;QD=17.44;SB=-10.00	GT:AD:DP:GL:GQ	1/1:4,10:10:-28.01,-3.01,-0.01:30.03
+chr1	72195	.	T	C	61.39	PASS	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.33;MQ0=10;OQ=206.79;QD=10.34;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,7:10:-26.97,-3.01,-11.90:88.90
+chr1	73690	.	A	G	59.97	Indel	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=8.93;MQ=23.64;MQ0=3;QD=4.28;SB=-6.99	GT:AD:DP:GL:GQ	0/1:7,7:8:-11.69,-2.41,-21.22:92.80
+chr1	73692	.	G	A	71.09	Indel	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=3;HaplotypeScore=9.93;MQ=23.64;MQ0=3;QD=5.08;SB=-6.99	GT:AD:DP:GL:GQ	0/1:7,7:8:-12.80,-2.41,-18.45:99
+chr1	73996	.	A	T	22.55	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=27.59;MQ0=22;OQ=466.23;QD=7.40;SB=-57.87	GT:AD:DP:GL:GQ	0/1:36,27:38:-61.35,-11.44,-82.94:99
+chr1	74170	rs4118012	C	A	85.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=197.97;QD=32.99;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,6:6:-23.37,-1.81,-0.00:18.06
+chr1	74355	rs3871778	C	G	11.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.46;MQ0=2;OQ=92.52;QD=18.50;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,5:3:-12.74,-0.90,-0.00:9.03
+chr1	74885	.	G	A	80.42	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=18.46;MQ0=14;OQ=538.01;QD=13.12;SB=-187.68	GT:AD:DP:GL:GQ	0/1:20,21:26:-64.92,-7.83,-36.63:99
+chr1	80719	.	G	A	41.54	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=8.20;MQ0=31;QD=1.19;SB=-10.00	GT:AD:DP:GL:GQ	0/1:32,2:3:-8.34,-0.91,-2.50:15.90
+chr1	81004	rs4245761	G	T	39.81	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=13.75;MQ0=7;QD=3.32;SB=-10.00	GT:AD:DP:GL:GQ	1/1:7,5:2:-7.39,-0.60,-0.00:6.02
+chr1	81077	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=13;HaplotypeScore=2.26;MQ=18.21;MQ0=7;OQ=85.86;QD=5.05;SB=-62.92	GT:AD:DP:GL:GQ	0/1:11,6:5:-13.38,-1.51,-3.74:22.35
+chr1	81199	rs4245763	A	T	30.68	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=13.70;MQ0=7;QD=3.07;SB=-10.00	GT:AD:DP:GL:GQ	1/1:6,4:2:-6.48,-0.60,-0.00:6.01
+chr1	81378	.	A	C	3.99	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=33.30;MQ0=0;OQ=188.72;QD=4.72;SB=-114.61	GT:AD:DP:GL:GQ	0/1:31,9:34:-32.39,-10.24,-89.64:99
+chr1	81399	rs6702460	G	T	307.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=32.81;MQ0=0;OQ=1379.58;QD=33.65;SB=-370.87	GT:AD:DP:GL:GQ	1/1:0,41:37:-141.55,-11.14,-0.01:99
+chr1	81444	rs1524604	G	A	325.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.68;MQ0=1;OQ=1101.93;QD=36.73;SB=-340.44	GT:AD:DP:GL:GQ	1/1:0,30:28:-113.78,-8.43,-0.01:84.28
+chr1	81611	rs4256762	C	T	100.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=17.29;MQ0=34;OQ=684.35;QD=12.01;SB=-10.00	GT:AD:DP:GL:GQ	1/1:14,43:19:-75.91,-5.72,-3.90:18.23
+chr1	82517	.	T	C	0.75	PASS	AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=13.00;MQ0=6;OQ=70.17;QD=3.19;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,22:3:-10.51,-0.90,-0.00:9.03
+chr1	86134	.	C	G	0.28	PASS	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=17.64;MQ0=31;OQ=214.58;QD=2.38;SB=-33.05	GT:AD:DP:GL:GQ	0/1:81,9:51:-40.11,-15.36,-187.83:99
+chr1	88546	.	G	A	0.08	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.25;MQ0=8;OQ=736.28;QD=19.90;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,24:26:-84.74,-7.83,-23.08:99
+chr1	88616	rs4504463	T	C	1.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.27;MQ0=29;OQ=80.37;QD=1.55;SB=-10.00	GT:AD:DP:GL:GQ	0/1:43,9:21:-17.65,-6.33,-64.09:99
+chr1	88704	.	G	A	26.43	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=13.14;MQ0=25;QD=0.76;SB=-10.00	GT:AD:DP:GL:GQ	0/1:33,2:8:-8.34,-2.41,-22.88:59.26
+chr1	88715	.	A	G	0.29	PASS	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=13.96;MQ0=21;OQ=53.96;QD=1.74;SB=-10.00	GT:AD:DP:GL:GQ	0/1:28,3:8:-11.09,-2.41,-20.54:86.80
+chr1	88808	.	C	T	3.03	PASS	AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.56;MQ0=9;OQ=459.05;QD=18.36;SB=-49.56	GT:AD:DP:GL:GQ	1/1:1,24:12:-49.49,-3.61,-0.00:36.12
+chr1	88856	rs1851939	G	A	178.37	HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=30.10;MQ0=10;QD=3.64;SB=-37.62	GT:AD:DP:GL:GQ	0/1:36,12:37:-32.26,-11.14,-102.50:99
+chr1	88918	.	C	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=6.89;MQ=32.20;MQ0=8;OQ=309.74;QD=3.64;SB=-68.70	GT:AD:DP:GL:GQ	0/1:64,21:74:-56.55,-22.29,-199.33:99
+chr1	88963	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=30.09;MQ=26.41;MQ0=31;OQ=291.13;QD=2.62;SB=-116.74	GT:AD:DP:GL:GQ	0/1:88,23:71:-53.80,-21.40,-203.68:99
+chr1	88966	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=24.42;MQ=26.07;MQ0=32;OQ=253.10;QD=2.32;SB=-149.24	GT:AD:DP:GL:GQ	0/1:88,21:67:-48.78,-20.19,-197.64:99
+chr1	89000	.	A	G	0.14	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=15.31;MQ0=39;OQ=157.34;QD=2.76;SB=-51.84	GT:AD:DP:GL:GQ	0/1:48,9:10:-22.04,-3.02,-12.09:90.71
+chr1	89029	.	C	T	23.46	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.84;MQ=12.16;MQ0=50;QD=0.36;SB=5.02	GT:AD:DP:GL:GQ	0/1:50,16:9:-8.34,-2.71,-21.03:56.28
+chr1	89043	.	T	C	25.04	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=9.57;MQ0=58;QD=0.36;SB=-0.97	GT:AD:DP:GL:GQ	0/1:54,16:6:-7.59,-1.81,-16.33:57.86
+chr1	89188	.	C	T	0.06	PASS	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=1;HaplotypeScore=2.43;MQ=17.90;MQ0=10;OQ=61.10;QD=3.39;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,3:7:-11.50,-2.11,-14.49:93.93
+chr1	89528	.	C	T	1.15	PASS	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=22.04;MQ0=0;OQ=168.19;QD=24.03;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,6:5:-20.38,-1.51,-0.00:15.05
+chr1	90974	rs62639107	G	T	14.16	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=10.20;MQ0=34;QD=0.33;SB=-0.97	GT:AD:DP:GL:GQ	0/1:33,10:6:-6.49,-1.81,-14.67:46.83
+chr1	91131	.	G	A	0.50	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=10.39;MQ0=55;OQ=206.73;QD=2.79;SB=-10.00	GT:AD:DP:GL:GQ	0/1:41,33:9:-26.67,-2.71,-7.60:48.84
+chr1	91212	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=134;Dels=0.01;HRun=13;HaplotypeScore=35.68;MQ=19.40;MQ0=63;OQ=147.19;QD=1.10;SB=-6.99	GT:AD:DP:GL:GQ	0/1:107,25:41:-30.37,-12.37,-109.55:99
+chr1	91252	.	A	C	43.23	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=1;HaplotypeScore=36.75;MQ=16.93;MQ0=85;QD=0.29;SB=-10.00	GT:AD:DP:GL:GQ	0/1:138,10:43:-20.56,-12.95,-127.64:76.06
+chr1	91549	.	A	G	49.47	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=209;Dels=0.00;HRun=0;HaplotypeScore=15.98;MQ=27.81;MQ0=39;QD=0.24;SB=65.80	GT:AD:DP:GL:GQ	0/1:179,30:144:-51.61,-43.38,-519.29:82.31
+chr1	91758	.	G	A	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.60;MQ=22.49;MQ0=25;OQ=143.40;QD=2.17;SB=15.64	GT:AD:DP:GL:GQ	0/1:56,10:34:-27.86,-10.24,-97.22:99
+chr1	91835	.	T	C	60.94	PASS	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.01;MQ0=36;OQ=785.45;QD=10.47;SB=-10.00	GT:AD:DP:GL:GQ	0/1:43,32:33:-91.79,-9.96,-12.24:22.78
+chr1	91851	rs4109800	G	C	35.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.96;MQ0=33;OQ=1198.57;QD=15.98;SB=-10.00	GT:AD:DP:GL:GQ	0/1:41,34:33:-133.08,-9.94,-16.89:69.53
+chr1	91938	.	G	A	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=2.53;MQ=14.92;MQ0=47;OQ=298.50;QD=3.21;SB=-10.00	GT:AD:DP:GL:GQ	0/1:77,15:21:-39.46,-6.32,-39.15:99
+chr1	92459	rs3912701	G	A	1.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=1.98;MQ=17.65;MQ0=34;OQ=809.52;QD=14.99;SB=-10.00	GT:AD:DP:GL:GQ	1/1:30,24:20:-84.54,-6.02,-0.00:60.20
+chr1	92527	rs4618909	A	G	1.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=1;HaplotypeScore=7.26;MQ=22.11;MQ0=40;OQ=1083.35;QD=10.62;SB=-10.00	GT:AD:DP:GL:GQ	0/1:55,47:51:-126.98,-15.36,-75.91:99
+chr1	92632	rs3872168	C	A	251.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.40;MQ0=16;OQ=274.62;QD=10.98;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,25:9:-31.05,-2.71,-0.00:27.07
+chr1	92814	.	C	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=1;HaplotypeScore=9.83;MQ=30.05;MQ0=21;OQ=659.75;QD=3.88;SB=-292.33	GT:AD:DP:GL:GQ	0/1:135,35:144:-112.64,-43.38,-415.54:99
+chr1	93070	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=1;HaplotypeScore=8.90;MQ=17.00;MQ0=65;OQ=190.64;QD=1.91;SB=-10.00	GT:AD:DP:GL:GQ	0/1:83,17:34:-32.59,-10.25,-92.04:99
+chr1	93104	rs62642109	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=24.91;MQ=20.20;MQ0=60;OQ=819.40;QD=6.83;SB=-0.98	GT:AD:DP:GL:GQ	0/1:72,48:57:-102.42,-17.19,-99.00:99
+chr1	93113	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=17.60;MQ=21.02;MQ0=51;OQ=474.12;QD=4.23;SB=5.03	GT:AD:DP:GL:GQ	0/1:79,33:56:-67.57,-16.87,-129.01:99
+chr1	93181	.	T	C	7.86	PASS	AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=15.97;MQ0=67;OQ=759.85;QD=7.17;SB=20.10	GT:AD:DP:GL:GQ	0/1:53,53:35:-89.81,-10.54,-44.53:99
+chr1	93248	rs62639110	G	A	30.22	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=8.07;MQ0=76;QD=0.36;SB=-10.00	GT:AD:DP:GL:GQ	0/1:62,22:6:-8.11,-1.81,-14.17:63.05
+chr1	93307	.	G	A	47.02	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=5.80;MQ0=48;QD=0.94;SB=-10.00	GT:AD:DP:GL:GQ	1/1:44,6:2:-8.11,-0.60,-0.00:6.02
+chr1	93757	.	T	C	30.28	LowQual	AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=10.09;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,2:2:-6.44,-0.60,-0.00:6.01
+chr1	93896	rs4287120	T	C	0.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=174;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=4.84;MQ0=151;OQ=128.63;QD=0.74;SB=-81.37	GT:AD:DP:GL:GQ	1/1:41,133:5:-16.43,-1.51,-0.00:15.04
+chr1	93971	rs4492556	A	G	12.01	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=2.58;MQ=7.18;MQ0=71;QD=0.15;SB=-31.93	GT:AD:DP:GL:GQ	0/1:47,34:7:-6.57,-2.11,-19.60:44.57
+chr1	94001	.	G	T	0.94	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=16.11;MQ0=45;OQ=194.11;QD=3.35;SB=-41.38	GT:AD:DP:GL:GQ	0/1:51,7:13:-26.61,-3.91,-21.51:99
+chr1	94049	rs4288537	T	C	0.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=10.96;MQ=20.93;MQ0=24;OQ=438.79;QD=10.45;SB=-71.88	GT:AD:DP:GL:GQ	0/1:18,24:17:-52.28,-5.12,-8.24:31.18
+chr1	94088	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=3.06;MQ=13.40;MQ0=57;OQ=79.42;QD=1.15;SB=-38.36	GT:AD:DP:GL:GQ	0/1:64,5:10:-14.24,-3.02,-19.96:99
+chr1	94312	.	C	A	18.04	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=10.70;MQ0=65;QD=0.24;SB=-10.00	GT:AD:DP:GL:GQ	0/1:72,2:9:-7.79,-2.71,-24.60:50.81
+chr1	98160	rs4109806	A	C	199.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.46;MQ0=21;OQ=505.68;QD=12.97;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,39:15:-54.16,-4.52,-0.00:45.14
+chr1	98173	.	T	C	2.30	PASS	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=16.05;MQ0=20;OQ=109.74;QD=3.05;SB=-45.95	GT:AD:DP:GL:GQ	0/1:14,22:12:-17.87,-3.61,-27.89:99
+chr1	98191	rs4109805	A	G	15.99	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=16.84;MQ0=14;QD=0.50;SB=5.05	GT:AD:DP:GL:GQ	0/1:28,4:15:-9.39,-4.52,-49.05:48.72
+chr1	98276	rs4457511	T	G	0.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=9.15;MQ=5.64;MQ0=97;OQ=125.84;QD=1.20;SB=-67.98	GT:AD:DP:GL:GQ	0/1:81,24:6:-17.67,-1.81,-3.90:20.89
+chr1	99188	.	T	C	0.10	PASS	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=8.00;MQ0=82;OQ=57.15;QD=0.64;SB=-10.00	GT:AD:DP:GL:GQ	0/1:85,4:6:-10.81,-1.81,-11.97:89.99
+chr1	99237	.	G	A	48.25	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=4.41;MQ0=117;QD=0.40;SB=-10.00	GT:AD:DP:GL:GQ	1/1:114,6:2:-8.23,-0.60,-0.00:6.02
+chr1	99503	rs4126043	T	A	232.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.79;MQ0=3;OQ=79.29;QD=11.33;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,7:3:-11.42,-0.90,-0.00:9.03
+chr1	110568	rs4117992	T	C	36.28	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=12.09;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:2:-7.04,-0.60,-0.00:6.02
+chr1	110846	.	C	T	29.97	PASS	AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=21.24;MQ0=9;OQ=175.53;QD=12.54;SB=-93.11	GT:AD:DP:GL:GQ	1/1:6,8:5:-21.11,-1.51,-0.00:15.05
+chr1	110872	rs1851943	C	T	61.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.59;MQ0=3;OQ=127.11;QD=18.16;SB=-91.11	GT:AD:DP:GL:GQ	1/1:0,7:4:-16.25,-1.20,-0.00:12.04
+chr1	117436	.	G	A	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=9.09;MQ0=104;OQ=195.33;QD=1.58;SB=-97.57	GT:AD:DP:GL:GQ	0/1:100,24:19:-28.54,-5.73,-40.13:99
+chr1	119192	.	C	G	13.29	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=6.87;MQ0=19;QD=0.58;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,8:1:-4.59,-0.30,-0.00:1.76
+chr1	125911	rs11531330	C	T	87.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=18.40;MQ0=3;OQ=89.79;QD=11.22;SB=-10.00	GT:AD:DP:GL:GQ	1/1:4,3:3:-12.47,-0.90,-0.00:9.03
+chr1	217782	.	A	T	46.88	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=14.40;MQ0=4;QD=5.86;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,8:2:-8.10,-0.60,-0.00:6.02
+chr1	219536	rs6678242	A	C	214.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=14.88;MQ0=9;OQ=112.38;QD=6.61;SB=-45.01	GT:AD:DP:GL:GQ	1/1:0,17:4:-14.77,-1.20,-0.00:12.04
+chr1	219731	.	C	T	12.21	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.96;MQ0=44;QD=0.17;SB=38.14	GT:AD:DP:GL:GQ	0/1:62,9:27:-12.61,-8.14,-82.06:44.77
+chr1	219921	rs12239119	T	G	63.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=23.26;MQ0=4;OQ=606.74;QD=25.28;SB=-312.56	GT:AD:DP:GL:GQ	1/1:0,24:18:-64.26,-5.42,-0.01:54.16
+chr1	221068	rs10047119	T	A	39.88	DPFilter;HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=254;Dels=0.00;HRun=1;HaplotypeScore=6.12;MQ=8.79;MQ0=135;QD=0.16;SB=-10.00	GT:AD:DP:GL:GQ	1/1:167,87:2:-7.40,-0.60,-0.00:6.02
+chr1	221077	rs10047174	C	A	38.69	DPFilter;HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=271;Dels=0.00;HRun=0;HaplotypeScore=6.64;MQ=8.55;MQ0=150;QD=0.14;SB=-10.00	GT:AD:DP:GL:GQ	1/1:181,90:2:-7.28,-0.60,-0.00:6.02
+chr1	221092	rs10047175	C	A	39.69	DPFilter;HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=283;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=7.57;MQ0=174;QD=0.14;SB=-10.00	GT:AD:DP:GL:GQ	1/1:201,82:2:-7.38,-0.60,-0.00:6.02
+chr1	221109	rs10047121	T	C	34.28	DPFilter;HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=275;Dels=0.00;HRun=0;HaplotypeScore=3.23;MQ=7.06;MQ0=184;QD=0.12;SB=-10.00	GT:AD:DP:GL:GQ	1/1:197,78:2:-6.84,-0.60,-0.00:6.02
+chr1	221318	.	T	A	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=241;Dels=0.00;HRun=0;HaplotypeScore=2.80;MQ=19.94;MQ0=85;OQ=462.52;QD=1.92;SB=39.55	GT:AD:DP:GL:GQ	0/1:212,29:108:-82.07,-32.53,-323.83:99
+chr1	221343	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=261;Dels=0.00;HRun=0;HaplotypeScore=2.12;MQ=22.79;MQ0=47;OQ=408.64;QD=1.57;SB=-215.29	GT:AD:DP:GL:GQ	0/1:222,38:157:-91.46,-47.31,-595.18:99
+chr1	221367	rs10047230	G	A	0.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=11.19;MQ=25.20;MQ0=11;OQ=1571.46;QD=5.65;SB=-527.77	GT:AD:DP:GL:GQ	0/1:197,80:212:-224.34,-63.91,-509.11:99
+chr1	221389	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=260;Dels=0.00;HRun=1;HaplotypeScore=1.74;MQ=24.37;MQ0=22;OQ=840.34;QD=3.23;SB=-412.02	GT:AD:DP:GL:GQ	0/1:209,50:201:-147.86,-60.54,-597.88:99
+chr1	221420	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=210;Dels=0.00;HRun=1;HaplotypeScore=4.60;MQ=20.04;MQ0=77;OQ=83.18;QD=0.40;SB=26.98	GT:AD:DP:GL:GQ	0/1:192,14:117:-46.84,-35.24,-385.27:99
+chr1	222364	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=186;Dels=0.03;HRun=0;HaplotypeScore=32.96;MQ=22.76;MQ0=12;OQ=2072.95;QD=11.14;SB=59.21	GT:AD:DP:GL:GQ	0/1:70,111:137:-251.84,-41.26,-268.25:99
+chr1	222793	.	C	G	25.72	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=260;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=16.62;MQ0=87;QD=0.10;SB=81.54	GT:AD:DP:GL:GQ	0/1:230,30:110:-38.99,-33.14,-447.79:58.55
+chr1	223336	.	C	G	28.20	PASS	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=35.25;MQ0=2;OQ=1925.92;QD=21.40;SB=-854.31	GT:AD:DP:GL:GQ	0/1:39,51:87:-222.09,-26.21,-160.96:99
+chr1	224095	rs8179512	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=229;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=15.51;MQ0=125;OQ=91.58;QD=0.40;SB=-45.96	GT:AD:DP:GL:GQ	0/1:203,26:89:-39.28,-26.84,-255.40:99
+chr1	224171	rs7195389	A	G	40.71	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=269;Dels=0.00;HRun=0;HaplotypeScore=47.18;MQ=22.11;MQ0=18;QD=0.15;SB=122.50	GT:AD:DP:GL:GQ	0/1:232,36:234:-77.87,-70.51,-842.48:73.55
+chr1	224176	rs56055731	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=276;Dels=0.00;HRun=1;HaplotypeScore=39.67;MQ=21.41;MQ0=32;OQ=545.76;QD=1.98;SB=-248.71	GT:AD:DP:GL:GQ	0/1:242,34:226:-125.93,-68.07,-709.89:99
+chr1	224241	rs62053733	A	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=216;Dels=0.00;HRun=0;HaplotypeScore=20.29;MQ=17.49;MQ0=74;OQ=1752.30;QD=8.11;SB=-714.08	GT:AD:DP:GL:GQ	0/1:103,113:104:-209.87,-31.36,-152.51:99
+chr1	224344	rs8179403	T	A	166.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=163;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=23.92;MQ0=45;OQ=2824.26;QD=17.33;SB=-725.16	GT:AD:DP:GL:GQ	0/1:38,125:108:-318.26,-32.55,-66.31:99
+chr1	224419	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=1;HaplotypeScore=18.87;MQ=14.35;MQ0=100;OQ=127.03;QD=0.68;SB=8.05	GT:AD:DP:GL:GQ	0/1:161,26:49:-30.75,-14.76,-153.48:99
+chr1	224472	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=261;Dels=0.00;HRun=1;HaplotypeScore=6.53;MQ=15.44;MQ0=125;OQ=992.61;QD=3.80;SB=-39.67	GT:AD:DP:GL:GQ	0/1:177,84:84:-127.86,-25.32,-192.69:99
+chr1	224623	rs7548182	A	T	1.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.00;HRun=3;HaplotypeScore=1.37;MQ=26.54;MQ0=23;OQ=863.08;QD=8.07;SB=50.19	GT:AD:DP:GL:GQ	0/1:39,68:64:-108.87,-19.28,-138.61:99
+chr1	225707	rs6603780	C	G	0.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=6.28;MQ=15.73;MQ0=150;OQ=1742.87;QD=6.27;SB=-566.38	GT:AD:DP:GL:GQ	0/1:147,131:57:-194.74,-17.17,-58.86:99
+chr1	225839	rs6422503	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=215;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=34.58;MQ0=26;OQ=4599.62;QD=21.39;SB=-1688.57	GT:AD:DP:GL:GQ	0/1:70,145:162:-458.96,-48.79,-124.49:99
+chr1	226216	.	T	C	24.03	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=3.20;MQ=9.23;MQ0=93;QD=0.13;SB=-10.00	GT:AD:DP:GL:GQ	0/1:162,19:7:-7.79,-2.11,-21.54:56.85
+chr1	227048	.	C	A	43.64	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=2.13;MQ=9.30;MQ0=121;QD=0.28;SB=-44.79	GT:AD:DP:GL:GQ	0/1:134,21:22:-14.27,-6.63,-62.25:76.48
+chr1	227333	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=5.51;MQ=14.65;MQ0=59;OQ=58.63;QD=0.42;SB=-10.00	GT:AD:DP:GL:GQ	0/1:125,16:25:-16.68,-7.54,-70.62:91.47
+chr1	227353	.	C	A	20.49	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=140;Dels=0.00;HRun=1;HaplotypeScore=4.94;MQ=14.92;MQ0=62;QD=0.15;SB=-10.00	GT:AD:DP:GL:GQ	0/1:122,18:29:-14.07,-8.74,-90.83:53.29
+chr1	227461	rs28618397	A	G	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=144;Dels=0.00;HRun=0;HaplotypeScore=6.94;MQ=8.17;MQ0=115;OQ=63.90;QD=0.44;SB=-10.00	GT:AD:DP:GL:GQ	0/1:131,13:8:-12.09,-2.41,-14.97:96.73
+chr1	227626	.	G	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=4.92;MQ=20.49;MQ0=18;OQ=315.55;QD=1.73;SB=-168.42	GT:AD:DP:GL:GQ	0/1:163,19:138:-76.40,-41.57,-437.40:99
+chr1	227735	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=14.30;MQ=17.08;MQ0=35;OQ=66.90;QD=0.75;SB=20.77	GT:AD:DP:GL:GQ	0/1:78,11:41:-22.33,-12.35,-159.24:99
+chr1	230298	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=1;HaplotypeScore=4.58;MQ=24.72;MQ0=17;OQ=319.24;QD=2.47;SB=-97.27	GT:AD:DP:GL:GQ	0/1:109,19:104:-66.59,-31.38,-356.71:99
+chr1	230890	.	G	A	0.28	PASS	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=4.05;MQ=28.42;MQ0=10;OQ=452.11;QD=3.77;SB=-186.08	GT:AD:DP:GL:GQ	0/1:99,21:95:-77.11,-28.62,-272.62:99
+chr1	231027	rs1917217	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=16;HaplotypeScore=20.40;MQ=32.62;MQ0=10;OQ=363.52;QD=5.05;SB=32.11	GT:AD:DP:GL:GQ	0/1:47,24:50:-54.70,-15.07,-118.26:99
+chr1	231044	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=16;HaplotypeScore=28.71;MQ=27.06;MQ0=9;OQ=128.09;QD=1.69;SB=39.29	GT:AD:DP:GL:GQ	0/1:63,12:57:-36.63,-20.54,-166.03:99
+chr1	231045	.	A	T	16.10	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=26.04;MQ=26.31;MQ0=9;QD=0.22;SB=44.16	GT:AD:DP:GL:GQ	0/1:63,8:54:-21.15,-16.27,-182.36:48.82
+chr1	231183	.	A	G	0.09	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=8.45;MQ=28.02;MQ0=10;OQ=325.16;QD=6.25;SB=-110.63	GT:AD:DP:GL:GQ	0/1:19,32:27:-43.95,-8.15,-48.50:99
+chr1	231232	rs11490246	C	T	142.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=27.55;MQ0=9;OQ=1010.69;QD=16.84;SB=-258.84	GT:AD:DP:GL:GQ	1/1:0,59:26:-104.66,-7.83,-0.01:78.25
+chr1	234887	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=210;Dels=0.00;HRun=0;HaplotypeScore=14.30;MQ=23.11;MQ0=12;OQ=591.52;QD=2.82;SB=-248.32	GT:AD:DP:GL:GQ	0/1:173,36:184:-117.86,-55.42,-542.00:99
+chr1	235002	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=3;HaplotypeScore=1.45;MQ=7.75;MQ0=92;OQ=65.10;QD=0.63;SB=-6.99	GT:AD:DP:GL:GQ	0/1:88,15:7:-11.90,-2.11,-15.26:97.93
+chr1	235268	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=1;HaplotypeScore=31.21;MQ=26.04;MQ0=17;OQ=96.26;QD=2.53;SB=-57.31	GT:AD:DP:GL:GQ	0/1:24,12:15:-17.43,-4.52,-39.23:99
+chr1	235318	.	C	G	0.88	PASS	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=31.66;MQ0=1;OQ=172.25;QD=9.57;SB=-27.84	GT:AD:DP:GL:GQ	0/1:12,6:17:-25.63,-5.12,-44.90:99
+chr1	237291	rs62639107	G	T	22.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=12.32;MQ0=83;OQ=830.85;QD=6.59;SB=-342.75	GT:AD:DP:GL:GQ	0/1:51,75:34:-96.61,-10.24,-28.48:99
+chr1	237573	.	T	C	21.25	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=174;Dels=0.00;HRun=0;HaplotypeScore=8.41;MQ=14.44;MQ0=98;QD=0.12;SB=17.09	GT:AD:DP:GL:GQ	0/1:155,19:37:-16.55,-11.15,-125.38:54.05
+chr1	238151	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=9.86;MQ0=83;OQ=59.88;QD=0.63;SB=-10.00	GT:AD:DP:GL:GQ	0/1:91,4:10:-12.29,-3.01,-24.61:92.72
+chr1	238167	rs4109800	G	C	1.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=9.69;MQ0=81;OQ=122.76;QD=1.31;SB=-10.00	GT:AD:DP:GL:GQ	0/1:83,11:9:-18.27,-2.71,-21.24:99
+chr1	238254	.	G	A	14.34	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=10.94;MQ0=73;QD=0.13;SB=-10.00	GT:AD:DP:GL:GQ	0/1:101,9:10:-7.71,-3.01,-28.55:47.01
+chr1	242992	rs4109808	G	C	0.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=205;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=17.96;MQ0=77;OQ=316.33;QD=1.54;SB=11.07	GT:AD:DP:GL:GQ	0/1:143,62:81:-59.32,-24.40,-284.11:99
+chr1	244543	rs62639119	A	G	39.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=1.69;MQ=13.13;MQ0=71;OQ=645.60;QD=5.98;SB=-100.72	GT:AD:DP:GL:GQ	0/1:56,52:34:-78.09,-10.25,-42.39:99
+chr1	244959	rs4096710	C	T	45.82	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=3.93;MQ=13.07;MQ0=59;QD=0.54;SB=-26.62	GT:AD:DP:GL:GQ	0/1:74,11:15:-12.39,-4.52,-39.32:78.66
+chr1	245030	rs4247528	T	G	34.76	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=14.80;MQ0=42;QD=0.49;SB=8.04	GT:AD:DP:GL:GQ	0/1:62,9:14:-10.98,-4.22,-38.66:67.59
+chr1	245496	.	A	G	44.84	LowQual	AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.49;MQ0=2;QD=7.47;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,5:2:-7.89,-0.60,-0.00:6.02
+chr1	314685	.	A	T	13.26	PASS	AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.75;MQ=14.76;MQ0=13;OQ=314.43;QD=11.65;SB=-42.39	GT:AD:DP:GL:GQ	1/1:12,15:9:-35.03,-2.71,-0.00:27.09
+chr1	314938	.	G	C	1.97	PASS	AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=12.45;MQ0=16;OQ=80.86;QD=3.23;SB=-10.00	GT:AD:DP:GL:GQ	1/1:16,9:3:-11.58,-0.91,-0.00:9.03
+chr1	314990	.	T	C	42.83	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=12.15;MQ0=12;QD=2.14;SB=-10.00	GT:AD:DP:GL:GQ	1/1:10,10:2:-7.69,-0.60,-0.00:6.02
+chr1	354114	rs3905534	G	T	4.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=2;HaplotypeScore=1.96;MQ=17.14;MQ0=8;OQ=149.39;QD=8.30;SB=-10.00	GT:AD:DP:GL:GQ	0/1:10,8:10:-21.23,-3.01,-14.53:99
+chr1	374336	rs4959767	C	G	48.85	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=9.01;MQ=5.04;MQ0=75;QD=0.57;SB=-10.00	GT:AD:DP:GL:GQ	1/1:78,7:2:-8.29,-0.60,-0.00:6.02
+chr1	374388	rs4120938	C	T	0.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=7.85;MQ=3.88;MQ0=74;OQ=50.25;QD=0.61;SB=-10.00	GT:AD:DP:GL:GQ	1/1:76,7:2:-8.43,-0.60,-0.00:6.02
+chr1	374916	.	A	C	6.13	PASS	AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.92;MQ0=3;OQ=209.71;QD=17.48;SB=-40.56	GT:AD:DP:GL:GQ	1/1:2,10:8:-24.56,-2.41,-0.01:24.03
+chr1	391491	.	T	G	33.28	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=1;HaplotypeScore=4.00;MQ=5.85;MQ0=67;QD=0.45;SB=-10.00	GT:AD:DP:GL:GQ	0/1:70,4:3:-7.51,-0.90,-3.44:25.36
+chr1	394166	.	C	T	0.46	PASS	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=7.89;MQ0=95;OQ=178.49;QD=1.75;SB=-10.00	GT:AD:DP:GL:GQ	0/1:96,6:7:-23.23,-2.11,-3.57:14.61
+chr1	394272	.	T	G	16.31	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=17.93;MQ0=35;OQ=484.03;QD=7.81;SB=-10.00	GT:AD:DP:GL:GQ	0/1:39,23:22:-58.31,-6.63,-19.38:99
+chr1	394291	rs12121306	C	T	153.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=16.59;MQ0=30;OQ=364.11;QD=7.75;SB=-10.00	GT:AD:DP:GL:GQ	0/1:31,16:14:-43.91,-4.22,-11.01:67.92
+chr1	394310	.	C	T	0.18	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=12.47;MQ0=36;OQ=147.86;QD=3.21;SB=-10.00	GT:AD:DP:GL:GQ	0/1:41,5:8:-20.48,-2.41,-10.61:81.97
+chr1	394537	.	G	A	2.58	PASS	AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=6.78;MQ=23.70;MQ0=52;OQ=1238.38;QD=11.79;SB=-421.21	GT:AD:DP:GL:GQ	0/1:65,40:50:-142.19,-15.07,-44.99:99
+chr1	394765	.	A	G	0.18	PASS	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=7.43;MQ0=57;OQ=65.19;QD=1.07;SB=-10.00	GT:AD:DP:GL:GQ	0/1:58,3:4:-11.01,-1.20,-3.46:22.51
+chr1	394834	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=7.99;MQ=12.79;MQ0=47;OQ=202.79;QD=3.56;SB=-10.00	GT:AD:DP:GL:GQ	0/1:49,8:10:-26.57,-3.01,-12.50:94.91
+chr1	394837	.	A	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=7.99;MQ=12.80;MQ0=51;OQ=216.52;QD=3.49;SB=-10.00	GT:AD:DP:GL:GQ	0/1:48,14:11:-28.25,-3.31,-11.97:86.56
+chr1	404035	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=20.45;MQ=17.63;MQ0=51;OQ=155.60;QD=2.22;SB=-84.79	GT:AD:DP:GL:GQ	0/1:62,8:17:-23.97,-5.12,-38.73:99
+chr1	511466	rs3902909	G	A	114.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.37;MQ0=1;OQ=299.83;QD=6.00;SB=-10.00	GT:AD:DP:GL:GQ	0/1:35,15:40:-45.34,-12.07,-85.80:99
+chr1	513688	rs61767343	C	T	0.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=5.41;MQ=21.22;MQ0=15;OQ=264.79;QD=2.88;SB=32.01	GT:AD:DP:GL:GQ	0/1:78,14:66:-49.68,-19.91,-161.21:99
+chr1	522943	.	G	A	31.72	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=14;HaplotypeScore=31.16;MQ=21.11;MQ0=30;QD=0.33;SB=74.23	GT:AD:DP:GL:GQ	0/1:84,11:55:-23.03,-16.58,-166.54:64.56
+chr1	523155	.	C	T	20.46	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=7.86;MQ=11.23;MQ0=37;QD=0.34;SB=-10.00	GT:AD:DP:GL:GQ	0/1:56,5:10:-8.34,-3.02,-25.17:53.26
+chr1	523163	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=7.11;MQ=11.49;MQ0=30;OQ=99.30;QD=1.99;SB=-10.00	GT:AD:DP:GL:GQ	0/1:37,13:9:-15.92,-2.71,-17.34:99
+chr1	523812	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=9.50;MQ=11.52;MQ0=31;OQ=145.45;QD=2.05;SB=-10.00	GT:AD:DP:GL:GQ	0/1:61,10:10:-20.85,-3.02,-13.58:99
+chr1	523821	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=9.21;MQ=15.64;MQ0=25;OQ=121.38;QD=1.84;SB=-10.00	GT:AD:DP:GL:GQ	0/1:57,9:12:-19.04,-3.62,-21.78:99
+chr1	523868	.	G	A	13.34	PASS	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.79;MQ0=4;OQ=177.69;QD=5.08;SB=-10.00	GT:AD:DP:GL:GQ	0/1:21,14:15:-25.58,-4.53,-24.67:99
+chr1	524029	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=26.24;MQ0=29;OQ=72.18;QD=0.99;SB=-17.85	GT:AD:DP:GL:GQ	0/1:58,15:34:-20.75,-10.24,-100.17:99
+chr1	524055	rs6680723	C	T	0.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=2;HaplotypeScore=11.94;MQ=30.97;MQ0=23;OQ=525.09;QD=5.30;SB=-269.67	GT:AD:DP:GL:GQ	0/1:68,31:65:-75.37,-19.58,-166.45:99
+chr1	524061	rs6680725	C	T	44.53	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=14.45;MQ=31.89;MQ0=22;QD=0.42;SB=98.20	GT:AD:DP:GL:GQ	0/1:92,13:70:-28.85,-21.11,-204.21:77.37
+chr1	524105	rs2792879	C	T	49.58	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=35.66;MQ0=5;QD=0.40;SB=82.58	GT:AD:DP:GL:GQ	0/1:106,18:95:-36.89,-28.65,-274.71:82.42
+chr1	524187	.	G	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=48;Dels=0.02;HRun=0;HaplotypeScore=13.69;MQ=38.72;MQ0=2;OQ=392.49;QD=8.18;SB=-133.62	GT:AD:DP:GL:GQ	0/1:25,22:25:-49.77,-7.23,-31.06:99
+chr1	524410	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=27.66;MQ=40.25;MQ0=9;OQ=582.52;QD=5.34;SB=-205.05	GT:AD:DP:GL:GQ	0/1:82,27:83:-86.53,-25.00,-225.34:99
+chr1	524592	rs61767348	C	T	0.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=35.17;MQ0=0;OQ=230.33;QD=1.84;SB=-71.36	GT:AD:DP:GL:GQ	0/1:109,16:125:-63.96,-37.65,-391.79:99
+chr1	524704	.	C	G	0.30	PASS	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=15.62;MQ0=42;OQ=247.71;QD=3.26;SB=-10.00	GT:AD:DP:GL:GQ	0/1:63,13:16:-32.88,-4.82,-37.64:99
+chr1	525671	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=125;Dels=0.00;HRun=0;HaplotypeScore=16.72;MQ=18.80;MQ0=44;OQ=189.70;QD=1.52;SB=-93.64	GT:AD:DP:GL:GQ	0/1:113,12:40:-34.30,-12.05,-118.97:99
+chr1	525779	.	A	G	0.63	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=22.14;MQ0=11;OQ=348.30;QD=4.15;SB=-47.83	GT:AD:DP:GL:GQ	0/1:66,18:49:-52.88,-14.76,-137.92:99
+chr1	525958	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=25.63;MQ=21.45;MQ0=28;OQ=60.59;QD=0.61;SB=-44.97	GT:AD:DP:GL:GQ	0/1:86,13:50:-24.43,-15.08,-139.15:93.42
+chr1	526007	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=23.90;MQ=27.74;MQ0=20;OQ=72.77;QD=0.52;SB=-61.14	GT:AD:DP:GL:GQ	0/1:119,22:81:-34.97,-24.41,-279.63:99
+chr1	526679	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=6.10;MQ=15.23;MQ0=50;OQ=159.06;QD=1.64;SB=-10.00	GT:AD:DP:GL:GQ	0/1:72,25:19:-24.93,-5.74,-37.85:99
+chr1	526910	.	C	T	33.12	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=15.09;MQ=12.21;MQ0=78;QD=0.31;SB=8.05	GT:AD:DP:GL:GQ	0/1:95,11:28:-15.03,-8.43,-86.21:65.95
+chr1	527066	rs1109924	C	T	18.08	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.21;MQ=24.80;MQ0=20;QD=0.22;SB=56.20	GT:AD:DP:GL:GQ	0/1:74,8:55:-21.66,-16.57,-168.07:50.84
+chr1	527350	rs1105044	C	T	0.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=5.45;MQ=30.46;MQ0=9;OQ=109.38;QD=3.91;SB=5.03	GT:AD:DP:GL:GQ	0/1:19,9:14:-18.45,-4.22,-27.73:99
+chr1	527399	.	C	G	0.15	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.45;MQ=22.48;MQ0=26;OQ=195.21;QD=3.42;SB=2.03	GT:AD:DP:GL:GQ	0/1:49,8:23:-29.74,-6.93,-66.80:99
+chr1	527400	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=1;HaplotypeScore=5.09;MQ=22.50;MQ0=26;OQ=149.94;QD=2.50;SB=3.82	GT:AD:DP:GL:GQ	0/1:51,8:23:-28.15,-9.87,-58.83:99
+chr1	527445	.	C	G	0.06	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=15.27;MQ0=33;OQ=120.74;QD=2.05;SB=-43.89	GT:AD:DP:GL:GQ	0/1:47,12:21:-21.68,-6.33,-71.74:99
+chr1	530476	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=20.30;MQ0=34;OQ=101.99;QD=0.68;SB=16.46	GT:AD:DP:GL:GQ	0/1:135,15:110:-46.63,-33.14,-338.24:99
+chr1	534258	rs61769278	G	A	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=121;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=9.91;MQ0=64;OQ=75.11;QD=0.62;SB=-10.00	GT:AD:DP:GL:GQ	0/1:81,40:6:-12.60,-1.81,-10.89:90.82
+chr1	534650	rs61769279	G	C	10.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=22.82;MQ0=11;OQ=171.47;QD=4.76;SB=-10.00	GT:AD:DP:GL:GQ	0/1:26,10:21:-26.76,-6.33,-62.71:99
+chr1	536560	rs12025928	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=3;HaplotypeScore=20.90;MQ=24.04;MQ0=6;OQ=206.19;QD=3.49;SB=8.06	GT:AD:DP:GL:GQ	0/1:26,33:37:-35.06,-11.16,-99.03:99
+chr1	536665	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=53.76;MQ=25.56;MQ0=32;OQ=200.39;QD=1.71;SB=-106.47	GT:AD:DP:GL:GQ	0/1:92,25:66:-43.22,-19.90,-241.56:99
+chr1	536668	rs61769283	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=116;Dels=0.00;HRun=0;HaplotypeScore=52.49;MQ=25.44;MQ0=31;OQ=176.14;QD=1.52;SB=-101.57	GT:AD:DP:GL:GQ	0/1:89,25:62:-39.59,-18.70,-187.95:99
+chr1	536745	rs9438485	T	C	0.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=10.16;MQ=22.38;MQ0=21;OQ=208.92;QD=2.37;SB=-117.20	GT:AD:DP:GL:GQ	0/1:59,28:39:-35.93,-11.75,-108.78:99
+chr1	536815	rs9438487	T	C	0.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=5.65;MQ=26.07;MQ0=22;OQ=487.78;QD=3.81;SB=-195.14	GT:AD:DP:GL:GQ	0/1:76,52:82:-76.77,-24.71,-234.35:99
+chr1	536828	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=25.55;MQ0=22;OQ=75.76;QD=0.57;SB=28.89	GT:AD:DP:GL:GQ	0/1:122,12:82:-35.59,-24.73,-235.80:99
+chr1	537100	.	G	A	12.85	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=13.16;MQ0=46;QD=0.12;SB=-7.00	GT:AD:DP:GL:GQ	0/1:81,22:25:-12.08,-7.53,-73.93:45.46
+chr1	537113	.	C	T	31	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=12.14;MQ0=51;QD=0.29;SB=-6.99	GT:AD:DP:GL:GQ	0/1:84,22:18:-11.81,-5.42,-56.12:63.83
+chr1	537596	.	G	A	46.75	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=0;HaplotypeScore=23.62;MQ=12.88;MQ0=95;QD=0.28;SB=83.26	GT:AD:DP:GL:GQ	0/1:155,15:50:-23.03,-15.07,-148.87:79.59
+chr1	537643	rs9438495	T	C	0.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=12.92;MQ0=56;OQ=64.59;QD=0.65;SB=29.12	GT:AD:DP:GL:GQ	0/1:83,15:29:-18.49,-8.74,-88.70:97.43
+chr1	540378	.	T	C	1.66	PASS	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=10.44;MQ0=61;OQ=250.82;QD=2.82;SB=-10.00	GT:AD:DP:GL:GQ	0/1:69,20:17:-33.49,-5.12,-26.69:99
+chr1	543605	.	G	A	0.71	PASS	AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=19.26;MQ0=44;OQ=534.14;QD=4.38;SB=-165.55	GT:AD:DP:GL:GQ	0/1:95,27:72:-78.41,-21.71,-168.45:99
+chr1	544671	rs4120954	G	A	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=1;HaplotypeScore=17.61;MQ=20.21;MQ0=40;OQ=184.77;QD=1.55;SB=-112.49	GT:AD:DP:GL:GQ	0/1:103,16:61:-40.15,-18.39,-172.29:99
+chr1	549231	.	A	G	0.07	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=20.37;MQ0=37;OQ=179.14;QD=2.21;SB=30.55	GT:AD:DP:GL:GQ	0/1:67,14:40:-33.25,-12.05,-121.81:99
+chr1	549235	.	C	G	0.42	PASS	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=3.80;MQ=21.34;MQ0=35;OQ=329.96;QD=4.12;SB=-9.65	GT:AD:DP:GL:GQ	0/1:65,15:43:-49.24,-12.96,-142.49:99
+chr1	549756	.	G	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=4.27;MQ=22.29;MQ0=22;OQ=255.07;QD=4.40;SB=-111.11	GT:AD:DP:GL:GQ	0/1:45,13:33:-38.73,-9.94,-83.62:99
+chr1	551019	.	T	G	0.10	PASS	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=26.98;MQ0=20;OQ=197.80;QD=2.50;SB=4.26	GT:AD:DP:GL:GQ	0/1:67,12:53:-39.03,-15.96,-159.29:99
+chr1	551526	rs3908981	C	A	0.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=9.51;MQ0=72;OQ=83.63;QD=0.93;SB=-10.00	GT:AD:DP:GL:GQ	0/1:72,18:8:-14.06,-2.41,-15.23:99
+chr1	552065	.	T	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=19.90;MQ0=42;OQ=77.24;QD=1.04;SB=-15.93	GT:AD:DP:GL:GQ	0/1:68,6:22:-17.64,-6.63,-61.21:99
+chr1	553226	.	C	T	0.19	PASS	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=3;HaplotypeScore=1.62;MQ=24.97;MQ0=44;OQ=605.74;QD=6.51;SB=-203.18	GT:AD:DP:GL:GQ	0/1:67,26:42:-76.51,-12.65,-84.24:99
+chr1	553488	.	T	C	0.79	PASS	AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=309.81;QD=34.42;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,9:9:-34.57,-2.71,-0.00:27.09
+chr1	555282	rs55668158	C	G	1.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=7.94;MQ=40.12;MQ0=17;OQ=1152.38;QD=10.38;SB=-595.15	GT:AD:DP:GL:GQ	0/1:77,33:92:-146.24,-27.72,-249.40:99
+chr1	555454	rs7416152	C	T	0.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=134;Dels=0.00;HRun=0;HaplotypeScore=6.80;MQ=46.34;MQ0=10;OQ=133.21;QD=0.99;SB=31.52	GT:AD:DP:GL:GQ	0/1:100,33:107:-48.84,-32.23,-339.95:99
+chr1	555839	rs9283151	C	T	3.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=45.60;MQ0=9;OQ=549.78;QD=4.07;SB=-291.62	GT:AD:DP:GL:GQ	0/1:100,35:123:-95.32,-37.06,-353.94:99
+chr1	555911	rs6421780	G	A	0.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=11.39;MQ=39.59;MQ0=14;OQ=584.19;QD=4.56;SB=-299.10	GT:AD:DP:GL:GQ	0/1:90,32:104:-93.03,-31.32,-293.74:99
+chr1	557751	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=2961;Dels=0.00;HRun=2;HaplotypeScore=55.38;MQ=12.90;MQ0=2051;OQ=15633.32;QD=5.28;SB=59.42	GT:AD:DP:GL:GQ	0/1:109,2851:490:-1562.33,-147.66,-305.00:99
+chr1	558077	.	C	T	9.05	PASS	AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=3.52;MQ=45.73;MQ0=8;OQ=1080.95;QD=8.72;SB=-436.58	GT:AD:DP:GL:GQ	0/1:87,37:109:-144.24,-32.87,-230.68:99
+chr1	559290	rs55665739	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=606;Dels=0.00;HRun=3;HaplotypeScore=17.31;MQ=15.96;MQ0=469;OQ=1033.33;QD=1.71;SB=-487.92	GT:AD:DP:GL:GQ	0/1:561,45:103:-137.67,-31.06,-222.34:99
+chr1	559575	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=286;Dels=0.00;HRun=0;HaplotypeScore=67.59;MQ=29.40;MQ0=143;OQ=1081.89;QD=3.78;SB=-504.88	GT:AD:DP:GL:GQ	0/1:248,38:131:-150.96,-39.49,-301.87:99
+chr1	560501	rs3912527	T	C	0.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=42.53;MQ0=1;OQ=256.32;QD=2.44;SB=101.36	GT:AD:DP:GL:GQ	0/1:81,24:98:-58.45,-29.53,-320.39:99
+chr1	561486	rs4951848	T	G	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.00;HRun=3;HaplotypeScore=1.10;MQ=14.41;MQ0=91;OQ=408.98;QD=3.27;SB=-10.00	GT:AD:DP:GL:GQ	0/1:75,49:28:-52.62,-8.43,-47.04:99
+chr1	561492	rs4951847	T	C	0.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=117;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=12.50;MQ0=93;OQ=266.80;QD=2.28;SB=-10.00	GT:AD:DP:GL:GQ	0/1:73,44:19:-35.69,-5.72,-37.10:99
+chr1	561756	rs4092521	C	A	0.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=234;Dels=0.00;HRun=0;HaplotypeScore=3.92;MQ=28.08;MQ0=93;OQ=133.54;QD=0.57;SB=-15.37	GT:AD:DP:GL:GQ	0/1:211,23:136:-57.61,-40.97,-421.13:99
+chr1	574427	rs4317776	G	T	26.75	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=197;Dels=0.00;HRun=9;HaplotypeScore=3.53;MQ=6.95;MQ0=179;QD=0.14;SB=-30.89	GT:AD:DP:GL:GQ	0/1:180,17:17:-11.08,-5.12,-48.02:59.57
+chr1	575363	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=0;HaplotypeScore=13.77;MQ=11.89;MQ0=66;OQ=93.79;QD=0.87;SB=-10.00	GT:AD:DP:GL:GQ	0/1:97,11:18:-18.09,-5.43,-51.57:99
+chr1	575571	.	A	G	44.95	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=5.95;MQ=12.50;MQ0=35;QD=0.49;SB=-7.00	GT:AD:DP:GL:GQ	0/1:88,3:9:-10.49,-2.71,-23.69:77.78
+chr1	575656	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=0;HaplotypeScore=17.86;MQ=21.34;MQ0=33;OQ=102.29;QD=0.86;SB=-15.11	GT:AD:DP:GL:GQ	0/1:101,18:60:-31.59,-18.08,-183.63:99
+chr1	577203	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=2;HaplotypeScore=18.06;MQ=18.60;MQ0=50;OQ=68.56;QD=0.90;SB=-15.46	GT:AD:DP:GL:GQ	0/1:71,5:16:-14.96,-4.82,-42.28:99
+chr1	578945	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=108;Dels=0.01;HRun=3;HaplotypeScore=26.60;MQ=35.12;MQ0=11;OQ=422.46;QD=3.91;SB=-212.09	GT:AD:DP:GL:GQ	0/1:86,21:88:-72.04,-26.51,-252.61:99
+chr1	581862	rs428603	C	T	12.84	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=117;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=16.17;MQ0=62;QD=0.11;SB=5.04	GT:AD:DP:GL:GQ	0/1:112,5:25:-12.07,-7.53,-76.64:45.44
+chr1	582131	rs2808300	G	T	0.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=133;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=20.19;MQ0=60;OQ=103.03;QD=0.77;SB=74.25	GT:AD:DP:GL:GQ	0/1:113,20:71:-34.97,-21.38,-223.52:99
+chr1	590341	.	G	A	2.32	PASS	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=4.02;MQ=31.66;MQ0=1;OQ=697.92;QD=5.91;SB=-148.83	GT:AD:DP:GL:GQ	0/1:88,30:101:-103.52,-30.45,-248.69:99
+chr1	591004	.	C	T	96.57	PASS	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=34.15;MQ0=0;OQ=697.04;QD=7.58;SB=-276.23	GT:AD:DP:GL:GQ	0/1:66,26:89:-99.83,-26.84,-204.19:99
+chr1	591498	rs2531322	C	A	0.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=129;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=32.80;MQ0=0;OQ=356.51;QD=2.76;SB=131.06	GT:AD:DP:GL:GQ	0/1:108,21:125:-76.61,-37.67,-331.80:99
+chr1	592316	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=5.89;MQ=8.09;MQ0=42;OQ=58.17;QD=0.88;SB=-10.00	GT:AD:DP:GL:GQ	0/1:52,12:5:-10.61,-1.51,-6.31:48.04
+chr1	592508	rs2686868	C	T	15.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=1;HaplotypeScore=3.16;MQ=34.52;MQ0=0;OQ=1500.76;QD=12.61;SB=-645.23	GT:AD:DP:GL:GQ	0/1:71,48:113:-187.40,-34.04,-240.50:99
+chr1	616184	rs2808330	A	G	13.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.61;MQ0=5;OQ=348.18;QD=3.38;SB=86.31	GT:AD:DP:GL:GQ	0/1:75,28:95:-66.73,-28.63,-299.16:99
+chr1	625884	rs3857304	G	A	2.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=6.38;MQ0=48;OQ=115.97;QD=2.23;SB=-51.67	GT:AD:DP:GL:GQ	1/1:47,5:4:-15.13,-1.21,-0.00:12.03
+chr1	625907	rs4030160	G	A	213.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=11.50;MQ0=27;OQ=320.38;QD=8.90;SB=-93.34	GT:AD:DP:GL:GQ	1/1:25,11:9:-35.62,-2.71,-0.00:27.09
+chr1	625979	rs3871845	G	C	249.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=11.96;MQ0=27;OQ=358.10;QD=9.68;SB=-129.40	GT:AD:DP:GL:GQ	1/1:26,11:9:-39.40,-2.71,-0.00:27.09
+chr1	626181	rs3873089	G	A	177.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.43;MQ0=3;OQ=376.84;QD=28.99;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,13:10:-41.27,-3.01,-0.00:30.10
+chr1	638976	.	C	T	0.12	PASS	AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=4.06;MQ=23.85;MQ0=8;OQ=648.49;QD=24.02;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,27:17:-68.44,-5.12,-0.00:51.17
+chr1	640686	.	A	G	25.04	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=6.84;MQ0=102;QD=0.23;SB=-10.00	GT:AD:DP:GL:GQ	0/1:98,10:6:-7.60,-1.81,-15.47:57.87
+chr1	641012	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=157;Dels=0.00;HRun=1;HaplotypeScore=5.72;MQ=12.45;MQ0=138;OQ=282.66;QD=1.80;SB=-113.62	GT:AD:DP:GL:GQ	0/1:142,15:18:-36.97,-5.42,-32.71:99
+chr1	647651	.	G	C	91.46	PASS	AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=15.14;MQ0=31;OQ=441.56;QD=9.39;SB=-238.61	GT:AD:DP:GL:GQ	1/1:28,19:11:-47.74,-3.31,-0.00:33.11
+chr1	652720	rs62639125	G	A	47.02	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=8.82;MQ0=19;QD=1.42;SB=-10.00	GT:AD:DP:GL:GQ	1/1:13,20:2:-8.11,-0.60,-0.00:6.02
+chr1	652960	rs61769340	G	C	105.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=20.58;MQ0=11;OQ=1522.59;QD=27.68;SB=-684.47	GT:AD:DP:GL:GQ	1/1:10,45:39:-155.88,-11.77,-0.03:99
+chr1	656406	.	G	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=11.93;MQ0=83;OQ=127.34;QD=1.14;SB=-0.98	GT:AD:DP:GL:GQ	0/1:95,17:17:-21.14,-5.12,-45.67:99
+chr1	662072	.	G	A	11.72	PASS	AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=4.71;MQ=27.50;MQ0=7;OQ=1481.48;QD=11.06;SB=-511.41	GT:AD:DP:GL:GQ	0/1:80,54:118:-187.00,-35.57,-233.79:99
+chr1	662535	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=1;HaplotypeScore=4.63;MQ=12.94;MQ0=86;OQ=221.86;QD=1.71;SB=-10.00	GT:AD:DP:GL:GQ	0/1:117,13:31:-34.81,-9.34,-77.61:99
+chr1	664297	.	A	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=1;HaplotypeScore=8.91;MQ=25.89;MQ0=44;OQ=139.99;QD=0.72;SB=29.32	GT:AD:DP:GL:GQ	0/1:135,59:118:-52.83,-35.54,-396.03:99
+chr1	664319	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=197;Dels=0.00;HRun=1;HaplotypeScore=4.98;MQ=25.84;MQ0=39;OQ=562.89;QD=2.86;SB=-70.36	GT:AD:DP:GL:GQ	0/1:152,44:131:-101.81,-42.24,-385.33:99
+chr1	665009	.	G	A	0.15	PASS	AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=7.66;MQ=13.29;MQ0=30;OQ=394.21;QD=6.36;SB=-10.00	GT:AD:DP:GL:GQ	1/1:20,42:11:-43.01,-3.32,-0.01:33.10
+chr1	665981	.	C	T	314.88	PASS	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.49;MQ0=9;OQ=1228.86;QD=15.36;SB=-521.03	GT:AD:DP:GL:GQ	0/1:42,38:68:-146.65,-20.48,-114.04:99
+chr1	678857	.	T	C	37.39	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=9.96;MQ0=52;QD=0.58;SB=-41.94	GT:AD:DP:GL:GQ	0/1:58,5:10:-10.04,-3.02,-24.70:70.23
+chr1	681407	.	T	A	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;HRun=13;HaplotypeScore=8.39;MQ=28.14;MQ0=23;OQ=991.49;QD=17.71;SB=-487.41	GT:AD:DP:GL:GQ	1/1:17,39:33:-109.19,-9.95,-6.46:34.91
+chr1	681927	.	C	G	40.97	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=4.89;MQ=4.61;MQ0=72;QD=0.54;SB=-10.00	GT:AD:DP:GL:GQ	0/1:72,2:3:-8.29,-0.90,-4.05:31.44
+chr1	684740	rs1829739	A	C	31.20	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=3;HaplotypeScore=24.15;MQ=12.41;MQ0=41;QD=0.60;SB=-34.97	GT:AD:DP:GL:GQ	0/1:47,5:9:-9.12,-2.71,-21.21:64.03
+chr1	684742	.	C	A	14.57	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=37.61;MQ=12.41;MQ0=41;QD=0.28;SB=-31.35	GT:AD:DP:GL:GQ	0/1:46,6:9:-7.44,-2.71,-24.53:47.25
+chr1	684781	.	C	T	48.14	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.66;MQ=4.69;MQ0=46;QD=1.00;SB=-49.56	GT:AD:DP:GL:GQ	1/1:40,8:2:-8.22,-0.60,-0.00:6.02
+chr1	684978	.	A	T	38.37	PASS	AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.29;MQ0=2;OQ=86.08;QD=14.35;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,6:3:-12.10,-0.90,-0.00:9.03
+chr1	690691	rs6685320	T	A	0.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=41.41;MQ0=1;OQ=71.22;QD=0.76;SB=149.48	GT:AD:DP:GL:GQ	0/1:83,11:90:-37.51,-27.11,-298.94:99
+chr1	692785	.	C	T	0.89	PASS	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=27.63;MQ0=14;OQ=282.72;QD=2.30;SB=-80.41	GT:AD:DP:GL:GQ	0/1:107,16:98:-61.07,-29.52,-300.46:99
+chr1	692834	.	C	T	2.02	PASS	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=26.70;MQ0=10;OQ=722.71;QD=6.12;SB=-381.76	GT:AD:DP:GL:GQ	0/1:89,29:108:-108.08,-32.53,-294.03:99
+chr1	692878	rs12124557	G	C	71.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.28;MQ0=34;OQ=350.61;QD=4.61;SB=-168.38	GT:AD:DP:GL:GQ	0/1:61,15:41:-50.70,-12.35,-126.27:99
+chr1	694230	rs9727436	T	C	8.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=32.48;MQ0=2;OQ=333.56;QD=17.56;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,18:12:-36.95,-3.62,-0.01:36.08
+chr1	695745	.	G	A	102.02	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=41.82;MQ0=0;OQ=1169.68;QD=16.02;SB=-501.47	GT:AD:DP:GL:GQ	0/1:36,37:71:-141.66,-21.41,-112.07:99
+chr1	696231	rs12029736	A	G	92.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=39.21;MQ0=1;OQ=1205.31;QD=20.78;SB=-587.73	GT:AD:DP:GL:GQ	0/1:5,53:49:-138.60,-14.79,-16.39:15.94
+chr1	696641	.	G	A	0.05	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=11.92;MQ=21.76;MQ0=28;OQ=1527.01;QD=18.18;SB=-47.56	GT:AD:DP:GL:GQ	1/1:26,58:39:-156.30,-11.75,-0.02:99
+chr1	704290	rs12028261	G	A	67.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.14;MQ=38.97;MQ0=0;OQ=1407.21;QD=35.18;SB=-656.37	GT:AD:DP:GL:GQ	1/1:0,40:36:-144.32,-10.85,-0.01:99
+chr1	705211	rs3131984	T	G	181.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=48.59;MQ0=0;OQ=1797.71;QD=32.69;SB=-808.10	GT:AD:DP:GL:GQ	1/1:0,55:52:-183.37,-15.66,-0.02:99
+chr1	705859	rs4614203	A	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=9;HaplotypeScore=9.09;MQ=20.66;MQ0=19;OQ=690.18;QD=13.80;SB=-46.39	GT:AD:DP:GL:GQ	1/1:1,48:20:-72.61,-6.03,-0.01:60.18
+chr1	708249	rs10900602	A	G	1.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.93;MQ=25.93;MQ0=21;OQ=1118.18;QD=17.47;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,63:38:-115.46,-11.48,-0.05:99
+chr1	708418	rs10751453	T	C	415.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.69;MQ0=5;OQ=1667.51;QD=27.79;SB=-566.12	GT:AD:DP:GL:GQ	1/1:4,56:54:-174.43,-16.28,-4.09:99
+chr1	710103	rs3121393	T	C	439.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.62;MQ0=19;OQ=1791.16;QD=20.59;SB=-717.22	GT:AD:DP:GL:GQ	1/1:0,87:51:-182.72,-15.36,-0.02:99
+chr1	710660	rs3115846	G	A	23.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=0.95;MQ=32.94;MQ0=7;OQ=1843.21;QD=32.91;SB=-738.02	GT:AD:DP:GL:GQ	1/1:0,56:47:-187.92,-14.16,-0.01:99
+chr1	713754	rs2977670	G	C	680.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.16;MQ0=0;OQ=1954.35;QD=36.87;SB=-819.16	GT:AD:DP:GL:GQ	1/1:0,53:49:-199.05,-14.78,-0.03:99
+chr1	714052	.	G	A	38.81	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=1;HaplotypeScore=27.06;MQ=47.82;MQ0=13;QD=0.40;SB=-19.66	GT:AD:DP:GL:GQ	0/1:88,9:69:-27.95,-20.79,-220.66:71.64
+chr1	714724	rs12123401	G	A	77.21	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=38.16;MQ=32.18;MQ0=19;QD=1.19;SB=53.18	GT:AD:DP:GL:GQ	0/1:50,14:32:-20.64,-9.64,-97.41:99
+chr1	714732	rs12735556	C	A	597.50	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=35.96;MQ=32.37;MQ0=15;QD=9.34;SB=-186.20	GT:AD:DP:GL:GQ	0/1:31,30:31:-72.37,-9.34,-42.36:99
+chr1	714734	rs12735557	C	G	606.51	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=32.96;MQ=32.01;MQ0=15;QD=9.48;SB=-232.37	GT:AD:DP:GL:GQ	0/1:31,33:32:-73.58,-9.64,-63.94:99
+chr1	714811	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=1;HaplotypeScore=105.18;MQ=32.80;MQ0=13;OQ=394.82;QD=4.11;SB=-25.79	GT:AD:DP:GL:GQ	0/1:48,48:42:-55.42,-12.65,-93.88:99
+chr1	714830	.	G	A	44.58	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=2;HaplotypeScore=123.02;MQ=32.55;MQ0=17;QD=0.46;SB=2.03	GT:AD:DP:GL:GQ	0/1:60,27:26:-15.57,-7.83,-82.81:77.42
+chr1	714865	.	G	A	118.87	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=2;HaplotypeScore=72.07;MQ=36.16;MQ0=17;QD=1.19;SB=45.52	GT:AD:DP:GL:GQ	0/1:83,11:39:-26.94,-11.77,-99.77:99
+chr1	714869	.	G	A	210.22	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=70.54;MQ=36.82;MQ0=18;QD=2.08;SB=89.30	GT:AD:DP:GL:GQ	0/1:78,22:52:-39.97,-15.66,-154.79:99
+chr1	714870	.	G	C	132.10	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=64.77;MQ=36.96;MQ0=18;QD=1.33;SB=86.32	GT:AD:DP:GL:GQ	0/1:81,18:51:-31.86,-15.37,-195.72:99
+chr1	714885	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=11.63;MQ=42.34;MQ0=19;OQ=59.67;QD=0.80;SB=57.28	GT:AD:DP:GL:GQ	0/1:59,16:42:-21.91,-12.66,-130.29:92.50
+chr1	714965	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=93;Dels=0.06;HRun=0;HaplotypeScore=109.90;MQ=37.50;MQ0=15;OQ=104.38;QD=1.12;SB=93.07	GT:AD:DP:GL:GQ	0/1:76,7:50:-34.61,-20.89,-189.48:99
+chr1	714987	.	A	T	75.82	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=80;Dels=0.03;HRun=1;HaplotypeScore=85.54;MQ=37.34;MQ0=12;QD=0.95;SB=77.28	GT:AD:DP:GL:GQ	0/1:70,6:44:-26.77,-15.90,-141.85:99
+chr1	714990	.	A	G	169.75	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=75;Dels=0.04;HRun=1;HaplotypeScore=76.84;MQ=38.08;MQ0=11;QD=2.26;SB=1.07	GT:AD:DP:GL:GQ	0/1:50,19:44:-36.22,-15.96,-136.58:99
+chr1	714991	.	A	G	49.83	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=75;Dels=0.01;HRun=0;HaplotypeScore=63.75;MQ=38.08;MQ0=11;QD=0.66;SB=86.30	GT:AD:DP:GL:GQ	0/1:68,6:44:-21.52,-13.26,-154.68:82.67
+chr1	714995	.	C	A	39.02	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=2;HaplotypeScore=68.11;MQ=38.07;MQ0=12;QD=0.54;SB=48.86	GT:AD:DP:GL:GQ	0/1:52,10:39:-31.66,-24.48,-125.33:71.86
+chr1	715012	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=28.31;MQ=43.81;MQ0=11;OQ=81.07;QD=1.33;SB=77.26	GT:AD:DP:GL:GQ	0/1:50,6:42:-27.43,-16.04,-129.03:99
+chr1	715014	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=28.31;MQ=44.76;MQ0=10;OQ=135.00;QD=2.29;SB=80.30	GT:AD:DP:GL:GQ	0/1:48,10:43:-29.74,-12.96,-149.46:99
+chr1	715704	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=1;HaplotypeScore=25.25;MQ=54.80;MQ0=2;OQ=145.06;QD=1.23;SB=-43.38	GT:AD:DP:GL:GQ	0/1:97,21:107:-50.01,-32.22,-342.89:99
+chr1	716048	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=178;Dels=0.00;HRun=1;HaplotypeScore=18.47;MQ=39.54;MQ0=8;OQ=52.50;QD=0.29;SB=34.27	GT:AD:DP:GL:GQ	0/1:78,99:81:-32.94,-24.40,-274.16:85.34
+chr1	716061	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=0;HaplotypeScore=21.67;MQ=39.51;MQ0=6;OQ=115.15;QD=0.62;SB=43.85	GT:AD:DP:GL:GQ	0/1:135,49:85:-40.41,-25.61,-331.38:99
+chr1	716222	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=2;HaplotypeScore=139.36;MQ=31.95;MQ0=27;OQ=92.92;QD=0.79;SB=-50.76	GT:AD:DP:GL:GQ	0/1:103,13:47:-26.73,-14.16,-149.22:99
+chr1	716344	rs3131980	T	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=39.71;MQ=55.45;MQ0=6;OQ=2415.81;QD=31.79;SB=-1086.51	GT:AD:DP:GL:GQ	1/1:2,74:68:-245.18,-20.48,-0.02:99
+chr1	716802	rs4520358	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=160;Dels=0.00;HRun=0;HaplotypeScore=127.95;MQ=28.01;MQ0=48;OQ=1542.52;QD=9.64;SB=-717.92	GT:AD:DP:GL:GQ	0/1:109,49:76:-180.46,-22.93,-134.20:99
+chr1	716807	rs3131979	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.00;HRun=1;HaplotypeScore=146.45;MQ=27.53;MQ0=52;OQ=2520.74;QD=14.92;SB=-1257.54	GT:AD:DP:GL:GQ	0/1:69,89:79:-286.20,-30.85,-56.55:99
+chr1	717392	.	A	G	3.52	PASS	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.37;MQ=24.74;MQ0=13;OQ=554.36;QD=8.66;SB=-175.95	GT:AD:DP:GL:GQ	0/1:36,28:38:-70.17,-11.45,-77.18:99
+chr1	717776	.	A	G	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=36.84;MQ0=8;OQ=198.21;QD=1.82;SB=-48.31	GT:AD:DP:GL:GQ	0/1:82,26:93:-51.12,-28.02,-315.62:99
+chr1	717825	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=45.12;MQ0=3;OQ=93.24;QD=0.90;SB=-41.95	GT:AD:DP:GL:GQ	0/1:87,17:97:-41.83,-29.22,-341.26:99
+chr1	718022	rs3131978	C	T	227.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.78;MQ0=12;OQ=2206.38;QD=27.93;SB=-528.20	GT:AD:DP:GL:GQ	1/1:0,79:55:-224.24,-16.57,-0.01:99
+chr1	718105	rs3131977	C	G	701.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.42;MQ0=9;OQ=2564.24;QD=33.30;SB=-886.52	GT:AD:DP:GL:GQ	1/1:0,77:61:-260.03,-18.38,-0.02:99
+chr1	718468	rs2977661	C	A	0.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=44.88;MQ0=1;OQ=306.65;QD=3.13;SB=125.41	GT:AD:DP:GL:GQ	0/1:81,17:92:-61.67,-27.72,-254.10:99
+chr1	719542	rs4951859	C	G	20.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=0.73;MQ=51.87;MQ0=0;OQ=2314.11;QD=40.60;SB=-1158.05	GT:AD:DP:GL:GQ	1/1:0,57:55:-235.02,-16.58,-0.02:99
+chr1	722635	.	G	A	178.90	PASS	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.65;MQ0=17;OQ=703.25;QD=9.38;SB=-329.31	GT:AD:DP:GL:GQ	0/1:40,35:48:-88.07,-14.46,-95.92:99
+chr1	723861	rs3094321	C	T	2.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=4.03;MQ=14.10;MQ0=13;OQ=171.30;QD=5.53;SB=-52.67	GT:AD:DP:GL:GQ	1/1:0,31:5:-20.69,-1.51,-0.00:15.05
+chr1	723905	rs3115866	G	A	435.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.45;MQ0=11;OQ=1488.74;QD=31.02;SB=-417.55	GT:AD:DP:GL:GQ	1/1:0,48:37:-152.47,-11.14,-0.01:99
+chr1	724152	rs2427932	G	A	28.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=40.65;MQ0=10;OQ=544.36;QD=7.78;SB=29.11	GT:AD:DP:GL:GQ	0/1:46,24:57:-74.91,-17.19,-123.40:99
+chr1	724325	rs12564807	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.02;HRun=14;HaplotypeScore=12.95;MQ=25.23;MQ0=25;OQ=486.84;QD=10.36;SB=-195.27	GT:AD:DP:GL:GQ	0/1:7,39:20:-57.99,-6.03,-17.33:99
+chr1	724354	rs7518433	T	C	213.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=16.24;MQ0=8;OQ=108.50;QD=7.23;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,15:4:-14.38,-1.21,-0.00:12.04
+chr1	724429	.	G	A	5.67	PASS	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=39.71;MQ0=12;OQ=1919.08;QD=16.26;SB=-856.39	GT:AD:DP:GL:GQ	0/1:56,62:102:-225.91,-30.72,-172.49:99
+chr1	724483	rs2427930	A	G	156.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=45.92;MQ0=8;OQ=1015.40;QD=8.46;SB=-368.74	GT:AD:DP:GL:GQ	0/1:73,47:110:-137.96,-33.13,-289.42:99
+chr1	724814	rs61770166	A	G	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.01;HRun=0;HaplotypeScore=8.00;MQ=38.81;MQ0=11;OQ=57.16;QD=0.57;SB=101.37	GT:AD:DP:GL:GQ	0/1:74,25:85:-34.30,-25.30,-302.54:90
+chr1	725289	rs10900603	G	A	319.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.84;MQ0=12;OQ=1308.47;QD=22.56;SB=-614.32	GT:AD:DP:GL:GQ	1/1:0,58:33:-134.44,-9.94,-0.01:99
+chr1	727603	rs3893479	G	A	3.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=20.83;MQ0=35;OQ=241.46;QD=3.71;SB=-122.11	GT:AD:DP:GL:GQ	0/1:49,15:27:-35.56,-8.14,-65.14:99
+chr1	729005	rs2340527	T	A	17.56	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=11;HaplotypeScore=0.00;MQ=42.93;MQ0=12;QD=0.18;SB=2.25	GT:AD:DP:GL:GQ	0/1:70,25:68:-25.52,-20.49,-222.57:50.31
+chr1	729073	rs2427917	A	G	0.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=3;HaplotypeScore=1.32;MQ=36.83;MQ0=11;OQ=1725.34;QD=25.00;SB=-386.59	GT:AD:DP:GL:GQ	1/1:8,61:54:-180.20,-16.27,-4.08:99
+chr1	729289	rs3131973	A	G	242.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.01;MQ0=22;OQ=768.10;QD=13.48;SB=-48.96	GT:AD:DP:GL:GQ	1/1:0,57:23:-80.40,-6.93,-0.01:69.20
+chr1	729391	rs3094317	G	A	25.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=29.31;MQ0=14;OQ=1050.45;QD=23.87;SB=-501.02	GT:AD:DP:GL:GQ	1/1:0,44:27:-108.64,-8.13,-0.01:81.26
+chr1	731442	rs3115865	T	C	10.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=14.78;MQ0=18;OQ=257.65;QD=3.79;SB=-147.73	GT:AD:DP:GL:GQ	1/1:0,68:9:-29.35,-2.71,-0.01:27.07
+chr1	732688	.	A	G	132.94	PASS	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=40.79;MQ0=0;OQ=1231.30;QD=15.02;SB=-638.22	GT:AD:DP:GL:GQ	0/1:40,42:81:-150.81,-24.40,-157.55:99
+chr1	732884	rs2488925	T	C	45.12	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=12.78;MQ0=54;QD=0.47;SB=-0.97	GT:AD:DP:GL:GQ	0/1:72,25:9:-10.51,-2.71,-24.07:77.96
+chr1	732935	rs2488505	C	A	405.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=25.42;MQ0=21;OQ=984.68;QD=12.62;SB=-456.35	GT:AD:DP:GL:GQ	1/1:10,68:28:-102.06,-8.43,-0.01:84.26
+chr1	734986	rs61823337	A	C	21.52	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=121;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=22.23;MQ0=45;QD=0.18;SB=23.10	GT:AD:DP:GL:GQ	0/1:104,17:71:-26.81,-21.38,-234.10:54.33
+chr1	735210	rs2488501	T	C	0.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=117;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=29.20;MQ0=16;OQ=204.37;QD=1.75;SB=-126.97	GT:AD:DP:GL:GQ	0/1:101,16:100:-53.85,-30.13,-340.21:99
+chr1	736231	rs3925106	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=38.77;MQ0=4;OQ=87.62;QD=1.33;SB=28.85	GT:AD:DP:GL:GQ	0/1:58,8:62:-30.72,-18.67,-192.09:99
+chr1	736257	rs28622890	G	A	34.58	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=41.58;MQ0=5;QD=0.43;SB=53.57	GT:AD:DP:GL:GQ	0/1:73,8:73:-28.75,-22.01,-217.76:67.42
+chr1	737271	rs2427896	G	A	1.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.89;MQ0=27;OQ=95.91;QD=0.96;SB=26.10	GT:AD:DP:GL:GQ	0/1:78,22:62:-31.55,-18.68,-198.47:99
+chr1	737583	rs2488922	A	G	0.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=42.10;MQ0=2;OQ=266.56;QD=2.17;SB=-121.05	GT:AD:DP:GL:GQ	0/1:92,31:105:-61.60,-31.66,-333.56:99
+chr1	738741	rs2519043	G	T	42.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=26.82;MQ0=11;OQ=2109.65;QD=29.30;SB=-875.26	GT:AD:DP:GL:GQ	1/1:7,65:57:-214.56,-17.17,-0.01:99
+chr1	739128	rs2519041	G	A	43.02	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=8.37;MQ0=49;QD=0.61;SB=-10.00	GT:AD:DP:GL:GQ	1/1:19,51:2:-7.71,-0.60,-0.00:6.02
+chr1	739546	rs12184332	C	T	184.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=12.22;MQ0=29;OQ=412.05;QD=9.81;SB=-172.22	GT:AD:DP:GL:GQ	1/1:0,15:11:-44.79,-3.31,-0.00:33.11
+chr1	739719	rs12409679	C	T	476.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.16;MQ0=31;OQ=1249.90;QD=19.53;SB=-559.74	GT:AD:DP:GL:GQ	1/1:9,55:32:-128.58,-9.64,-0.01:96.31
+chr1	739852	rs12409693	C	T	32.23	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=4;HaplotypeScore=0.83;MQ=11.24;MQ0=16;QD=1.29;SB=-3.98	GT:AD:DP:GL:GQ	0/1:9,16:4:-7.71,-1.20,-7.59:63.88
+chr1	739860	rs12410209	A	G	6.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=11.03;MQ0=14;OQ=69.01;QD=3.14;SB=-6.99	GT:AD:DP:GL:GQ	0/1:7,15:4:-11.39,-1.20,-4.06:28.52
+chr1	742429	rs3094315	G	A	709.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.17;MQ0=0;OQ=3081.43;QD=40.02;SB=-1319.35	GT:AD:DP:GL:GQ	1/1:0,77:77:-311.75,-23.19,-0.02:99
+chr1	742584	rs3131972	A	G	25.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=3;HaplotypeScore=0.95;MQ=43.52;MQ0=0;OQ=2970.98;QD=35.37;SB=-1399.49	GT:AD:DP:GL:GQ	1/1:0,84:83:-300.71,-25.00,-0.02:99
+chr1	742757	rs3131971	T	C	41.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.21;MQ=23.17;MQ0=17;OQ=516.07;QD=12.59;SB=-10.00	GT:AD:DP:GL:GQ	1/1:4,37:19:-55.23,-5.74,-0.04:57.08
+chr1	743132	rs3115861	C	G	14.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=27.06;MQ0=17;OQ=1234.23;QD=26.26;SB=-15.29	GT:AD:DP:GL:GQ	1/1:0,46:29:-129.86,-11.46,-2.85:86.17
+chr1	743268	rs3115860	C	A	75.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.75;MQ0=7;OQ=486.16;QD=22.10;SB=-153.55	GT:AD:DP:GL:GQ	1/1:0,22:14:-52.20,-4.22,-0.00:42.13
+chr1	743288	rs3131970	T	C	362.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.31;MQ0=12;OQ=231.44;QD=11.57;SB=-100.85	GT:AD:DP:GL:GQ	1/1:0,20:8:-26.73,-2.41,-0.01:24.06
+chr1	743337	rs2073814	C	G	1.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=4;HaplotypeScore=1.47;MQ=27.30;MQ0=10;OQ=1125.84;QD=30.43;SB=-429.30	GT:AD:DP:GL:GQ	1/1:1,36:27:-116.18,-8.13,-0.01:81.27
+chr1	743712	rs56101360	G	T	37.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=10.96;MQ0=18;OQ=73.40;QD=3.50;SB=-44.39	GT:AD:DP:GL:GQ	1/1:0,21:3:-10.83,-0.90,-0.00:9.03
+chr1	744045	rs3131969	A	G	233.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.14;MQ0=6;OQ=1104.31;QD=23.50;SB=-502.19	GT:AD:DP:GL:GQ	1/1:0,47:36:-114.05,-10.86,-0.03:99
+chr1	744055	rs3131968	A	G	489.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.65;MQ0=5;OQ=1245.81;QD=27.08;SB=-566.90	GT:AD:DP:GL:GQ	1/1:0,46:40:-128.20,-12.07,-0.04:99
+chr1	744197	rs3131967	T	C	119.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=53.80;MQ0=2;OQ=2119.16;QD=28.26;SB=-841.48	GT:AD:DP:GL:GQ	1/1:1,74:67:-215.56,-20.21,-0.06:99
+chr1	744366	rs3115859	G	A	143.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.48;MQ0=0;OQ=2152.98;QD=37.77;SB=-958.79	GT:AD:DP:GL:GQ	1/1:0,55:55:-218.90,-16.57,-0.02:99
+chr1	744827	rs3131966	C	T	120.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=47.82;MQ0=1;OQ=2882.74;QD=38.96;SB=-1406.06	GT:AD:DP:GL:GQ	1/1:1,73:72:-291.88,-21.69,-0.02:99
+chr1	745638	rs3131965	A	G	37.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.96;MQ=59.56;MQ0=0;OQ=1308.09;QD=25.16;SB=-645.91	GT:AD:DP:GL:GQ	1/1:2,50:45:-138.61,-13.58,-4.21:93.63
+chr1	745750	rs3131964	C	G	3.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=53.42;MQ0=0;OQ=1959.71;QD=42.60;SB=-541.05	GT:AD:DP:GL:GQ	1/1:0,46:45:-199.57,-13.56,-0.01:99
+chr1	745753	rs3115858	A	T	53.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=52.51;MQ0=0;OQ=1749.78;QD=37.23;SB=-548.77	GT:AD:DP:GL:GQ	1/1:0,47:47:-178.57,-14.15,-0.01:99
+chr1	745791	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=2;HaplotypeScore=18.24;MQ=43.86;MQ0=9;OQ=50.05;QD=0.65;SB=68.26	GT:AD:DP:GL:GQ	0/1:71,6:65:-27.87,-19.59,-256.05:82.88
+chr1	745803	rs3115857	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=56.59;MQ=40.14;MQ0=10;OQ=1678.77;QD=22.69;SB=-752.72	GT:AD:DP:GL:GQ	0/1:24,50:53:-187.11,-15.98,-16.89:9.18
+chr1	745905	.	G	C	40.04	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=1;HaplotypeScore=109.46;MQ=39.52;MQ0=1;QD=0.47;SB=41.16	GT:AD:DP:GL:GQ	0/1:44,42:46:-21.15,-13.87,-174.52:72.88
+chr1	745926	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=1;HaplotypeScore=71.25;MQ=39.59;MQ0=1;OQ=190.93;QD=2.22;SB=53.16	GT:AD:DP:GL:GQ	0/1:47,39:55:-38.95,-16.57,-157.39:99
+chr1	745944	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=34.08;MQ=37.55;MQ0=2;OQ=183.15;QD=2.23;SB=41.15	GT:AD:DP:GL:GQ	0/1:68,13:63:-40.58,-18.98,-189.40:99
+chr1	745947	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=35.45;MQ=37.64;MQ0=2;OQ=144.60;QD=1.76;SB=41.13	GT:AD:DP:GL:GQ	0/1:61,21:63:-36.72,-18.98,-195.32:99
+chr1	745969	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=26.39;MQ=43.31;MQ0=1;OQ=191.12;QD=2.62;SB=65.24	GT:AD:DP:GL:GQ	0/1:56,17:62:-41.07,-18.68,-205.74:99
+chr1	745970	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=53.14;MQ=43.05;MQ0=1;OQ=181.87;QD=2.46;SB=65.22	GT:AD:DP:GL:GQ	0/1:57,13:62:-40.15,-18.68,-186.08:99
+chr1	746120	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=2;HaplotypeScore=45.83;MQ=41.92;MQ0=5;OQ=178.43;QD=2.66;SB=1.10	GT:AD:DP:GL:GQ	0/1:36,31:38:-32.58,-11.45,-99.35:99
+chr1	746127	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=64.18;MQ=39.79;MQ0=5;OQ=90.17;QD=1.29;SB=23.10	GT:AD:DP:GL:GQ	0/1:61,9:40:-24.35,-12.05,-113.93:99
+chr1	746131	rs12567639	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=86.22;MQ=40.15;MQ0=5;OQ=1193.97;QD=14.74;SB=-198.46	GT:AD:DP:GL:GQ	0/1:23,47:41:-137.40,-14.72,-24.14:94.15
+chr1	746140	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=67.36;MQ=39.96;MQ0=6;OQ=451.51;QD=4.47;SB=-226.37	GT:AD:DP:GL:GQ	0/1:64,37:56:-65.31,-16.87,-128.04:99
+chr1	746183	rs61768169	G	A	45.64	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=15.14;MQ=43.93;MQ0=4;QD=0.48;SB=0.06	GT:AD:DP:GL:GQ	0/1:84,10:80:-31.96,-24.11,-251.75:78.48
+chr1	746197	.	C	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=9.62;MQ=45.83;MQ0=2;OQ=266.46;QD=3.10;SB=-143.52	GT:AD:DP:GL:GQ	0/1:62,24:69:-50.72,-20.79,-191.84:99
+chr1	746210	.	C	G	29.36	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=1;HaplotypeScore=12.28;MQ=48.57;MQ0=1;QD=0.39;SB=83.30	GT:AD:DP:GL:GQ	0/1:61,15:60:-24.30,-18.08,-232.38:62.19
+chr1	746211	.	A	C	19.28	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=12.28;MQ=48.88;MQ0=1;QD=0.26;SB=56.68	GT:AD:DP:GL:GQ	0/1:55,20:60:-23.28,-18.07,-191.05:52.07
+chr1	746241	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=1;HaplotypeScore=37.04;MQ=43.41;MQ0=2;OQ=460.88;QD=4.90;SB=-102.94	GT:AD:DP:GL:GQ	0/1:66,28:77:-72.58,-23.21,-260.56:99
+chr1	746243	rs3131963	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=38.28;MQ=42.00;MQ0=2;OQ=2225.83;QD=20.61;SB=-986.67	GT:AD:DP:GL:GQ	0/1:37,71:77:-249.07,-23.20,-37.48:99
+chr1	746259	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=53.13;MQ=42.82;MQ0=2;OQ=115.63;QD=1.04;SB=-45.40	GT:AD:DP:GL:GQ	0/1:89,21:81:-39.28,-24.43,-223.64:99
+chr1	746271	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=0;HaplotypeScore=62.70;MQ=43.89;MQ0=1;OQ=73.67;QD=0.68;SB=-12.36	GT:AD:DP:GL:GQ	0/1:82,19:79:-37.12,-26.47,-271.48:99
+chr1	746467	rs3131962	A	G	256.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.92;MQ0=2;OQ=1247.82;QD=23.54;SB=-557.88	GT:AD:DP:GL:GQ	1/1:1,52:40:-128.40,-12.06,-0.04:99
+chr1	747503	rs3115853	G	A	25.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=3.30;MQ=58.23;MQ0=2;OQ=3098.30;QD=37.78;SB=-1549.56	GT:AD:DP:GL:GQ	1/1:0,81:79:-317.18,-27.31,-3.76:99
+chr1	747597	rs4951929	C	T	626.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=2652.10;QD=38.44;SB=-1324.28	GT:AD:DP:GL:GQ	1/1:0,69:67:-268.81,-20.18,-0.02:99
+chr1	747799	rs4951862	C	A	77.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=57.90;MQ0=0;OQ=1743.44;QD=32.90;SB=-442.30	GT:AD:DP:GL:GQ	1/1:0,53:51:-177.95,-15.36,-0.02:99
+chr1	748007	rs3131956	A	G	613.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=1973.59;QD=34.03;SB=-931.61	GT:AD:DP:GL:GQ	1/1:0,58:58:-200.97,-17.48,-0.03:99
+chr1	748187	rs3131955	T	C	137.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=57.23;MQ0=0;OQ=1684.65;QD=30.08;SB=-868.87	GT:AD:DP:GL:GQ	1/1:0,56:51:-172.08,-15.37,-0.03:99
+chr1	748489	rs3131954	C	T	606.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.38;MQ0=0;OQ=1957.02;QD=37.63;SB=-957.97	GT:AD:DP:GL:GQ	1/1:0,52:51:-199.31,-15.37,-0.02:99
+chr1	749563	rs3115852	T	C	295.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.43;MQ0=19;OQ=1638.73;QD=24.46;SB=-694.62	GT:AD:DP:GL:GQ	1/1:0,67:46:-167.47,-13.85,-0.01:99
+chr1	749700	rs3115851	T	A	246.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=37.92;MQ0=12;OQ=2113.34;QD=28.18;SB=-566.84	GT:AD:DP:GL:GQ	1/1:0,75:55:-214.93,-16.56,-0.01:99
+chr1	750775	rs1048488	C	T	147.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=55.79;MQ0=0;OQ=2544.23;QD=37.42;SB=-1282.72	GT:AD:DP:GL:GQ	1/1:0,68:64:-258.02,-19.28,-0.02:99
+chr1	751010	rs3115850	T	C	532.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.77;MQ0=0;OQ=2501.23;QD=35.73;SB=-1116.81	GT:AD:DP:GL:GQ	1/1:0,70:69:-253.73,-20.78,-0.02:99
+chr1	751595	rs2286139	C	T	599.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=41.46;MQ0=7;OQ=1283.06;QD=32.08;SB=-543.21	GT:AD:DP:GL:GQ	1/1:0,40:32:-131.90,-9.64,-0.01:96.32
+chr1	751615	rs1057213	C	T	31.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=31.78;MQ0=12;OQ=906.27;QD=25.17;SB=-453.10	GT:AD:DP:GL:GQ	1/1:0,36:23:-94.22,-6.93,-0.00:69.23
+chr1	751674	rs1057212	G	A	293.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=15.73;MQ0=12;OQ=176.65;QD=10.39;SB=-51.56	GT:AD:DP:GL:GQ	1/1:0,17:5:-21.22,-1.51,-0.00:15.05
+chr1	752136	rs3115849	G	A	60.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.04;MQ0=8;OQ=733.35;QD=26.19;SB=-160.21	GT:AD:DP:GL:GQ	1/1:0,28:19:-76.93,-5.73,-0.01:57.18
+chr1	752452	rs3115848	G	C	110.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=44.19;MQ0=1;OQ=1521.80;QD=34.59;SB=-621.54	GT:AD:DP:GL:GQ	1/1:1,43:40:-155.80,-12.08,-0.04:99
+chr1	752455	rs3131950	C	G	3.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=4.46;MQ=42.62;MQ0=2;OQ=1386.15;QD=32.24;SB=-555.07	GT:AD:DP:GL:GQ	1/1:1,42:36:-142.24,-10.87,-0.04:99
+chr1	752464	rs3131949	T	C	84.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=40.87;MQ0=2;OQ=1077.25;QD=28.35;SB=-454.51	GT:AD:DP:GL:GQ	1/1:1,37:32:-111.32,-9.64,-0.01:96.27
+chr1	752495	rs3131948	T	A	77.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=37.91;MQ0=2;OQ=926.17;QD=28.94;SB=-390.81	GT:AD:DP:GL:GQ	1/1:1,31:26:-96.21,-7.83,-0.01:78.23
+chr1	753257	rs3115847	G	A	0.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=27.21;MQ0=9;OQ=840.10;QD=24.71;SB=-20.92	GT:AD:DP:GL:GQ	1/1:5,28:22:-89.90,-8.89,-2.30:65.88
+chr1	755968	rs2519015	T	A	366.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.21;MQ0=48;OQ=1019.18;QD=12.90;SB=-121.94	GT:AD:DP:GL:GQ	1/1:23,56:29:-105.51,-8.74,-0.01:87.26
+chr1	757643	rs2905042	G	A	71.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=34.85;MQ0=1;OQ=1607.55;QD=32.81;SB=-663.38	GT:AD:DP:GL:GQ	1/1:0,49:41:-164.35,-12.35,-0.01:99
+chr1	758116	rs2977608	A	C	58.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=47.69;MQ0=11;OQ=2396.98;QD=30.34;SB=-914.67	GT:AD:DP:GL:GQ	1/1:4,75:68:-243.30,-20.48,-0.02:99
+chr1	759692	rs2977607	C	A	65.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=47.39;MQ0=6;OQ=1539.69;QD=31.42;SB=-733.73	GT:AD:DP:GL:GQ	1/1:0,49:42:-157.56,-12.65,-0.01:99
+chr1	759938	rs2977606	C	T	514.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.63;MQ0=7;OQ=1693.07;QD=33.20;SB=-574.34	GT:AD:DP:GL:GQ	1/1:0,51:44:-172.91,-13.26,-0.01:99
+chr1	760431	rs3131943	A	G	213.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=31.32;MQ0=2;OQ=527.61;QD=27.77;SB=-87.92	GT:AD:DP:GL:GQ	1/1:0,19:16:-56.35,-4.82,-0.00:48.14
+chr1	760781	rs3095826	T	G	40.05	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=15.14;MQ0=8;QD=3.64;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,11:2:-7.41,-0.60,-0.00:6.02
+chr1	761273	rs2519006	C	T	29.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.96;MQ=27.71;MQ0=20;OQ=1719.34;QD=22.33;SB=-558.69	GT:AD:DP:GL:GQ	1/1:18,59:45:-179.00,-13.55,-3.48:99
+chr1	761686	rs2977605	T	C	284.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.99;MQ0=4;OQ=744.87;QD=26.60;SB=-283.54	GT:AD:DP:GL:GQ	1/1:0,28:24:-78.09,-7.24,-0.02:72.16
+chr1	762618	rs2905039	A	C	494.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.90;MQ0=0;OQ=1864.52;QD=29.13;SB=-798.77	GT:AD:DP:GL:GQ	1/1:0,64:60:-190.09,-18.09,-0.06:99
+chr1	764599	rs28830877	A	C	154.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=49.78;MQ0=3;OQ=2217.13;QD=30.37;SB=-1008.12	GT:AD:DP:GL:GQ	1/1:0,73:64:-225.32,-19.28,-0.02:99
+chr1	764648	rs28873693	G	A	193.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=40.27;MQ0=2;OQ=1900.97;QD=32.22;SB=-951.98	GT:AD:DP:GL:GQ	1/1:0,59:49:-193.70,-14.76,-0.02:99
+chr1	764732	rs55994826	G	A	15.73	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=36.88;MQ0=1;QD=0.58;SB=17.08	GT:AD:DP:GL:GQ	0/1:24,3:23:-11.77,-6.93,-72.32:48.45
+chr1	764737	rs28810152	A	C	715.74	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=38.33;MQ0=0;QD=28.63;SB=-297.55	GT:AD:DP:GL:GQ	1/1:0,25:22:-75.17,-6.63,-0.01:66.18
+chr1	764742	.	A	T	46.72	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=39.13;MQ0=0;QD=2.03;SB=-38.86	GT:AD:DP:GL:GQ	0/1:19,4:18:-13.38,-5.42,-51.11:79.56
+chr1	764746	.	G	A	393.33	SnpCluster	AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=40.70;MQ0=1;QD=17.88;SB=-221.92	GT:AD:DP:GL:GQ	0/1:8,14:19:-48.34,-5.72,-22.76:99
+chr1	764763	rs28797844	C	G	118.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=44.74;MQ0=1;OQ=234.91;QD=8.39;SB=-89.25	GT:AD:DP:GL:GQ	0/1:20,8:26:-34.62,-7.84,-73.94:99
+chr1	764786	rs28769076	G	C	293.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=38.71;MQ0=4;OQ=1154.38;QD=32.98;SB=-346.74	GT:AD:DP:GL:GQ	1/1:0,35:27:-119.03,-8.14,-0.01:81.27
+chr1	765119	.	T	G	7.65	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=15.72;MQ0=15;OQ=87.25;QD=4.15;SB=-66.98	GT:AD:DP:GL:GQ	0/1:15,6:6:-13.82,-1.81,-7.64:58.28
+chr1	765289	rs2905037	G	A	284.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=48.40;MQ0=0;OQ=3000.65;QD=37.51;SB=-1455.38	GT:AD:DP:GL:GQ	1/1:0,80:75:-303.67,-22.59,-0.02:99
+chr1	765522	rs2905035	A	G	84.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=40.77;MQ0=3;OQ=2096.78;QD=30.39;SB=-645.26	GT:AD:DP:GL:GQ	1/1:0,68:58:-213.28,-17.47,-0.02:99
+chr1	766409	rs12124819	A	G	273.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=3.66;MQ=51.01;MQ0=0;OQ=1354.31;QD=15.75;SB=-621.86	GT:AD:DP:GL:GQ	0/1:41,45:85:-164.32,-25.60,-163.76:99
+chr1	766985	rs2980319	A	T	684.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.93;MQ0=0;OQ=2347.43;QD=37.26;SB=-849.94	GT:AD:DP:GL:GQ	1/1:0,63:62:-238.35,-18.68,-0.02:99
+chr1	768432	rs2977615	A	G	315.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=46.80;MQ0=5;OQ=1414.86;QD=25.27;SB=-618.23	GT:AD:DP:GL:GQ	1/1:0,56:46:-145.13,-13.88,-0.05:99
+chr1	769890	rs2977613	G	T	314.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=53.23;MQ0=0;OQ=2549.06;QD=34.45;SB=-1034.15	GT:AD:DP:GL:GQ	1/1:0,74:70:-258.51,-21.09,-0.02:99
+chr1	770648	rs2977612	T	A	316.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=55.02;MQ0=0;OQ=2471.78;QD=34.81;SB=-1070.63	GT:AD:DP:GL:GQ	1/1:1,70:68:-253.32,-20.49,-2.56:99
+chr1	773167	rs2980295	T	C	625.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.46;MQ0=0;OQ=2479.28;QD=34.43;SB=-1064.87	GT:AD:DP:GL:GQ	1/1:0,72:71:-251.54,-21.39,-0.02:99
+chr1	774913	rs2905062	G	A	647.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.25;MQ0=0;OQ=2057.09;QD=38.09;SB=-793.69	GT:AD:DP:GL:GQ	1/1:0,54:52:-209.31,-15.66,-0.01:99
+chr1	775852	rs2980300	T	C	398.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.91;MQ0=0;OQ=1925.83;QD=36.34;SB=-289.45	GT:AD:DP:GL:GQ	1/1:0,53:52:-196.18,-15.66,-0.01:99
+chr1	776110	rs59319764	G	A	135.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=22.95;MQ0=5;OQ=708.27;QD=21.46;SB=-330.44	GT:AD:DP:GL:GQ	1/1:5,28:18:-74.41,-5.42,-0.00:54.18
+chr1	776673	rs2905061	G	A	271.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.77;MQ0=2;OQ=243.21;QD=12.80;SB=-51.67	GT:AD:DP:GL:GQ	1/1:0,19:7:-27.90,-2.11,-0.00:21.07
+chr1	776882	rs2905060	C	T	28.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.47;MQ0=13;OQ=680.11;QD=21.25;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,32:18:-71.60,-5.42,-0.01:54.17
+chr1	776908	.	C	G	26.94	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=23.04;MQ0=7;QD=1.35;SB=-10.00	GT:AD:DP:GL:GQ	0/1:11,8:6:-7.79,-1.82,-13.09:59.77
+chr1	776998	rs28753393	A	G	1.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=22.78;MQ0=8;OQ=492.59;QD=20.52;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,24:14:-52.85,-4.22,-0.00:42.13
+chr1	777048	rs2905058	G	A	64.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=2.66;MQ=17.04;MQ0=12;OQ=310.80;QD=12.43;SB=-128.67	GT:AD:DP:GL:GQ	1/1:0,25:9:-34.67,-2.71,-0.01:27.08
+chr1	777068	rs2905057	G	A	256.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=15.61;MQ0=17;OQ=265.15;QD=9.14;SB=-131.67	GT:AD:DP:GL:GQ	1/1:0,29:8:-30.10,-2.41,-0.01:24.07
+chr1	777125	rs2905056	C	G	369.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=42.20;MQ0=14;OQ=1716.63;QD=32.39;SB=-514.60	GT:AD:DP:GL:GQ	1/1:0,53:39:-175.26,-11.75,-0.01:99
+chr1	777262	rs2905055	G	T	436.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=43.93;MQ0=5;OQ=1457.00;QD=33.11;SB=-678.96	GT:AD:DP:GL:GQ	1/1:0,44:39:-149.29,-11.74,-0.01:99
+chr1	777290	.	C	T	29.42	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=32.80;MQ0=5;OQ=855.45;QD=17.11;SB=-308.80	GT:AD:DP:GL:GQ	0/1:21,29:44:-102.09,-13.26,-62.10:99
+chr1	777548	rs2905054	G	T	500.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.40;MQ0=0;OQ=2267.93;QD=36.00;SB=-851.89	GT:AD:DP:GL:GQ	1/1:0,63:62:-230.39,-18.67,-0.01:99
+chr1	777707	rs2905053	C	T	334.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=44.44;MQ0=2;OQ=3957.07;QD=39.57;SB=-1940.72	GT:AD:DP:GL:GQ	1/1:0,100:95:-394.71,-28.61,-0.02:99
+chr1	778576	rs2980306	T	C	128.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=33.51;MQ0=34;OQ=1562.02;QD=19.05;SB=-268.41	GT:AD:DP:GL:GQ	1/1:13,69:45:-159.81,-13.56,-0.02:99
+chr1	778703	rs10157303	T	C	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=3;HaplotypeScore=7.41;MQ=38.85;MQ0=14;OQ=444.81;QD=5.30;SB=-42.81	GT:AD:DP:GL:GQ	0/1:40,44:57:-64.95,-17.19,-138.39:99
+chr1	778707	rs10159337	C	G	0.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=6.67;MQ=39.47;MQ0=14;OQ=423.04;QD=5.29;SB=32.36	GT:AD:DP:GL:GQ	0/1:47,33:53:-61.57,-15.98,-162.13:99
+chr1	778752	rs10159341	C	T	0.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.10;MQ=43.79;MQ0=4;OQ=82.84;QD=1.45;SB=53.17	GT:AD:DP:GL:GQ	0/1:50,7:44:-24.83,-13.27,-122.87:99
+chr1	778808	.	G	C	4.86	PASS	AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=23.40;MQ0=13;OQ=99.43;QD=5.52;SB=-51.47	GT:AD:DP:GL:GQ	1/1:11,7:3:-13.43,-0.90,-0.00:9.03
+chr1	778958	.	C	G	0.12	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=6.83;MQ=13.77;MQ0=12;OQ=373.21;QD=7.46;SB=-3.98	GT:AD:DP:GL:GQ	0/1:40,10:17:-45.73,-5.12,-29.92:99
+chr1	778962	rs10158938	G	A	0.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=6.77;MQ=13.74;MQ0=12;OQ=114.14;QD=2.24;SB=-77.09	GT:AD:DP:GL:GQ	0/1:17,34:17:-19.83,-5.13,-36.56:99
+chr1	779001	.	C	G	62.18	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=43.25;MQ=17.50;MQ0=24;QD=0.60;SB=-3.98	GT:AD:DP:GL:GQ	0/1:92,11:44:-22.76,-13.26,-160.88:95.02
+chr1	779004	.	G	C	379.18	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=41.31;MQ=17.52;MQ0=26;QD=3.61;SB=-3.98	GT:AD:DP:GL:GQ	0/1:83,21:42:-55.98,-14.78,-128.84:99
+chr1	779007	.	G	C	125.98	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=41.47;MQ=17.84;MQ0=24;QD=1.21;SB=-3.98	GT:AD:DP:GL:GQ	0/1:82,22:45:-29.45,-13.56,-167.32:99
+chr1	779046	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=13.36;MQ=16.85;MQ0=30;OQ=85.18;QD=0.76;SB=-0.98	GT:AD:DP:GL:GQ	0/1:103,9:39:-23.55,-11.75,-110.84:99
+chr1	779119	rs3131939	T	C	14.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=38.97;MQ0=6;OQ=1691.71;QD=26.03;SB=-847.52	GT:AD:DP:GL:GQ	1/1:0,65:53:-172.80,-15.99,-0.05:99
+chr1	782126	rs1044922	A	G	199.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=35.10;MQ0=8;OQ=1304.52;QD=20.38;SB=-463.86	GT:AD:DP:GL:GQ	1/1:3,61:42:-134.08,-12.67,-0.04:99
+chr1	782343	rs2905036	C	T	605.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=44.88;MQ0=2;OQ=3789.97;QD=39.07;SB=-1780.39	GT:AD:DP:GL:GQ	1/1:0,97:94:-378.00,-28.32,-0.03:99
+chr1	783071	rs2905029	C	G	4.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=24.02;MQ0=7;OQ=636.50;QD=15.91;SB=29.13	GT:AD:DP:GL:GQ	0/1:20,20:32:-76.58,-9.64,-67.00:99
+chr1	783292	rs2519067	T	C	14.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=32.87;MQ0=7;OQ=1046.72;QD=28.29;SB=-162.84	GT:AD:DP:GL:GQ	1/1:5,32:30:-108.26,-9.03,-0.01:90.27
+chr1	785455	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=20;HaplotypeScore=3.33;MQ=47.34;MQ0=4;OQ=246.17;QD=4.48;SB=-56.75	GT:AD:DP:GL:GQ	0/1:43,12:47:-42.06,-14.16,-132.17:99
+chr1	786397	.	T	C	0.59	PASS	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=41.18;MQ0=9;OQ=325.37;QD=4.52;SB=-24.72	GT:AD:DP:GL:GQ	0/1:50,22:59:-53.59,-17.77,-179.67:99
+chr1	786590	rs2909612	G	T	160.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=27.34;MQ0=10;OQ=1960.56;QD=30.63;SB=-1001.80	GT:AD:DP:GL:GQ	1/1:0,64:54:-199.65,-16.26,-0.01:99
+chr1	786630	rs12076540	G	A	0.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=7.41;MQ=41.01;MQ0=13;OQ=2659.94;QD=26.60;SB=-1327.51	GT:AD:DP:GL:GQ	0/1:23,77:83:-294.28,-25.01,-36.59:99
+chr1	786634	rs2909613	T	C	0.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=7.24;MQ=42.00;MQ0=12;OQ=84.11;QD=0.83;SB=12.37	GT:AD:DP:GL:GQ	0/1:80,21:85:-37.30,-25.61,-300.66:99
+chr1	786902	.	A	G	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=48.19;MQ0=15;OQ=198.92;QD=1.55;SB=-72.06	GT:AD:DP:GL:GQ	0/1:96,32:111:-56.61,-33.43,-385.87:99
+chr1	787026	.	G	A	14.82	LowQual	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=46.76;MQ0=8;QD=0.17;SB=-27.80	GT:AD:DP:GL:GQ	0/1:74,15:80:-28.85,-24.10,-261.80:47.51
+chr1	787041	.	A	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=44.71;MQ0=13;OQ=84.25;QD=0.90;SB=-23.86	GT:AD:DP:GL:GQ	0/1:71,22:80:-37.92,-26.21,-271.06:99
+chr1	787889	rs4951864	C	T	266.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=45.78;MQ0=1;OQ=2714.18;QD=38.77;SB=-989.31	GT:AD:DP:GL:GQ	1/1:1,69:67:-275.02,-20.18,-0.01:99
+chr1	789326	rs4245756	T	C	211.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=58.75;MQ0=0;OQ=3107.92;QD=34.53;SB=-1502.55	GT:AD:DP:GL:GQ	1/1:0,90:89:-314.41,-26.81,-0.04:99
+chr1	789870	rs6681049	T	C	615.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=47.06;MQ0=1;OQ=2660.56;QD=34.55;SB=-1115.14	GT:AD:DP:GL:GQ	1/1:0,77:73:-269.66,-21.99,-0.02:99
+chr1	790246	rs4951931	C	T	190.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=47.97;MQ0=4;OQ=2808.35;QD=36.95;SB=-1258.17	GT:AD:DP:GL:GQ	1/1:1,75:70:-284.44,-21.09,-0.02:99
+chr1	791806	rs7516866	C	T	78.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=49.91;MQ0=4;OQ=2127.43;QD=34.88;SB=-1017.37	GT:AD:DP:GL:GQ	1/1:0,61:56:-216.36,-16.88,-0.03:99
+chr1	791858	rs7553084	G	A	0.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=36.92;MQ0=13;OQ=63.33;QD=1.47;SB=-33.64	GT:AD:DP:GL:GQ	0/1:29,14:21:-15.95,-6.33,-55.40:96.17
+chr1	791869	rs9700144	T	C	36.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=30.98;MQ0=16;OQ=499.95;QD=11.90;SB=-156.35	GT:AD:DP:GL:GQ	0/1:18,24:19:-59.00,-5.72,-11.19:54.70
+chr1	791956	rs7553197	G	A	67.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=36.93;MQ0=8;OQ=1294.09;QD=27.53;SB=-402.66	GT:AD:DP:GL:GQ	1/1:3,44:34:-133.00,-10.24,-0.01:99
+chr1	792054	.	G	A	0.09	PASS	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=2.92;MQ=30.80;MQ0=19;OQ=223.16;QD=2.37;SB=-57.50	GT:AD:DP:GL:GQ	0/1:66,28:40:-37.67,-12.07,-95.70:99
+chr1	792085	rs61768213	G	A	0.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=11.76;MQ=27.41;MQ0=19;OQ=204.34;QD=1.93;SB=-8.44	GT:AD:DP:GL:GQ	0/1:88,18:55:-40.31,-16.60,-140.17:99
+chr1	792094	rs59334306	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=46.76;MQ=26.45;MQ0=20;OQ=280.32;QD=2.64;SB=-7.86	GT:AD:DP:GL:GQ	0/1:75,30:53:-47.28,-15.96,-151.37:99
+chr1	792103	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=25.85;MQ=29.18;MQ0=20;OQ=339.53;QD=3.09;SB=-172.66	GT:AD:DP:GL:GQ	0/1:84,26:61:-55.65,-18.41,-142.90:99
+chr1	792163	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=94;Dels=0.02;HRun=3;HaplotypeScore=9.77;MQ=36.34;MQ0=8;OQ=472.25;QD=5.02;SB=-153.68	GT:AD:DP:GL:GQ	0/1:49,43:64:-69.50,-18.99,-156.72:99
+chr1	792183	.	G	A	7.22	PASS	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=4.86;MQ=42.20;MQ0=9;OQ=1359.41;QD=15.27;SB=-245.27	GT:AD:DP:GL:GQ	0/1:36,53:59:-157.01,-17.79,-57.64:99
+chr1	792201	.	G	A	0.06	PASS	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=43.46;MQ0=8;OQ=234.21;QD=2.47;SB=6.27	GT:AD:DP:GL:GQ	0/1:68,27:69:-47.53,-20.82,-170.85:99
+chr1	792244	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=1;HaplotypeScore=3.46;MQ=47.18;MQ0=4;OQ=75.38;QD=1.05;SB=92.33	GT:AD:DP:GL:GQ	0/1:49,23:53:-26.79,-15.97,-181.50:99
+chr1	793978	rs9725068	G	A	105.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.47;MQ0=13;OQ=1474.93;QD=26.34;SB=-321.42	GT:AD:DP:GL:GQ	1/1:0,56:37:-151.09,-11.15,-0.01:99
+chr1	794403	rs11240778	T	C	115.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.32;MQ0=0;OQ=2475.68;QD=30.95;SB=-1150.98	GT:AD:DP:GL:GQ	1/1:0,80:77:-251.22,-23.23,-0.07:99
+chr1	797375	rs10751454	A	G	614.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.93;MQ0=1;OQ=2184.15;QD=34.67;SB=-971.41	GT:AD:DP:GL:GQ	1/1:0,63:61:-222.02,-18.37,-0.02:99
+chr1	797624	rs4951932	C	A	532.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.69;MQ0=0;OQ=2699.27;QD=36.48;SB=-1270.15	GT:AD:DP:GL:GQ	1/1:0,74:72:-273.52,-21.68,-0.01:99
+chr1	798086	rs4951933	G	C	74.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=48.23;MQ0=3;OQ=1918.57;QD=25.24;SB=-881.14	GT:AD:DP:GL:GQ	1/1:5,71:54:-198.81,-16.33,-3.37:99
+chr1	798494	rs11240779	G	A	160.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=54.32;MQ0=0;OQ=2346.63;QD=37.85;SB=-859.15	GT:AD:DP:GL:GQ	1/1:0,62:60:-238.27,-18.08,-0.02:99
+chr1	798785	rs6594027	G	A	211.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.48;MQ=43.75;MQ0=6;OQ=1743.42;QD=29.06;SB=-625.73	GT:AD:DP:GL:GQ	1/1:3,57:47:-180.84,-14.16,-2.92:99
+chr1	798791	rs11240780	C	T	1.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.98;MQ=44.87;MQ0=5;OQ=1874.68;QD=30.73;SB=-625.19	GT:AD:DP:GL:GQ	1/1:3,58:49:-194.73,-14.76,-3.68:99
+chr1	801153	rs6683530	G	C	58.35	Indel	AC=1;AF=0.50;AN=2;DB;DP=8;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=47.12;MQ0=0;QD=7.29;SB=-48.46	GT:AD:DP:GL:GQ	0/1:3,5:6:-10.93,-1.81,-12.15:91.19
+chr1	801443	.	G	C	0.04	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=38.48;MQ0=1;OQ=52.85;QD=17.62;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:2:-8.69,-0.60,-0.00:6.02
+chr1	801493	.	G	A	49.74	LowQual	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=43.23;MQ0=0;QD=5.53;SB=-18.25	GT:AD:DP:GL:GQ	0/1:2,4:4:-12.63,-4.37,-6.30:19.25
+chr1	801563	.	C	G	14.05	LowQual	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=3.71;MQ=42.60;MQ0=0;QD=1.40;SB=-3.98	GT:AD:DP:GL:GQ	0/1:8,2:7:-6.79,-2.12,-21.33:46.71
+chr1	801598	.	T	C	10.44	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=49.26;MQ0=0;OQ=130.47;QD=6.21;SB=-25.63	GT:AD:DP:GL:GQ	0/1:13,8:15:-20.85,-4.52,-36.05:99
+chr1	801628	.	C	T	6.09	PASS	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=52.56;MQ0=0;OQ=245.60;QD=14.45;SB=-39.65	GT:AD:DP:GL:GQ	0/1:7,10:12:-31.46,-3.62,-11.96:83.42
+chr1	802130	rs7541694	A	G	69.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=3.34;MQ=55.65;MQ0=0;OQ=1955.23;QD=29.18;SB=-933.35	GT:AD:DP:GL:GQ	1/1:0,67:63:-199.17,-19.00,-0.06:99
+chr1	802147	rs7545373	C	G	33.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=3.57;MQ=55.54;MQ0=0;OQ=2348.31;QD=37.27;SB=-1198.48	GT:AD:DP:GL:GQ	1/1:2,61:60:-246.74,-18.09,-8.33:97.66
+chr1	802165	.	G	A	18.16	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.79;MQ=55.42;MQ0=0;QD=0.31;SB=71.21	GT:AD:DP:GL:GQ	0/1:51,8:51:-20.46,-15.37,-155.58:50.93
+chr1	802175	.	C	T	26.53	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=55.08;MQ0=0;QD=0.48;SB=56.20	GT:AD:DP:GL:GQ	0/1:46,8:48:-20.39,-14.46,-154.35:59.35
+chr1	802189	.	G	A	11.38	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=55.49;MQ0=0;QD=0.20;SB=56.19	GT:AD:DP:GL:GQ	0/1:49,8:51:-19.75,-15.37,-163.52:43.89
+chr1	802470	.	T	C	21.38	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=54.38;MQ0=1;QD=0.34;SB=62.23	GT:AD:DP:GL:GQ	0/1:57,6:59:-23.19,-17.77,-210.98:54.19
+chr1	802488	.	G	T	29.03	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=53.89;MQ0=1;QD=0.53;SB=65.21	GT:AD:DP:GL:GQ	0/1:49,6:52:-21.85,-15.66,-163.62:61.86
+chr1	802614	rs4246500	T	C	405.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=1600.84;QD=34.80;SB=-568.88	GT:AD:DP:GL:GQ	1/1:0,46:45:-163.68,-13.56,-0.02:99
+chr1	803503	rs16973606	A	G	11.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.56;MQ=28.75;MQ0=1;OQ=1669.54;QD=28.30;SB=-566.93	GT:AD:DP:GL:GQ	1/1:0,58:52:-170.59,-15.68,-0.05:99
+chr1	803610	rs4970388	G	A	620.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.63;MQ0=0;OQ=2297.43;QD=38.94;SB=-1171.71	GT:AD:DP:GL:GQ	1/1:0,59:58:-233.34,-17.47,-0.02:99
+chr1	803950	.	C	A	24.11	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=7.91;MQ=35.01;MQ0=10;QD=0.32;SB=59.14	GT:AD:DP:GL:GQ	0/1:54,21:50:-20.76,-15.06,-152.32:56.93
+chr1	803957	rs61768235	A	G	0.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=7.75;MQ=34.03;MQ0=10;OQ=322.16;QD=4.30;SB=35.12	GT:AD:DP:GL:GQ	0/1:42,30:47:-49.67,-14.18,-120.05:99
+chr1	803968	.	C	T	1.63	PASS	AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=30.80;MQ0=12;OQ=418.55;QD=4.81;SB=59.13	GT:AD:DP:GL:GQ	0/1:53,34:61:-63.53,-18.39,-146.32:99
+chr1	804010	rs4268301	G	C	0.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=6.53;MQ=32.14;MQ0=12;OQ=1062.36;QD=10.84;SB=53.20	GT:AD:DP:GL:GQ	0/1:43,55:71:-130.91,-21.39,-167.36:99
+chr1	804023	.	C	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=2;HaplotypeScore=7.44;MQ=36.24;MQ0=5;OQ=967.44;QD=10.63;SB=62.24	GT:AD:DP:GL:GQ	0/1:48,43:70:-121.12,-21.09,-190.26:99
+chr1	804036	.	A	T	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=7.15;MQ=36.45;MQ0=7;OQ=717.66;QD=8.34;SB=65.21	GT:AD:DP:GL:GQ	0/1:47,38:68:-95.53,-20.48,-155.46:99
+chr1	804078	rs4468103	A	G	426.89	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=12.81;MQ=43.94;MQ0=3;QD=5.62;SB=77.26	GT:AD:DP:GL:GQ	0/1:53,23:63:-64.96,-18.98,-178.46:99
+chr1	804080	rs34234497	C	A	381.14	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=12.71;MQ=43.70;MQ0=3;QD=4.95;SB=89.27	GT:AD:DP:GL:GQ	0/1:53,24:67:-61.57,-20.18,-178.60:99
+chr1	804083	.	C	A	27.31	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=12.71;MQ=43.58;MQ0=4;QD=0.34;SB=86.24	GT:AD:DP:GL:GQ	0/1:70,11:67:-26.19,-20.18,-214.42:60.14
+chr1	804127	rs4571914	C	T	3.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=96;Dels=0.00;HRun=1;HaplotypeScore=3.93;MQ=47.10;MQ0=4;OQ=2988.66;QD=31.13;SB=-1433.34	GT:AD:DP:GL:GQ	1/1:3,93:75:-302.47,-22.59,-0.02:99
+chr1	804160	.	T	A	1.44	PASS	AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=46.18;MQ0=5;OQ=470.49;QD=4.06;SB=48.91	GT:AD:DP:GL:GQ	0/1:72,44:82:-75.03,-24.70,-237.11:99
+chr1	804163	.	T	A	0.61	PASS	AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=45.72;MQ0=5;OQ=536.43;QD=4.62;SB=45.90	GT:AD:DP:GL:GQ	0/1:71,45:81:-81.32,-24.40,-231.88:99
+chr1	804176	.	C	T	0.11	PASS	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=42.84;MQ0=5;OQ=284.28;QD=2.41;SB=31.59	GT:AD:DP:GL:GQ	0/1:90,28:84:-57.01,-25.30,-251.94:99
+chr1	804255	rs61768236	C	T	415.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=27.82;MQ0=7;OQ=1235.94;QD=11.44;SB=-464.41	GT:AD:DP:GL:GQ	0/1:49,59:70:-147.96,-21.08,-123.48:99
+chr1	804268	rs61768237	T	C	267.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.38;MQ0=8;OQ=1449.21;QD=11.32;SB=-624.62	GT:AD:DP:GL:GQ	0/1:53,75:88:-174.71,-26.51,-156.34:99
+chr1	804322	.	T	C	170.65	PASS	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.67;MQ0=9;OQ=1734.45;QD=11.19;SB=-540.49	GT:AD:DP:GL:GQ	0/1:72,83:118:-212.27,-35.54,-249.66:99
+chr1	804353	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=4;HaplotypeScore=24.21;MQ=44.77;MQ0=2;OQ=299.39;QD=2.32;SB=-27.46	GT:AD:DP:GL:GQ	0/1:106,23:112:-66.96,-33.74,-330.98:99
+chr1	804358	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=1;HaplotypeScore=23.14;MQ=46.13;MQ0=0;OQ=958.19;QD=8.33;SB=-257.80	GT:AD:DP:GL:GQ	0/1:68,47:100:-129.23,-30.12,-232.16:99
+chr1	804472	.	A	T	0.19	PASS	AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=48.14;MQ0=4;OQ=798.74;QD=6.89;SB=107.38	GT:AD:DP:GL:GQ	0/1:75,41:98:-112.67,-29.52,-266.53:99
+chr1	804474	.	A	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=2;HaplotypeScore=5.00;MQ=47.90;MQ0=4;OQ=704.41;QD=6.18;SB=101.34	GT:AD:DP:GL:GQ	0/1:73,41:96:-102.63,-28.91,-247.09:99
+chr1	804544	.	A	T	0.11	PASS	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=3.62;MQ=40.45;MQ0=6;OQ=406.04;QD=3.15;SB=95.34	GT:AD:DP:GL:GQ	0/1:99,30:89:-70.69,-26.81,-271.16:99
+chr1	804557	.	A	C	0.23	PASS	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=3.14;MQ=40.10;MQ0=5;OQ=416.51;QD=3.82;SB=86.28	GT:AD:DP:GL:GQ	0/1:65,43:73:-66.93,-21.99,-180.79:99
+chr1	804573	.	G	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=8.85;MQ=43.02;MQ0=4;OQ=579.16;QD=6.16;SB=83.29	GT:AD:DP:GL:GQ	0/1:56,38:69:-81.99,-20.79,-176.35:99
+chr1	804594	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=7.80;MQ=47.78;MQ0=4;OQ=294.82;QD=3.04;SB=104.36	GT:AD:DP:GL:GQ	0/1:66,31:74:-55.06,-22.29,-235.53:99
+chr1	804605	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=13.95;MQ=49.87;MQ0=3;OQ=284.24;QD=2.81;SB=113.40	GT:AD:DP:GL:GQ	0/1:73,28:82:-56.44,-24.73,-279.54:99
+chr1	804976	.	T	C	11.87	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=17.62;MQ=47.74;MQ0=10;QD=0.07;SB=128.44	GT:AD:DP:GL:GQ	0/1:107,52:112:-38.18,-33.74,-401.64:44.42
+chr1	805001	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=241;Dels=0.00;HRun=1;HaplotypeScore=76.93;MQ=42.40;MQ0=12;OQ=1246.68;QD=5.17;SB=146.50	GT:AD:DP:GL:GQ	0/1:129,112:153:-174.09,-46.14,-468.17:99
+chr1	805002	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=0;HaplotypeScore=75.93;MQ=42.40;MQ0=13;OQ=1673.16;QD=6.89;SB=-6.76	GT:AD:DP:GL:GQ	0/1:105,138:154:-217.01,-46.41,-335.99:99
+chr1	805021	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=298;Dels=0.00;HRun=1;HaplotypeScore=153.68;MQ=38.48;MQ0=13;OQ=1337.90;QD=4.49;SB=-19.37	GT:AD:DP:GL:GQ	0/1:146,152:156:-184.06,-46.99,-421.14:99
+chr1	805031	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=318;Dels=0.00;HRun=0;HaplotypeScore=207.07;MQ=37.99;MQ0=12;OQ=1684.06;QD=5.30;SB=131.37	GT:AD:DP:GL:GQ	0/1:175,143:165:-221.39,-49.70,-405.98:99
+chr1	805042	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=340;Dels=0.00;HRun=0;HaplotypeScore=155.12;MQ=37.32;MQ0=17;OQ=677.06;QD=1.99;SB=140.48	GT:AD:DP:GL:GQ	0/1:285,55:199:-130.92,-59.93,-605.02:99
+chr1	805044	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=339;Dels=0.00;HRun=1;HaplotypeScore=156.13;MQ=36.94;MQ0=19;OQ=889.27;QD=2.62;SB=-0.09	GT:AD:DP:GL:GQ	0/1:243,95:179:-146.12,-53.91,-499.80:99
+chr1	805060	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=354;Dels=0.00;HRun=0;HaplotypeScore=82.46;MQ=36.20;MQ0=28;OQ=262.53;QD=0.74;SB=131.47	GT:AD:DP:GL:GQ	0/1:269,85:206:-91.58,-62.05,-725.20:99
+chr1	805070	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=335;Dels=0.00;HRun=0;HaplotypeScore=72.27;MQ=36.04;MQ0=29;OQ=243.31;QD=0.73;SB=122.43	GT:AD:DP:GL:GQ	0/1:284,51:196:-86.65,-59.04,-686.22:99
+chr1	805096	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=276;Dels=0.00;HRun=1;HaplotypeScore=49.35;MQ=36.73;MQ0=27;OQ=2126.16;QD=7.70;SB=101.36	GT:AD:DP:GL:GQ	0/1:81,194:152:-261.68,-45.78,-320.28:99
+chr1	805097	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=277;Dels=0.00;HRun=0;HaplotypeScore=50.14;MQ=36.84;MQ0=27;OQ=2166.21;QD=7.82;SB=104.34	GT:AD:DP:GL:GQ	0/1:80,196:153:-269.55,-49.64,-287.57:99
+chr1	805200	.	G	T	14.62	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=163;Dels=0.00;HRun=0;HaplotypeScore=25.70;MQ=44.88;MQ0=22;QD=0.09;SB=134.45	GT:AD:DP:GL:GQ	0/1:137,26:122:-41.47,-36.74,-399.49:47.31
+chr1	805236	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=3;HaplotypeScore=58.62;MQ=48.88;MQ0=19;OQ=385.49;QD=2.77;SB=18.48	GT:AD:DP:GL:GQ	0/1:87,52:105:-73.46,-31.63,-322.22:99
+chr1	805261	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=234;Dels=0.00;HRun=0;HaplotypeScore=375.75;MQ=40.95;MQ0=20;OQ=701.87;QD=3.00;SB=-184.24	GT:AD:DP:GL:GQ	0/1:132,101:136:-114.44,-40.97,-420.32:99
+chr1	805262	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=0;HaplotypeScore=355.61;MQ=40.41;MQ0=21;OQ=112.78;QD=0.47;SB=-10.32	GT:AD:DP:GL:GQ	0/1:195,42:136:-62.96,-48.40,-549.49:99
+chr1	805283	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=350;Dels=0.00;HRun=0;HaplotypeScore=86.54;MQ=35.73;MQ0=32;OQ=70.17;QD=0.20;SB=7.66	GT:AD:DP:GL:GQ	0/1:314,35:208:-72.95,-62.65,-681.33:99
+chr1	805284	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=355;Dels=0.00;HRun=0;HaplotypeScore=88.37;MQ=35.41;MQ0=32;OQ=4656.41;QD=13.12;SB=-1324.68	GT:AD:DP:GL:GQ	0/1:83,272:209:-464.64,-62.96,-333.94:99
+chr1	805326	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=520;Dels=0.00;HRun=0;HaplotypeScore=98.56;MQ=31.27;MQ0=33;OQ=692.81;QD=1.33;SB=-240.64	GT:AD:DP:GL:GQ	0/1:439,81:305:-164.43,-91.87,-1058.15:99
+chr1	805332	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=545;Dels=0.00;HRun=2;HaplotypeScore=105.70;MQ=31.02;MQ0=35;OQ=141.69;QD=0.26;SB=-23.90	GT:AD:DP:GL:GQ	0/1:483,62:326:-115.64,-98.18,-1059.59:99
+chr1	805355	.	A	G	982.52	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=566;Dels=0.00;HRun=0;HaplotypeScore=511.67;MQ=31.08;MQ0=42;QD=1.74;SB=-163.90	GT:AD:DP:GL:GQ	0/1:444,82:337:-230.52,-128.98,-1164.43:99
+chr1	805360	.	A	G	1795.44	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=565;Dels=0.00;HRun=0;HaplotypeScore=478.07;MQ=31.09;MQ0=46;QD=3.18;SB=-791.73	GT:AD:DP:GL:GQ	0/1:432,132:335:-287.21,-104.38,-1038.16:99
+chr1	805365	.	T	C	1655.74	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=542;Dels=0.00;HRun=0;HaplotypeScore=449.89;MQ=31.32;MQ0=44;QD=3.05;SB=-765.34	GT:AD:DP:GL:GQ	0/1:385,157:321:-265.54,-96.68,-1024.45:99
+chr1	805383	rs61768238	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=498;Dels=0.00;HRun=3;HaplotypeScore=98.26;MQ=31.16;MQ0=41;OQ=7913.78;QD=15.89;SB=-2299.71	GT:AD:DP:GL:GQ	0/1:75,423:268:-790.38,-80.71,-278.68:99
+chr1	805386	rs61768239	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=483;Dels=0.00;HRun=1;HaplotypeScore=91.10;MQ=31.39;MQ0=41;OQ=3141.51;QD=6.50;SB=-667.16	GT:AD:DP:GL:GQ	0/1:227,256:265:-397.24,-79.81,-626.74:99
+chr1	805419	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=411;Dels=0.00;HRun=1;HaplotypeScore=30.13;MQ=32.93;MQ0=34;OQ=719.57;QD=1.75;SB=-330.57	GT:AD:DP:GL:GQ	0/1:225,186:205:-136.99,-61.75,-686.74:99
+chr1	805436	rs61768240	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=352;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=34.71;MQ0=24;OQ=2408.76;QD=6.84;SB=-1167.64	GT:AD:DP:GL:GQ	0/1:93,259:163:-293.26,-49.10,-323.35:99
+chr1	805464	.	T	C	90.93	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=2;HaplotypeScore=145.78;MQ=37.92;MQ0=13;QD=0.36;SB=50.70	GT:AD:DP:GL:GQ	0/1:218,34:131:-51.84,-39.46,-473.80:99
+chr1	805469	.	G	A	411.01	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=232;Dels=0.00;HRun=0;HaplotypeScore=129.65;MQ=39.23;MQ0=10;QD=1.77;SB=-144.72	GT:AD:DP:GL:GQ	0/1:163,68:125:-82.03,-37.65,-380.30:99
+chr1	805474	.	C	T	980.44	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=4;HaplotypeScore=70.79;MQ=41.63;MQ0=7;QD=4.83;SB=-326.68	GT:AD:DP:GL:GQ	0/1:87,114:116:-136.29,-34.97,-264.49:99
+chr1	805480	.	G	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=196;Dels=0.00;HRun=1;HaplotypeScore=5.97;MQ=42.07;MQ0=5;OQ=803.65;QD=4.10;SB=-259.91	GT:AD:DP:GL:GQ	0/1:87,109:116:-118.58,-34.93,-301.30:99
+chr1	805558	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=180;Dels=0.00;HRun=0;HaplotypeScore=21.59;MQ=45.69;MQ0=3;OQ=812.25;QD=4.51;SB=-279.67	GT:AD:DP:GL:GQ	0/1:110,69:130:-123.67,-39.16,-392.54:99
+chr1	805591	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=218;Dels=0.00;HRun=0;HaplotypeScore=34.23;MQ=41.40;MQ0=5;OQ=1850.17;QD=8.49;SB=-635.41	GT:AD:DP:GL:GQ	0/1:84,134:148:-232.88,-44.58,-338.13:99
+chr1	805603	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=239;Dels=0.00;HRun=0;HaplotypeScore=49.54;MQ=40.33;MQ0=6;OQ=1757.35;QD=7.35;SB=-559.93	GT:AD:DP:GL:GQ	0/1:109,130:154:-225.41,-46.39,-351.31:99
+chr1	805620	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=274;Dels=0.00;HRun=0;HaplotypeScore=50.16;MQ=37.51;MQ0=8;OQ=230.26;QD=0.84;SB=134.91	GT:AD:DP:GL:GQ	0/1:246,28:171:-77.81,-51.50,-552.70:99
+chr1	805666	.	G	A	1332.87	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=339;Dels=0.00;HRun=0;HaplotypeScore=203.60;MQ=35.75;MQ0=0;QD=3.93;SB=119.41	GT:AD:DP:GL:GQ	0/1:281,58:223:-203.73,-67.16,-610.84:99
+chr1	805667	.	T	G	1225.05	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=341;Dels=0.00;HRun=2;HaplotypeScore=286.55;MQ=35.76;MQ0=2;QD=3.59;SB=122.41	GT:AD:DP:GL:GQ	0/1:261,66:222:-230.10,-104.31,-623.63:99
+chr1	805699	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=311;Dels=0.00;HRun=0;HaplotypeScore=73.71;MQ=35.76;MQ0=12;OQ=1765.48;QD=5.68;SB=-47.39	GT:AD:DP:GL:GQ	0/1:139,171:182:-234.66,-54.83,-454.10:99
+chr1	805716	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=281;Dels=0.00;HRun=1;HaplotypeScore=131.75;MQ=37.99;MQ0=12;OQ=2170.35;QD=7.72;SB=-121.23	GT:AD:DP:GL:GQ	0/1:87,193:163:-269.41,-49.09,-357.63:99
+chr1	805720	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=0;HaplotypeScore=145.61;MQ=38.29;MQ0=13;OQ=527.98;QD=1.87;SB=137.43	GT:AD:DP:GL:GQ	0/1:237,44:165:-105.78,-49.70,-509.42:99
+chr1	805742	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=1;HaplotypeScore=47.83;MQ=40.90;MQ0=15;OQ=1225.89;QD=5.11;SB=-296.81	GT:AD:DP:GL:GQ	0/1:97,143:138:-167.44,-41.57,-348.72:99
+chr1	805786	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=3.15;MQ=44.26;MQ0=7;OQ=155.59;QD=0.86;SB=-81.22	GT:AD:DP:GL:GQ	0/1:95,86:108:-51.37,-32.53,-383.93:99
+chr1	805792	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=9.50;MQ=44.61;MQ0=6;OQ=192.56;QD=1.10;SB=-88.24	GT:AD:DP:GL:GQ	0/1:93,82:108:-55.07,-32.53,-377.29:99
+chr1	805825	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=46.58;MQ0=3;OQ=327.36;QD=1.98;SB=-101.34	GT:AD:DP:GL:GQ	0/1:95,70:115:-70.67,-34.65,-378.60:99
+chr1	805831	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=154;Dels=0.00;HRun=0;HaplotypeScore=10.96;MQ=47.14;MQ0=3;OQ=324.94;QD=2.11;SB=-17.64	GT:AD:DP:GL:GQ	0/1:97,57:110:-68.91,-33.13,-331.34:99
+chr1	805897	.	G	T	104.51	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=35.45;MQ=51.05;MQ0=2;QD=0.74;SB=119.34	GT:AD:DP:GL:GQ	0/1:121,19:121:-50.18,-36.44,-386.79:99
+chr1	805898	.	C	A	129.42	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=35.61;MQ=51.05;MQ0=2;QD=0.91;SB=116.38	GT:AD:DP:GL:GQ	0/1:123,19:121:-52.67,-36.45,-375.35:99
+chr1	805905	.	T	G	13.51	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=25.14;MQ=52.44;MQ0=2;QD=0.10;SB=92.42	GT:AD:DP:GL:GQ	0/1:98,32:107:-36.84,-32.23,-356.89:46.15
+chr1	806044	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=16.71;MQ=40.59;MQ0=35;OQ=921.37;QD=5.06;SB=-438.60	GT:AD:DP:GL:GQ	0/1:71,111:106:-127.34,-31.92,-261.51:99
+chr1	806066	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=250;Dels=0.00;HRun=1;HaplotypeScore=9.43;MQ=37.37;MQ0=38;OQ=287.57;QD=1.15;SB=103.29	GT:AD:DP:GL:GQ	0/1:214,36:146:-76.01,-43.97,-467.77:99
+chr1	806081	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=255;Dels=0.00;HRun=0;HaplotypeScore=39.62;MQ=37.88;MQ0=27;OQ=908.24;QD=3.56;SB=97.71	GT:AD:DP:GL:GQ	0/1:178,77:158:-141.71,-47.60,-556.49:99
+chr1	806157	.	T	C	806.81	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=0;HaplotypeScore=71.06;MQ=40.64;MQ0=4;QD=3.75;SB=110.40	GT:AD:DP:GL:GQ	0/1:92,123:126:-121.92,-37.95,-368.73:99
+chr1	806159	.	A	C	141.17	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=219;Dels=0.00;HRun=0;HaplotypeScore=72.96;MQ=40.68;MQ0=4;QD=0.64;SB=110.38	GT:AD:DP:GL:GQ	0/1:166,49:128:-59.78,-42.38,-415.09:99
+chr1	806180	.	A	G	18.74	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=200;Dels=0.00;HRun=0;HaplotypeScore=59.33;MQ=41.65;MQ0=4;QD=0.09;SB=116.41	GT:AD:DP:GL:GQ	0/1:140,60:110:-38.29,-33.13,-408.92:51.52
+chr1	806197	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=1;HaplotypeScore=58.42;MQ=43.62;MQ0=5;OQ=190.94;QD=0.95;SB=134.47	GT:AD:DP:GL:GQ	0/1:110,91:116:-57.32,-34.94,-409.71:99
+chr1	806222	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=4;HaplotypeScore=6.94;MQ=47.96;MQ0=4;OQ=291.81;QD=1.80;SB=146.43	GT:AD:DP:GL:GQ	0/1:98,64:114:-66.80,-34.33,-354.69:99
+chr1	806232	.	T	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=151;Dels=0.00;HRun=1;HaplotypeScore=11.98;MQ=49.02;MQ0=3;OQ=233.87;QD=1.55;SB=140.48	GT:AD:DP:GL:GQ	0/1:96,55:110:-59.80,-33.13,-362.79:99
+chr1	806258	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=0;HaplotypeScore=10.30;MQ=50.03;MQ0=8;OQ=407.17;QD=2.51;SB=100.40	GT:AD:DP:GL:GQ	0/1:106,56:126:-81.95,-37.95,-384.61:99
+chr1	806268	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=1;HaplotypeScore=25.82;MQ=48.78;MQ0=9;OQ=670.14;QD=4.09;SB=84.39	GT:AD:DP:GL:GQ	0/1:109,55:126:-108.24,-37.95,-362.57:99
+chr1	806273	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=0;HaplotypeScore=24.82;MQ=48.14;MQ0=9;OQ=549.55;QD=3.23;SB=88.59	GT:AD:DP:GL:GQ	0/1:119,51:130:-97.39,-39.15,-372.33:99
+chr1	806316	.	T	G	0.95	PASS	AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=0;HaplotypeScore=6.00;MQ=41.01;MQ0=11;OQ=1685.25;QD=7.49;SB=-248.74	GT:AD:DP:GL:GQ	0/1:86,139:148:-216.38,-44.57,-322.16:99
+chr1	806332	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=267;Dels=0.00;HRun=0;HaplotypeScore=118.47;MQ=40.66;MQ0=10;OQ=669.93;QD=2.51;SB=-242.01	GT:AD:DP:GL:GQ	0/1:204,61:176:-123.31,-53.03,-632.31:99
+chr1	806338	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=0;HaplotypeScore=122.42;MQ=40.64;MQ0=8;OQ=2439.01;QD=9.17;SB=-856.79	GT:AD:DP:GL:GQ	0/1:98,144:180:-333.38,-86.20,-389.89:99
+chr1	806349	.	G	A	3132.30	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=280;Dels=0.07;HRun=0;HaplotypeScore=186.48;MQ=39.25;MQ0=4;QD=11.19;SB=-1153.15	GT:AD:DP:GL:GQ	0/1:91,170:182:-371.34,-54.83,-329.61:99
+chr1	806378	rs61768241	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=371;Dels=0.00;HRun=0;HaplotypeScore=37.20;MQ=35.74;MQ0=10;OQ=1136.07;QD=3.06;SB=-392.71	GT:AD:DP:GL:GQ	0/1:284,87:244:-190.38,-73.49,-742.15:99
+chr1	806405	.	A	T	171.83	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=402;Dels=0.02;HRun=5;HaplotypeScore=383.28;MQ=34.90;MQ0=14;QD=0.43;SB=-100.81	GT:AD:DP:GL:GQ	0/1:350,43:240:-91.25,-70.78,-803.92:99
+chr1	806411	.	A	T	5745.19	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=405;Dels=0.00;HRun=5;HaplotypeScore=552.66;MQ=35.31;MQ0=14;QD=14.19;SB=-2306.85	GT:AD:DP:GL:GQ	0/1:102,301:243:-573.52,-72.58,-344.41:99
+chr1	806412	.	A	T	2395.75	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=407;Dels=0.00;HRun=0;HaplotypeScore=506.57;MQ=35.27;MQ0=14;QD=5.89;SB=-1049.34	GT:AD:DP:GL:GQ	0/1:219,186:244:-315.74,-72.89,-600.57:99
+chr1	806419	.	G	T	930.64	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=433;Dels=0.00;HRun=4;HaplotypeScore=220.68;MQ=34.42;MQ0=17;QD=2.15;SB=-419.01	GT:AD:DP:GL:GQ	0/1:342,91:258:-174.05,-77.70,-758.54:99
+chr1	806424	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=450;Dels=0.00;HRun=4;HaplotypeScore=249.41;MQ=33.94;MQ0=20;OQ=971.28;QD=2.16;SB=-437.51	GT:AD:DP:GL:GQ	0/1:358,92:263:-179.62,-79.21,-806.78:99
+chr1	806430	rs61768242	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=441;Dels=0.01;HRun=1;HaplotypeScore=160.65;MQ=34.18;MQ0=22;OQ=1511.20;QD=3.43;SB=-624.36	GT:AD:DP:GL:GQ	0/1:304,134:257:-231.81,-77.41,-730.64:99
+chr1	806460	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=368;Dels=0.01;HRun=0;HaplotypeScore=18.13;MQ=35.78;MQ0=21;OQ=826.67;QD=2.25;SB=-89.07	GT:AD:DP:GL:GQ	0/1:306,59:217:-150.70,-64.75,-660.76:99
+chr1	806471	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=38.11;MQ0=12;OQ=2295.87;QD=7.92;SB=-836.85	GT:AD:DP:GL:GQ	0/1:88,202:166:-282.86,-49.99,-314.28:99
+chr1	806472	.	T	G	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=284;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=38.55;MQ0=12;OQ=2108.07;QD=7.42;SB=-683.52	GT:AD:DP:GL:GQ	0/1:91,193:165:-263.78,-49.69,-338.75:99
+chr1	806498	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=2;HaplotypeScore=28.30;MQ=42.69;MQ0=9;OQ=436.81;QD=2.11;SB=-20.91	GT:AD:DP:GL:GQ	0/1:161,46:144:-90.38,-43.41,-400.65:99
+chr1	806543	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=1;HaplotypeScore=100.50;MQ=43.92;MQ0=14;OQ=975.93;QD=5.00;SB=-107.11	GT:AD:DP:GL:GQ	0/1:89,101:124:-149.49,-48.61,-281.82:99
+chr1	806545	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=211;Dels=0.00;HRun=0;HaplotypeScore=104.33;MQ=43.14;MQ0=16;OQ=1451.12;QD=6.88;SB=-262.10	GT:AD:DP:GL:GQ	0/1:103,108:137:-189.66,-41.27,-324.56:99
+chr1	806559	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=338;Dels=0.00;HRun=5;HaplotypeScore=96.33;MQ=38.72;MQ0=24;OQ=1155.72;QD=3.42;SB=-374.82	GT:AD:DP:GL:GQ	0/1:243,83:209:-199.57,-80.72,-560.52:99
+chr1	806579	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=382;Dels=0.00;HRun=0;HaplotypeScore=77.21;MQ=36.57;MQ0=25;OQ=319.95;QD=0.84;SB=31.35	GT:AD:DP:GL:GQ	0/1:306,63:241:-152.76,-117.48,-790.42:99
+chr1	806588	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=408;Dels=0.00;HRun=0;HaplotypeScore=158.67;MQ=35.58;MQ0=25;OQ=4390.20;QD=10.76;SB=-833.37	GT:AD:DP:GL:GQ	0/1:156,252:245:-438.02,-73.80,-510.93:99
+chr1	806591	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=423;Dels=0.00;HRun=0;HaplotypeScore=153.73;MQ=35.14;MQ0=25;OQ=116.80;QD=0.28;SB=22.12	GT:AD:DP:GL:GQ	0/1:359,64:250:-90.26,-75.29,-922.92:99
+chr1	806599	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=465;Dels=0.00;HRun=3;HaplotypeScore=92.78;MQ=34.88;MQ0=25;OQ=533.96;QD=1.15;SB=-62.62	GT:AD:DP:GL:GQ	0/1:398,67:259:-134.68,-78.00,-790.36:99
+chr1	806614	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=552;Dels=0.00;HRun=4;HaplotypeScore=128.97;MQ=33.43;MQ0=27;OQ=171.34;QD=0.31;SB=81.53	GT:AD:DP:GL:GQ	0/1:512,39:328:-122.57,-102.16,-1083.77:99
+chr1	806616	.	A	C	48.77	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=560;Dels=0.00;HRun=0;HaplotypeScore=145.79;MQ=33.35;MQ0=27;QD=0.09;SB=125.19	GT:AD:DP:GL:GQ	0/1:521,38:333:-108.15,-99.99,-1104.08:81.61
+chr1	806647	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=500;Dels=0.00;HRun=1;HaplotypeScore=106.37;MQ=33.16;MQ0=15;OQ=6479.54;QD=12.96;SB=-2653.75	GT:AD:DP:GL:GQ	0/1:87,413:252:-646.95,-75.89,-317.53:99
+chr1	806652	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=463;Dels=0.00;HRun=0;HaplotypeScore=119.18;MQ=33.47;MQ0=16;OQ=6167.91;QD=13.32;SB=-2596.35	GT:AD:DP:GL:GQ	0/1:76,386:224:-615.79,-67.46,-279.43:99
+chr1	806659	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=412;Dels=0.00;HRun=0;HaplotypeScore=138.09;MQ=33.68;MQ0=14;OQ=4821.66;QD=11.70;SB=-2064.94	GT:AD:DP:GL:GQ	0/1:127,285:208:-481.17,-62.64,-276.81:99
+chr1	806663	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=403;Dels=0.00;HRun=1;HaplotypeScore=116.74;MQ=34.29;MQ0=14;OQ=4902.23;QD=12.16;SB=-2019.44	GT:AD:DP:GL:GQ	0/1:76,327:212:-489.22,-63.85,-279.67:99
+chr1	806698	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=346;Dels=0.00;HRun=0;HaplotypeScore=104.08;MQ=36.06;MQ0=23;OQ=205.16;QD=0.59;SB=41.51	GT:AD:DP:GL:GQ	0/1:305,41:216:-88.85,-65.05,-740.73:99
+chr1	806719	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=212;Dels=0.00;HRun=0;HaplotypeScore=400.08;MQ=40.22;MQ0=20;OQ=582.43;QD=2.75;SB=89.75	GT:AD:DP:GL:GQ	0/1:145,66:134:-101.59,-40.07,-419.05:99
+chr1	806735	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=218;Dels=0.00;HRun=0;HaplotypeScore=24.14;MQ=41.77;MQ0=24;OQ=129.16;QD=0.59;SB=143.49	GT:AD:DP:GL:GQ	0/1:169,49:138:-57.78,-41.58,-482.40:99
+chr1	806755	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=0;HaplotypeScore=72.66;MQ=42.05;MQ0=23;OQ=1702.34;QD=7.99;SB=-97.29	GT:AD:DP:GL:GQ	0/1:86,127:148:-218.09,-44.57,-348.93:99
+chr1	806758	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=212;Dels=0.00;HRun=0;HaplotypeScore=66.82;MQ=42.51;MQ0=24;OQ=101.05;QD=0.48;SB=140.48	GT:AD:DP:GL:GQ	0/1:180,31:147:-57.67,-44.28,-533.12:99
+chr1	806774	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=0;HaplotypeScore=33.98;MQ=43.76;MQ0=28;OQ=1370.17;QD=7.29;SB=4.43	GT:AD:DP:GL:GQ	0/1:94,94:136:-181.26,-40.96,-326.53:99
+chr1	806807	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=247;Dels=0.00;HRun=1;HaplotypeScore=84.17;MQ=41.43;MQ0=32;OQ=1901.04;QD=7.70;SB=-364.66	GT:AD:DP:GL:GQ	0/1:93,133:161:-255.61,-62.23,-399.73:99
+chr1	806819	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=264;Dels=0.00;HRun=1;HaplotypeScore=51.78;MQ=39.46;MQ0=35;OQ=117.55;QD=0.45;SB=-52.87	GT:AD:DP:GL:GQ	0/1:235,29:167:-65.33,-50.29,-569.53:99
+chr1	806835	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=0;HaplotypeScore=24.93;MQ=38.15;MQ0=32;OQ=3184.79;QD=11.46;SB=-1086.54	GT:AD:DP:GL:GQ	0/1:75,203:179:-375.67,-53.91,-276.38:99
+chr1	806857	.	A	G	426.69	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=388;Dels=0.00;HRun=0;HaplotypeScore=416.26;MQ=36.42;MQ0=33;QD=1.10;SB=-205.00	GT:AD:DP:GL:GQ	0/1:336,52:260:-124.27,-78.32,-915.07:99
+chr1	806858	.	A	C	2180.12	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=390;Dels=0.00;HRun=1;HaplotypeScore=419.10;MQ=36.36;MQ0=33;QD=5.59;SB=-410.18	GT:AD:DP:GL:GQ	0/1:135,134:259:-523.35,-302.06,-691.29:99
+chr1	806860	.	T	C	364.40	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=414;Dels=0.02;HRun=1;HaplotypeScore=391.10;MQ=36.35;MQ0=33;QD=0.88;SB=-200.49	GT:AD:DP:GL:GQ	0/1:360,44:277:-126.33,-86.61,-1004.70:99
+chr1	806864	.	G	A	1874.70	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=430;Dels=0.00;HRun=0;HaplotypeScore=443.75;MQ=36.02;MQ0=32;QD=4.36;SB=-378.35	GT:AD:DP:GL:GQ	0/1:340,90:284:-276.29,-85.54,-766.79:99
+chr1	806872	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=439;Dels=0.00;HRun=3;HaplotypeScore=61.91;MQ=35.95;MQ0=27;OQ=241.94;QD=0.55;SB=-56.85	GT:AD:DP:GL:GQ	0/1:394,45:294:-116.03,-88.55,-994.05:99
+chr1	806914	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=433;Dels=0.00;HRun=1;HaplotypeScore=82.84;MQ=36.13;MQ0=15;OQ=91.45;QD=0.21;SB=145.33	GT:AD:DP:GL:GQ	0/1:380,53:292:-100.38,-87.95,-1073.99:99
+chr1	806929	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=394;Dels=0.00;HRun=1;HaplotypeScore=53.78;MQ=36.16;MQ0=12;OQ=628.62;QD=1.60;SB=165.96	GT:AD:DP:GL:GQ	0/1:300,94:257:-143.55,-77.40,-778.57:99
+chr1	806933	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=384;Dels=0.00;HRun=1;HaplotypeScore=52.56;MQ=36.30;MQ0=13;OQ=624.21;QD=1.63;SB=148.11	GT:AD:DP:GL:GQ	0/1:298,86:253:-141.91,-76.20,-801.85:99
+chr1	807097	rs4970387	A	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=141;Dels=0.00;HRun=4;HaplotypeScore=35.71;MQ=49.47;MQ0=9;OQ=3569.50;QD=25.32;SB=-1647.14	GT:AD:DP:GL:GQ	1/1:0,141:95:-355.95,-28.62,-0.03:99
+chr1	807120	.	C	T	28.74	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=5;HaplotypeScore=8.47;MQ=47.00;MQ0=10;QD=0.19;SB=107.30	GT:AD:DP:GL:GQ	0/1:82,66:90:-33.27,-27.11,-295.41:61.57
+chr1	807127	.	C	G	240.31	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=32.57;MQ=46.64;MQ0=10;QD=1.61;SB=107.38	GT:AD:DP:GL:GQ	0/1:80,69:92:-55.04,-27.72,-340.23:99
+chr1	807132	.	T	C	652.10	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=1;HaplotypeScore=41.20;MQ=46.24;MQ0=10;QD=4.29;SB=107.38	GT:AD:DP:GL:GQ	0/1:77,75:102:-99.22,-30.73,-310.86:99
+chr1	807136	.	C	A	59.03	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=2;HaplotypeScore=75.46;MQ=45.64;MQ0=10;QD=0.36;SB=6.21	GT:AD:DP:GL:GQ	0/1:135,27:108:-41.72,-32.53,-330.47:91.87
+chr1	807137	.	T	G	132.15	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=74.46;MQ=45.79;MQ0=10;QD=0.83;SB=113.39	GT:AD:DP:GL:GQ	0/1:140,19:114:-50.84,-34.34,-356.98:99
+chr1	807144	.	G	C	321.19	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=33.44;MQ=44.89;MQ0=10;QD=1.96;SB=17.66	GT:AD:DP:GL:GQ	0/1:131,27:122:-82.39,-46.99,-445.41:99
+chr1	807168	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=236.47;MQ=42.45;MQ0=9;OQ=1209.57;QD=6.91;SB=-394.74	GT:AD:DP:GL:GQ	0/1:124,51:131:-163.71,-39.47,-414.74:99
+chr1	807169	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=262.45;MQ=42.56;MQ0=9;OQ=108.48;QD=0.61;SB=74.80	GT:AD:DP:GL:GQ	0/1:162,17:135:-54.79,-40.66,-456.43:99
+chr1	807188	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=186;Dels=0.01;HRun=8;HaplotypeScore=227.66;MQ=43.88;MQ0=1;OQ=1264.52;QD=6.80;SB=-460.79	GT:AD:DP:GL:GQ	0/1:118,67:149:-174.32,-44.58,-377.47:99
+chr1	807190	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=0;HaplotypeScore=246.34;MQ=43.75;MQ0=1;OQ=529.31;QD=2.86;SB=137.46	GT:AD:DP:GL:GQ	0/1:148,37:145:-99.89,-43.67,-443.33:99
+chr1	807204	.	A	C	36.37	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=0;HaplotypeScore=12.98;MQ=42.45;MQ0=6;QD=0.19;SB=109.90	GT:AD:DP:GL:GQ	0/1:167,21:153:-53.00,-46.08,-519.54:69.21
+chr1	807245	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=1;HaplotypeScore=17.90;MQ=38.97;MQ0=18;OQ=1145.58;QD=6.94;SB=-550.34	GT:AD:DP:GL:GQ	0/1:87,78:121:-154.28,-36.44,-312.35:99
+chr1	807259	.	G	A	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=39.36;MQ0=20;OQ=646.71;QD=4.25;SB=-192.93	GT:AD:DP:GL:GQ	0/1:96,56:108:-100.48,-32.53,-300.21:99
+chr1	807350	rs4082611	G	A	0.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=9.97;MQ=44.42;MQ0=8;OQ=866.67;QD=5.70;SB=98.31	GT:AD:DP:GL:GQ	0/1:80,69:106:-125.51,-35.56,-282.07:99
+chr1	807353	.	C	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=8.92;MQ=43.77;MQ0=8;OQ=867.33;QD=5.45;SB=95.29	GT:AD:DP:GL:GQ	0/1:76,83:108:-122.54,-32.52,-265.26:99
+chr1	807384	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=0;HaplotypeScore=61.52;MQ=40.31;MQ0=13;OQ=503.09;QD=2.47;SB=116.39	GT:AD:DP:GL:GQ	0/1:145,57:132:-93.37,-39.78,-338.75:99
+chr1	807385	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=1;HaplotypeScore=61.52;MQ=40.32;MQ0=13;OQ=1779.01;QD=8.76;SB=73.73	GT:AD:DP:GL:GQ	0/1:76,126:131:-220.64,-39.46,-278.09:99
+chr1	807400	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=1;HaplotypeScore=26.31;MQ=38.88;MQ0=12;OQ=2472.80;QD=10.18;SB=76.74	GT:AD:DP:GL:GQ	0/1:81,162:155:-297.25,-46.69,-297.33:99
+chr1	807412	rs4082610	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=262;Dels=0.00;HRun=4;HaplotypeScore=30.19;MQ=38.31;MQ0=9;OQ=2516.42;QD=9.60;SB=119.38	GT:AD:DP:GL:GQ	0/1:109,153:168:-305.53,-50.60,-311.50:99
+chr1	807432	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=262;Dels=0.00;HRun=0;HaplotypeScore=25.55;MQ=38.32;MQ0=6;OQ=4433.84;QD=16.92;SB=-160.81	GT:AD:DP:GL:GQ	0/1:80,182:176:-442.38,-53.03,-343.20:99
+chr1	807469	.	C	T	416.75	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=210;Dels=0.00;HRun=0;HaplotypeScore=92.28;MQ=41.14;MQ0=1;QD=1.98;SB=-49.34	GT:AD:DP:GL:GQ	0/1:84,126:97:-74.18,-29.22,-280.73:99
+chr1	807471	.	A	C	318.15	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=2;HaplotypeScore=90.45;MQ=41.29;MQ0=1;QD=1.49;SB=-31.35	GT:AD:DP:GL:GQ	0/1:85,128:99:-64.91,-29.81,-297.50:99
+chr1	807475	.	C	T	356.15	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=0;HaplotypeScore=174.77;MQ=40.93;MQ0=2;QD=1.67;SB=-36.29	GT:AD:DP:GL:GQ	0/1:85,128:101:-69.35,-30.45,-273.00:99
+chr1	807484	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=1;HaplotypeScore=266.19;MQ=40.31;MQ0=2;OQ=100.09;QD=0.47;SB=95.09	GT:AD:DP:GL:GQ	0/1:168,47:127:-51.55,-38.26,-450.15:99
+chr1	807508	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=1;HaplotypeScore=7.00;MQ=41.28;MQ0=4;OQ=211.72;QD=1.14;SB=90.69	GT:AD:DP:GL:GQ	0/1:142,43:119:-60.30,-35.84,-379.49:99
+chr1	807527	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=161;Dels=0.00;HRun=2;HaplotypeScore=9.95;MQ=41.68;MQ0=7;OQ=177.85;QD=1.10;SB=146.44	GT:AD:DP:GL:GQ	0/1:119,42:108:-53.60,-32.53,-346.10:99
+chr1	807556	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=1;HaplotypeScore=66.91;MQ=41.77;MQ0=6;OQ=532.40;QD=3.89;SB=-236.01	GT:AD:DP:GL:GQ	0/1:68,69:85:-82.13,-25.60,-230.23:99
+chr1	807561	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=140;Dels=0.00;HRun=0;HaplotypeScore=70.93;MQ=41.65;MQ0=7;OQ=124.65;QD=0.89;SB=101.32	GT:AD:DP:GL:GQ	0/1:96,44:87:-41.95,-26.20,-282.69:99
+chr1	807571	rs34106744	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=3;HaplotypeScore=33.63;MQ=41.31;MQ0=9;OQ=377.46;QD=2.80;SB=-157.65	GT:AD:DP:GL:GQ	0/1:62,73:80:-65.12,-24.09,-230.06:99
+chr1	807588	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=29.86;MQ=39.35;MQ0=12;OQ=1527.96;QD=9.32;SB=-255.65	GT:AD:DP:GL:GQ	0/1:60,104:105:-187.72,-31.65,-191.88:99
+chr1	807611	.	G	C	0.98	PASS	AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=7.78;MQ=38.64;MQ0=13;OQ=1984.90;QD=11.81;SB=-213.08	GT:AD:DP:GL:GQ	0/1:60,108:111:-235.21,-33.44,-245.33:99
+chr1	807628	.	G	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=0;HaplotypeScore=15.09;MQ=38.17;MQ0=13;OQ=1889.96;QD=9.74;SB=-59.93	GT:AD:DP:GL:GQ	0/1:68,126:123:-229.33,-37.05,-239.27:99
+chr1	807662	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=324;Dels=0.00;HRun=0;HaplotypeScore=5.25;MQ=35.02;MQ0=24;OQ=5029.36;QD=15.52;SB=-1355.57	GT:AD:DP:GL:GQ	0/1:79,245:206:-501.94,-62.04,-299.38:99
+chr1	807698	rs61768243	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=413;Dels=0.00;HRun=1;HaplotypeScore=119.83;MQ=33.65;MQ0=41;OQ=7356.92;QD=17.81;SB=-2911.42	GT:AD:DP:GL:GQ	0/1:85,328:252:-734.69,-75.92,-368.28:99
+chr1	807726	rs61768244	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=451;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=33.55;MQ0=36;OQ=2315.76;QD=5.13;SB=-928.19	GT:AD:DP:GL:GQ	0/1:303,148:263:-314.08,-79.22,-727.35:99
+chr1	807759	rs4034377	A	C	755.20	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=336;Dels=0.00;HRun=0;HaplotypeScore=236.06;MQ=33.74;MQ0=39;QD=2.25;SB=-109.97	GT:AD:DP:GL:GQ	0/1:260,76:175:-131.50,-52.70,-521.92:99
+chr1	807761	.	A	G	2451.79	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=328;Dels=0.00;HRun=0;HaplotypeScore=310.08;MQ=33.84;MQ0=39;QD=7.47;SB=-739.45	GT:AD:DP:GL:GQ	0/1:164,163:171:-299.96,-51.50,-359.62:99
+chr1	807766	rs3969819	A	C	564.07	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=320;Dels=0.00;HRun=0;HaplotypeScore=284.38;MQ=33.76;MQ0=45;QD=1.76;SB=-303.05	GT:AD:DP:GL:GQ	0/1:266,53:164:-109.08,-49.39,-509.36:99
+chr1	807787	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=301;Dels=0.00;HRun=1;HaplotypeScore=10.94;MQ=35.09;MQ0=34;OQ=678.04;QD=2.25;SB=50.87	GT:AD:DP:GL:GQ	0/1:179,122:124:-108.43,-37.34,-358.12:99
+chr1	807799	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=330;Dels=0.00;HRun=1;HaplotypeScore=46.01;MQ=35.31;MQ0=34;OQ=1300.39;QD=3.94;SB=-358.87	GT:AD:DP:GL:GQ	0/1:191,139:161:-181.81,-48.48,-410.83:99
+chr1	807817	rs4034379	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=305;Dels=0.00;HRun=0;HaplotypeScore=40.59;MQ=36.43;MQ0=47;OQ=1097.69;QD=3.60;SB=-508.19	GT:AD:DP:GL:GQ	0/1:205,100:154:-159.44,-46.39,-521.49:99
+chr1	807831	rs4034380	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=324;Dels=0.00;HRun=0;HaplotypeScore=53.25;MQ=36.07;MQ0=54;OQ=860.18;QD=2.65;SB=-52.35	GT:AD:DP:GL:GQ	0/1:235,89:165:-139.00,-49.70,-477.57:99
+chr1	807843	rs61768247	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=340;Dels=0.00;HRun=3;HaplotypeScore=25.24;MQ=35.61;MQ0=59;OQ=2917.98;QD=8.58;SB=-1176.92	GT:AD:DP:GL:GQ	0/1:93,247:179:-348.99,-53.91,-340.62:99
+chr1	807878	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=340;Dels=0.00;HRun=3;HaplotypeScore=1.68;MQ=33.99;MQ0=59;OQ=2636.13;QD=7.75;SB=-1148.59	GT:AD:DP:GL:GQ	0/1:141,199:182:-321.71,-54.82,-379.20:99
+chr1	807900	rs61768248	A	G	107.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=254;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=36.51;MQ0=52;OQ=2423.92;QD=9.54;SB=-510.71	GT:AD:DP:GL:GQ	0/1:72,182:155:-292.36,-46.69,-288.83:99
+chr1	807921	rs4034381	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=238;Dels=0.00;HRun=0;HaplotypeScore=52.91;MQ=37.12;MQ0=38;OQ=730.38;QD=3.07;SB=87.15	GT:AD:DP:GL:GQ	0/1:169,69:152:-122.12,-45.80,-464.61:99
+chr1	807923	rs2311679	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=238;Dels=0.00;HRun=1;HaplotypeScore=53.91;MQ=36.90;MQ0=37;OQ=150.90;QD=0.63;SB=114.49	GT:AD:DP:GL:GQ	0/1:205,33:149:-63.25,-44.87,-483.89:99
+chr1	807940	rs61768249	C	T	132.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=201;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=39.52;MQ0=18;OQ=2365.28;QD=11.77;SB=-227.57	GT:AD:DP:GL:GQ	0/1:70,131:135:-280.47,-40.66,-242.20:99
+chr1	807969	.	G	T	0.34	PASS	AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=0;HaplotypeScore=3.99;MQ=40.13;MQ0=16;OQ=852.49;QD=4.24;SB=25.59	GT:AD:DP:GL:GQ	0/1:139,62:138:-130.10,-41.57,-369.51:99
+chr1	807986	.	G	A	410.65	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=0;HaplotypeScore=37.75;MQ=40.61;MQ0=11;QD=2.15;SB=32.93	GT:AD:DP:GL:GQ	0/1:73,117:91:-71.78,-27.44,-235.41:99
+chr1	807989	.	A	G	41.79	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=1;HaplotypeScore=63.74;MQ=41.32;MQ0=11;QD=0.24;SB=71.44	GT:AD:DP:GL:GQ	0/1:71,104:80:-31.56,-24.09,-295.20:74.62
+chr1	807990	.	G	T	63.48	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=1;HaplotypeScore=63.74;MQ=41.32;MQ0=11;QD=0.36;SB=71.41	GT:AD:DP:GL:GQ	0/1:71,104:79:-33.42,-23.79,-250.10:96.32
+chr1	808001	rs2311681	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.00;HRun=1;HaplotypeScore=145.95;MQ=39.96;MQ0=12;OQ=189.55;QD=1.02;SB=-28.87	GT:AD:DP:GL:GQ	0/1:68,100:81:-53.53,-31.29,-271.83:99
+chr1	808002	.	C	T	30.08	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=1;HaplotypeScore=147.95;MQ=39.81;MQ0=12;QD=0.16;SB=5.97	GT:AD:DP:GL:GQ	0/1:124,64:83:-31.29,-25.00,-266.30:62.91
+chr1	808027	rs3969820	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=178;Dels=0.00;HRun=0;HaplotypeScore=57.38;MQ=38.17;MQ0=19;OQ=723.18;QD=4.06;SB=-165.45	GT:AD:DP:GL:GQ	0/1:134,44:108:-108.14,-32.53,-287.08:99
+chr1	808030	.	A	G	1086.71	DPFilter;HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=167;Dels=0.00;HRun=0;HaplotypeScore=42.92;MQ=38.47;MQ0=18;QD=6.51;SB=-568.31	GT:AD:DP:GL:GQ	0/1:57,109:99:-141.80,-29.84,-220.97:99
+chr1	808043	.	A	G	970.86	DPFilter;HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=1;HaplotypeScore=39.52;MQ=39.24;MQ0=20;QD=6.11;SB=-490.82	GT:AD:DP:GL:GQ	0/1:58,101:92:-128.08,-27.71,-229.15:99
+chr1	808058	rs4068670	A	G	19.55	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=148;Dels=0.00;HRun=0;HaplotypeScore=41.67;MQ=39.19;MQ0=26;QD=0.13;SB=-33.62	GT:AD:DP:GL:GQ	0/1:54,74:61:-37.68,-32.44,-211.21:52.34
+chr1	808064	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=1;HaplotypeScore=40.55;MQ=38.61;MQ0=24;OQ=246.33;QD=1.85;SB=-81.77	GT:AD:DP:GL:GQ	0/1:48,85:54:-44.19,-16.27,-162.59:99
+chr1	808071	.	C	T	20.12	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=40.24;MQ=40.16;MQ0=22;QD=0.15;SB=14.54	GT:AD:DP:GL:GQ	0/1:54,82:58:-22.76,-17.47,-182.75:52.91
+chr1	808112	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=227;Dels=0.00;HRun=2;HaplotypeScore=125.36;MQ=37.91;MQ0=32;OQ=1776.62;QD=7.83;SB=-160.46	GT:AD:DP:GL:GQ	0/1:73,153:125:-218.60,-37.66,-274.51:99
+chr1	808131	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=257;Dels=0.00;HRun=1;HaplotypeScore=46.49;MQ=37.72;MQ0=22;OQ=2127.72;QD=8.28;SB=-282.13	GT:AD:DP:GL:GQ	0/1:106,150:146:-260.04,-43.99,-307.83:99
+chr1	808143	rs2871830	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=266;Dels=0.00;HRun=0;HaplotypeScore=22.61;MQ=37.96;MQ0=21;OQ=255.61;QD=0.96;SB=23.44	GT:AD:DP:GL:GQ	0/1:214,51:151:-74.35,-45.50,-504.23:99
+chr1	808170	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=251;Dels=0.00;HRun=1;HaplotypeScore=39.92;MQ=39.75;MQ0=13;OQ=386.02;QD=1.54;SB=116.39	GT:AD:DP:GL:GQ	0/1:201,50:155:-88.58,-46.69,-468.07:99
+chr1	808187	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=220;Dels=0.00;HRun=7;HaplotypeScore=162.06;MQ=41.27;MQ0=11;OQ=363.00;QD=1.65;SB=17.72	GT:AD:DP:GL:GQ	0/1:176,44:136:-80.56,-40.98,-399.39:99
+chr1	808189	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=0;HaplotypeScore=288.29;MQ=41.39;MQ0=11;OQ=708.25;QD=3.28;SB=-149.01	GT:AD:DP:GL:GQ	0/1:142,53:138:-146.61,-72.50,-410.59:99
+chr1	808297	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=196;Dels=0.00;HRun=0;HaplotypeScore=21.45;MQ=38.78;MQ0=17;OQ=1228.84;QD=6.27;SB=-563.99	GT:AD:DP:GL:GQ	0/1:75,120:104:-157.52,-31.35,-213.62:99
+chr1	808336	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=1;HaplotypeScore=34.12;MQ=34.50;MQ0=28;OQ=414.84;QD=1.47;SB=-185.55	GT:AD:DP:GL:GQ	0/1:228,54:155:-91.47,-46.70,-585.75:99
+chr1	808347	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=0;HaplotypeScore=78.29;MQ=34.29;MQ0=30;OQ=600.10;QD=2.16;SB=-67.28	GT:AD:DP:GL:GQ	0/1:221,39:151:-138.41,-75.12,-545.71:99
+chr1	808349	rs61768250	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=274;Dels=0.00;HRun=0;HaplotypeScore=172.09;MQ=34.47;MQ0=30;OQ=2858.46;QD=10.43;SB=-822.44	GT:AD:DP:GL:GQ	0/1:82,190:149:-334.02,-44.89,-232.77:99
+chr1	808359	.	C	T	950.38	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=269;Dels=0.00;HRun=0;HaplotypeScore=192.43;MQ=34.52;MQ0=31;QD=3.53;SB=-243.11	GT:AD:DP:GL:GQ	0/1:178,83:148:-142.90,-44.58,-399.15:99
+chr1	808362	.	G	A	76.04	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=113.80;MQ=34.64;MQ0=30;QD=0.28;SB=96.15	GT:AD:DP:GL:GQ	0/1:234,29:151:-56.37,-45.49,-495.71:99
+chr1	808363	.	C	A	14.91	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=113.80;MQ=34.60;MQ0=34;QD=0.05;SB=125.29	GT:AD:DP:GL:GQ	0/1:250,29:157:-52.05,-47.29,-518.11:47.61
+chr1	808367	.	G	A	731.54	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=0;HaplotypeScore=120.25;MQ=34.34;MQ0=33;QD=2.52;SB=-82.29	GT:AD:DP:GL:GQ	0/1:229,61:165:-126.14,-49.70,-491.32:99
+chr1	808394	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=235;Dels=0.00;HRun=0;HaplotypeScore=10.16;MQ=37.74;MQ0=26;OQ=126.55;QD=0.54;SB=56.98	GT:AD:DP:GL:GQ	0/1:188,47:147:-60.25,-44.31,-434.17:99
+chr1	808413	.	T	G	317.98	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=2;HaplotypeScore=72.86;MQ=40.13;MQ0=20;QD=1.94;SB=-24.43	GT:AD:DP:GL:GQ	0/1:121,43:105:-66.71,-31.62,-317.98:99
+chr1	808417	.	G	A	68.93	DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=67.03;MQ=42.13;MQ0=16;QD=0.46;SB=83.26	GT:AD:DP:GL:GQ	0/1:135,13:103:-41.21,-31.03,-340.99:99
+chr1	808421	.	G	A	1042.35	DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=46.56;MQ=44.72;MQ0=15;QD=7.72;SB=-112.51	GT:AD:DP:GL:GQ	0/1:67,68:99:-137.34,-29.83,-234.94:99
+chr1	808447	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=2;HaplotypeScore=11.26;MQ=49.75;MQ0=9;OQ=392.50;QD=3.54;SB=-21.38	GT:AD:DP:GL:GQ	0/1:71,40:86:-68.46,-25.93,-223.10:99
+chr1	808451	.	A	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=1;HaplotypeScore=9.78;MQ=50.21;MQ0=9;OQ=368.72;QD=3.29;SB=-63.61	GT:AD:DP:GL:GQ	0/1:73,39:88:-66.66,-26.51,-263.45:99
+chr1	808566	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=42.07;MQ=40.72;MQ0=9;OQ=262.25;QD=1.45;SB=83.19	GT:AD:DP:GL:GQ	0/1:73,108:86:-55.43,-25.93,-233.09:99
+chr1	808594	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=249;Dels=0.00;HRun=0;HaplotypeScore=18.85;MQ=37.64;MQ0=16;OQ=690.50;QD=2.77;SB=110.37	GT:AD:DP:GL:GQ	0/1:80,169:110:-105.47,-33.14,-280.23:99
+chr1	808641	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=283;Dels=0.00;HRun=1;HaplotypeScore=21.83;MQ=33.64;MQ0=19;OQ=2063.93;QD=7.29;SB=28.04	GT:AD:DP:GL:GQ	0/1:72,211:133:-249.73,-40.06,-265.59:99
+chr1	808664	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=245;Dels=0.00;HRun=1;HaplotypeScore=236.43;MQ=34.77;MQ0=16;OQ=159.51;QD=0.65;SB=12.22	GT:AD:DP:GL:GQ	0/1:197,22:147:-105.83,-86.60,-492.17:99
+chr1	808677	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=233;Dels=0.00;HRun=0;HaplotypeScore=83.64;MQ=35.28;MQ0=11;OQ=206.00;QD=0.88;SB=113.55	GT:AD:DP:GL:GQ	0/1:190,43:144:-67.26,-43.38,-499.53:99
+chr1	808728	.	C	A	203.60	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=1;HaplotypeScore=31.96;MQ=45.04;MQ0=12;QD=1.82;SB=15.39	GT:AD:DP:GL:GQ	0/1:87,25:80:-47.74,-24.10,-238.32:99
+chr1	808731	.	C	T	444.24	SnpCluster	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=24.97;MQ=46.65;MQ0=11;QD=4.04;SB=-165.40	GT:AD:DP:GL:GQ	0/1:69,41:86:-73.64,-25.93,-224.50:99
+chr1	808732	.	G	A	408.16	SnpCluster	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=24.97;MQ=46.65;MQ0=11;QD=3.71;SB=-130.98	GT:AD:DP:GL:GQ	0/1:69,41:85:-69.72,-25.62,-220.30:99
+chr1	808802	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=47.94;MQ=46.85;MQ0=10;OQ=50.85;QD=0.45;SB=55.37	GT:AD:DP:GL:GQ	0/1:67,39:74:-30.66,-22.29,-262.89:83.69
+chr1	808813	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=9.12;MQ=42.90;MQ0=8;OQ=68.22;QD=0.48;SB=65.92	GT:AD:DP:GL:GQ	0/1:121,22:85:-35.73,-25.62,-328.85:99
+chr1	808837	.	A	G	640.03	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=0;HaplotypeScore=190.29;MQ=37.94;MQ0=4;QD=3.42;SB=66.67	GT:AD:DP:GL:GQ	0/1:64,123:88:-93.80,-26.51,-252.52:99
+chr1	808839	.	G	A	725.93	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=188;Dels=0.01;HRun=3;HaplotypeScore=118.63;MQ=37.90;MQ0=4;QD=3.86;SB=63.76	GT:AD:DP:GL:GQ	0/1:65,112:89:-102.68,-26.81,-229.73:99
+chr1	808842	.	A	G	234.46	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=1;HaplotypeScore=215.12;MQ=37.45;MQ0=5;QD=1.20;SB=62.67	GT:AD:DP:GL:GQ	0/1:152,43:87:-52.93,-26.20,-300.50:99
+chr1	808844	.	C	A	211.39	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=1;HaplotypeScore=139.43;MQ=37.30;MQ0=5;QD=1.09;SB=62.33	GT:AD:DP:GL:GQ	0/1:151,43:87:-50.63,-26.20,-257.94:99
+chr1	808878	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=228;Dels=0.00;HRun=0;HaplotypeScore=11.87;MQ=35.54;MQ0=6;OQ=484.59;QD=2.13;SB=67.42	GT:AD:DP:GL:GQ	0/1:69,159:88:-78.25,-26.50,-268.80:99
+chr1	808900	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=211;Dels=0.00;HRun=0;HaplotypeScore=53.01;MQ=34.26;MQ0=7;OQ=319.52;QD=1.51;SB=101.36	GT:AD:DP:GL:GQ	0/1:68,143:78:-58.73,-23.49,-234.89:99
+chr1	808952	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=30.36;MQ0=16;OQ=684.75;QD=4.08;SB=-303.13	GT:AD:DP:GL:GQ	0/1:69,99:91:-99.17,-27.41,-260.34:99
+chr1	808969	rs57185426	C	T	0.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=167;Dels=0.00;HRun=0;HaplotypeScore=6.98;MQ=27.19;MQ0=22;OQ=1308.35;QD=7.83;SB=-543.36	GT:AD:DP:GL:GQ	0/1:64,103:97:-163.35,-29.23,-183.79:99
+chr1	809028	rs61768251	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=24.74;MQ=37.22;MQ0=19;OQ=1197.89;QD=7.88;SB=-487.91	GT:AD:DP:GL:GQ	0/1:69,83:107:-155.31,-32.23,-252.53:99
+chr1	809058	.	T	C	0.11	PASS	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=4.46;MQ=47.89;MQ0=8;OQ=300.60;QD=2.95;SB=-111.38	GT:AD:DP:GL:GQ	0/1:71,31:84:-58.65,-25.31,-262.00:99
+chr1	809087	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=12.78;MQ=44.45;MQ0=38;OQ=174.63;QD=1.20;SB=29.35	GT:AD:DP:GL:GQ	0/1:79,66:90:-47.85,-27.11,-283.45:99
+chr1	809147	.	A	G	708.22	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=385;Dels=0.00;HRun=0;HaplotypeScore=142.43;MQ=32.08;MQ0=67;QD=1.84;SB=-338.08	GT:AD:DP:GL:GQ	0/1:273,112:167:-124.42,-50.31,-531.00:99
+chr1	809152	.	A	G	2828.87	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=380;Dels=0.00;HRun=0;HaplotypeScore=142.28;MQ=32.36;MQ0=64;QD=7.44;SB=-821.16	GT:AD:DP:GL:GQ	0/1:76,304:165:-335.87,-49.70,-295.78:99
+chr1	809155	.	G	A	906.28	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=379;Dels=0.00;HRun=1;HaplotypeScore=107.83;MQ=32.25;MQ0=64;QD=2.39;SB=-437.76	GT:AD:DP:GL:GQ	0/1:271,108:165:-143.61,-49.69,-484.11:99
+chr1	809196	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=249;Dels=0.00;HRun=2;HaplotypeScore=63.80;MQ=34.67;MQ0=22;OQ=1194.90;QD=4.80;SB=-269.68	GT:AD:DP:GL:GQ	0/1:67,182:101:-153.20,-30.42,-236.52:99
+chr1	809260	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=41.08;MQ0=8;OQ=376.66;QD=3.30;SB=116.36	GT:AD:DP:GL:GQ	0/1:80,34:93:-68.96,-28.01,-266.36:99
+chr1	809273	.	T	C	463.34	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=121;Dels=0.00;HRun=0;HaplotypeScore=8.66;MQ=40.73;MQ0=7;QD=3.83;SB=119.42	GT:AD:DP:GL:GQ	0/1:85,36:100:-79.74,-30.12,-319.61:99
+chr1	809278	.	T	A	448.40	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=125;Dels=0.00;HRun=0;HaplotypeScore=9.66;MQ=40.70;MQ0=10;QD=3.59;SB=128.40	GT:AD:DP:GL:GQ	0/1:95,30:101:-78.54,-30.42,-301.76:99
+chr1	809279	.	C	A	472.08	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=0;HaplotypeScore=9.66;MQ=40.57;MQ0=10;QD=3.72;SB=128.43	GT:AD:DP:GL:GQ	0/1:97,30:103:-81.51,-31.02,-300.46:99
+chr1	809374	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=0;HaplotypeScore=40.85;MQ=49.25;MQ0=14;OQ=274.74;QD=2.18;SB=128.46	GT:AD:DP:GL:GQ	0/1:85,41:95:-59.38,-28.62,-356.10:99
+chr1	809396	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=153;Dels=0.03;HRun=0;HaplotypeScore=81.33;MQ=46.63;MQ0=11;OQ=370.18;QD=2.42;SB=128.42	GT:AD:DP:GL:GQ	0/1:90,59:107:-71.93,-31.63,-311.43:99
+chr1	809418	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=208;Dels=0.00;HRun=0;HaplotypeScore=18.59;MQ=42.45;MQ0=17;OQ=1574.87;QD=7.57;SB=-383.90	GT:AD:DP:GL:GQ	0/1:84,123:141:-203.25,-42.48,-331.17:99
+chr1	809463	.	T	C	270.15	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=218;Dels=0.00;HRun=0;HaplotypeScore=113.69;MQ=41.23;MQ0=17;QD=1.24;SB=22.33	GT:AD:DP:GL:GQ	0/1:180,37:141:-72.78,-42.48,-486.18:99
+chr1	809466	.	G	A	91.66	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=2;HaplotypeScore=122.84;MQ=41.24;MQ0=16;QD=0.43;SB=110.32	GT:AD:DP:GL:GQ	0/1:181,32:144:-55.83,-43.38,-458.71:99
+chr1	809470	.	T	C	630.75	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=208;Dels=0.00;HRun=2;HaplotypeScore=238.78;MQ=41.40;MQ0=14;QD=3.03;SB=-114.41	GT:AD:DP:GL:GQ	0/1:153,55:135:-107.03,-40.67,-427.65:99
+chr1	809480	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=183;Dels=0.00;HRun=0;HaplotypeScore=103.82;MQ=41.73;MQ0=11;OQ=1974.03;QD=10.79;SB=-338.07	GT:AD:DP:GL:GQ	0/1:66,116:122:-237.45,-36.76,-206.62:99
+chr1	809721	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=3;HaplotypeScore=9.02;MQ=53.95;MQ0=4;OQ=80.85;QD=0.86;SB=59.35	GT:AD:DP:GL:GQ	0/1:75,18:84:-36.67,-25.30,-283.82:99
+chr1	809780	rs6605057	A	G	0.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=11.81;MQ=56.13;MQ0=2;OQ=3054.85;QD=32.85;SB=-1362.55	GT:AD:DP:GL:GQ	1/1:0,93:85:-309.09,-25.60,-0.02:99
+chr1	809879	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=0;HaplotypeScore=59.97;MQ=40.35;MQ0=14;OQ=622.51;QD=3.19;SB=42.71	GT:AD:DP:GL:GQ	0/1:76,119:98:-95.05,-29.52,-272.29:99
+chr1	809895	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=1;HaplotypeScore=66.59;MQ=38.60;MQ0=19;OQ=465.46;QD=2.28;SB=92.30	GT:AD:DP:GL:GQ	0/1:110,94:92:-77.54,-27.71,-254.54:99
+chr1	809906	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=0;HaplotypeScore=107.86;MQ=38.19;MQ0=19;OQ=204.28;QD=1.02;SB=98.35	GT:AD:DP:GL:GQ	0/1:163,38:93:-51.72,-28.01,-294.59:99
+chr1	810152	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=23.45;MQ=46.60;MQ0=18;OQ=256.17;QD=1.80;SB=89.22	GT:AD:DP:GL:GQ	0/1:80,62:93:-56.93,-28.03,-260.32:99
+chr1	810179	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=166;Dels=0.00;HRun=0;HaplotypeScore=40.97;MQ=43.29;MQ0=18;OQ=423.48;QD=2.55;SB=-10.82	GT:AD:DP:GL:GQ	0/1:90,76:99:-75.44,-29.81,-289.52:99
+chr1	810200	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=157;Dels=0.00;HRun=0;HaplotypeScore=91.89;MQ=44.44;MQ0=8;OQ=93.53;QD=0.60;SB=79.37	GT:AD:DP:GL:GQ	0/1:113,44:97:-41.85,-29.21,-309.84:99
+chr1	810211	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=3;HaplotypeScore=28.81;MQ=44.83;MQ0=8;OQ=438.48;QD=2.67;SB=-23.86	GT:AD:DP:GL:GQ	0/1:92,72:104:-78.46,-31.33,-303.09:99
+chr1	810249	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=0;HaplotypeScore=54.95;MQ=45.56;MQ0=5;OQ=532.92;QD=3.29;SB=-263.19	GT:AD:DP:GL:GQ	0/1:92,70:108:-89.11,-32.53,-336.39:99
+chr1	810266	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=0;HaplotypeScore=6.95;MQ=49.31;MQ0=7;OQ=320.58;QD=2.31;SB=3.34	GT:AD:DP:GL:GQ	0/1:87,51:105:-66.97,-31.63,-352.01:99
+chr1	810282	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=2;HaplotypeScore=2.11;MQ=50.38;MQ0=7;OQ=214.82;QD=1.51;SB=75.99	GT:AD:DP:GL:GQ	0/1:98,44:111:-58.20,-33.43,-338.53:99
+chr1	810326	.	T	C	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=51.92;MQ0=10;OQ=89.69;QD=0.81;SB=59.40	GT:AD:DP:GL:GQ	0/1:87,24:95:-40.87,-28.62,-338.92:99
+chr1	810564	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=0;HaplotypeScore=14.88;MQ=44.23;MQ0=6;OQ=498.14;QD=2.90;SB=-150.99	GT:AD:DP:GL:GQ	0/1:102,70:118:-88.65,-35.55,-364.99:99
+chr1	810629	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=38.71;MQ=50.61;MQ0=2;OQ=253.97;QD=2.29;SB=-143.03	GT:AD:DP:GL:GQ	0/1:83,27:94:-56.99,-28.31,-290.69:99
+chr1	810683	.	T	C	21.46	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=45.49;MQ0=13;QD=0.17;SB=104.38	GT:AD:DP:GL:GQ	0/1:80,50:88:-31.93,-26.50,-325.33:54.27
+chr1	810696	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=154;Dels=0.00;HRun=0;HaplotypeScore=34.97;MQ=44.00;MQ0=14;OQ=294.30;QD=1.91;SB=110.32	GT:AD:DP:GL:GQ	0/1:85,69:98:-62.23,-29.52,-298.08:99
+chr1	810711	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=0;HaplotypeScore=44.23;MQ=40.46;MQ0=17;OQ=839.07;QD=4.51;SB=107.39	GT:AD:DP:GL:GQ	0/1:81,105:106:-119.13,-31.94,-347.53:99
+chr1	810733	.	C	A	43.01	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=1;HaplotypeScore=56.61;MQ=40.22;MQ0=16;QD=0.19;SB=125.38	GT:AD:DP:GL:GQ	0/1:192,33:131:-47.04,-39.45,-426.81:75.84
+chr1	810794	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=3;HaplotypeScore=52.64;MQ=44.21;MQ0=2;OQ=1066.68;QD=5.73;SB=31.06	GT:AD:DP:GL:GQ	0/1:92,94:128:-148.50,-38.55,-332.75:99
+chr1	810798	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=183;Dels=0.00;HRun=0;HaplotypeScore=60.51;MQ=44.84;MQ0=1;OQ=1224.15;QD=6.69;SB=34.50	GT:AD:DP:GL:GQ	0/1:93,90:127:-163.96,-38.27,-393.95:99
+chr1	810830	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=3;HaplotypeScore=77.56;MQ=44.23;MQ0=2;OQ=74.26;QD=0.42;SB=98.47	GT:AD:DP:GL:GQ	0/1:145,25:125:-59.06,-48.35,-399.04:99
+chr1	810842	.	C	G	7.71	PASS	AC=1;AF=0.50;AN=2;DP=180;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=44.02;MQ0=3;OQ=1687.26;QD=9.37;SB=-373.48	GT:AD:DP:GL:GQ	0/1:84,96:131:-211.48,-39.47,-372.20:99
+chr1	810901	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=76.75;MQ=45.85;MQ0=4;OQ=1193.00;QD=8.40;SB=-508.15	GT:AD:DP:GL:GQ	0/1:72,70:110:-155.72,-33.14,-263.20:99
+chr1	810906	.	T	C	38.41	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=0;HaplotypeScore=84.75;MQ=46.22;MQ0=3;QD=0.29;SB=-42.29	GT:AD:DP:GL:GQ	0/1:104,29:99:-36.95,-29.82,-359.79:71.24
+chr1	810914	rs2871831	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=29.97;MQ=47.06;MQ0=6;OQ=781.68;QD=6.20;SB=-314.19	GT:AD:DP:GL:GQ	0/1:70,55:96:-110.36,-28.91,-259.38:99
+chr1	810923	.	A	T	0.10	PASS	AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=1;HaplotypeScore=7.81;MQ=46.94;MQ0=8;OQ=838.41;QD=6.60;SB=-348.34	GT:AD:DP:GL:GQ	0/1:70,57:101:-117.55,-30.42,-266.19:99
+chr1	810974	rs61768253	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=159;Dels=0.00;HRun=0;HaplotypeScore=90.96;MQ=39.12;MQ0=31;OQ=376.97;QD=2.37;SB=-131.06	GT:AD:DP:GL:GQ	0/1:90,68:97:-70.20,-29.22,-313.33:99
+chr1	810984	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=2;HaplotypeScore=97.32;MQ=34.90;MQ0=35;OQ=108.00;QD=0.52;SB=94.23	GT:AD:DP:GL:GQ	0/1:166,41:109:-46.91,-32.83,-360.50:99
+chr1	810998	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=239;Dels=0.00;HRun=0;HaplotypeScore=73.35;MQ=33.36;MQ0=43;OQ=73.40;QD=0.31;SB=-50.06	GT:AD:DP:GL:GQ	0/1:185,54:123:-47.67,-37.04,-404.38:99
+chr1	811006	rs61768254	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=248;Dels=0.00;HRun=1;HaplotypeScore=66.91;MQ=33.49;MQ0=48;OQ=832.91;QD=3.36;SB=-277.39	GT:AD:DP:GL:GQ	0/1:106,142:128:-125.13,-38.56,-331.35:99
+chr1	811069	rs35186927	T	A	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=481;Dels=0.00;HRun=1;HaplotypeScore=3.93;MQ=31.63;MQ0=35;OQ=1139.00;QD=2.37;SB=-237.78	GT:AD:DP:GL:GQ	0/1:346,135:257:-194.59,-77.40,-784.30:99
+chr1	811112	rs2311684	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=350;Dels=0.00;HRun=0;HaplotypeScore=77.41;MQ=35.82;MQ0=8;OQ=2362.85;QD=6.75;SB=-654.92	GT:AD:DP:GL:GQ	0/1:216,134:219:-305.59,-66.02,-466.00:99
+chr1	811131	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=248;Dels=0.00;HRun=0;HaplotypeScore=87.33;MQ=41.16;MQ0=2;OQ=4074.75;QD=16.43;SB=-1430.41	GT:AD:DP:GL:GQ	0/1:100,147:200:-406.47,-62.90,-355.42:99
+chr1	811184	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=2;HaplotypeScore=27.77;MQ=43.71;MQ0=0;OQ=460.52;QD=3.74;SB=149.45	GT:AD:DP:GL:GQ	0/1:91,32:108:-81.87,-32.53,-317.70:99
+chr1	811205	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=2;HaplotypeScore=18.01;MQ=44.82;MQ0=0;OQ=329.41;QD=2.86;SB=146.50	GT:AD:DP:GL:GQ	0/1:87,28:104:-67.56,-31.33,-345.48:99
+chr1	811285	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=37.25;MQ=40.88;MQ0=3;OQ=828.79;QD=5.53;SB=-15.76	GT:AD:DP:GL:GQ	0/1:66,84:93:-114.20,-28.04,-207.99:99
+chr1	811292	.	G	C	33.11	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=58.15;MQ=39.23;MQ0=3;QD=0.21;SB=95.35	GT:AD:DP:GL:GQ	0/1:79,14:72:-31.92,-25.33,-286.41:65.95
+chr1	811309	.	A	C	218.07	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=180;Dels=0.00;HRun=0;HaplotypeScore=95.42;MQ=36.77;MQ0=3;QD=1.21;SB=75.78	GT:AD:DP:GL:GQ	0/1:95,84:77:-48.28,-23.19,-225.41:99
+chr1	811313	.	C	A	77.35	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=190;Dels=0.00;HRun=1;HaplotypeScore=126.41;MQ=36.87;MQ0=1;QD=0.41;SB=64.94	GT:AD:DP:GL:GQ	0/1:128,61:85:-36.63,-25.61,-260.99:99
+chr1	811315	.	G	A	900.17	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=189;Dels=0.00;HRun=1;HaplotypeScore=96.44;MQ=36.96;MQ0=1;QD=4.76;SB=64.69	GT:AD:DP:GL:GQ	0/1:57,131:88:-122.19,-28.89,-207.10:99
+chr1	811336	.	T	C	533.21	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=37.36;MQ0=1;QD=2.63;SB=59.62	GT:AD:DP:GL:GQ	0/1:62,140:81:-81.01,-24.41,-227.12:99
+chr1	811339	.	T	C	458.52	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=200;Dels=0.00;HRun=1;HaplotypeScore=44.80;MQ=38.07;MQ0=1;QD=2.29;SB=92.33	GT:AD:DP:GL:GQ	0/1:65,135:85:-74.74,-25.60,-261.77:99
+chr1	811347	.	T	G	278.98	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=226;Dels=0.00;HRun=3;HaplotypeScore=134.53;MQ=37.01;MQ0=0;QD=1.23;SB=83.27	GT:AD:DP:GL:GQ	0/1:65,161:80:-55.28,-24.10,-233.47:99
+chr1	811354	.	C	T	677.91	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=233;Dels=0.00;HRun=0;HaplotypeScore=163.01;MQ=36.31;MQ0=0;QD=2.91;SB=83.23	GT:AD:DP:GL:GQ	0/1:63,170:82:-95.80,-24.72,-187.92:99
+chr1	811362	.	C	T	454.65	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=226.76;MQ=36.80;MQ0=0;QD=1.97;SB=83.14	GT:AD:DP:GL:GQ	0/1:64,167:80:-72.88,-24.13,-190.51:99
+chr1	811364	.	T	C	196.31	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=230;Dels=0.00;HRun=1;HaplotypeScore=66.22;MQ=36.51;MQ0=0;QD=0.85;SB=79.92	GT:AD:DP:GL:GQ	0/1:84,145:75:-47.99,-25.07,-244.42:99
+chr1	811375	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=93.49;MQ=37.41;MQ0=0;OQ=1696.08;QD=7.34;SB=71.11	GT:AD:DP:GL:GQ	0/1:93,137:119:-208.77,-35.88,-209.62:99
+chr1	811378	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=239;Dels=0.00;HRun=1;HaplotypeScore=193.97;MQ=37.86;MQ0=0;OQ=1149.75;QD=4.81;SB=77.23	GT:AD:DP:GL:GQ	0/1:188,51:123:-155.31,-37.05,-314.47:99
+chr1	811386	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=227;Dels=0.00;HRun=2;HaplotypeScore=163.58;MQ=38.25;MQ0=0;OQ=516.99;QD=2.28;SB=29.28	GT:AD:DP:GL:GQ	0/1:149,78:121:-91.43,-36.45,-384.88:99
+chr1	811400	.	C	T	562.85	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=209;Dels=0.00;HRun=0;HaplotypeScore=151.19;MQ=39.64;MQ0=0;QD=2.69;SB=23.60	GT:AD:DP:GL:GQ	0/1:96,113:102:-90.30,-30.73,-291.44:99
+chr1	811402	.	C	T	93.97	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=206;Dels=0.00;HRun=1;HaplotypeScore=101.45;MQ=39.46;MQ0=1;QD=0.46;SB=62.16	GT:AD:DP:GL:GQ	0/1:188,18:99:-42.50,-29.82,-326.30:99
+chr1	811408	.	G	T	250.46	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=192;Dels=0.00;HRun=0;HaplotypeScore=79.23;MQ=40.75;MQ0=2;QD=1.30;SB=59.20	GT:AD:DP:GL:GQ	0/1:111,80:98:-57.85,-29.52,-298.59:99
+chr1	811413	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=0;HaplotypeScore=67.52;MQ=40.58;MQ0=2;OQ=77.44;QD=0.41;SB=62.19	GT:AD:DP:GL:GQ	0/1:97,91:86:-36.94,-25.92,-277.54:99
+chr1	811430	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=4;HaplotypeScore=58.87;MQ=40.65;MQ0=2;OQ=63.77;QD=0.39;SB=65.24	GT:AD:DP:GL:GQ	0/1:88,76:92:-37.38,-27.72,-324.79:96.61
+chr1	811435	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=19.26;MQ=40.95;MQ0=1;OQ=266.78;QD=1.72;SB=71.27	GT:AD:DP:GL:GQ	0/1:84,71:100:-60.08,-30.12,-340.43:99
+chr1	811443	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=2;HaplotypeScore=30.32;MQ=41.18;MQ0=1;OQ=189.19;QD=1.39;SB=77.28	GT:AD:DP:GL:GQ	0/1:79,56:91:-52.39,-30.19,-304.45:99
+chr1	811635	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=82.21;MQ=40.79;MQ0=16;OQ=141.45;QD=0.98;SB=-89.35	GT:AD:DP:GL:GQ	0/1:111,34:74:-39.73,-22.30,-281.80:99
+chr1	811650	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=95.82;MQ=42.47;MQ0=12;OQ=224.58;QD=1.65;SB=-61.36	GT:AD:DP:GL:GQ	0/1:66,70:76:-48.64,-22.89,-228.84:99
+chr1	811656	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=71.17;MQ=43.15;MQ0=11;OQ=112.09;QD=0.87;SB=-75.98	GT:AD:DP:GL:GQ	0/1:102,27:76:-37.39,-22.90,-238.94:99
+chr1	811750	rs6677354	A	G	0.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=4.05;MQ=50.03;MQ0=0;OQ=1811.37;QD=31.78;SB=-810.16	GT:AD:DP:GL:GQ	1/1:0,56:52:-184.74,-15.66,-0.02:99
+chr1	811789	rs35660652	C	G	23.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=4.89;MQ=49.27;MQ0=1;OQ=933.21;QD=16.97;SB=-483.19	GT:AD:DP:GL:GQ	0/1:25,30:48:-111.08,-14.47,-94.44:99
+chr1	811811	rs6671445	T	C	60.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=51.17;MQ0=1;OQ=1096.50;QD=26.11;SB=-519.10	GT:AD:DP:GL:GQ	1/1:0,42:35:-113.27,-10.56,-0.03:99
+chr1	811899	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=32.15;MQ=43.49;MQ0=20;OQ=124.06;QD=1.01;SB=92.32	GT:AD:DP:GL:GQ	0/1:62,60:72:-37.38,-21.69,-248.07:99
+chr1	812359	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=1;HaplotypeScore=23.61;MQ=48.84;MQ0=1;OQ=66.32;QD=0.77;SB=71.21	GT:AD:DP:GL:GQ	0/1:52,34:57:-27.09,-17.17,-171.46:99
+chr1	812367	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=15.11;MQ=47.39;MQ0=1;OQ=182.54;QD=1.77;SB=-16.56	GT:AD:DP:GL:GQ	0/1:55,46:66:-41.42,-19.89,-213.25:99
+chr1	812395	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=147;Dels=0.00;HRun=0;HaplotypeScore=16.89;MQ=44.59;MQ0=4;OQ=290.02;QD=1.97;SB=-35.46	GT:AD:DP:GL:GQ	0/1:75,71:87:-58.50,-26.21,-278.39:99
+chr1	812396	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=12.57;MQ=44.24;MQ0=4;OQ=510.01;QD=3.40;SB=-121.97	GT:AD:DP:GL:GQ	0/1:77,73:89:-81.09,-26.81,-250.00:99
+chr1	812452	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=237;Dels=0.00;HRun=1;HaplotypeScore=44.19;MQ=38.30;MQ0=6;OQ=174.18;QD=0.73;SB=140.46	GT:AD:DP:GL:GQ	0/1:178,59:128:-59.25,-38.55,-429.97:99
+chr1	812470	.	G	A	3027.24	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=2;HaplotypeScore=95.67;MQ=37.00;MQ0=5;QD=11.38;SB=-136.01	GT:AD:DP:GL:GQ	0/1:72,177:161:-375.45,-69.45,-279.59:99
+chr1	812474	.	A	G	225.39	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=0;HaplotypeScore=98.08;MQ=36.45;MQ0=4;QD=0.80;SB=107.36	GT:AD:DP:GL:GQ	0/1:225,57:173:-77.95,-52.13,-605.26:99
+chr1	812476	.	G	A	4194.86	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=280;Dels=0.00;HRun=1;HaplotypeScore=148.97;MQ=36.56;MQ0=4;QD=14.98;SB=-125.96	GT:AD:DP:GL:GQ	0/1:71,208:172:-418.49,-51.81,-254.37:99
+chr1	812496	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=383;Dels=0.00;HRun=3;HaplotypeScore=110.05;MQ=34.24;MQ0=3;OQ=4072.28;QD=10.63;SB=-60.38	GT:AD:DP:GL:GQ	0/1:191,192:229:-406.23,-68.97,-420.64:99
+chr1	812509	.	A	G	1306.01	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=390;Dels=0.00;HRun=0;HaplotypeScore=338.39;MQ=34.90;MQ0=4;QD=3.35;SB=113.39	GT:AD:DP:GL:GQ	0/1:88,302:134:-174.25,-40.36,-354.14:99
+chr1	812511	.	C	T	253.04	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=392;Dels=0.00;HRun=1;HaplotypeScore=342.27;MQ=34.93;MQ0=3;QD=0.65;SB=107.37	GT:AD:DP:GL:GQ	0/1:210,181:105:-60.21,-31.62,-326.58:99
+chr1	812536	.	C	T	6216.93	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=431;Dels=0.00;HRun=0;HaplotypeScore=21.13;MQ=33.82;MQ0=5;QD=14.42;SB=89.30	GT:AD:DP:GL:GQ	0/1:86,345:239:-620.69,-71.99,-300.06:99
+chr1	812546	.	A	T	6301.61	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=411;Dels=0.00;HRun=5;HaplotypeScore=527.01;MQ=34.23;MQ0=5;QD=15.33;SB=95.32	GT:AD:DP:GL:GQ	0/1:107,219:261:-629.16,-251.98,-546.86:99
+chr1	812557	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=384;Dels=0.00;HRun=0;HaplotypeScore=98.60;MQ=34.24;MQ0=5;OQ=4742.49;QD=12.35;SB=92.31	GT:AD:DP:GL:GQ	0/1:201,182:235:-473.25,-70.78,-414.34:99
+chr1	812581	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=273;Dels=0.00;HRun=0;HaplotypeScore=142.64;MQ=35.76;MQ0=4;OQ=1205.24;QD=4.41;SB=74.26	GT:AD:DP:GL:GQ	0/1:167,71:149:-175.85,-52.04,-375.17:99
+chr1	812582	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=267;Dels=0.00;HRun=0;HaplotypeScore=141.33;MQ=35.99;MQ0=4;OQ=1716.18;QD=6.43;SB=71.26	GT:AD:DP:GL:GQ	0/1:103,164:146:-218.89,-43.99,-346.52:99
+chr1	812608	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=1;HaplotypeScore=67.91;MQ=41.17;MQ0=4;OQ=693.18;QD=4.20;SB=50.19	GT:AD:DP:GL:GQ	0/1:102,63:97:-101.82,-29.21,-294.33:99
+chr1	812623	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=28.33;MQ=46.60;MQ0=1;OQ=165.38;QD=1.61;SB=41.15	GT:AD:DP:GL:GQ	0/1:59,44:68:-40.30,-20.48,-216.18:99
+chr1	812625	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=1;HaplotypeScore=28.33;MQ=46.70;MQ0=1;OQ=134.52;QD=1.27;SB=44.17	GT:AD:DP:GL:GQ	0/1:60,46:69:-37.52,-20.78,-218.11:99
+chr1	812637	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=0;HaplotypeScore=37.48;MQ=47.73;MQ0=2;OQ=214.50;QD=1.87;SB=-61.85	GT:AD:DP:GL:GQ	0/1:67,48:77:-47.94,-23.20,-220.91:99
+chr1	812655	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=121;Dels=0.00;HRun=0;HaplotypeScore=33.89;MQ=47.71;MQ0=3;OQ=405.95;QD=3.35;SB=-136.06	GT:AD:DP:GL:GQ	0/1:68,53:87:-70.08,-26.20,-247.74:99
+chr1	812661	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=2;HaplotypeScore=21.84;MQ=47.58;MQ0=5;OQ=365.64;QD=2.95;SB=-168.82	GT:AD:DP:GL:GQ	0/1:87,37:88:-66.35,-26.51,-263.64:99
+chr1	812666	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=21.15;MQ=47.18;MQ0=5;OQ=451.13;QD=3.67;SB=-190.13	GT:AD:DP:GL:GQ	0/1:65,57:86:-74.30,-25.91,-260.71:99
+chr1	812725	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=2;HaplotypeScore=17.99;MQ=47.07;MQ0=7;OQ=51.25;QD=0.37;SB=36.23	GT:AD:DP:GL:GQ	0/1:99,33:95:-37.06,-28.65,-279.36:84.09
+chr1	812740	.	T	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=2;HaplotypeScore=10.99;MQ=47.57;MQ0=4;OQ=391.52;QD=3.08;SB=-178.55	GT:AD:DP:GL:GQ	0/1:69,58:85:-68.04,-25.60,-259.04:99
+chr1	812742	.	A	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=1;HaplotypeScore=11.99;MQ=46.41;MQ0=4;OQ=355.87;QD=2.58;SB=-160.38	GT:AD:DP:GL:GQ	0/1:72,66:89:-65.67,-26.80,-277.85:99
+chr1	812772	.	C	A	4524.81	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=340;Dels=0.00;HRun=1;HaplotypeScore=205.36;MQ=35.68;MQ0=5;QD=13.31;SB=-1151.01	GT:AD:DP:GL:GQ	0/1:83,257:202:-451.48,-60.83,-296.00:99
+chr1	812774	.	G	A	5465.17	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=359;Dels=0.00;HRun=1;HaplotypeScore=230.04;MQ=35.29;MQ0=5;QD=15.22;SB=-1392.69	GT:AD:DP:GL:GQ	0/1:83,276:217:-545.52,-65.36,-295.35:99
+chr1	812778	.	A	C	2967.60	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=395;Dels=0.00;HRun=0;HaplotypeScore=217.58;MQ=34.63;MQ0=8;QD=7.51;SB=-725.51	GT:AD:DP:GL:GQ	0/1:219,176:242:-372.92,-72.88,-512.65:99
+chr1	812823	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=734;Dels=0.00;HRun=0;HaplotypeScore=134.36;MQ=30.02;MQ0=41;OQ=617.75;QD=0.84;SB=-157.33	GT:AD:DP:GL:GQ	0/1:653,81:442:-198.19,-133.13,-1425.62:99
+chr1	812838	rs657923	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=716;Dels=0.00;HRun=1;HaplotypeScore=212.74;MQ=29.97;MQ0=41;OQ=1388.92;QD=1.94;SB=-7.94	GT:AD:DP:GL:GQ	0/1:599,117:439:-274.39,-132.21,-1407.52:99
+chr1	812875	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=465;Dels=0.00;HRun=0;HaplotypeScore=110.91;MQ=32.05;MQ0=37;OQ=83.36;QD=0.18;SB=55.37	GT:AD:DP:GL:GQ	0/1:398,67:296:-100.77,-89.15,-980.63:99
+chr1	812885	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=346;Dels=0.00;HRun=1;HaplotypeScore=111.42;MQ=33.27;MQ0=30;OQ=5208.47;QD=15.05;SB=-2233.36	GT:AD:DP:GL:GQ	0/1:69,277:208:-519.85,-62.65,-238.95:99
+chr1	812886	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=335;Dels=0.00;HRun=1;HaplotypeScore=55.46;MQ=33.49;MQ0=30;OQ=451.06;QD=1.35;SB=-154.07	GT:AD:DP:GL:GQ	0/1:302,33:200:-108.62,-60.23,-633.51:99
+chr1	812900	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=183;Dels=0.00;HRun=0;HaplotypeScore=14.94;MQ=39.79;MQ0=13;OQ=813.81;QD=4.45;SB=92.87	GT:AD:DP:GL:GQ	0/1:73,110:100:-114.78,-30.12,-260.13:99
+chr1	812923	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=27.88;MQ=50.22;MQ0=2;OQ=306.33;QD=2.95;SB=-30.81	GT:AD:DP:GL:GQ	0/1:70,34:81:-58.31,-24.40,-238.03:99
+chr1	812935	.	G	A	2.07	PASS	AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=2.66;MQ=47.53;MQ0=2;OQ=744.11;QD=5.55;SB=-223.02	GT:AD:DP:GL:GQ	0/1:69,65:96:-106.61,-28.92,-247.13:99
+chr1	812951	.	G	T	11.25	PASS	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=43.90;MQ0=5;OQ=1351.36;QD=8.72;SB=-400.31	GT:AD:DP:GL:GQ	0/1:63,92:108:-170.95,-32.53,-225.30:99
+chr1	812975	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=0;HaplotypeScore=28.65;MQ=40.87;MQ0=15;OQ=1862.55;QD=9.36;SB=-484.23	GT:AD:DP:GL:GQ	0/1:66,132:123:-230.20,-40.66,-212.95:99
+chr1	812981	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=1;HaplotypeScore=40.75;MQ=39.82;MQ0=15;OQ=1797.82;QD=8.86;SB=-460.63	GT:AD:DP:GL:GQ	0/1:63,140:120:-219.20,-36.14,-217.08:99
+chr1	812999	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=293;Dels=0.00;HRun=3;HaplotypeScore=112.34;MQ=35.70;MQ0=17;OQ=746.50;QD=2.55;SB=103.46	GT:AD:DP:GL:GQ	0/1:201,92:175:-130.64,-52.71,-522.15:99
+chr1	813018	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=409;Dels=0.00;HRun=4;HaplotypeScore=24.00;MQ=34.51;MQ0=18;OQ=2503.76;QD=6.12;SB=-85.25	GT:AD:DP:GL:GQ	0/1:266,142:285:-339.49,-85.83,-765.92:99
+chr1	813030	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=463;Dels=0.00;HRun=0;HaplotypeScore=48.87;MQ=34.17;MQ0=19;OQ=2316.95;QD=5.00;SB=-56.40	GT:AD:DP:GL:GQ	0/1:312,151:338:-336.77,-101.79,-911.65:99
+chr1	813038	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=491;Dels=0.00;HRun=0;HaplotypeScore=299.82;MQ=33.86;MQ0=19;OQ=574.58;QD=1.17;SB=49.00	GT:AD:DP:GL:GQ	0/1:442,49:363:-170.06,-109.32,-1157.10:99
+chr1	813041	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=493;Dels=0.00;HRun=0;HaplotypeScore=391.76;MQ=34.08;MQ0=19;OQ=10262.92;QD=20.82;SB=-1216.69	GT:AD:DP:GL:GQ	0/1:84,408:369:-1025.29,-114.38,-315.19:99
+chr1	813055	.	T	G	5105.47	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=534;Dels=0.00;HRun=1;HaplotypeScore=573.54;MQ=33.39;MQ0=15;QD=9.56;SB=-804.21	GT:AD:DP:GL:GQ	0/1:355,179:410:-509.55,-123.48,-999.47:99
+chr1	813070	.	G	T	1334.14	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=573;Dels=0.00;HRun=1;HaplotypeScore=588.05;MQ=33.10;MQ0=9;QD=2.33;SB=-193.13	GT:AD:DP:GL:GQ	0/1:472,101:440:-269.21,-132.51,-1306.87:99
+chr1	813073	.	C	G	2805.72	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=592;Dels=0.00;HRun=1;HaplotypeScore=532.94;MQ=33.08;MQ0=8;QD=4.74;SB=-566.71	GT:AD:DP:GL:GQ	0/1:469,123:455:-420.94,-137.09,-1553.33:99
+chr1	813077	.	G	A	139.61	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=606;Dels=0.00;HRun=1;HaplotypeScore=787.16;MQ=33.34;MQ0=7;QD=0.23;SB=20.29	GT:AD:DP:GL:GQ	0/1:564,42:462:-156.39,-139.14,-1597.16:99
+chr1	813078	.	C	G	7856.82	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=607;Dels=0.00;HRun=1;HaplotypeScore=894.22;MQ=33.34;MQ0=7;QD=12.94;SB=-567.18	GT:AD:DP:GL:GQ	0/1:367,165:476:-784.68,-363.52,-1514.16:99
+chr1	813086	.	C	G	6412.49	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=625;Dels=0.00;HRun=0;HaplotypeScore=667.82;MQ=33.46;MQ0=7;QD=10.26;SB=-767.41	GT:AD:DP:GL:GQ	0/1:438,186:509:-640.25,-153.35,-1590.01:99
+chr1	813088	.	G	A	7116.40	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=627;Dels=0.00;HRun=1;HaplotypeScore=625.87;MQ=33.36;MQ0=7;QD=11.35;SB=-863.76	GT:AD:DP:GL:GQ	0/1:405,186:507:-710.64,-256.24,-1344.66:99
+chr1	813094	.	C	T	2968.23	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=620;Dels=0.00;HRun=0;HaplotypeScore=211.21;MQ=33.22;MQ0=9;QD=4.79;SB=-1023.50	GT:AD:DP:GL:GQ	0/1:481,139:495:-449.19,-149.09,-1385.37:99
+chr1	813107	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=546;Dels=0.00;HRun=0;HaplotypeScore=55.14;MQ=33.11;MQ0=20;OQ=871.93;QD=1.60;SB=-175.62	GT:AD:DP:GL:GQ	0/1:477,69:368:-201.32,-110.84,-1286.63:99
+chr1	813112	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=540;Dels=0.00;HRun=1;HaplotypeScore=215.40;MQ=33.46;MQ0=24;OQ=633.86;QD=1.17;SB=-102.54	GT:AD:DP:GL:GQ	0/1:489,51:349:-171.78,-105.11,-1109.57:99
+chr1	813120	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=452;Dels=0.00;HRun=0;HaplotypeScore=223.96;MQ=34.07;MQ0=26;OQ=8026.64;QD=17.76;SB=-2723.00	GT:AD:DP:GL:GQ	0/1:104,348:294:-801.66,-88.56,-349.63:99
+chr1	813123	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=449;Dels=0.00;HRun=0;HaplotypeScore=337.04;MQ=33.84;MQ0=28;OQ=7271.87;QD=16.20;SB=-2574.23	GT:AD:DP:GL:GQ	0/1:72,377:266:-726.19,-80.11,-257.87:99
+chr1	813133	.	G	C	2818.75	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=399;Dels=0.00;HRun=0;HaplotypeScore=373.63;MQ=34.21;MQ0=30;QD=7.06;SB=-1307.24	GT:AD:DP:GL:GQ	0/1:279,119:209:-348.13,-62.97,-562.66:99
+chr1	813135	.	A	G	6195.50	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=391;Dels=0.00;HRun=0;HaplotypeScore=305.70;MQ=34.41;MQ0=29;QD=15.85;SB=-2650.19	GT:AD:DP:GL:GQ	0/1:69,321:237:-618.55,-71.38,-275.07:99
+chr1	813142	.	T	C	345.82	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=364;Dels=0.00;HRun=1;HaplotypeScore=286.54;MQ=33.82;MQ0=33;QD=0.95;SB=-108.69	GT:AD:DP:GL:GQ	0/1:317,47:188:-94.49,-56.62,-663.95:99
+chr1	813148	.	C	A	1435.04	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=349;Dels=0.00;HRun=2;HaplotypeScore=161.77;MQ=34.46;MQ0=34;QD=4.11;SB=-365.32	GT:AD:DP:GL:GQ	0/1:282,67:257:-224.19,-77.40,-705.20:99
+chr1	813156	.	T	A	297.72	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=308;Dels=0.00;HRun=0;HaplotypeScore=111.01;MQ=35.71;MQ0=35;QD=0.97;SB=9.92	GT:AD:DP:GL:GQ	0/1:276,32:221:-99.61,-66.55,-759.37:99
+chr1	813157	.	G	C	549.74	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=307;Dels=0.00;HRun=0;HaplotypeScore=111.01;MQ=35.86;MQ0=35;QD=1.79;SB=-210.25	GT:AD:DP:GL:GQ	0/1:247,59:221:-124.85,-66.59,-828.88:99
+chr1	813168	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=254;Dels=0.00;HRun=2;HaplotypeScore=4.86;MQ=37.54;MQ0=37;OQ=984.94;QD=3.88;SB=44.86	GT:AD:DP:GL:GQ	0/1:209,45:173:-153.88,-52.11,-496.83:99
+chr1	813186	.	G	C	76.25	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=160;Dels=0.00;HRun=0;HaplotypeScore=72.20;MQ=40.71;MQ0=36;QD=0.48;SB=71.95	GT:AD:DP:GL:GQ	0/1:148,12:83:-35.91,-25.01,-332.34:99
+chr1	813187	.	A	G	513.33	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=147;Dels=0.00;HRun=1;HaplotypeScore=71.20;MQ=41.66;MQ0=35;QD=3.49;SB=-73.38	GT:AD:DP:GL:GQ	0/1:75,50:94:-82.93,-28.31,-287.29:99
+chr1	813188	.	C	A	79.88	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=1;HaplotypeScore=71.20;MQ=41.50;MQ0=35;QD=0.55;SB=44.61	GT:AD:DP:GL:GQ	0/1:120,26:78:-34.77,-23.49,-243.41:99
+chr1	813189	.	C	A	521.18	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=67.21;MQ=41.65;MQ0=35;QD=3.62;SB=-1.36	GT:AD:DP:GL:GQ	0/1:108,26:91:-101.37,-45.97,-249.59:99
+chr1	813208	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=2;HaplotypeScore=18.83;MQ=43.26;MQ0=23;OQ=418.24;QD=3.37;SB=-54.23	GT:AD:DP:GL:GQ	0/1:61,63:76:-68.00,-22.89,-206.10:99
+chr1	813240	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=154;Dels=0.00;HRun=2;HaplotypeScore=43.28;MQ=41.04;MQ0=25;OQ=943.89;QD=6.13;SB=-68.91	GT:AD:DP:GL:GQ	0/1:64,90:92:-125.38,-27.71,-227.61:99
+chr1	813250	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=0;HaplotypeScore=62.53;MQ=37.95;MQ0=22;OQ=226.25;QD=1.16;SB=14.99	GT:AD:DP:GL:GQ	0/1:153,42:96:-54.82,-28.92,-298.56:99
+chr1	813271	.	T	C	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=249;Dels=0.00;HRun=0;HaplotypeScore=8.46;MQ=34.98;MQ0=19;OQ=1147.61;QD=4.61;SB=-134.40	GT:AD:DP:GL:GQ	0/1:63,186:103:-149.07,-31.02,-256.47:99
+chr1	813292	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=382;Dels=0.00;HRun=2;HaplotypeScore=102.43;MQ=30.92;MQ0=23;OQ=1986.60;QD=5.20;SB=-566.46	GT:AD:DP:GL:GQ	0/1:105,277:133:-242.00,-40.06,-276.00:99
+chr1	813307	.	A	G	32.13	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=535;Dels=0.00;HRun=0;HaplotypeScore=181.84;MQ=30.25;MQ0=27;QD=0.06;SB=46.55	GT:AD:DP:GL:GQ	0/1:504,31:255:-83.31,-76.81,-935.22:64.97
+chr1	813316	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=619;Dels=0.00;HRun=2;HaplotypeScore=75.11;MQ=29.97;MQ0=27;OQ=3157.81;QD=5.10;SB=-1462.71	GT:AD:DP:GL:GQ	0/1:382,237:331:-418.76,-99.69,-846.79:99
+chr1	813335	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=826;Dels=0.00;HRun=1;HaplotypeScore=136.91;MQ=30.11;MQ0=21;OQ=7119.57;QD=8.62;SB=-2280.77	GT:AD:DP:GL:GQ	0/1:537,288:549:-710.96,-165.36,-1364.58:99
+chr1	813362	.	A	G	16357.98	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=920;Dels=0.00;HRun=1;HaplotypeScore=446.32;MQ=30.10;MQ0=24;QD=17.78;SB=-5014.09	GT:AD:DP:GL:GQ	0/1:273,494:683:-1634.80,-554.43,-1400.88:99
+chr1	813367	.	T	C	20902.62	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=914;Dels=0.00;HRun=0;HaplotypeScore=426.41;MQ=30.28;MQ0=24;QD=22.87;SB=-7448.46	GT:AD:DP:GL:GQ	0/1:141,716:687:-2089.26,-358.04,-691.48:99
+chr1	813368	rs13302980	T	C	206.93	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=916;Dels=0.00;HRun=0;HaplotypeScore=426.41;MQ=30.25;MQ0=24;QD=0.23;SB=-118.41	GT:AD:DP:GL:GQ	0/1:843,73:685:-230.32,-206.34,-2521.41:99
+chr1	813385	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=888;Dels=0.00;HRun=0;HaplotypeScore=40.71;MQ=30.82;MQ0=25;OQ=1088.75;QD=1.23;SB=-408.14	GT:AD:DP:GL:GQ	0/1:783,105:699:-322.70,-210.54,-2232.26:99
+chr1	813404	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=750;Dels=0.00;HRun=2;HaplotypeScore=134.73;MQ=32.26;MQ0=17;OQ=670.55;QD=0.89;SB=-191.51	GT:AD:DP:GL:GQ	0/1:685,65:613:-254.96,-184.62,-2037.75:99
+chr1	813405	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=741;Dels=0.00;HRun=2;HaplotypeScore=133.74;MQ=32.36;MQ0=17;OQ=1633.92;QD=2.21;SB=-672.01	GT:AD:DP:GL:GQ	0/1:597,144:607:-349.50,-182.82,-2122.95:99
+chr1	813418	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=590;Dels=0.00;HRun=0;HaplotypeScore=47.11;MQ=33.33;MQ0=15;OQ=65.79;QD=0.11;SB=206.84	GT:AD:DP:GL:GQ	0/1:544,46:476:-153.22,-143.35,-1574.37:98.63
+chr1	813443	.	T	G	3848.11	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=275;Dels=0.00;HRun=0;HaplotypeScore=38.86;MQ=37.99;MQ0=5;QD=13.99;SB=-1241.58	GT:AD:DP:GL:GQ	0/1:79,195:186:-383.81,-56.02,-279.85:99
+chr1	813451	.	C	T	1033.45	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=197;Dels=0.01;HRun=0;HaplotypeScore=22.13;MQ=41.75;MQ0=4;QD=5.25;SB=-217.95	GT:AD:DP:GL:GQ	0/1:81,115:114:-140.97,-34.34,-279.86:99
+chr1	813452	.	A	G	765.89	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=186;Dels=0.01;HRun=0;HaplotypeScore=26.12;MQ=42.21;MQ0=4;QD=4.12;SB=-130.38	GT:AD:DP:GL:GQ	0/1:79,106:109:-112.71,-32.84,-316.56:99
+chr1	813514	rs61768255	T	A	0.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=40.18;MQ0=52;OQ=194.92;QD=1.28;SB=-18.62	GT:AD:DP:GL:GQ	0/1:64,87:75:-45.36,-22.59,-238.39:99
+chr1	813576	.	G	T	36.42	DPFilter;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=256;Dels=0.00;HRun=0;HaplotypeScore=114.90;MQ=32.12;MQ0=13;QD=0.14;SB=80.27	GT:AD:DP:GL:GQ	0/1:231,25:108:-39.45,-32.53,-355.25:69.25
+chr1	813577	.	C	T	12.25	DPFilter;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=253;Dels=0.00;HRun=0;HaplotypeScore=118.76;MQ=32.29;MQ0=11;QD=0.05;SB=83.28	GT:AD:DP:GL:GQ	0/1:222,24:110:-47.87,-43.39,-370.50:44.82
+chr1	813595	.	G	A	14.36	DPFilter;Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=304;Dels=0.02;HRun=3;HaplotypeScore=679.47;MQ=32.56;MQ0=1;QD=0.05;SB=59.22	GT:AD:DP:GL:GQ	0/1:279,19:122:-44.63,-39.92,-398.76:47.04
+chr1	813600	.	G	A	274.89	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=326;Dels=0.00;HRun=2;HaplotypeScore=874.07;MQ=32.03;MQ0=1;QD=0.84;SB=65.24	GT:AD:DP:GL:GQ	0/1:247,78:142:-73.54,-42.77,-440.28:99
+chr1	813603	.	G	A	897.36	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=326;Dels=0.00;HRun=2;HaplotypeScore=1015.89;MQ=31.94;MQ0=0;QD=2.75;SB=17.55	GT:AD:DP:GL:GQ	0/1:201,125:138:-134.59,-41.57,-374.40:99
+chr1	813618	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=385;Dels=0.01;HRun=2;HaplotypeScore=1064.00;MQ=30.68;MQ0=0;OQ=4144.71;QD=10.77;SB=-60.77	GT:AD:DP:GL:GQ	0/1:139,193:174:-413.47,-52.40,-263.62:99
+chr1	813640	.	G	A	6008.25	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=492;Dels=0.03;HRun=2;HaplotypeScore=778.76;MQ=30.34;MQ0=0;QD=12.21;SB=-280.67	GT:AD:DP:GL:GQ	0/1:225,249:279:-599.83,-82.23,-444.10:99
+chr1	813644	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=499;Dels=0.00;HRun=2;HaplotypeScore=589.76;MQ=30.13;MQ0=0;OQ=1319.59;QD=2.64;SB=-65.34	GT:AD:DP:GL:GQ	0/1:370,128:286:-221.39,-86.15,-815.48:99
+chr1	813653	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=493;Dels=0.00;HRun=1;HaplotypeScore=439.06;MQ=30.75;MQ0=0;OQ=617.48;QD=1.25;SB=-157.65	GT:AD:DP:GL:GQ	0/1:455,38:256:-142.14,-77.10,-775.99:99
+chr1	813667	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=450;Dels=0.03;HRun=0;HaplotypeScore=1087.09;MQ=31.84;MQ0=0;OQ=612.31;QD=1.36;SB=24.15	GT:AD:DP:GL:GQ	0/1:310,99:290:-203.97,-139.46,-953.68:99
+chr1	813680	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=385;Dels=0.03;HRun=2;HaplotypeScore=1191.21;MQ=32.81;MQ0=0;OQ=1213.04;QD=3.15;SB=-10.63	GT:AD:DP:GL:GQ	0/1:276,97:229:-193.56,-68.97,-645.40:99
+chr1	813720	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=252;Dels=0.06;HRun=1;HaplotypeScore=327.60;MQ=37.03;MQ0=0;OQ=194.28;QD=0.77;SB=110.38	GT:AD:DP:GL:GQ	0/1:205,33:146:-66.38,-43.67,-457.57:99
+chr1	813729	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=0;HaplotypeScore=373.81;MQ=39.70;MQ0=0;OQ=281.23;QD=1.50;SB=15.00	GT:AD:DP:GL:GQ	0/1:127,60:111:-64.84,-33.43,-345.95:99
+chr1	813820	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=81;Dels=0.05;HRun=2;HaplotypeScore=42.41;MQ=49.74;MQ0=3;OQ=162.06;QD=2.00;SB=-100.42	GT:AD:DP:GL:GQ	0/1:56,21:59:-37.26,-17.77,-183.03:99
+chr1	813869	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=73.61;MQ=47.62;MQ0=2;OQ=155.20;QD=1.94;SB=41.14	GT:AD:DP:GL:GQ	0/1:71,9:54:-35.07,-16.26,-160.29:99
+chr1	813877	.	G	A	25.05	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=66.85;MQ=49.86;MQ0=1;QD=0.34;SB=32.11	GT:AD:DP:GL:GQ	0/1:64,9:51:-21.15,-15.36,-169.54:57.88
+chr1	813907	.	G	A	23.05	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=73;Dels=0.04;HRun=1;HaplotypeScore=56.30;MQ=49.27;MQ0=1;QD=0.32;SB=38.13	GT:AD:DP:GL:GQ	0/1:63,7:54:-21.25,-15.66,-171.08:55.87
+chr1	813910	.	G	A	12.29	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=61.37;MQ=49.27;MQ0=1;QD=0.17;SB=35.12	GT:AD:DP:GL:GQ	0/1:63,10:55:-21.06,-16.57,-179.39:44.87
+chr1	813923	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=75;Dels=0.03;HRun=2;HaplotypeScore=23.38;MQ=50.12;MQ0=1;OQ=138.74;QD=1.85;SB=-24.20	GT:AD:DP:GL:GQ	0/1:50,23:55:-33.43,-16.28,-173.24:99
+chr1	813957	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=2;HaplotypeScore=18.68;MQ=43.32;MQ0=1;OQ=871.71;QD=6.86;SB=-275.74	GT:AD:DP:GL:GQ	0/1:65,62:85:-116.06,-25.61,-200.91:99
+chr1	813978	.	A	C	0.71	PASS	AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=39.28;MQ0=4;OQ=705.69;QD=4.77;SB=-252.74	GT:AD:DP:GL:GQ	0/1:54,94:80:-97.95,-24.09,-193.62:99
+chr1	814078	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=1;HaplotypeScore=6.42;MQ=36.79;MQ0=24;OQ=486.46;QD=2.55;SB=-267.20	GT:AD:DP:GL:GQ	0/1:63,128:82:-76.63,-24.70,-247.64:99
+chr1	814121	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=39.43;MQ=40.45;MQ0=17;OQ=289.94;QD=1.73;SB=-38.08	GT:AD:DP:GL:GQ	0/1:70,98:82:-56.99,-24.71,-295.92:99
+chr1	814147	.	C	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=151;Dels=0.00;HRun=0;HaplotypeScore=14.17;MQ=45.92;MQ0=13;OQ=964.78;QD=6.39;SB=-366.58	GT:AD:DP:GL:GQ	0/1:82,69:112:-133.50,-33.74,-285.66:99
+chr1	814171	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=1;HaplotypeScore=20.78;MQ=44.66;MQ0=14;OQ=904.13;QD=5.38;SB=-364.51	GT:AD:DP:GL:GQ	0/1:83,85:118:-129.23,-35.54,-305.53:99
+chr1	814202	.	C	A	1692.96	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=197;Dels=0.09;HRun=0;HaplotypeScore=162.31;MQ=41.97;MQ0=8;QD=8.59;SB=-578.48	GT:AD:DP:GL:GQ	0/1:79,100:139:-213.84,-41.26,-286.69:99
+chr1	814220	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=0;HaplotypeScore=50.82;MQ=39.65;MQ0=8;OQ=329.14;QD=1.52;SB=-86.50	GT:AD:DP:GL:GQ	0/1:161,56:136:-77.16,-40.96,-423.94:99
+chr1	814233	.	G	A	2067.86	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=0;HaplotypeScore=147.47;MQ=38.66;MQ0=13;QD=9.23;SB=-544.97	GT:AD:DP:GL:GQ	0/1:105,119:132:-249.86,-39.79,-228.63:99
+chr1	814239	.	A	G	1315.30	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=220;Dels=0.00;HRun=1;HaplotypeScore=123.50;MQ=38.45;MQ0=13;QD=5.98;SB=-142.40	GT:AD:DP:GL:GQ	0/1:70,150:114:-169.16,-34.34,-278.17:99
+chr1	814242	.	A	G	554.64	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=125.56;MQ=38.13;MQ0=16;QD=2.40;SB=-155.01	GT:AD:DP:GL:GQ	0/1:172,59:130:-97.91,-39.16,-422.03:99
+chr1	814256	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=245;Dels=0.00;HRun=0;HaplotypeScore=21.41;MQ=37.07;MQ0=15;OQ=2324.45;QD=9.49;SB=-360.77	GT:AD:DP:GL:GQ	0/1:68,177:144:-279.11,-43.38,-270.96:99
+chr1	814273	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=59.92;MQ=36.71;MQ0=15;OQ=51.68;QD=0.19;SB=122.32	GT:AD:DP:GL:GQ	0/1:221,49:163:-60.05,-51.60,-506.38:84.51
+chr1	814274	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=269;Dels=0.00;HRun=0;HaplotypeScore=59.77;MQ=36.62;MQ0=15;OQ=1850.48;QD=6.88;SB=-407.81	GT:AD:DP:GL:GQ	0/1:149,120:153:-234.45,-46.12,-315.76:99
+chr1	814294	.	A	G	2410.03	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=2;HaplotypeScore=103.79;MQ=37.05;MQ0=15;QD=9.06;SB=-443.47	GT:AD:DP:GL:GQ	0/1:75,191:153:-290.38,-46.10,-295.34:99
+chr1	814296	.	G	A	1211.04	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=274;Dels=0.00;HRun=0;HaplotypeScore=219.20;MQ=36.82;MQ0=15;QD=4.42;SB=-351.23	GT:AD:DP:GL:GQ	0/1:200,74:158:-171.99,-47.60,-420.58:99
+chr1	814301	.	A	G	978.34	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=274;Dels=0.00;HRun=0;HaplotypeScore=220.77;MQ=36.41;MQ0=15;QD=3.57;SB=-180.08	GT:AD:DP:GL:GQ	0/1:73,201:110:-134.26,-33.14,-291.65:99
+chr1	814305	.	T	C	45.78	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=0;HaplotypeScore=232.83;MQ=35.76;MQ0=15;QD=0.16;SB=-43.14	GT:AD:DP:GL:GQ	0/1:206,71:102:-38.59,-30.73,-365.14:78.61
+chr1	814318	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=0;HaplotypeScore=167.17;MQ=36.26;MQ0=13;OQ=2113.99;QD=7.60;SB=-387.55	GT:AD:DP:GL:GQ	0/1:72,191:148:-269.75,-55.07,-295.63:99
+chr1	814320	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=280;Dels=0.00;HRun=0;HaplotypeScore=167.17;MQ=36.49;MQ0=13;OQ=746.17;QD=2.66;SB=-108.14	GT:AD:DP:GL:GQ	0/1:218,62:140:-120.08,-42.18,-412.31:99
+chr1	814333	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=285;Dels=0.00;HRun=0;HaplotypeScore=281.15;MQ=35.53;MQ0=9;OQ=1990.33;QD=6.98;SB=-447.96	GT:AD:DP:GL:GQ	0/1:95,190:142:-245.09,-42.77,-288.22:99
+chr1	814346	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=251;Dels=0.00;HRun=0;HaplotypeScore=225.23;MQ=36.32;MQ0=4;OQ=1683.84;QD=6.71;SB=-421.88	GT:AD:DP:GL:GQ	0/1:107,144:128:-210.24,-38.57,-269.23:99
+chr1	814360	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=2;HaplotypeScore=149.83;MQ=38.08;MQ0=4;OQ=172.19;QD=0.77;SB=51.61	GT:AD:DP:GL:GQ	0/1:195,28:117:-55.74,-35.24,-362.13:99
+chr1	814384	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=1;HaplotypeScore=42.51;MQ=45.49;MQ0=3;OQ=551.67;QD=3.70;SB=-145.33	GT:AD:DP:GL:GQ	0/1:76,73:99:-88.27,-29.82,-286.26:99
+chr1	814428	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=10.58;MQ=49.14;MQ0=17;OQ=342.52;QD=2.63;SB=-111.49	GT:AD:DP:GL:GQ	0/1:82,48:99:-67.35,-29.82,-298.71:99
+chr1	814439	.	C	T	20.82	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=47.72;MQ0=20;QD=0.14;SB=152.46	GT:AD:DP:GL:GQ	0/1:137,12:115:-40.00,-34.64,-383.60:53.62
+chr1	814456	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=1;HaplotypeScore=15.28;MQ=46.84;MQ0=26;OQ=753.94;QD=4.65;SB=-138.63	GT:AD:DP:GL:GQ	0/1:92,70:122:-115.43,-36.75,-321.50:99
+chr1	814470	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=189;Dels=0.00;HRun=1;HaplotypeScore=31.58;MQ=44.82;MQ0=39;OQ=884.58;QD=4.68;SB=-229.69	GT:AD:DP:GL:GQ	0/1:97,92:121:-128.25,-36.50,-368.74:99
+chr1	814488	.	C	A	76.03	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=247;Dels=0.00;HRun=0;HaplotypeScore=105.09;MQ=41.14;MQ0=41;QD=0.31;SB=176.55	GT:AD:DP:GL:GQ	0/1:229,16:148:-55.47,-44.58,-476.50:99
+chr1	814489	.	C	G	69.13	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=248;Dels=0.00;HRun=0;HaplotypeScore=89.81;MQ=41.12;MQ0=41;QD=0.28;SB=176.62	GT:AD:DP:GL:GQ	0/1:231,17:149:-55.10,-44.90,-596.57:99
+chr1	814495	.	T	C	1858.16	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=258;Dels=0.00;HRun=0;HaplotypeScore=56.93;MQ=40.44;MQ0=47;QD=7.20;SB=-760.45	GT:AD:DP:GL:GQ	0/1:92,166:157:-236.40,-47.30,-370.00:99
+chr1	814529	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=433;Dels=0.00;HRun=0;HaplotypeScore=120.51;MQ=38.11;MQ0=39;OQ=500.57;QD=1.16;SB=-243.42	GT:AD:DP:GL:GQ	0/1:383,50:261:-131.95,-78.61,-806.43:99
+chr1	814534	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=446;Dels=0.00;HRun=0;HaplotypeScore=107.63;MQ=38.32;MQ0=36;OQ=359.59;QD=0.81;SB=-173.49	GT:AD:DP:GL:GQ	0/1:401,44:272:-121.18,-81.93,-841.90:99
+chr1	814540	.	A	G	36.54	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=477;Dels=0.00;HRun=1;HaplotypeScore=62.33;MQ=38.25;MQ0=37;QD=0.08;SB=123.17	GT:AD:DP:GL:GQ	0/1:445,32:265:-86.76,-79.83,-986.21:69.37
+chr1	814554	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=529;Dels=0.00;HRun=0;HaplotypeScore=89.36;MQ=37.97;MQ0=32;OQ=9731.93;QD=18.40;SB=-1976.66	GT:AD:DP:GL:GQ	0/1:80,449:318:-972.19,-95.79,-281.92:99
+chr1	814557	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=552;Dels=0.00;HRun=0;HaplotypeScore=97.56;MQ=38.01;MQ0=31;OQ=8661.84;QD=15.69;SB=-1680.73	GT:AD:DP:GL:GQ	0/1:195,357:340:-865.18,-102.42,-472.42:99
+chr1	814572	rs564838	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=625;Dels=0.00;HRun=1;HaplotypeScore=63.63;MQ=38.08;MQ0=27;OQ=2371.32;QD=3.79;SB=-326.77	GT:AD:DP:GL:GQ	0/1:480,145:413:-364.80,-124.39,-1136.05:99
+chr1	814627	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=504;Dels=0.00;HRun=1;HaplotypeScore=183.33;MQ=39.27;MQ0=14;OQ=10984.00;QD=21.79;SB=-1265.89	GT:AD:DP:GL:GQ	0/1:67,203:343:-1097.40,-537.50,-676.52:99
+chr1	814675	.	G	A	2732.90	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=265;Dels=0.00;HRun=1;HaplotypeScore=261.45;MQ=41.69;MQ0=11;QD=10.31;SB=-108.93	GT:AD:DP:GL:GQ	0/1:161,102:166:-330.09,-53.51,-314.61:99
+chr1	814679	.	A	G	2402.46	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=237;Dels=0.00;HRun=1;HaplotypeScore=135.51;MQ=41.79;MQ0=13;QD=10.14;SB=-20.34	GT:AD:DP:GL:GQ	0/1:70,167:146:-287.52,-43.99,-273.83:99
+chr1	814680	.	C	T	2092.18	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=238;Dels=0.00;HRun=0;HaplotypeScore=134.51;MQ=41.43;MQ0=17;QD=8.79;SB=-7.62	GT:AD:DP:GL:GQ	0/1:151,86:144:-255.88,-43.38,-283.23:99
+chr1	814701	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=219;Dels=0.00;HRun=0;HaplotypeScore=51.82;MQ=41.75;MQ0=19;OQ=1622.55;QD=7.41;SB=-75.48	GT:AD:DP:GL:GQ	0/1:87,132:141:-208.02,-42.48,-267.24:99
+chr1	814708	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=0;HaplotypeScore=76.68;MQ=40.68;MQ0=25;OQ=2028.26;QD=9.14;SB=-58.81	GT:AD:DP:GL:GQ	0/1:84,138:144:-249.49,-43.38,-267.28:99
+chr1	814713	rs563211	T	C	1374.69	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=232;Dels=0.00;HRun=0;HaplotypeScore=105.58;MQ=40.40;MQ0=29;QD=5.93;SB=29.72	GT:AD:DP:GL:GQ	0/1:146,86:143:-183.83,-43.08,-359.04:99
+chr1	814720	.	T	C	689.97	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=0;HaplotypeScore=108.11;MQ=39.59;MQ0=32;QD=2.84;SB=46.65	GT:AD:DP:GL:GQ	0/1:85,157:115:-106.92,-34.64,-346.63:99
+chr1	814722	.	C	G	183.01	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=254;Dels=0.00;HRun=0;HaplotypeScore=126.09;MQ=39.61;MQ0=33;QD=0.72;SB=68.61	GT:AD:DP:GL:GQ	0/1:217,37:122:-58.35,-36.76,-472.38:99
+chr1	814737	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=299;Dels=0.00;HRun=0;HaplotypeScore=30.86;MQ=38.18;MQ0=38;OQ=2218.82;QD=7.42;SB=-36.77	GT:AD:DP:GL:GQ	0/1:186,113:186:-281.20,-56.03,-416.78:99
+chr1	814767	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=365;Dels=0.00;HRun=2;HaplotypeScore=49.56;MQ=35.63;MQ0=43;OQ=5264.89;QD=14.42;SB=-427.42	GT:AD:DP:GL:GQ	0/1:96,269:216:-525.49,-65.13,-366.09:99
+chr1	814784	.	A	G	211.71	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=402;Dels=0.00;HRun=0;HaplotypeScore=324.91;MQ=34.66;MQ0=41;QD=0.53;SB=-28.05	GT:AD:DP:GL:GQ	0/1:357,45:243:-97.65,-73.19,-885.32:99
+chr1	814787	.	A	G	1988.10	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=404;Dels=0.00;HRun=0;HaplotypeScore=288.76;MQ=34.45;MQ0=41;QD=4.92;SB=-448.31	GT:AD:DP:GL:GQ	0/1:239,165:199:-262.08,-59.99,-467.56:99
+chr1	814790	.	G	A	2076.12	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=406;Dels=0.00;HRun=0;HaplotypeScore=289.81;MQ=34.38;MQ0=42;QD=5.11;SB=-426.20	GT:AD:DP:GL:GQ	0/1:294,112:245:-284.69,-73.80,-651.34:99
+chr1	814794	.	G	C	5521.90	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=400;Dels=0.00;HRun=0;HaplotypeScore=359.70;MQ=34.34;MQ0=40;QD=13.80;SB=-919.83	GT:AD:DP:GL:GQ	0/1:77,252:207:-551.19,-211.22,-478.27:99
+chr1	814804	.	C	T	88.70	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=434;Dels=0.00;HRun=1;HaplotypeScore=347.22;MQ=35.87;MQ0=35;QD=0.20;SB=-33.30	GT:AD:DP:GL:GQ	0/1:387,47:188:-68.79,-56.64,-599.68:99
+chr1	814807	.	A	C	912.16	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=446;Dels=0.00;HRun=1;HaplotypeScore=302.12;MQ=36.31;MQ0=35;QD=2.05;SB=-348.23	GT:AD:DP:GL:GQ	0/1:319,127:242:-167.40,-72.90,-690.79:99
+chr1	814811	.	C	T	8629.57	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=472;Dels=0.00;HRun=2;HaplotypeScore=321.44;MQ=36.81;MQ0=35;QD=18.28;SB=-2662.56	GT:AD:DP:GL:GQ	0/1:133,339:310:-861.96,-93.38,-350.61:99
+chr1	814815	.	G	A	1219.97	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=497;Dels=0.00;HRun=1;HaplotypeScore=253.88;MQ=37.19;MQ0=33;QD=2.45;SB=-308.28	GT:AD:DP:GL:GQ	0/1:414,82:332:-225.30,-100.02,-991.58:99
+chr1	814833	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=552;Dels=0.00;HRun=0;HaplotypeScore=30.66;MQ=38.93;MQ0=25;OQ=13138.69;QD=23.80;SB=-5564.86	GT:AD:DP:GL:GQ	0/1:68,484:387:-1312.87,-116.58,-241.99:99
+chr1	814846	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=600;Dels=0.00;HRun=1;HaplotypeScore=69.54;MQ=39.19;MQ0=23;OQ=3136.64;QD=5.23;SB=-1237.78	GT:AD:DP:GL:GQ	0/1:435,165:409:-440.13,-123.18,-1039.78:99
+chr1	814879	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=693;Dels=0.00;HRun=0;HaplotypeScore=388.69;MQ=39.91;MQ0=7;OQ=8125.01;QD=11.72;SB=-2578.04	GT:AD:DP:GL:GQ	0/1:409,284:467:-811.50,-140.66,-960.39:99
+chr1	814880	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=692;Dels=0.00;HRun=2;HaplotypeScore=381.90;MQ=39.95;MQ0=7;OQ=2413.57;QD=3.49;SB=-960.49	GT:AD:DP:GL:GQ	0/1:533,158:465:-387.57,-142.93,-1289.43:99
+chr1	814900	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=699;Dels=0.00;HRun=0;HaplotypeScore=119.56;MQ=39.22;MQ0=14;OQ=14541.95;QD=20.80;SB=-4000.09	GT:AD:DP:GL:GQ	0/1:90,605:445:-1453.20,-134.09,-272.14:99
+chr1	814929	.	C	T	1261.33	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=562;Dels=0.00;HRun=0;HaplotypeScore=644.78;MQ=37.11;MQ0=29;QD=2.24;SB=-29.99	GT:AD:DP:GL:GQ	0/1:384,176:313:-223.70,-94.28,-953.66:99
+chr1	814931	.	T	C	7350.11	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=554;Dels=0.00;HRun=4;HaplotypeScore=616.85;MQ=36.93;MQ0=28;QD=13.27;SB=-1896.86	GT:AD:DP:GL:GQ	0/1:148,405:309:-734.01,-93.08,-440.40:99
+chr1	814932	rs4475692	G	A	10783.24	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=554;Dels=0.00;HRun=0;HaplotypeScore=621.95;MQ=36.79;MQ0=29;QD=19.46;SB=-2129.22	GT:AD:DP:GL:GQ	0/1:174,298:306:-1077.32,-380.57,-459.91:99
+chr1	814939	.	G	A	1306.21	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=568;Dels=0.00;HRun=1;HaplotypeScore=479.84;MQ=36.20;MQ0=35;QD=2.30;SB=-170.45	GT:AD:DP:GL:GQ	0/1:402,165:327:-232.39,-98.48,-986.51:99
+chr1	814952	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=543;Dels=0.00;HRun=0;HaplotypeScore=51.53;MQ=35.74;MQ0=35;OQ=140.17;QD=0.26;SB=144.16	GT:AD:DP:GL:GQ	0/1:482,61:349:-122.41,-105.11,-1207.38:99
+chr1	814967	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=541;Dels=0.00;HRun=0;HaplotypeScore=312.71;MQ=35.10;MQ0=40;OQ=7468.20;QD=13.80;SB=-2338.34	GT:AD:DP:GL:GQ	0/1:256,284:360:-745.82,-108.45,-622.35:99
+chr1	814975	.	C	T	35.90	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=483;Dels=0.00;HRun=0;HaplotypeScore=80.80;MQ=34.88;MQ0=44;QD=0.07;SB=387.40	GT:AD:DP:GL:GQ	0/1:418,42:326:-167.53,-160.66,-1098.08:68.73
+chr1	815007	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=591;Dels=0.00;HRun=1;HaplotypeScore=71.67;MQ=32.27;MQ0=41;OQ=5134.52;QD=8.69;SB=-1587.17	GT:AD:DP:GL:GQ	0/1:388,203:408:-512.45,-122.89,-966.60:99
+chr1	815060	rs7417801	G	A	11239.90	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=650;Dels=0.00;HRun=0;HaplotypeScore=316.82;MQ=33.42;MQ0=19;QD=17.29;SB=-4737.34	GT:AD:DP:GL:GQ	0/1:178,470:421:-1122.99,-126.87,-458.77:99
+chr1	815061	.	C	T	1691.04	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=650;Dels=0.00;HRun=1;HaplotypeScore=315.98;MQ=33.65;MQ0=19;QD=2.60;SB=-738.44	GT:AD:DP:GL:GQ	0/1:537,113:421:-299.19,-126.80,-1266.58:99
+chr1	815070	rs61768257	T	C	12258.60	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=631;Dels=0.00;HRun=0;HaplotypeScore=343.15;MQ=33.97;MQ0=16;QD=19.43;SB=-5504.71	GT:AD:DP:GL:GQ	0/1:80,551:412:-1224.86,-124.09,-309.22:99
+chr1	815113	rs61768258	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=470;Dels=0.00;HRun=0;HaplotypeScore=109.35;MQ=33.63;MQ0=24;OQ=6584.76;QD=14.01;SB=-2185.39	GT:AD:DP:GL:GQ	0/1:114,356:254:-657.48,-76.51,-273.29:99
+chr1	815129	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=382;Dels=0.00;HRun=3;HaplotypeScore=48.33;MQ=33.58;MQ0=23;OQ=4485.00;QD=11.74;SB=-986.12	GT:AD:DP:GL:GQ	0/1:120,260:190:-447.50,-57.26,-260.95:99
+chr1	815155	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=321;Dels=0.00;HRun=2;HaplotypeScore=58.38;MQ=34.02;MQ0=21;OQ=1737.47;QD=5.41;SB=15.00	GT:AD:DP:GL:GQ	0/1:189,132:155:-223.72,-46.69,-361.30:99
+chr1	815170	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=270;Dels=0.00;HRun=0;HaplotypeScore=137.94;MQ=34.80;MQ0=19;OQ=2424.70;QD=8.98;SB=14.59	GT:AD:DP:GL:GQ	0/1:64,205:125:-283.44,-37.69,-171.56:99
+chr1	815209	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=4;HaplotypeScore=80.30;MQ=38.66;MQ0=0;OQ=2224.65;QD=10.44;SB=11.50	GT:AD:DP:GL:GQ	0/1:67,146:136:-266.72,-40.97,-258.01:99
+chr1	815222	.	C	G	180.27	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=2;HaplotypeScore=142.18;MQ=38.40;MQ0=0;QD=0.81;SB=9.29	GT:AD:DP:GL:GQ	0/1:186,36:136:-62.35,-41.04,-500.13:99
+chr1	815223	.	G	T	2117.77	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=1;HaplotypeScore=129.82;MQ=38.70;MQ0=0;QD=9.80;SB=21.09	GT:AD:DP:GL:GQ	0/1:67,149:140:-257.24,-42.18,-220.42:99
+chr1	815225	.	C	A	1105.29	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=2;HaplotypeScore=129.82;MQ=38.83;MQ0=0;QD=5.09;SB=62.22	GT:AD:DP:GL:GQ	0/1:119,82:139:-174.62,-60.81,-341.62:99
+chr1	815273	rs13303179	G	A	2565.92	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=228;Dels=0.03;HRun=0;HaplotypeScore=354.84;MQ=39.22;MQ0=2;QD=11.25;SB=-1159.78	GT:AD:DP:GL:GQ	0/1:137,80:90:-286.39,-26.51,-60.11:99
+chr1	815278	.	G	T	761.09	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=1;HaplotypeScore=623.87;MQ=38.93;MQ0=0;QD=3.17;SB=80.36	GT:AD:DP:GL:GQ	0/1:181,48:118:-132.78,-53.39,-296.79:99
+chr1	815284	.	A	T	612.72	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=234;Dels=0.01;HRun=0;HaplotypeScore=131.40;MQ=39.54;MQ0=0;QD=2.62;SB=-4.85	GT:AD:DP:GL:GQ	0/1:70,108:89:-96.12,-31.56,-237.53:99
+chr1	815299	.	C	T	462.61	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=1;HaplotypeScore=228.02;MQ=37.95;MQ0=1;QD=1.71;SB=107.29	GT:AD:DP:GL:GQ	0/1:137,134:104:-80.88,-31.33,-296.80:99
+chr1	815300	.	A	G	825.50	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=268;Dels=0.00;HRun=0;HaplotypeScore=227.74;MQ=37.73;MQ0=1;QD=3.08;SB=104.37	GT:AD:DP:GL:GQ	0/1:110,156:125:-123.50,-37.66,-346.20:99
+chr1	815308	.	A	G	1233.06	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=264;Dels=0.00;HRun=0;HaplotypeScore=419.76;MQ=37.40;MQ0=1;QD=4.67;SB=68.40	GT:AD:DP:GL:GQ	0/1:127,137:154:-172.99,-46.40,-402.39:99
+chr1	815312	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=276;Dels=0.00;HRun=0;HaplotypeScore=183.65;MQ=36.17;MQ0=1;OQ=3931.91;QD=14.25;SB=-32.81	GT:AD:DP:GL:GQ	0/1:62,214:156:-392.19,-47.02,-185.37:99
+chr1	815328	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=297;Dels=0.00;HRun=0;HaplotypeScore=61.42;MQ=35.05;MQ0=1;OQ=1563.62;QD=5.26;SB=37.57	GT:AD:DP:GL:GQ	0/1:210,87:190:-216.89,-57.25,-456.11:99
+chr1	815333	.	A	G	262.79	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=299;Dels=0.00;HRun=0;HaplotypeScore=239.02;MQ=35.16;MQ0=1;QD=0.88;SB=12.36	GT:AD:DP:GL:GQ	0/1:257,42:214:-94.06,-64.49,-716.97:99
+chr1	815339	.	G	A	1298.73	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=284;Dels=0.00;HRun=1;HaplotypeScore=174.26;MQ=34.74;MQ0=1;QD=4.57;SB=28.57	GT:AD:DP:GL:GQ	0/1:213,70:192:-191.01,-57.85,-488.27:99
+chr1	815340	.	C	A	157.45	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=166.11;MQ=34.52;MQ0=1;QD=0.56;SB=56.17	GT:AD:DP:GL:GQ	0/1:238,39:195:-77.77,-58.74,-595.87:99
+chr1	815347	.	C	T	431.68	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=149.67;MQ=34.21;MQ0=1;QD=1.59;SB=13.61	GT:AD:DP:GL:GQ	0/1:219,52:183:-101.60,-55.14,-567.56:99
+chr1	815356	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=0;HaplotypeScore=134.05;MQ=33.48;MQ0=1;OQ=648.64;QD=2.30;SB=53.15	GT:AD:DP:GL:GQ	0/1:240,42:173:-120.28,-52.13,-519.88:99
+chr1	815363	.	G	A	778.46	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=288;Dels=0.00;HRun=0;HaplotypeScore=145.91;MQ=33.47;MQ0=1;QD=2.70;SB=9.52	GT:AD:DP:GL:GQ	0/1:221,66:188:-137.76,-56.63,-540.20:99
+chr1	815371	.	T	A	4591.13	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=275;Dels=0.00;HRun=0;HaplotypeScore=258.43;MQ=32.98;MQ0=1;QD=16.70;SB=38.12	GT:AD:DP:GL:GQ	0/1:49,226:171:-458.11,-51.51,-170.42:99
+chr1	815373	.	A	T	533.41	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=286;Dels=0.00;HRun=2;HaplotypeScore=261.79;MQ=33.03;MQ0=1;QD=1.87;SB=35.14	GT:AD:DP:GL:GQ	0/1:246,39:154:-103.02,-46.39,-455.31:99
+chr1	815376	.	C	A	1170.34	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=0;HaplotypeScore=127.10;MQ=33.82;MQ0=1;QD=4.15;SB=38.15	GT:AD:DP:GL:GQ	0/1:188,94:146:-164.30,-43.98,-347.79:99
+chr1	815381	.	G	A	252.28	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=299;Dels=0.00;HRun=0;HaplotypeScore=149.34;MQ=33.65;MQ0=1;QD=0.84;SB=44.17	GT:AD:DP:GL:GQ	0/1:261,37:167:-78.82,-50.30,-512.70:99
+chr1	815393	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=275;Dels=0.00;HRun=2;HaplotypeScore=32.62;MQ=34.43;MQ0=1;OQ=361.63;QD=1.32;SB=59.23	GT:AD:DP:GL:GQ	0/1:214,61:130:-78.62,-39.18,-425.44:99
+chr1	815401	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=262;Dels=0.00;HRun=0;HaplotypeScore=139.53;MQ=35.48;MQ0=0;OQ=534.52;QD=2.04;SB=65.23	GT:AD:DP:GL:GQ	0/1:204,58:105:-88.37,-31.63,-309.51:99
+chr1	815405	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=256;Dels=0.00;HRun=0;HaplotypeScore=139.38;MQ=35.34;MQ0=0;OQ=1047.66;QD=4.09;SB=65.23	GT:AD:DP:GL:GQ	0/1:61,195:95:-136.67,-28.62,-215.61:99
+chr1	815412	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=227;Dels=0.00;HRun=1;HaplotypeScore=225.15;MQ=36.20;MQ0=0;OQ=276.35;QD=1.22;SB=65.25	GT:AD:DP:GL:GQ	0/1:61,166:74:-53.21,-22.29,-232.02:99
+chr1	815417	rs4970337	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=202;Dels=0.00;HRun=1;HaplotypeScore=585.49;MQ=36.06;MQ0=0;OQ=1433.41;QD=7.10;SB=-630.86	GT:AD:DP:GL:GQ	1/1:20,53:52:-158.74,-15.68,-11.81:38.71
+chr1	815425	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=183;Dels=0.00;HRun=0;HaplotypeScore=313.15;MQ=35.48;MQ0=0;OQ=58.46;QD=0.32;SB=65.13	GT:AD:DP:GL:GQ	0/1:47,51:54:-25.40,-16.27,-162.78:91.30
+chr1	815458	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=13.84;MQ=40.96;MQ0=1;OQ=53.27;QD=0.51;SB=62.22	GT:AD:DP:GL:GQ	0/1:68,36:55:-25.19,-16.58,-184.48:86.11
+chr1	815470	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=23.44;MQ=43.10;MQ0=1;OQ=126.81;QD=1.44;SB=62.23	GT:AD:DP:GL:GQ	0/1:44,44:50:-31.03,-15.06,-165.46:99
+chr1	815557	.	T	C	22.78	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=1;HaplotypeScore=22.31;MQ=51.18;MQ0=1;QD=0.27;SB=2.47	GT:AD:DP:GL:GQ	0/1:71,13:68:-26.06,-20.50,-237.08:55.60
+chr1	815639	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=2;HaplotypeScore=38.60;MQ=52.07;MQ0=2;OQ=197.56;QD=2.27;SB=80.29	GT:AD:DP:GL:GQ	0/1:75,12:73:-45.07,-22.03,-247.37:99
+chr1	815714	rs4549984	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=282;Dels=0.00;HRun=0;HaplotypeScore=45.55;MQ=35.23;MQ0=6;OQ=3065.05;QD=10.87;SB=-490.50	GT:AD:DP:GL:GQ	0/1:131,151:198:-369.43,-59.64,-380.00:99
+chr1	815740	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=388;Dels=0.00;HRun=1;HaplotypeScore=91.19;MQ=33.31;MQ0=8;OQ=203.81;QD=0.53;SB=46.30	GT:AD:DP:GL:GQ	0/1:351,35:273:-111.13,-87.46,-857.56:99
+chr1	815759	.	A	T	981.66	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=425;Dels=0.00;HRun=0;HaplotypeScore=319.89;MQ=33.30;MQ0=16;QD=2.31;SB=-282.31	GT:AD:DP:GL:GQ	0/1:309,70:292:-258.47,-157.02,-944.68:99
+chr1	815760	.	C	A	1978.15	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=424;Dels=0.00;HRun=3;HaplotypeScore=319.89;MQ=33.21;MQ0=16;QD=4.67;SB=-361.60	GT:AD:DP:GL:GQ	0/1:311,113:290:-288.45,-87.35,-755.50:99
+chr1	815761	.	C	A	1757.71	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=422;Dels=0.00;HRun=1;HaplotypeScore=319.47;MQ=33.03;MQ0=16;QD=4.17;SB=-393.48	GT:AD:DP:GL:GQ	0/1:295,112:286:-275.36,-96.30,-763.46:99
+chr1	815762	.	A	G	1602.96	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=423;Dels=0.00;HRun=0;HaplotypeScore=319.57;MQ=33.04;MQ0=16;QD=3.79;SB=-325.52	GT:AD:DP:GL:GQ	0/1:273,113:288:-310.25,-146.67,-857.16:99
+chr1	815765	.	G	A	2936.95	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=427;Dels=0.00;HRun=3;HaplotypeScore=320.41;MQ=33.17;MQ0=17;QD=6.88;SB=-566.97	GT:AD:DP:GL:GQ	0/1:277,150:291:-384.73,-87.75,-614.82:99
+chr1	815777	.	C	T	24.19	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=434;Dels=0.00;HRun=0;HaplotypeScore=73.54;MQ=32.97;MQ0=17;QD=0.06;SB=99.73	GT:AD:DP:GL:GQ	0/1:393,41:292:-93.65,-87.95,-958.63:57.01
+chr1	815780	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=432;Dels=0.00;HRun=1;HaplotypeScore=75.21;MQ=32.79;MQ0=17;OQ=115.11;QD=0.27;SB=79.01	GT:AD:DP:GL:GQ	0/1:399,33:289:-101.84,-87.05,-1076.94:99
+chr1	815810	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=3;HaplotypeScore=40.23;MQ=35.68;MQ0=17;OQ=207.08;QD=0.78;SB=-57.21	GT:AD:DP:GL:GQ	0/1:229,35:180:-78.22,-54.22,-636.76:99
+chr1	815845	.	C	G	0.13	PASS	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=5.72;MQ=49.45;MQ0=9;OQ=487.79;QD=4.69;SB=-262.79	GT:AD:DP:GL:GQ	0/1:68,36:85:-77.68,-25.61,-285.79:99
+chr1	815857	.	T	A	21.33	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=5.01;MQ=54.04;MQ0=5;QD=0.23;SB=16.48	GT:AD:DP:GL:GQ	0/1:77,14:82:-30.11,-24.70,-281.02:54.14
+chr1	815931	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=2;HaplotypeScore=25.80;MQ=41.76;MQ0=34;OQ=413.34;QD=2.70;SB=-90.95	GT:AD:DP:GL:GQ	0/1:89,64:100:-74.74,-30.13,-291.31:99
+chr1	815936	.	T	G	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=41.51;MQ0=35;OQ=307.08;QD=1.93;SB=-87.61	GT:AD:DP:GL:GQ	0/1:91,68:101:-64.41,-30.42,-308.26:99
+chr1	815949	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=1;HaplotypeScore=25.06;MQ=39.71;MQ0=34;OQ=456.33;QD=2.82;SB=-102.31	GT:AD:DP:GL:GQ	0/1:134,28:100:-79.04,-30.12,-319.08:99
+chr1	815979	.	A	G	1177.05	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=1;HaplotypeScore=140.50;MQ=42.13;MQ0=3;QD=7.18;SB=-203.16	GT:AD:DP:GL:GQ	0/1:88,76:129:-159.86,-38.87,-326.00:99
+chr1	815980	.	T	C	32.10	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=144.97;MQ=42.03;MQ0=3;QD=0.19;SB=-40.00	GT:AD:DP:GL:GQ	0/1:145,23:122:-43.25,-36.76,-439.68:64.94
+chr1	815986	.	A	G	296.02	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=2;HaplotypeScore=92.41;MQ=40.86;MQ0=3;QD=1.64;SB=-47.33	GT:AD:DP:GL:GQ	0/1:153,28:121:-69.34,-36.45,-404.50:99
+chr1	816000	.	G	A	125.95	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=173;Dels=0.00;HRun=1;HaplotypeScore=82.29;MQ=39.25;MQ0=3;QD=0.73;SB=53.66	GT:AD:DP:GL:GQ	0/1:159,14:109:-48.71,-32.83,-348.18:99
+chr1	816001	.	G	A	216.96	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=171;Dels=0.00;HRun=0;HaplotypeScore=91.06;MQ=39.38;MQ0=3;QD=1.27;SB=50.65	GT:AD:DP:GL:GQ	0/1:127,38:117:-81.21,-56.23,-367.68:99
+chr1	816004	.	G	A	219.09	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=0;HaplotypeScore=92.89;MQ=39.19;MQ0=0;QD=1.27;SB=56.64	GT:AD:DP:GL:GQ	0/1:125,47:119:-61.04,-35.85,-362.44:99
+chr1	816007	.	G	A	88.79	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=173;Dels=0.02;HRun=1;HaplotypeScore=88.30;MQ=38.80;MQ0=0;QD=0.51;SB=95.33	GT:AD:DP:GL:GQ	0/1:131,39:117:-47.40,-35.24,-375.36:99
+chr1	816018	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=196;Dels=0.00;HRun=1;HaplotypeScore=112.53;MQ=36.89;MQ0=0;OQ=274.62;QD=1.40;SB=-52.14	GT:AD:DP:GL:GQ	0/1:173,23:109:-63.59,-32.85,-401.41:99
+chr1	816026	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=509.63;MQ=37.96;MQ0=0;OQ=1247.86;QD=6.86;SB=56.18	GT:AD:DP:GL:GQ	0/1:108,73:128:-166.63,-38.56,-316.49:99
+chr1	816043	.	A	G	1178.79	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=281;Dels=0.00;HRun=0;HaplotypeScore=614.45;MQ=34.94;MQ0=1;QD=4.19;SB=56.21	GT:AD:DP:GL:GQ	0/1:198,83:191:-178.71,-57.55,-539.60:99
+chr1	816057	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=287;Dels=0.00;HRun=0;HaplotypeScore=198.13;MQ=34.34;MQ0=4;OQ=1603.81;QD=5.59;SB=62.23	GT:AD:DP:GL:GQ	0/1:144,109:196:-293.22,-129.56,-512.85:99
+chr1	816072	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=309;Dels=0.00;HRun=0;HaplotypeScore=33.06;MQ=33.48;MQ0=15;OQ=115.32;QD=0.37;SB=71.18	GT:AD:DP:GL:GQ	0/1:282,15:160:-71.44,-56.63,-531.53:99
+chr1	816077	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=299;Dels=0.00;HRun=0;HaplotypeScore=55.33;MQ=33.49;MQ0=15;OQ=4794.59;QD=16.04;SB=68.22	GT:AD:DP:GL:GQ	0/1:81,218:173:-478.46,-52.11,-201.39:99
+chr1	816088	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=1;HaplotypeScore=51.57;MQ=34.30;MQ0=16;OQ=4463.53;QD=16.06;SB=62.23	GT:AD:DP:GL:GQ	0/1:58,220:169:-445.35,-50.90,-214.04:99
+chr1	816103	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=237;Dels=0.00;HRun=0;HaplotypeScore=38.99;MQ=36.26;MQ0=16;OQ=1889.47;QD=7.97;SB=68.20	GT:AD:DP:GL:GQ	0/1:61,152:117:-237.42,-45.19,-199.18:99
+chr1	816115	.	C	T	1441.66	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=202;Dels=0.00;HRun=0;HaplotypeScore=145.73;MQ=37.27;MQ0=15;QD=7.14;SB=68.18	GT:AD:DP:GL:GQ	0/1:132,70:112:-181.22,-33.77,-214.53:99
+chr1	816118	.	A	T	125.43	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=0;HaplotypeScore=164.12;MQ=38.34;MQ0=15;QD=0.66;SB=77.28	GT:AD:DP:GL:GQ	0/1:145,37:109:-58.41,-42.58,-369.08:99
+chr1	816122	.	G	C	132.11	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=159.96;MQ=38.91;MQ0=15;QD=0.73;SB=80.30	GT:AD:DP:GL:GQ	0/1:155,27:96:-45.43,-28.94,-364.83:99
+chr1	816123	.	A	G	766.79	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=157.96;MQ=38.91;MQ0=14;QD=4.28;SB=80.30	GT:AD:DP:GL:GQ	0/1:86,89:106:-121.93,-41.97,-306.67:99
+chr1	816140	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=2;HaplotypeScore=35.96;MQ=45.77;MQ0=9;OQ=496.37;QD=3.82;SB=92.32	GT:AD:DP:GL:GQ	0/1:81,49:95:-81.53,-28.61,-273.48:99
+chr1	817130	rs2879698	C	T	1.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=7.86;MQ=52.69;MQ0=4;OQ=2390.21;QD=32.30;SB=-1172.34	GT:AD:DP:GL:GQ	1/1:5,69:61:-242.62,-18.38,-0.02:99
+chr1	817140	rs4246498	T	C	134.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=52.12;MQ0=4;OQ=2043.04;QD=29.61;SB=-1026.82	GT:AD:DP:GL:GQ	1/1:0,69:59:-207.91,-17.78,-0.03:99
+chr1	817186	rs4970386	C	T	31.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=4.56;MQ=51.33;MQ0=3;OQ=2194.13;QD=35.39;SB=-970.28	GT:AD:DP:GL:GQ	1/1:3,59:55:-223.01,-16.57,-0.01:99
+chr1	819196	rs9778019	G	A	567.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.32;MQ0=0;OQ=1941.14;QD=39.62;SB=-968.30	GT:AD:DP:GL:GQ	1/1:0,49:49:-197.71,-14.76,-0.01:99
+chr1	819500	rs4437820	C	T	68.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.98;MQ=47.44;MQ0=2;OQ=2599.35;QD=37.13;SB=-1006.03	GT:AD:DP:GL:GQ	1/1:0,70:64:-263.53,-19.28,-0.01:99
+chr1	819787	.	G	A	25.28	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=51.75;MQ0=1;QD=0.29;SB=104.31	GT:AD:DP:GL:GQ	0/1:80,8:75:-28.42,-22.61,-220.79:58.10
+chr1	820044	rs28444699	A	G	2.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=5.59;MQ=55.18;MQ0=2;OQ=1994.05;QD=28.49;SB=-1022.00	GT:AD:DP:GL:GQ	1/1:9,61:60:-210.82,-18.07,-7.83:99
+chr1	820670	rs6422669	G	C	266.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.30;MQ0=1;OQ=1743.26;QD=40.54;SB=-467.22	GT:AD:DP:GL:GQ	1/1:1,42:42:-177.93,-12.66,-0.02:99
+chr1	821139	rs4024798	C	T	0.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=239;Dels=0.00;HRun=1;HaplotypeScore=9.98;MQ=39.26;MQ0=24;OQ=434.25;QD=1.82;SB=23.91	GT:AD:DP:GL:GQ	0/1:189,50:167:-97.03,-50.32,-487.12:99
+chr1	821171	rs477080	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=308;Dels=0.00;HRun=0;HaplotypeScore=33.10;MQ=34.56;MQ0=43;OQ=282.37;QD=0.92;SB=137.47	GT:AD:DP:GL:GQ	0/1:233,75:190:-88.75,-57.23,-688.44:99
+chr1	821352	rs4970385	C	T	0.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=12.93;MQ=49.51;MQ0=5;OQ=2978.23;QD=32.02;SB=-1308.26	GT:AD:DP:GL:GQ	1/1:14,79:78:-308.32,-23.50,-6.91:99
+chr1	821772	rs9697642	C	T	1.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=6.48;MQ=53.07;MQ0=1;OQ=2639.96;QD=38.26;SB=-935.74	GT:AD:DP:GL:GQ	1/1:1,68:65:-267.59,-19.58,-0.01:99
+chr1	821923	rs9697378	G	A	628.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=46.85;MQ0=2;OQ=2615.06;QD=34.87;SB=-1164.40	GT:AD:DP:GL:GQ	1/1:9,66:67:-268.90,-20.18,-3.81:99
+chr1	821929	rs9697380	G	C	204.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=46.00;MQ0=2;OQ=2952.34;QD=37.85;SB=-1375.91	GT:AD:DP:GL:GQ	1/1:9,69:70:-303.53,-21.09,-4.71:99
+chr1	821975	rs9697725	T	C	60.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=42.31;MQ0=7;OQ=2446.13;QD=25.75;SB=-880.44	GT:AD:DP:GL:GQ	1/1:20,75:74:-256.35,-22.29,-8.15:99
+chr1	822041	rs13302934	A	G	54.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=37.41;MQ0=11;OQ=2291.03;QD=26.64;SB=-1047.92	GT:AD:DP:GL:GQ	1/1:17,69:67:-236.77,-20.18,-4.08:99
+chr1	822181	rs4500250	C	A	165.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=54.49;MQ0=0;OQ=2287.58;QD=33.15;SB=-1055.56	GT:AD:DP:GL:GQ	1/1:2,67:63:-232.36,-18.97,-0.02:99
+chr1	822261	rs4553118	T	C	105.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=53.16;MQ0=0;OQ=2074.16;QD=32.41;SB=-1031.91	GT:AD:DP:GL:GQ	1/1:0,64:58:-211.02,-17.47,-0.02:99
+chr1	827077	.	G	C	11.08	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1103.43;QD=20.06;SB=-557.74	GT:AD:DP:GL:GQ	0/1:23,32:50:-128.70,-15.07,-86.51:99
+chr1	832688	rs7519340	A	G	206.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.92;MQ0=0;OQ=2256.38;QD=34.19;SB=-897.99	GT:AD:DP:GL:GQ	1/1:0,66:64:-229.25,-19.28,-0.02:99
+chr1	833268	rs11516185	A	G	180.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=58.03;MQ0=0;OQ=720.81;QD=12.65;SB=-270.98	GT:AD:DP:GL:GQ	0/1:24,33:50:-90.45,-15.09,-82.68:99
+chr1	834163	rs61769713	C	G	7.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=34.66;MQ0=0;OQ=386.18;QD=32.18;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,12:11:-42.22,-3.32,-0.01:33.11
+chr1	834187	rs61769714	G	A	6.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=34.17;MQ0=0;OQ=258.44;QD=25.84;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,9:8:-29.44,-2.42,-0.01:24.06
+chr1	834206	rs61769715	A	G	21	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=32.88;MQ0=0;OQ=98.47;QD=14.07;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,7:4:-13.38,-1.21,-0.00:12.03
+chr1	834961	.	T	G	0.56	PASS	AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;HRun=2;HaplotypeScore=0.74;MQ=16.23;MQ0=3;OQ=70.14;QD=6.38;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,10:3:-10.50,-0.90,-0.00:9.03
+chr1	835146	rs7366404	G	T	7.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=37.00;MQ0=0;OQ=260.28;QD=32.54;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,8:8:-29.61,-2.41,-0.00:24.08
+chr1	836201	rs4970334	A	G	56.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.61;MQ=57.95;MQ0=0;OQ=1280.53;QD=26.68;SB=-522.83	GT:AD:DP:GL:GQ	1/1:0,47:43:-131.69,-12.98,-0.05:99
+chr1	836352	rs4970333	T	C	54.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.98;MQ=58.58;MQ0=0;OQ=1607.31;QD=32.80;SB=-789.15	GT:AD:DP:GL:GQ	1/1:0,49:46:-164.33,-13.86,-0.02:99
+chr1	837113	rs7416129	G	A	502.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=3431.98;QD=39.91;SB=-1125.99	GT:AD:DP:GL:GQ	1/1:0,85:84:-342.20,-25.31,-0.02:99
+chr1	839861	rs13303222	A	G	170.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=59.09;MQ0=0;OQ=2748.15;QD=33.51;SB=-1203.79	GT:AD:DP:GL:GQ	1/1:0,81:78:-278.43,-23.50,-0.03:99
+chr1	840081	rs6664536	T	A	113.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=58.64;MQ0=0;OQ=1837.58;QD=35.34;SB=-814.88	GT:AD:DP:GL:GQ	1/1:0,52:50:-187.36,-15.06,-0.02:99
+chr1	840234	rs6679046	G	T	614.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.48;MQ0=0;OQ=2550.23;QD=33.56;SB=-1032.51	GT:AD:DP:GL:GQ	1/1:0,76:73:-258.64,-22.00,-0.04:99
+chr1	840643	rs6657440	C	T	589.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=2334.22;QD=36.47;SB=-836.99	GT:AD:DP:GL:GQ	1/1:0,64:61:-237.03,-18.38,-0.02:99
+chr1	841253	.	G	T	87.70	PASS	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=59.70;MQ0=0;OQ=1174.44;QD=15.25;SB=-547.82	GT:AD:DP:GL:GQ	0/1:37,40:75:-143.32,-22.59,-125.03:99
+chr1	841362	rs4970465	A	G	15.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=2.07;MQ=60.00;MQ0=0;OQ=1972.18;QD=30.34;SB=-856.55	GT:AD:DP:GL:GQ	1/1:0,65:61:-200.85,-18.39,-0.05:99
+chr1	841500	.	G	C	11.73	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=3;HaplotypeScore=11.47;MQ=56.60;MQ0=0;QD=0.26;SB=59.23	GT:AD:DP:GL:GQ	0/1:36,10:33:-14.38,-9.96,-126.72:44.27
+chr1	841620	rs62677860	A	G	51.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=60.00;MQ0=0;OQ=1201.63;QD=27.31;SB=-317.48	GT:AD:DP:GL:GQ	1/1:0,43:38:-123.78,-11.46,-0.03:99
+chr1	841900	rs4970463	G	A	437.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=1176.31;QD=36.76;SB=-508.18	GT:AD:DP:GL:GQ	1/1:0,32:31:-121.23,-9.34,-0.01:93.29
+chr1	841926	rs28436996	G	A	99.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=58.05;MQ0=0;OQ=1247.42;QD=34.65;SB=-580.28	GT:AD:DP:GL:GQ	1/1:0,35:33:-128.34,-9.94,-0.01:99
+chr1	841996	rs7518702	C	T	517.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1573.23;QD=37.46;SB=-692.34	GT:AD:DP:GL:GQ	1/1:0,41:40:-160.92,-12.05,-0.01:99
+chr1	842738	rs13303369	C	T	76.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.63;MQ=58.47;MQ0=0;OQ=2145.17;QD=36.99;SB=-908.72	GT:AD:DP:GL:GQ	1/1:0,58:57:-218.13,-17.18,-0.03:99
+chr1	842827	rs4970461	T	G	8.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.36;MQ=59.03;MQ0=0;OQ=1414.13;QD=29.46;SB=-684.25	GT:AD:DP:GL:GQ	1/1:0,48:47:-145.05,-14.17,-0.05:99
+chr1	843817	rs1806509	C	A	190.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.61;MQ0=0;OQ=1993.99;QD=33.80;SB=-878.64	GT:AD:DP:GL:GQ	1/1:0,59:57:-203.01,-17.17,-0.02:99
+chr1	844640	rs13303019	A	G	51.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.20;MQ0=0;OQ=644.86;QD=22.24;SB=-345.42	GT:AD:DP:GL:GQ	1/1:0,29:23:-68.11,-6.95,-0.04:69.10
+chr1	844841	rs13303057	A	C	5.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.91;MQ=58.36;MQ0=0;OQ=1059.33;QD=26.48;SB=-412.87	GT:AD:DP:GL:GQ	1/1:0,40:35:-109.55,-10.55,-0.04:99
+chr1	844938	rs6673914	C	G	24.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.27;MQ0=0;OQ=1048.92;QD=37.46;SB=-371.18	GT:AD:DP:GL:GQ	1/1:0,28:26:-108.49,-7.84,-0.02:78.26
+chr1	847591	rs6689107	T	G	181.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.19;MQ0=0;OQ=1848.72;QD=32.43;SB=-803.49	GT:AD:DP:GL:GQ	1/1:0,57:54:-188.48,-16.27,-0.02:99
+chr1	848664	rs7418179	A	G	160.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=1692.05;QD=34.53;SB=-783.00	GT:AD:DP:GL:GQ	1/1:0,49:48:-172.81,-14.46,-0.02:99
+chr1	850279	rs61464428	G	A	12.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=57.66;MQ0=0;OQ=337.99;QD=33.80;SB=-134.01	GT:AD:DP:GL:GQ	1/1:0,10:10:-37.39,-3.02,-0.01:30.09
+chr1	850324	rs57465118	G	A	8.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=54.65;MQ0=0;OQ=218.19;QD=24.24;SB=-48.67	GT:AD:DP:GL:GQ	1/1:0,9:7:-25.40,-2.11,-0.00:21.06
+chr1	850384	rs57924093	C	A	117.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.88;MQ0=0;OQ=151.15;QD=25.19;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,5:5:-18.67,-1.51,-0.00:15.05
+chr1	850551	rs60837925	G	A	175.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.04;MQ0=0;OQ=188.60;QD=31.43;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,6:6:-22.43,-1.81,-0.00:18.06
+chr1	850660	.	G	T	32.80	LowQual	AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=65.19;MQ0=0;QD=16.40;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,2:2:-6.69,-0.60,-0.00:6.02
+chr1	850717	rs57816555	T	C	168.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.96;MQ0=0;OQ=139.82;QD=27.96;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,5:5:-17.54,-1.51,-0.00:15.04
+chr1	850871	rs28521172	G	C	136.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.04;MQ0=0;OQ=409.27;QD=34.11;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,12:11:-44.52,-3.32,-0.00:33.11
+chr1	851493	rs2879816	G	A	181.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=58.51;MQ0=0;OQ=1761.97;QD=35.24;SB=-837.99	GT:AD:DP:GL:GQ	1/1:0,50:46:-179.80,-13.86,-0.02:99
+chr1	851671	rs13302982	A	G	540.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.19;MQ0=0;OQ=1746.20;QD=30.64;SB=-800.68	GT:AD:DP:GL:GQ	1/1:0,57:56:-178.25,-16.89,-0.05:99
+chr1	851956	rs13303291	T	C	0.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=5;HaplotypeScore=0.79;MQ=59.54;MQ0=0;OQ=1647.69;QD=32.95;SB=-763.57	GT:AD:DP:GL:GQ	1/1:0,50:48:-168.38,-14.46,-0.02:99
+chr1	851987	rs13303101	A	G	75.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.28;MQ=58.42;MQ0=0;OQ=1718.71;QD=29.13;SB=-814.55	GT:AD:DP:GL:GQ	1/1:0,59:55:-175.51,-16.59,-0.06:99
+chr1	852246	rs6680268	C	T	87.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.89;MQ0=0;OQ=1535.86;QD=36.57;SB=-649.38	GT:AD:DP:GL:GQ	1/1:0,42:40:-157.19,-12.05,-0.02:99
+chr1	852252	rs6693546	A	G	8.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=57.97;MQ0=0;OQ=1460.23;QD=31.74;SB=-743.12	GT:AD:DP:GL:GQ	1/1:0,45:42:-149.63,-12.66,-0.02:99
+chr1	852729	rs3892970	C	T	119.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=1397.63;QD=34.09;SB=-551.29	GT:AD:DP:GL:GQ	1/1:0,41:38:-143.37,-11.46,-0.02:99
+chr1	852987	rs4040604	G	T	33.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=59.28;MQ0=0;OQ=1900.46;QD=32.77;SB=-758.90	GT:AD:DP:GL:GQ	1/1:0,58:55:-193.66,-16.57,-0.02:99
+chr1	853374	rs28626846	T	C	176.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=56.72;MQ0=0;OQ=383.16;QD=9.12;SB=-198.44	GT:AD:DP:GL:GQ	0/1:24,18:39:-53.37,-11.77,-80.00:99
+chr1	853419	rs7410998	G	A	181.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=49.05;MQ0=1;OQ=787.22;QD=31.49;SB=-167.67	GT:AD:DP:GL:GQ	1/1:1,24:21:-82.31,-6.33,-0.01:63.20
+chr1	853425	rs7417972	A	C	3.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=51.24;MQ0=1;OQ=853.26;QD=25.86;SB=-413.26	GT:AD:DP:GL:GQ	1/1:1,32:29:-88.94,-8.74,-0.03:87.12
+chr1	853552	rs7417994	A	G	58.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=47.89;MQ0=0;OQ=1045.12;QD=27.50;SB=-347.41	GT:AD:DP:GL:GQ	1/1:0,38:34:-108.13,-10.26,-0.03:99
+chr1	854589	rs2340590	T	A	319.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.35;MQ0=0;OQ=1082.41;QD=34.92;SB=-267.73	GT:AD:DP:GL:GQ	1/1:0,31:30:-111.84,-9.04,-0.02:90.27
+chr1	854618	rs2340589	A	G	2.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=1104.04;QD=28.31;SB=-284.44	GT:AD:DP:GL:GQ	1/1:0,39:37:-114.04,-11.17,-0.05:99
+chr1	854620	rs2340588	G	A	306.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=1407.34;QD=36.09;SB=-288.88	GT:AD:DP:GL:GQ	1/1:0,39:36:-144.33,-10.85,-0.01:99
+chr1	854801	.	G	A	27.13	PASS	AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=59.52;MQ0=0;OQ=1814.99;QD=37.81;SB=-848.99	GT:AD:DP:GL:GQ	1/1:0,48:46:-185.10,-13.86,-0.01:99
+chr1	856182	rs9988021	G	A	414.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=1807.60;QD=37.66;SB=-511.65	GT:AD:DP:GL:GQ	1/1:0,48:47:-184.36,-14.16,-0.02:99
+chr1	856756	rs2880024	T	C	439.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.61;MQ0=0;OQ=1661.89;QD=33.92;SB=-660.32	GT:AD:DP:GL:GQ	1/1:0,49:47:-169.79,-14.16,-0.01:99
+chr1	856783	rs2341361	A	G	391.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=1555.14;QD=34.56;SB=-535.20	GT:AD:DP:GL:GQ	1/1:0,45:44:-159.12,-13.26,-0.02:99
+chr1	857447	rs2341360	A	T	453.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1951.43;QD=37.53;SB=-755.79	GT:AD:DP:GL:GQ	1/1:0,51:51:-198.74,-15.36,-0.01:99
+chr1	858192	rs2341359	A	C	117.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=55.20;MQ0=0;OQ=1194.83;QD=30.64;SB=-603.64	GT:AD:DP:GL:GQ	1/1:0,39:36:-123.08,-10.85,-0.02:99
+chr1	858267	rs13302914	C	T	413.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.75;MQ0=0;OQ=1181.60;QD=33.76;SB=-589.79	GT:AD:DP:GL:GQ	1/1:0,35:32:-121.76,-9.65,-0.02:96.30
+chr1	858654	rs13303003	C	T	431.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=892.14;QD=35.69;SB=-459.35	GT:AD:DP:GL:GQ	1/1:1,24:23:-92.80,-6.93,-0.01:69.23
+chr1	858754	rs13303066	A	G	117.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=59.96;MQ0=0;OQ=1127.68;QD=32.22;SB=-537.22	GT:AD:DP:GL:GQ	1/1:0,35:32:-116.36,-9.64,-0.01:96.29
+chr1	858844	rs13303037	C	T	239.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.36;MQ0=0;OQ=920.18;QD=35.39;SB=-178.71	GT:AD:DP:GL:GQ	1/1:0,26:25:-95.62,-7.54,-0.02:75.23
+chr1	859186	rs13303207	T	C	5.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=2;HaplotypeScore=1.75;MQ=49.46;MQ0=0;OQ=860.62;QD=31.87;SB=-321.13	GT:AD:DP:GL:GQ	1/1:0,27:25:-89.66,-7.53,-0.01:75.22
+chr1	859220	.	G	T	15.33	LowQual	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=44.47;MQ0=0;QD=0.73;SB=-4.00	GT:AD:DP:GL:GQ	0/1:18,3:16:-9.63,-4.82,-45.13:48.04
+chr1	859232	rs13303328	G	T	26.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=42.12;MQ0=0;OQ=238.10;QD=15.87;SB=-41.94	GT:AD:DP:GL:GQ	0/1:4,11:12:-30.71,-3.62,-8.58:49.58
+chr1	859236	rs13303330	G	C	2.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=42.12;MQ0=0;OQ=289.97;QD=19.33;SB=-45.46	GT:AD:DP:GL:GQ	0/1:4,11:11:-35.60,-3.32,-10.54:72.26
+chr1	859264	rs13303353	G	C	17.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=37.87;MQ0=1;OQ=164.66;QD=13.72;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,7:8:-22.16,-2.41,-12.54:99
+chr1	859992	.	G	C	97.38	PASS	AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.96;MQ0=0;OQ=93.52;QD=10.39;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,9:3:-12.84,-0.90,-0.00:9.03
+chr1	860032	.	G	T	37.54	PASS	AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.43;MQ0=0;OQ=70.96;QD=5.46;SB=-10.00	GT:AD:DP:GL:GQ	1/1:8,5:3:-10.58,-0.90,-0.00:9.03
+chr1	860180	rs28451560	G	A	12.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.95;MQ0=0;OQ=73.11;QD=18.28;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,3:3:-10.80,-0.90,-0.00:9.03
+chr1	860766	rs13303094	T	C	16.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=59.17;MQ0=0;OQ=826.94;QD=29.53;SB=-125.69	GT:AD:DP:GL:GQ	1/1:0,28:25:-86.29,-7.54,-0.02:75.20
+chr1	861197	rs4072383	G	T	400.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.63;MQ0=0;OQ=731.30;QD=30.47;SB=-355.85	GT:AD:DP:GL:GQ	1/1:0,24:22:-76.73,-6.63,-0.01:66.18
+chr1	861546	rs4504834	G	A	1.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.70;MQ0=0;OQ=257.15;QD=25.71;SB=-133.67	GT:AD:DP:GL:GQ	1/1:0,10:8:-29.30,-2.41,-0.01:24.07
+chr1	863421	rs1110052	G	T	380.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=1308.42;QD=32.71;SB=-530.08	GT:AD:DP:GL:GQ	1/1:0,40:39:-134.45,-11.76,-0.03:99
+chr1	865499	.	C	T	29.46	LowQual	AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.04;MQ0=0;QD=4.91;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,2:5:-7.74,-1.51,-8.99:62.30
+chr1	865506	rs7411115	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=5;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=55.21;MQ0=0;OQ=112.00;QD=22.40;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,4:5:-15.99,-1.51,-3.39:18.84
+chr1	866063	.	G	C	0.28	PASS	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.80;MQ=60.00;MQ0=0;OQ=689.42;QD=21.54;SB=-257.43	GT:AD:DP:GL:GQ	0/1:12,20:31:-81.58,-9.35,-46.59:99
+chr1	866362	rs4372192	A	G	0.01	FDRtranche2.00to10.00	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=6;HaplotypeScore=0.89;MQ=56.86;MQ0=0;OQ=933.15;QD=29.16;SB=-432.49	GT:AD:DP:GL:GQ	1/1:0,31:29:-96.92,-8.74,-0.02:87.21
+chr1	867578	rs6605066	C	G	7.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=93.52;QD=31.17;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:3:-12.84,-0.90,-0.00:9.03
+chr1	867694	rs6672356	T	C	3.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=52.96;QD=17.65;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:3:-8.79,-0.91,-0.01:9.01
+chr1	868792	.	G	C	15.78	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=42;Dels=0.02;HRun=2;HaplotypeScore=22.45;MQ=51.57;MQ0=2;QD=0.38;SB=59.22	GT:AD:DP:GL:GQ	0/1:36,4:34:-14.81,-9.96,-119.24:48.50
+chr1	869539	rs6605067	G	A	19.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=0.58;MQ=56.16;MQ0=0;OQ=2221.47;QD=39.67;SB=-1054.70	GT:AD:DP:GL:GQ	1/1:0,56:55:-225.74,-16.57,-0.01:99
+chr1	869550	rs2839	T	C	133.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=56.64;MQ0=0;OQ=2001.68;QD=34.51;SB=-1024.77	GT:AD:DP:GL:GQ	1/1:0,58:57:-203.78,-17.17,-0.02:99
+chr1	870101	rs3748592	A	G	495.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.39;MQ0=0;OQ=1890.23;QD=34.37;SB=-862.36	GT:AD:DP:GL:GQ	1/1:0,55:54:-192.63,-16.27,-0.02:99
+chr1	871490	rs2272757	G	A	6.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.19;MQ=57.04;MQ0=0;OQ=1394.54;QD=37.69;SB=-510.64	GT:AD:DP:GL:GQ	1/1:0,37:36:-143.05,-10.85,-0.01:99
+chr1	872666	rs2340582	A	G	42.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=4.34;MQ=59.14;MQ0=0;OQ=1872.55;QD=34.68;SB=-917.03	GT:AD:DP:GL:GQ	1/1:0,54:54:-190.86,-16.27,-0.02:99
+chr1	873488	rs4970378	A	G	248.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=1449.35;QD=35.35;SB=-732.23	GT:AD:DP:GL:GQ	1/1:0,41:41:-148.53,-12.35,-0.01:99
+chr1	873762	.	T	G	3.38	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=2;HaplotypeScore=3.82;MQ=57.58;MQ0=0;OQ=623.05;QD=12.98;SB=-319.82	GT:AD:DP:GL:GQ	0/1:24,24:47:-79.75,-14.16,-84.17:99
+chr1	873892	.	A	C	58.62	SnpCluster	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=53.03;MQ0=0;QD=2.09;SB=-41.91	GT:AD:DP:GL:GQ	0/1:23,5:28:-17.58,-8.43,-82.84:91.46
+chr1	873894	.	C	T	82.90	SnpCluster	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.03;MQ0=0;QD=2.96;SB=-56.23	GT:AD:DP:GL:GQ	0/1:23,5:28:-20.01,-8.43,-84.10:99
+chr1	873895	.	C	T	48.24	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.20;MQ0=0;QD=1.56;SB=-25.58	GT:AD:DP:GL:GQ	0/1:26,5:28:-16.54,-8.43,-88.26:81.07
+chr1	873901	.	T	G	115.57	SnpCluster	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.52;MQ0=0;QD=3.50;SB=-81.81	GT:AD:DP:GL:GQ	0/1:26,7:33:-24.78,-9.94,-99.02:99
+chr1	873954	rs7522415	C	G	8.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.52;MQ=43.40;MQ0=0;OQ=1100.42;QD=22.93;SB=-415.98	GT:AD:DP:GL:GQ	0/1:16,32:45:-126.89,-13.56,-66.90:99
+chr1	873964	rs4970455	A	C	1.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=3;HaplotypeScore=2.44;MQ=43.46;MQ0=0;OQ=358.55;QD=6.77;SB=-63.88	GT:AD:DP:GL:GQ	0/1:38,15:50:-54.21,-15.07,-122.51:99
+chr1	874630	.	G	A	13.69	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=47.61;MQ0=0;OQ=1000.31;QD=21.75;SB=-485.51	GT:AD:DP:GL:GQ	0/1:17,29:46:-117.17,-13.86,-57.54:99
+chr1	874678	rs4246503	A	G	158.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=55.11;MQ0=0;OQ=1771.59;QD=30.03;SB=-814.69	GT:AD:DP:GL:GQ	1/1:0,59:55:-180.79,-16.58,-0.04:99
+chr1	875539	rs4970377	C	A	535.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.40;MQ0=0;OQ=2636.42;QD=36.12;SB=-1177.36	GT:AD:DP:GL:GQ	1/1:1,72:71:-267.24,-21.38,-0.02:99
+chr1	875552	rs4970452	G	A	0.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=10.99;MQ=56.01;MQ0=0;OQ=2730.82;QD=37.93;SB=-1364.34	GT:AD:DP:GL:GQ	1/1:1,71:70:-276.69,-21.09,-0.03:99
+chr1	875562	rs4970376	A	G	1.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=9.96;MQ=55.41;MQ0=0;OQ=2063.84;QD=30.35;SB=-1045.24	GT:AD:DP:GL:GQ	1/1:1,67:64:-210.02,-19.30,-0.05:99
+chr1	875869	rs4970375	T	C	458.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.16;MQ0=0;OQ=1904.11;QD=35.26;SB=-492.54	GT:AD:DP:GL:GQ	1/1:0,54:53:-194.01,-15.96,-0.01:99
+chr1	876651	rs10465242	G	A	37.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=58.78;MQ0=0;OQ=1853.33;QD=37.07;SB=-743.49	GT:AD:DP:GL:GQ	1/1:0,50:47:-188.93,-14.16,-0.01:99
+chr1	876680	rs10465241	C	T	139.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=1420.84;QD=37.39;SB=-598.99	GT:AD:DP:GL:GQ	1/1:0,38:38:-145.68,-11.45,-0.02:99
+chr1	877423	rs3748595	A	C	60.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=58.73;MQ0=0;OQ=1913.10;QD=31.88;SB=-946.06	GT:AD:DP:GL:GQ	1/1:0,60:56:-194.92,-16.87,-0.02:99
+chr1	877664	rs3828047	A	G	27.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=59.38;MQ0=0;OQ=1254.26;QD=33.90;SB=-513.49	GT:AD:DP:GL:GQ	1/1:0,37:36:-129.02,-10.84,-0.01:99
+chr1	878502	rs3748596	T	C	69.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=55.26;MQ0=0;OQ=1390.46;QD=33.11;SB=-577.30	GT:AD:DP:GL:GQ	1/1:0,42:41:-142.65,-12.35,-0.02:99
+chr1	878522	rs3748597	T	C	420.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.43;MQ0=0;OQ=1101.61;QD=31.47;SB=-433.56	GT:AD:DP:GL:GQ	1/1:0,35:33:-113.76,-9.94,-0.02:99
+chr1	879021	rs56262069	G	C	15.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=1649.51;QD=39.27;SB=-490.55	GT:AD:DP:GL:GQ	1/1:0,42:39:-168.56,-11.76,-0.02:99
+chr1	879022	rs13302945	A	C	102.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1299.59;QD=30.94;SB=-461.34	GT:AD:DP:GL:GQ	1/1:0,42:39:-133.56,-11.75,-0.02:99
+chr1	879501	rs13303206	G	C	38.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=58.78;MQ0=0;OQ=1536.75;QD=40.44;SB=-636.90	GT:AD:DP:GL:GQ	1/1:0,38:37:-157.27,-11.15,-0.01:99
+chr1	879576	rs13303051	C	A	192.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.48;MQ=59.05;MQ0=0;OQ=1663.22;QD=33.94;SB=-850.81	GT:AD:DP:GL:GQ	1/1:1,48:46:-169.92,-13.85,-0.01:99
+chr1	880884	rs13302957	G	A	138.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=59.32;MQ0=0;OQ=2228.59;QD=40.52;SB=-1097.37	GT:AD:DP:GL:GQ	1/1:0,55:55:-226.45,-16.57,-0.01:99
+chr1	880922	rs13303065	C	T	237.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2022.89;QD=39.66;SB=-914.68	GT:AD:DP:GL:GQ	1/1:0,51:51:-205.89,-15.36,-0.01:99
+chr1	881808	rs13303106	A	G	3.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.33;MQ=59.21;MQ0=0;OQ=1343.98;QD=25.36;SB=-644.88	GT:AD:DP:GL:GQ	1/1:0,53:43:-138.03,-12.97,-0.04:99
+chr1	882608	rs13303227	G	A	569.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2091.00;QD=38.72;SB=-899.68	GT:AD:DP:GL:GQ	1/1:0,54:53:-212.70,-15.97,-0.01:99
+chr1	883143	rs4970371	G	A	143.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=57.73;MQ0=0;OQ=2249.45;QD=37.49;SB=-940.26	GT:AD:DP:GL:GQ	1/1:0,60:57:-228.55,-17.17,-0.02:99
+chr1	883494	rs6605069	A	G	58.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=58.62;MQ0=0;OQ=2094.43;QD=32.73;SB=-870.68	GT:AD:DP:GL:GQ	1/1:0,64:60:-213.05,-18.07,-0.02:99
+chr1	883582	rs4970445	G	A	189.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.14;MQ0=0;OQ=1807.99;QD=33.48;SB=-798.52	GT:AD:DP:GL:GQ	1/1:1,53:49:-184.42,-14.78,-0.04:99
+chr1	884436	rs13303010	G	A	1.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=58.63;MQ0=0;OQ=585.11;QD=34.42;SB=-52.67	GT:AD:DP:GL:GQ	1/1:0,17:16:-62.10,-4.82,-0.01:48.15
+chr1	885569	rs13303327	G	A	161.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=61.07;MQ0=0;OQ=743.89;QD=37.19;SB=-245.00	GT:AD:DP:GL:GQ	1/1:0,20:20:-77.98,-6.03,-0.01:60.19
+chr1	887188	rs4970441	G	C	2.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=753.54;QD=39.66;SB=-289.25	GT:AD:DP:GL:GQ	1/1:0,19:18:-78.95,-5.42,-0.01:54.18
+chr1	887427	rs13303229	T	C	257.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1210.82;QD=33.63;SB=-286.61	GT:AD:DP:GL:GQ	1/1:0,36:36:-124.69,-10.85,-0.02:99
+chr1	888186	rs6605071	T	C	17.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=3.35;MQ=58.67;MQ0=0;OQ=1185.73;QD=33.88;SB=-618.22	GT:AD:DP:GL:GQ	1/1:0,35:34:-122.17,-10.24,-0.01:99
+chr1	889791	rs6677386	G	C	245.35	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=39.71;MQ0=0;QD=16.36;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,15:8:-28.14,-2.43,-0.02:24.07
+chr1	889800	.	G	T	344.36	SnpCluster	AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=39.12;MQ0=0;QD=28.70;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,12:11:-38.03,-3.31,-0.01:33.08
+chr1	889801	.	G	C	465.29	SnpCluster	AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=39.12;MQ0=0;QD=38.77;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,12:11:-50.12,-3.31,-0.00:33.11
+chr1	889805	.	G	A	501.88	SnpCluster	AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=39.71;MQ0=0;QD=33.46;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,15:14:-53.78,-4.22,-0.01:42.13
+chr1	889852	rs6669071	A	C	11.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=44.10;MQ0=0;OQ=318.72;QD=26.56;SB=-44.57	GT:AD:DP:GL:GQ	1/1:0,12:11:-35.46,-3.31,-0.01:33.07
+chr1	889864	rs28754834	G	A	283.84	Indel	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=44.79;MQ0=0;QD=31.54;SB=-93.34	GT:AD:DP:GL:GQ	1/1:0,9:8:-31.97,-2.41,-0.00:24.08
+chr1	889872	rs6704181	C	G	264.94	Indel	AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=42.50;MQ0=0;QD=33.12;SB=-56.93	GT:AD:DP:GL:GQ	1/1:0,8:7:-30.07,-2.11,-0.00:21.07
+chr1	890148	rs4970435	C	T	1.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=54.37;MQ0=0;OQ=1059.65;QD=35.32;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,29:28:-109.56,-8.43,-0.01:84.27
+chr1	890149	rs4970434	A	G	1.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=54.37;MQ0=0;OQ=1048.98;QD=34.97;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,30:29:-108.49,-8.74,-0.01:87.27
+chr1	890161	.	C	G	0.39	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.89;MQ=54.80;MQ0=0;OQ=464.33;QD=12.55;SB=-10.00	GT:AD:DP:GL:GQ	0/1:16,21:31:-59.09,-9.37,-60.44:99
+chr1	890593	rs3935066	G	A	1827.67	Indel	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=54.80;MQ0=0;QD=38.08;SB=-380.50	GT:AD:DP:GL:GQ	1/1:0,48:46:-186.37,-13.86,-0.02:99
+chr1	890835	rs9697711	T	G	5.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=3.09;MQ=57.77;MQ0=0;OQ=1087.73;QD=27.19;SB=-563.56	GT:AD:DP:GL:GQ	1/1:0,40:34:-112.38,-10.25,-0.03:99
+chr1	890886	rs13303351	T	C	4.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=5.09;MQ=56.17;MQ0=0;OQ=1868.96;QD=27.89;SB=-762.95	GT:AD:DP:GL:GQ	1/1:0,67:61:-190.56,-18.41,-0.08:99
+chr1	891422	rs13303160	G	A	335.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=1009.81;QD=38.84;SB=-456.35	GT:AD:DP:GL:GQ	1/1:0,26:26:-104.57,-7.83,-0.01:78.26
+chr1	891470	rs13302996	C	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=1288.09;QD=33.03;SB=-383.20	GT:AD:DP:GL:GQ	1/1:0,39:34:-132.43,-10.27,-0.04:99
+chr1	891515	rs2879814	A	G	4.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.80;MQ=59.05;MQ0=0;OQ=1360.05;QD=30.91;SB=-420.15	GT:AD:DP:GL:GQ	1/1:0,44:40:-139.61,-12.06,-0.03:99
+chr1	892627	rs28416780	C	G	985.40	Indel	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=3.73;MQ=60.94;MQ0=0;QD=29.86;SB=-516.60	GT:AD:DP:GL:GQ	1/1:0,33:26:-102.16,-7.86,-0.03:78.25
+chr1	892860	rs7524174	G	A	607.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2039.21;QD=35.78;SB=-884.69	GT:AD:DP:GL:GQ	1/1:0,57:52:-207.52,-15.67,-0.02:99
+chr1	893108	rs28690976	A	G	19.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=1.31;MQ=59.50;MQ0=0;OQ=1221.87;QD=33.02;SB=-508.55	GT:AD:DP:GL:GQ	1/1:0,37:34:-125.78,-10.24,-0.01:99
+chr1	893184	rs6669800	G	A	536.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1821.94;QD=35.04;SB=-645.66	GT:AD:DP:GL:GQ	1/1:0,52:47:-185.80,-14.16,-0.02:99
+chr1	895023	rs7555426	C	T	0.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.03;HRun=0;HaplotypeScore=12.36;MQ=55.36;MQ0=0;OQ=2346.52;QD=37.25;SB=-860.64	GT:AD:DP:GL:GQ	1/1:0,60:62:-238.26,-18.08,-0.02:99
+chr1	895028	rs7522959	A	G	167.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=55.43;MQ0=0;OQ=2120.68;QD=33.14;SB=-824.97	GT:AD:DP:GL:GQ	1/1:0,63:62:-215.68,-18.68,-0.03:99
+chr1	899282	rs28548431	C	T	198.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.43;MQ0=0;OQ=508.80;QD=15.42;SB=-237.75	GT:AD:DP:GL:GQ	0/1:15,18:31:-63.51,-9.35,-46.57:99
+chr1	899418	rs2340594	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=1231.29;QD=30.03;SB=-602.23	GT:AD:DP:GL:GQ	1/1:0,41:40:-126.75,-12.06,-0.03:99
+chr1	899631	rs2340593	A	G	106.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1110.83;QD=35.83;SB=-387.48	GT:AD:DP:GL:GQ	1/1:0,31:31:-114.68,-9.34,-0.01:93.28
+chr1	900257	rs28477686	C	T	200.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=716.99;QD=16.30;SB=-337.87	GT:AD:DP:GL:GQ	0/1:20,24:40:-87.03,-12.05,-62.41:99
+chr1	900301	rs6685581	A	G	61.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=58.90;MQ0=0;OQ=1025.59;QD=26.99;SB=-469.48	GT:AD:DP:GL:GQ	1/1:0,38:34:-106.18,-10.26,-0.04:99
+chr1	900766	rs4970429	T	C	21.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=1255.50;QD=27.90;SB=-520.11	GT:AD:DP:GL:GQ	1/1:0,45:41:-129.18,-12.37,-0.04:99
+chr1	901458	rs7417106	A	G	62.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=56.69;MQ0=0;OQ=1131.68;QD=22.63;SB=-392.29	GT:AD:DP:GL:GQ	1/1:0,48:37:-116.79,-11.16,-0.04:99
+chr1	901912	rs9803103	T	C	68.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.16;MQ0=0;OQ=72.78;QD=4.85;SB=-10.00	GT:AD:DP:GL:GQ	0/1:10,5:15:-15.08,-4.52,-39.48:99
+chr1	901966	rs9803017	G	A	5.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=48.89;MQ0=0;OQ=164.19;QD=23.46;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,5:5:-19.98,-1.51,-0.00:15.05
+chr1	903262	.	C	T	47.02	LowQual	AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.12;MQ0=0;QD=23.51;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,2:2:-8.11,-0.60,-0.00:6.02
+chr1	903752	rs2340596	G	A	213.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=58.63;MQ0=0;OQ=437.08;QD=12.86;SB=-239.73	GT:AD:DP:GL:GQ	0/1:19,15:34:-57.25,-10.26,-59.16:99
+chr1	904055	rs2340595	G	C	462.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1540.41;QD=36.68;SB=-743.79	GT:AD:DP:GL:GQ	1/1:0,42:38:-157.65,-11.46,-0.02:99
+chr1	904196	rs13302979	C	G	14.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=60.00;MQ0=0;OQ=238.96;QD=11.95;SB=-110.33	GT:AD:DP:GL:GQ	0/1:12,8:19:-32.91,-5.73,-43.20:99
+chr1	904715	rs13303368	G	C	150.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=58.83;MQ0=0;OQ=429.52;QD=11.93;SB=-165.16	GT:AD:DP:GL:GQ	0/1:21,15:34:-56.48,-10.25,-87.94:99
+chr1	904739	rs13302983	T	C	1.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=3.25;MQ=59.49;MQ0=0;OQ=1146.65;QD=25.48;SB=-382.24	GT:AD:DP:GL:GQ	1/1:0,45:37:-118.29,-11.16,-0.04:99
+chr1	904803	rs13303033	T	C	97.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=3.63;MQ=59.44;MQ0=0;OQ=505.70;QD=12.33;SB=-138.55	GT:AD:DP:GL:GQ	0/1:20,21:40:-65.92,-12.07,-67.38:99
+chr1	905090	rs13303355	A	G	1.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=8.34;MQ=56.14;MQ0=0;OQ=1675.03;QD=29.39;SB=-822.95	GT:AD:DP:GL:GQ	1/1:1,56:50:-171.12,-15.07,-0.03:99
+chr1	906412	rs6660139	A	G	108.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=506.06;QD=14.88;SB=-146.57	GT:AD:DP:GL:GQ	0/1:14,20:33:-63.84,-9.95,-51.10:99
+chr1	906453	rs28566954	G	A	282.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.36;MQ0=0;OQ=491.61;QD=13.66;SB=-253.24	GT:AD:DP:GL:GQ	0/1:20,16:35:-62.99,-10.55,-63.70:99
+chr1	906697	rs6694632	G	A	262.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.25;MQ0=0;OQ=424.41;QD=13.69;SB=-233.73	GT:AD:DP:GL:GQ	0/1:16,15:29:-54.46,-8.74,-53.31:99
+chr1	906923	rs6605058	C	G	4.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=59.45;MQ0=0;OQ=1718.51;QD=40.92;SB=-739.75	GT:AD:DP:GL:GQ	1/1:0,42:41:-175.45,-12.36,-0.02:99
+chr1	907503	rs41285816	G	A	149.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.47;MQ0=0;OQ=650.11;QD=15.12;SB=-327.85	GT:AD:DP:GL:GQ	0/1:21,22:41:-80.65,-12.35,-76.53:99
+chr1	908101	rs28552711	C	G	269.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.03;MQ0=0;OQ=561.89;QD=11.71;SB=-234.09	GT:AD:DP:GL:GQ	0/1:27,21:45:-73.04,-13.57,-111.91:99
+chr1	908247	rs13303118	G	T	75.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.58;MQ0=0;OQ=378.28;QD=8.60;SB=-112.78	GT:AD:DP:GL:GQ	0/1:27,17:40:-53.17,-12.06,-75.89:99
+chr1	908436	rs2341354	A	G	288.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.09;MQ0=0;OQ=687.85;QD=13.49;SB=-217.36	GT:AD:DP:GL:GQ	0/1:22,29:47:-86.23,-14.17,-83.30:99
+chr1	908990	rs28469033	T	C	203.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=58.06;MQ0=0;OQ=712.75;QD=12.29;SB=-242.27	GT:AD:DP:GL:GQ	0/1:29,28:55:-91.13,-16.57,-114.97:99
+chr1	909282	rs6605059	T	C	230.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=181.71;QD=7.57;SB=-100.01	GT:AD:DP:GL:GQ	0/1:13,11:22:-28.09,-6.63,-51.27:99
+chr1	909352	rs61606412	C	T	41.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=53.76;MQ0=0;OQ=576.99;QD=16.03;SB=-77.09	GT:AD:DP:GL:GQ	0/1:16,19:32:-70.62,-9.64,-54.85:99
+chr1	909718	.	G	A	32.42	PASS	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.35;MQ0=0;OQ=82.61;QD=6.35;SB=-28.51	GT:AD:DP:GL:GQ	0/1:9,4:13:-15.46,-3.92,-29.36:99
+chr1	909851	.	C	T	379.69	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=14.99;MQ=38.66;MQ0=0;QD=8.44;SB=-209.86	GT:AD:DP:GL:GQ	0/1:32,13:38:-52.70,-11.44,-90.66:99
+chr1	909854	.	C	A	33.53	Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=23.31;MQ=39.61;MQ0=0;QD=0.73;SB=-35.83	GT:AD:DP:GL:GQ	0/1:41,3:18:-18.90,-12.26,-52.66:66.37
+chr1	909858	.	T	A	34.25	Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=85.24;MQ=39.71;MQ0=0;QD=0.69;SB=-24.32	GT:AD:DP:GL:GQ	0/1:46,4:25:-14.24,-7.53,-79.28:67.09
+chr1	909861	rs2341357	A	C	442.96	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=92.23;MQ=37.93;MQ0=0;QD=9.23;SB=-187.18	GT:AD:DP:GL:GQ	0/1:13,31:32:-70.70,-23.12,-57.83:99
+chr1	909862	.	T	C	28.94	Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=90.34;MQ=37.54;MQ0=1;QD=0.59;SB=-27.89	GT:AD:DP:GL:GQ	0/1:45,4:23:-13.11,-6.93,-76.03:61.77
+chr1	909865	rs55746336	A	C	368.04	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=65.88;MQ=38.28;MQ0=1;QD=7.51;SB=-150.94	GT:AD:DP:GL:GQ	0/1:20,29:28:-48.52,-8.43,-49.13:99
+chr1	910511	rs6677020	T	C	126.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=58.99;MQ0=0;OQ=1842.74;QD=30.71;SB=-555.07	GT:AD:DP:GL:GQ	1/1:0,60:57:-187.90,-17.18,-0.04:99
+chr1	910596	rs6677131	T	C	281.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=1029.24;QD=25.10;SB=-459.07	GT:AD:DP:GL:GQ	1/1:0,41:35:-106.55,-10.56,-0.04:99
+chr1	911433	rs6662128	T	C	65.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=42.74;MQ0=0;OQ=1332.64;QD=27.76;SB=-494.18	GT:AD:DP:GL:GQ	1/1:0,48:43:-136.89,-12.97,-0.04:99
+chr1	911523	rs6703008	C	T	253.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.87;MQ0=0;OQ=592.10;QD=14.44;SB=-247.55	GT:AD:DP:GL:GQ	0/1:21,20:40:-74.55,-12.06,-68.34:99
+chr1	911579	rs13303278	C	A	321.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=57.82;MQ0=0;OQ=846.22;QD=16.27;SB=-412.14	GT:AD:DP:GL:GQ	0/1:22,30:49:-102.67,-14.76,-65.25:99
+chr1	911872	rs6693747	G	A	247.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=57.81;MQ0=0;OQ=692.72;QD=11.94;SB=-247.55	GT:AD:DP:GL:GQ	0/1:34,24:51:-87.93,-15.37,-94.90:99
+chr1	912939	rs6605060	A	G	422.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1569.95;QD=29.62;SB=-431.82	GT:AD:DP:GL:GQ	1/1:0,53:52:-160.64,-15.69,-0.06:99
+chr1	913322	rs9442609	A	G	120.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=58.95;MQ0=0;OQ=1780.01;QD=28.25;SB=-752.61	GT:AD:DP:GL:GQ	1/1:0,63:58:-181.64,-17.49,-0.06:99
+chr1	913612	rs9442610	T	C	76.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.45;MQ0=1;OQ=2496.82;QD=28.70;SB=-1150.17	GT:AD:DP:GL:GQ	1/1:1,86:79:-253.33,-23.82,-0.07:99
+chr1	913974	rs28447224	T	A	288.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.45;MQ0=0;OQ=731.87;QD=12.20;SB=-322.51	GT:AD:DP:GL:GQ	0/1:33,27:58:-93.94,-17.47,-123.87:99
+chr1	914034	.	A	T	3.99	PASS	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.53;MQ0=0;OQ=328.12;QD=3.57;SB=-36.46	GT:AD:DP:GL:GQ	0/1:74,18:90:-63.21,-27.12,-275.61:99
+chr1	914043	.	A	T	0.15	PASS	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=53.25;MQ0=0;OQ=310.60;QD=3.20;SB=-88.90	GT:AD:DP:GL:GQ	0/1:71,26:82:-59.05,-24.71,-248.58:99
+chr1	914057	rs36034299	T	A	46.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=4.71;MQ=52.48;MQ0=0;OQ=1254.45;QD=10.20;SB=-515.06	GT:AD:DP:GL:GQ	0/1:78,44:120:-164.87,-36.14,-292.57:99
+chr1	914062	rs34208189	G	T	4.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.00;HRun=1;HaplotypeScore=4.71;MQ=52.50;MQ0=0;OQ=1304.79;QD=10.87;SB=-551.46	GT:AD:DP:GL:GQ	0/1:72,47:118:-172.13,-38.37,-252.01:99
+chr1	914098	rs28489602	G	A	178.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=53.92;MQ0=0;OQ=1142.45;QD=9.29;SB=-414.29	GT:AD:DP:GL:GQ	0/1:80,43:115:-152.18,-34.65,-273.57:99
+chr1	914111	.	T	G	3.17	PASS	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=54.02;MQ0=0;OQ=717.31;QD=5.56;SB=-222.67	GT:AD:DP:GL:GQ	0/1:95,34:128:-113.56,-38.55,-355.41:99
+chr1	914118	rs59424352	T	G	15.06	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=131;Dels=0.00;HRun=2;HaplotypeScore=1.56;MQ=54.89;MQ0=0;QD=0.11;SB=-22.32	GT:AD:DP:GL:GQ	0/1:103,28:116:-39.71,-34.94,-387.42:47.76
+chr1	914126	rs28607403	A	T	0.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=56.46;MQ0=0;OQ=177.88;QD=1.41;SB=-25.34	GT:AD:DP:GL:GQ	0/1:106,20:118:-56.62,-35.55,-387.33:99
+chr1	914231	rs35562283	C	T	2.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=100;Dels=0.00;HRun=2;HaplotypeScore=2.10;MQ=59.39;MQ0=0;OQ=4072.19;QD=40.72;SB=-2034.20	GT:AD:DP:GL:GQ	1/1:0,100:100:-406.22,-30.12,-0.03:99
+chr1	914391	rs34712273	C	A	51.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=5.23;MQ=56.94;MQ0=0;OQ=1123.83;QD=11.59;SB=-531.23	GT:AD:DP:GL:GQ	0/1:55,42:95:-144.28,-28.62,-196.31:99
+chr1	914466	rs28422907	T	C	454.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=3679.99;QD=36.08;SB=-1782.71	GT:AD:DP:GL:GQ	1/1:0,102:101:-367.00,-30.42,-0.03:99
+chr1	914492	rs28622096	A	G	82.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=92;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=2947.74;QD=32.04;SB=-1451.63	GT:AD:DP:GL:GQ	1/1:0,92:91:-298.43,-27.44,-0.07:99
+chr1	914761	rs6665000	C	A	607.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3789.11;QD=37.15;SB=-1446.45	GT:AD:DP:GL:GQ	1/1:0,101:101:-377.91,-33.59,-3.42:99
+chr1	915547	rs6605061	T	C	196.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=57.81;MQ0=0;OQ=1982.79;QD=33.05;SB=-855.97	GT:AD:DP:GL:GQ	1/1:0,60:57:-201.89,-17.17,-0.03:99
+chr1	916214	rs6671243	C	T	469.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2468.85;QD=39.82;SB=-737.98	GT:AD:DP:GL:GQ	1/1:0,62:61:-250.48,-18.37,-0.01:99
+chr1	916294	rs4970403	A	T	304.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.55;MQ=59.43;MQ0=0;OQ=2680.54;QD=36.72;SB=-1154.05	GT:AD:DP:GL:GQ	1/1:1,72:71:-271.66,-21.39,-0.02:99
+chr1	916484	rs4970351	A	C	485.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=1740.98;QD=35.53;SB=-550.05	GT:AD:DP:GL:GQ	1/1:0,49:49:-177.70,-14.76,-0.01:99
+chr1	917172	rs2341362	T	C	555.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1855.09;QD=30.92;SB=-890.64	GT:AD:DP:GL:GQ	1/1:0,60:59:-189.15,-17.80,-0.06:99
+chr1	917604	rs6665587	G	A	343.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.08;MQ0=0;OQ=746.63;QD=16.23;SB=-250.74	GT:AD:DP:GL:GQ	0/1:23,23:45:-91.50,-13.55,-86.19:99
+chr1	918279	.	G	A	19.72	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=64.12;MQ0=0;OQ=347.49;QD=8.91;SB=-127.57	GT:AD:DP:GL:GQ	0/1:25,14:32:-47.68,-9.65,-62.78:99
+chr1	918383	rs35002855	A	G	36.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.30;MQ0=0;OQ=923.20;QD=27.98;SB=-310.47	GT:AD:DP:GL:GQ	1/1:0,33:30:-95.93,-9.05,-0.03:90.20
+chr1	918441	rs28394749	G	A	367.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=1345.86;QD=38.45;SB=-480.97	GT:AD:DP:GL:GQ	1/1:0,35:35:-138.18,-10.55,-0.01:99
+chr1	918699	rs9777703	C	T	463.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.88;MQ0=0;OQ=1525.43;QD=38.14;SB=-621.02	GT:AD:DP:GL:GQ	1/1:0,40:39:-156.14,-11.75,-0.01:99
+chr1	919053	rs9777939	A	G	223.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.27;MQ0=0;OQ=1351.32;QD=33.78;SB=-678.95	GT:AD:DP:GL:GQ	1/1:0,40:38:-138.73,-11.45,-0.01:99
+chr1	919179	rs9777893	C	T	85.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=55.86;MQ0=0;OQ=1631.07;QD=35.46;SB=-540.88	GT:AD:DP:GL:GQ	1/1:0,46:44:-166.72,-13.27,-0.03:99
+chr1	919184	rs13302916	A	C	0.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=5;HaplotypeScore=2.13;MQ=54.60;MQ0=0;OQ=1536.74;QD=31.36;SB=-480.03	GT:AD:DP:GL:GQ	1/1:0,49:45:-157.28,-13.56,-0.02:99
+chr1	919190	rs13302924	A	G	46.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=54.92;MQ0=0;OQ=1263.79;QD=24.30;SB=-518.21	GT:AD:DP:GL:GQ	1/1:0,52:42:-130.02,-12.68,-0.06:99
+chr1	919921	.	C	A	110.32	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=58.99;MQ0=0;OQ=1041.89;QD=15.10;SB=-490.89	GT:AD:DP:GL:GQ	0/1:34,35:65:-127.06,-19.58,-99.23:99
+chr1	920192	rs3128108	C	T	194.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.69;MQ0=0;OQ=711.37;QD=14.23;SB=-187.15	GT:AD:DP:GL:GQ	0/1:24,26:47:-88.59,-14.17,-77.59:99
+chr1	920240	rs3128109	C	T	215.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.70;MQ0=0;OQ=1131.05;QD=17.95;SB=-367.88	GT:AD:DP:GL:GQ	0/1:29,34:63:-135.38,-18.99,-92.17:99
+chr1	920396	rs3128110	C	G	210.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=58.26;MQ0=0;OQ=1157.59;QD=14.84;SB=-599.54	GT:AD:DP:GL:GQ	0/1:41,37:77:-142.27,-23.22,-177.91:99
+chr1	920430	rs3121574	A	G	364.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.06;MQ0=0;OQ=652.89;QD=9.60;SB=-349.53	GT:AD:DP:GL:GQ	0/1:41,27:65:-88.16,-19.59,-156.95:99
+chr1	920614	rs3128111	C	G	139.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=58.99;MQ0=0;OQ=1461.73;QD=21.18;SB=-736.36	GT:AD:DP:GL:GQ	0/1:28,41:68:-169.95,-20.49,-124.60:99
+chr1	920786	rs2710882	A	G	12.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.97;MQ=49.62;MQ0=0;OQ=1291.93;QD=28.71;SB=-670.84	GT:AD:DP:GL:GQ	1/1:0,45:41:-132.82,-12.37,-0.04:99
+chr1	920877	rs2710881	A	G	324.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.30;MQ0=0;OQ=966.43;QD=26.85;SB=-364.34	GT:AD:DP:GL:GQ	1/1:0,36:31:-100.25,-9.35,-0.03:93.22
+chr1	921029	rs2710880	A	G	58.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=3.24;MQ=56.56;MQ0=0;OQ=562.50;QD=14.06;SB=-270.38	GT:AD:DP:GL:GQ	0/1:15,25:36:-70.39,-10.85,-55.63:99
+chr1	921225	rs2799060	G	A	150.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.04;MQ=54.08;MQ0=0;OQ=614.91;QD=17.08;SB=-332.87	GT:AD:DP:GL:GQ	0/1:15,21:29:-73.51,-8.74,-35.50:99
+chr1	921371	rs2799061	T	A	126.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=52.82;MQ0=0;OQ=1479.30;QD=33.62;SB=-589.54	GT:AD:DP:GL:GQ	1/1:0,44:41:-151.53,-12.35,-0.02:99
+chr1	921411	rs2799062	G	T	122.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=53.36;MQ0=0;OQ=738.91;QD=16.06;SB=-235.96	GT:AD:DP:GL:GQ	0/1:19,27:43:-90.13,-12.95,-62.40:99
+chr1	921593	rs2005437	A	G	3.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=3.71;MQ=50.61;MQ0=0;OQ=1146.23;QD=32.75;SB=-497.46	GT:AD:DP:GL:GQ	1/1:0,35:33:-118.22,-9.94,-0.01:99
+chr1	921666	rs1891908	C	T	2.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.85;MQ=32.06;MQ0=2;OQ=160.89;QD=4.35;SB=-6.43	GT:AD:DP:GL:GQ	0/1:19,17:19:-25.09,-5.72,-45.39:99
+chr1	921743	rs2710878	G	A	0.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=13.34;MQ=30.42;MQ0=11;OQ=92.22;QD=1.77;SB=38.12	GT:AD:DP:GL:GQ	0/1:43,9:31:-21.85,-9.35,-87.56:99
+chr1	921798	rs59581901	T	C	0.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=13.36;MQ=44.02;MQ0=2;OQ=265.71;QD=4.66;SB=-27.22	GT:AD:DP:GL:GQ	0/1:37,20:42:-42.52,-12.66,-114.67:99
+chr1	921802	rs13303155	G	A	0.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=12.88;MQ=43.29;MQ0=2;OQ=165.28;QD=2.85;SB=-96.56	GT:AD:DP:GL:GQ	0/1:44,13:47:-33.98,-14.17,-116.58:99
+chr1	921917	rs13302969	G	T	74.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.19;MQ=21.41;MQ0=5;OQ=283.37;QD=8.86;SB=-65.73	GT:AD:DP:GL:GQ	0/1:6,26:13:-35.54,-3.92,-11.08:71.59
+chr1	921950	rs4350142	T	G	3.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=16.76;MQ0=5;OQ=77.67;QD=4.32;SB=-39.55	GT:AD:DP:GL:GQ	0/1:13,5:9:-13.76,-2.71,-16.22:99
+chr1	922320	rs1891910	G	A	55.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=54.96;MQ0=0;OQ=908.58;QD=18.93;SB=-365.40	GT:AD:DP:GL:GQ	0/1:20,28:47:-108.30,-14.16,-73.49:99
+chr1	922481	rs3128112	C	G	140.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.00;MQ0=0;OQ=2826.91;QD=42.19;SB=-1373.36	GT:AD:DP:GL:GQ	1/1:0,67:66:-286.30,-19.89,-0.02:99
+chr1	923653	rs9442392	G	A	34.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.66;MQ0=0;OQ=346.01;QD=17.30;SB=-99.62	GT:AD:DP:GL:GQ	0/1:8,12:18:-43.31,-5.43,-22.69:99
+chr1	923962	rs2710867	G	C	179.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.52;MQ0=0;OQ=491.87;QD=30.74;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,16:14:-52.79,-4.24,-0.02:42.13
+chr1	923969	rs2799063	A	G	177.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.52;MQ0=0;OQ=467.35;QD=31.16;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,15:15:-50.33,-4.52,-0.01:45.12
+chr1	923984	rs2488989	G	A	4.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=52.45;MQ0=0;OQ=54.72;QD=4.21;SB=-10.00	GT:AD:DP:GL:GQ	0/1:9,4:12:-12.37,-3.61,-31.32:87.56
+chr1	924007	rs9697551	C	G	2.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=52.65;MQ0=0;OQ=378.82;QD=37.88;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,10:10:-41.47,-3.01,-0.00:30.10
+chr1	925085	rs2298214	C	A	41.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=126.82;QD=15.85;SB=-10.00	GT:AD:DP:GL:GQ	0/1:3,5:8:-18.37,-2.41,-10.50:80.94
+chr1	925696	rs3128115	C	G	0.04	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=4;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=341.24;QD=28.44;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,12:10:-37.72,-3.03,-0.02:30.09
+chr1	925974	rs1936360	C	T	39.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=58.35;MQ0=0;OQ=214.61;QD=12.62;SB=-42.53	GT:AD:DP:GL:GQ	0/1:9,8:14:-28.97,-4.22,-22.12:99
+chr1	926057	rs3121570	A	G	2.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=311.77;QD=28.34;SB=-100.02	GT:AD:DP:GL:GQ	1/1:0,11:11:-34.77,-3.32,-0.01:33.06
+chr1	926073	rs3121569	C	A	189.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=295.10;QD=26.83;SB=-77.88	GT:AD:DP:GL:GQ	1/1:0,11:10:-33.10,-3.01,-0.01:30.07
+chr1	927551	rs2489000	T	C	23.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.20;MQ0=0;OQ=869.96;QD=30.00;SB=-383.48	GT:AD:DP:GL:GQ	1/1:0,29:26:-90.60,-7.84,-0.01:78.21
+chr1	927679	.	G	T	11.95	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=20;HaplotypeScore=4.44;MQ=51.49;MQ0=1;QD=0.30;SB=29.12	GT:AD:DP:GL:GQ	0/1:35,5:33:-14.39,-9.94,-101.16:44.50
+chr1	927979	rs2710869	T	G	68.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=52.06;MQ0=0;OQ=1400.53;QD=31.83;SB=-711.32	GT:AD:DP:GL:GQ	1/1:0,44:41:-143.66,-12.35,-0.02:99
+chr1	927988	rs2710868	G	A	255.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.36;MQ0=0;OQ=410.87;QD=10.02;SB=-73.54	GT:AD:DP:GL:GQ	0/1:27,14:38:-55.83,-11.46,-75.32:99
+chr1	928076	rs2799058	A	G	513.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.12;MQ0=1;OQ=1982.35;QD=34.78;SB=-956.40	GT:AD:DP:GL:GQ	1/1:0,57:56:-201.84,-16.87,-0.02:99
+chr1	929868	rs2799056	A	G	83.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=60.00;MQ0=0;OQ=292.67;QD=13.30;SB=-94.98	GT:AD:DP:GL:GQ	0/1:10,12:19:-38.28,-5.73,-31.90:99
+chr1	929959	rs4503294	C	T	66.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=59.48;MQ0=0;OQ=871.55;QD=19.81;SB=-434.84	GT:AD:DP:GL:GQ	0/1:17,27:40:-102.50,-12.06,-44.62:99
+chr1	931147	rs3128116	C	T	186.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=58.74;MQ0=0;OQ=584.87;QD=15.81;SB=-318.85	GT:AD:DP:GL:GQ	0/1:17,20:34:-72.02,-10.25,-50.30:99
+chr1	931197	rs57683598	G	A	242.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.63;MQ0=0;OQ=443.86;QD=13.05;SB=-202.91	GT:AD:DP:GL:GQ	0/1:19,15:33:-57.62,-9.95,-57.41:99
+chr1	931402	rs9778087	C	T	103.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.28;MQ=58.18;MQ0=0;OQ=521.73;QD=14.49;SB=-147.61	GT:AD:DP:GL:GQ	0/1:17,19:30:-64.50,-9.04,-41.68:99
+chr1	933113	rs3121568	C	T	81.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=27.66;MQ0=1;OQ=764.02;QD=34.73;SB=-301.68	GT:AD:DP:GL:GQ	1/1:1,21:20:-79.99,-6.02,-0.00:60.20
+chr1	933331	rs3121567	T	C	90.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=52.92;MQ0=0;OQ=1930.66;QD=28.39;SB=-605.93	GT:AD:DP:GL:GQ	1/1:0,67:59:-196.69,-17.79,-0.04:99
+chr1	933550	rs2465140	G	C	10.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=52.98;MQ0=0;OQ=1826.77;QD=24.04;SB=-482.83	GT:AD:DP:GL:GQ	0/1:29,47:76:-208.87,-22.91,-115.72:99
+chr1	933770	rs2488992	C	G	622.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=2496.05;QD=39.00;SB=-1249.63	GT:AD:DP:GL:GQ	1/1:1,63:62:-253.23,-18.70,-0.04:99
+chr1	933831	rs13303313	C	T	77.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=54.98;MQ0=1;OQ=1022.40;QD=21.30;SB=-421.46	GT:AD:DP:GL:GQ	0/1:17,31:46:-119.39,-13.87,-49.73:99
+chr1	934427	rs3128117	T	C	70.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=3.79;MQ=59.48;MQ0=0;OQ=1012.81;QD=12.50;SB=-424.88	GT:AD:DP:GL:GQ	0/1:46,35:81:-128.96,-24.40,-186.84:99
+chr1	934959	rs3135457	C	T	611.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.45;MQ0=0;OQ=2185.20;QD=35.82;SB=-904.70	GT:AD:DP:GL:GQ	1/1:0,61:55:-222.12,-16.57,-0.02:99
+chr1	934974	rs13303172	C	T	140.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=58.59;MQ0=0;OQ=2216.02;QD=34.63;SB=-887.19	GT:AD:DP:GL:GQ	1/1:0,63:58:-225.21,-17.48,-0.03:99
+chr1	935337	rs3121566	C	T	64.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=57.82;MQ0=0;OQ=2650.36;QD=37.33;SB=-1265.29	GT:AD:DP:GL:GQ	1/1:0,71:68:-268.65,-20.49,-0.03:99
+chr1	935475	rs3121565	C	T	3.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=5.58;MQ=54.82;MQ0=0;OQ=1712.26;QD=33.57;SB=-826.14	GT:AD:DP:GL:GQ	1/1:0,51:46:-174.83,-13.86,-0.02:99
+chr1	935997	rs2341364	T	G	377.30	Indel	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=10.97;MQ=57.32;MQ0=2;QD=7.12;SB=-202.78	GT:AD:DP:GL:GQ	0/1:37,16:48:-55.47,-14.46,-118.77:99
+chr1	935998	rs9723307	T	G	915.61	Indel	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=11.45;MQ=57.32;MQ0=2;QD=17.28;SB=-353.60	GT:AD:DP:GL:GQ	0/1:21,32:48:-109.30,-14.46,-57.43:99
+chr1	936897	rs2465126	G	A	228.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.52;MQ0=0;OQ=1823.18;QD=37.98;SB=-798.06	GT:AD:DP:GL:GQ	1/1:0,48:47:-185.92,-14.16,-0.02:99
+chr1	937401	rs2465125	C	T	186.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.20;MQ0=0;OQ=2163.80;QD=37.31;SB=-987.00	GT:AD:DP:GL:GQ	1/1:0,58:56:-219.99,-16.88,-0.02:99
+chr1	938555	rs2341365	G	A	140.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.55;MQ0=0;OQ=1650.26;QD=34.38;SB=-693.43	GT:AD:DP:GL:GQ	1/1:0,47:44:-168.63,-13.26,-0.02:99
+chr1	938733	rs4615788	C	G	63.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=59.05;MQ0=0;OQ=1777.68;QD=37.82;SB=-661.48	GT:AD:DP:GL:GQ	1/1:0,47:45:-181.39,-13.58,-0.03:99
+chr1	938784	rs15842	T	C	63.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=51.15;MQ0=0;OQ=1180.61;QD=25.67;SB=-593.57	GT:AD:DP:GL:GQ	1/1:0,46:38:-121.68,-11.46,-0.04:99
+chr1	939098	rs2465124	G	A	101.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=58.32;MQ0=0;OQ=1385.28;QD=35.52;SB=-635.85	GT:AD:DP:GL:GQ	1/1:0,39:36:-142.13,-10.85,-0.02:99
+chr1	939471	rs1921	G	A	210.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=59.46;MQ0=0;OQ=818.95;QD=19.05;SB=-428.80	GT:AD:DP:GL:GQ	0/1:17,25:41:-97.53,-12.36,-57.36:99
+chr1	939517	rs8997	A	G	93.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.52;MQ=58.71;MQ0=0;OQ=1127.57;QD=31.32;SB=-511.18	GT:AD:DP:GL:GQ	1/1:0,36:33:-116.36,-9.94,-0.02:99
+chr1	939788	rs2799070	C	T	122.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=60.00;MQ0=0;OQ=1513.64;QD=36.92;SB=-701.35	GT:AD:DP:GL:GQ	1/1:0,40:39:-154.96,-11.75,-0.01:99
+chr1	940106	rs1891906	A	C	58.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.38;MQ0=0;OQ=496.04;QD=13.41;SB=-49.04	GT:AD:DP:GL:GQ	0/1:19,18:37:-64.03,-11.14,-68.15:99
+chr1	940540	rs9331223	T	C	228.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=58.40;MQ0=0;OQ=564.77;QD=13.45;SB=-287.31	GT:AD:DP:GL:GQ	0/1:17,25:39:-71.52,-11.76,-66.74:99
+chr1	940579	rs2799069	A	T	132.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=57.66;MQ0=0;OQ=1217.27;QD=32.90;SB=-595.76	GT:AD:DP:GL:GQ	1/1:0,37:34:-125.32,-10.24,-0.01:99
+chr1	941146	rs9442363	C	T	200.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=29.19;MQ0=1;OQ=502.68;QD=12.89;SB=-262.28	GT:AD:DP:GL:GQ	0/1:16,22:28:-61.99,-8.44,-37.57:99
+chr1	941158	rs9442388	C	T	75.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.38;MQ=27.92;MQ0=1;OQ=496.98;QD=10.80;SB=-155.64	GT:AD:DP:GL:GQ	0/1:24,22:37:-64.14,-11.16,-65.52:99
+chr1	941185	rs9697362	C	T	0.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=4;HaplotypeScore=0.96;MQ=26.62;MQ0=0;OQ=1253.78;QD=25.59;SB=-636.34	GT:AD:DP:GL:GQ	1/1:0,49:34:-128.98,-10.25,-0.02:99
+chr1	941193	rs9697717	G	A	313.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.36;MQ0=0;OQ=1030.78;QD=25.77;SB=-468.62	GT:AD:DP:GL:GQ	1/1:0,40:27:-106.67,-8.14,-0.01:81.26
+chr1	941427	rs2465141	A	G	200.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.01;MQ=50.56;MQ0=1;OQ=585.65;QD=10.65;SB=-303.21	GT:AD:DP:GL:GQ	0/1:29,26:48:-76.32,-14.47,-98.65:99
+chr1	941491	.	A	T	28.08	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=45.78;MQ0=3;QD=0.52;SB=41.14	GT:AD:DP:GL:GQ	0/1:46,8:45:-19.65,-13.56,-148.74:60.91
+chr1	941866	rs3128118	G	A	182.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.48;MQ=58.42;MQ0=1;OQ=769.91;QD=13.27;SB=-278.19	GT:AD:DP:GL:GQ	0/1:30,27:54:-96.56,-16.28,-93.17:99
+chr1	942291	rs9442611	G	A	158.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=58.27;MQ0=0;OQ=928.32;QD=19.34;SB=-479.01	GT:AD:DP:GL:GQ	0/1:19,29:48:-110.59,-14.48,-59.61:99
+chr1	943087	rs4970390	C	T	107.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=50.43;MQ0=1;OQ=376.23;QD=6.60;SB=-175.84	GT:AD:DP:GL:GQ	0/1:38,19:49:-55.68,-14.78,-111.95:99
+chr1	943217	rs61766298	G	A	33.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=54.66;MQ0=1;OQ=355.20;QD=4.80;SB=-58.95	GT:AD:DP:GL:GQ	0/1:57,16:65:-58.41,-19.60,-158.72:99
+chr1	943541	rs2952918	T	C	3.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=5.78;MQ=53.39;MQ0=0;OQ=348.13;QD=8.70;SB=-186.61	GT:AD:DP:GL:GQ	0/1:24,16:38:-49.55,-11.46,-86.70:99
+chr1	943815	rs9442612	G	A	205.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=57.73;MQ0=0;OQ=533.79;QD=13.02;SB=-257.75	GT:AD:DP:GL:GQ	0/1:22,19:39:-68.42,-11.76,-70.56:99
+chr1	944640	rs61766299	C	A	104.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=57.66;MQ0=0;OQ=76.34;QD=7.63;SB=-34.38	GT:AD:DP:GL:GQ	0/1:6,4:9:-13.63,-2.71,-15.11:99
+chr1	946715	rs9777931	C	T	99.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=1.79;MQ=60.00;MQ0=0;OQ=313.20;QD=12.05;SB=-129.12	GT:AD:DP:GL:GQ	0/1:14,11:22:-41.23,-6.63,-41.31:99
+chr1	949018	rs3845291	G	A	42.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=1.63;MQ=59.54;MQ0=0;OQ=843.29;QD=16.87;SB=-349.52	GT:AD:DP:GL:GQ	0/1:23,27:47:-101.78,-14.17,-66.18:99
+chr1	949032	rs3845292	G	C	180	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.52;MQ0=0;OQ=777.11;QD=16.19;SB=-360.45	GT:AD:DP:GL:GQ	0/1:22,26:45:-94.57,-13.58,-90.66:99
+chr1	949094	rs4039721	G	A	273.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.09;MQ0=0;OQ=688.73;QD=16.80;SB=-366.42	GT:AD:DP:GL:GQ	0/1:19,22:36:-83.01,-10.86,-46.17:99
+chr1	950272	rs4970392	G	C	3.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=3;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=405.25;QD=17.62;SB=-227.38	GT:AD:DP:GL:GQ	0/1:10,13:21:-50.14,-6.33,-36.47:99
+chr1	951690	rs3121556	G	A	175.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=59.49;MQ0=0;OQ=541.95;QD=12.04;SB=-261.27	GT:AD:DP:GL:GQ	0/1:25,20:39:-69.24,-11.76,-65.32:99
+chr1	952469	rs4970393	G	A	53.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=4.24;MQ=58.80;MQ0=0;OQ=631.93;QD=18.06;SB=-331.90	GT:AD:DP:GL:GQ	0/1:14,21:33:-76.42,-9.95,-42.13:99
+chr1	952754	rs4970394	C	T	113.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=59.23;MQ0=0;OQ=488.22;QD=16.27;SB=-210.21	GT:AD:DP:GL:GQ	0/1:14,15:29:-60.84,-8.74,-49.96:99
+chr1	953112	rs2710870	C	T	198.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.50;MQ=60.00;MQ0=0;OQ=692.82;QD=14.74;SB=-280.19	GT:AD:DP:GL:GQ	0/1:24,23:46:-86.43,-13.86,-83.87:99
+chr1	953580	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=16;HaplotypeScore=1.95;MQ=42.79;MQ0=0;OQ=89.92;QD=8.17;SB=-0.97	GT:AD:DP:GL:GQ	0/1:7,4:8:-14.69,-2.41,-16.44:99
+chr1	953584	rs2465127	T	C	0.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=3;HaplotypeScore=3.77;MQ=52.61;MQ0=0;OQ=94.29;QD=7.86;SB=-65.34	GT:AD:DP:GL:GQ	0/1:4,8:9:-15.43,-2.71,-16.16:99
+chr1	954093	.	G	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=9.68;MQ=33.26;MQ0=5;OQ=209.72;QD=5.67;SB=-3.99	GT:AD:DP:GL:GQ	0/1:21,12:15:-28.78,-4.52,-24.72:99
+chr1	954161	rs61766303	C	G	18.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=31.02;MQ0=1;OQ=184.53;QD=5.27;SB=-0.98	GT:AD:DP:GL:GQ	0/1:19,16:16:-26.57,-4.83,-37.31:99
+chr1	954252	rs4970397	C	T	103.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=32.94;MQ0=3;OQ=204.52;QD=7.57;SB=-35.64	GT:AD:DP:GL:GQ	0/1:17,10:18:-29.16,-5.43,-34.74:99
+chr1	954703	rs4970343	T	C	2.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=6.47;MQ=58.52;MQ0=0;OQ=457.55;QD=14.30;SB=-98.71	GT:AD:DP:GL:GQ	0/1:14,18:30:-58.08,-9.04,-50.50:99
+chr1	954711	rs4970344	A	T	37.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.43;MQ0=0;OQ=626.99;QD=19.00;SB=-168.81	GT:AD:DP:GL:GQ	0/1:12,21:33:-75.92,-9.94,-45.13:99
+chr1	954872	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=20.43;MQ=48.78;MQ0=1;OQ=116.04;QD=3.14;SB=-52.28	GT:AD:DP:GL:GQ	0/1:25,12:25:-22.42,-7.54,-71.63:99
+chr1	955038	rs28373660	A	G	250.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=55.30;MQ0=0;OQ=611.00;QD=13.28;SB=-229.46	GT:AD:DP:GL:GQ	0/1:20,26:39:-76.13,-11.75,-66.91:99
+chr1	955106	.	A	G	23.39	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=10.05;MQ=39.47;MQ0=7;QD=0.46;SB=-5.58	GT:AD:DP:GL:GQ	0/1:38,13:31:-14.97,-9.35,-98.23:56.21
+chr1	955141	rs28433148	T	C	0.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.04;HRun=0;HaplotypeScore=16.86;MQ=40.85;MQ0=6;OQ=407.46;QD=7.41;SB=-215.36	GT:AD:DP:GL:GQ	0/1:25,28:41:-56.09,-12.06,-84.28:99
+chr1	955386	rs4970404	A	G	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.02;HRun=0;HaplotypeScore=18.83;MQ=42.69;MQ0=11;OQ=218.68;QD=3.58;SB=-113.62	GT:AD:DP:GL:GQ	0/1:39,21:33:-35.11,-9.95,-82.73:99
+chr1	955467	rs4970345	C	T	151.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=44.49;MQ0=2;OQ=398.93;QD=9.73;SB=-192.19	GT:AD:DP:GL:GQ	0/1:19,21:26:-51.01,-7.84,-42.93:99
+chr1	955802	rs4970398	A	T	97.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=47.03;MQ0=2;OQ=550.07;QD=10.19;SB=-184.73	GT:AD:DP:GL:GQ	0/1:27,27:47:-72.45,-14.16,-100.00:99
+chr1	955812	rs4970399	A	G	52.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.02;HRun=0;HaplotypeScore=3.69;MQ=45.58;MQ0=2;OQ=418.21;QD=7.47;SB=-156.96	GT:AD:DP:GL:GQ	0/1:27,28:43:-57.78,-12.67,-88.06:99
+chr1	955927	.	T	C	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.47;MQ=51.74;MQ0=5;OQ=79.40;QD=1.80;SB=-44.68	GT:AD:DP:GL:GQ	0/1:30,14:34:-21.47,-10.25,-106.58:99
+chr1	955942	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=21.62;MQ=50.59;MQ0=7;OQ=96.72;QD=1.97;SB=-71.62	GT:AD:DP:GL:GQ	0/1:29,17:31:-22.31,-9.35,-90.50:99
+chr1	956010	.	A	G	17.59	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=45.86;MQ0=9;QD=0.35;SB=1.17	GT:AD:DP:GL:GQ	0/1:36,13:34:-15.29,-10.25,-111.87:50.35
+chr1	957521	rs4970349	C	T	109.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.54;MQ=59.65;MQ0=0;OQ=696.48;QD=12.90;SB=-243.23	GT:AD:DP:GL:GQ	0/1:30,24:51:-88.30,-15.37,-100.68:99
+chr1	960023	.	C	T	7.39	PASS	AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=53.50;MQ0=0;OQ=70.28;QD=5.86;SB=-0.98	GT:AD:DP:GL:GQ	0/1:7,5:10:-13.33,-3.02,-17.80:99
+chr1	960078	rs9442364	G	C	190.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=59.38;QD=8.48;SB=-32.42	GT:AD:DP:GL:GQ	0/1:3,4:6:-11.04,-1.82,-11.54:92.22
+chr1	961087	rs2799055	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=6;HaplotypeScore=0.98;MQ=59.32;MQ0=0;OQ=442.07;QD=13.00;SB=-186.63	GT:AD:DP:GL:GQ	0/1:16,18:32:-57.14,-9.65,-55.82:99
+chr1	961230	rs2710883	T	C	342.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=662.38;QD=14.09;SB=-345.94	GT:AD:DP:GL:GQ	0/1:23,24:47:-83.68,-14.16,-90.90:99
+chr1	961997	rs3121575	C	T	135.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=582.22;QD=15.32;SB=-286.19	GT:AD:DP:GL:GQ	0/1:17,20:35:-72.05,-10.55,-56.30:99
+chr1	962043	rs4970350	G	A	118.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=762.03;QD=19.05;SB=-359.38	GT:AD:DP:GL:GQ	0/1:16,24:38:-90.95,-11.46,-47.96:99
+chr1	963199	rs2488993	A	G	276.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=691.22;QD=14.71;SB=-269.95	GT:AD:DP:GL:GQ	0/1:22,25:46:-86.26,-13.86,-87.86:99
+chr1	963240	rs2465129	G	A	277.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.66;MQ=58.44;MQ0=0;OQ=598.48;QD=15.35;SB=-309.81	GT:AD:DP:GL:GQ	0/1:19,20:36:-73.98,-10.85,-56.47:99
+chr1	963321	rs2465130	C	T	51.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=517.87;QD=11.26;SB=-211.85	GT:AD:DP:GL:GQ	0/1:28,18:43:-68.02,-12.95,-92.79:99
+chr1	963531	rs2488994	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=4;HaplotypeScore=7.50;MQ=58.37;MQ0=0;OQ=421.46;QD=9.80;SB=-94.66	GT:AD:DP:GL:GQ	0/1:26,17:40:-57.48,-12.05,-93.15:99
+chr1	964043	rs3121577	G	T	194.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=59.29;MQ0=0;OQ=740.60;QD=11.39;SB=-370.98	GT:AD:DP:GL:GQ	0/1:36,29:64:-96.63,-19.29,-128.48:99
+chr1	964062	rs2465131	C	T	262.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.28;MQ0=0;OQ=941.69;QD=14.71;SB=-361.86	GT:AD:DP:GL:GQ	0/1:34,30:62:-116.13,-18.68,-116.79:99
+chr1	964088	rs2488995	A	G	204.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=60.00;MQ0=0;OQ=709.06;QD=12.66;SB=-311.29	GT:AD:DP:GL:GQ	0/1:29,27:55:-90.77,-16.58,-108.13:99
+chr1	964159	rs2488996	A	G	168.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=2.14;MQ=59.09;MQ0=0;OQ=732.05;QD=15.91;SB=-365.63	GT:AD:DP:GL:GQ	0/1:18,28:43:-89.45,-12.96,-67.34:99
+chr1	964218	rs2488997	G	A	8.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=4.51;MQ=58.80;MQ0=0;OQ=657.04;QD=18.77;SB=-348.46	GT:AD:DP:GL:GQ	0/1:15,20:35:-79.53,-10.55,-53.54:99
+chr1	964219	rs2465132	T	C	152.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=58.80;MQ0=0;OQ=438.83;QD=12.54;SB=-221.28	GT:AD:DP:GL:GQ	0/1:15,20:33:-57.12,-9.95,-56.00:99
+chr1	964357	rs2465133	G	T	31.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=5.89;MQ=58.66;MQ0=0;OQ=971.31;QD=14.72;SB=-505.87	GT:AD:DP:GL:GQ	0/1:30,36:62:-119.10,-18.68,-97.98:99
+chr1	964433	rs2465134	T	G	140.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=2.32;MQ=58.54;MQ0=0;OQ=578.70;QD=12.58;SB=-251.93	GT:AD:DP:GL:GQ	0/1:22,23:38:-72.60,-11.45,-62.23:99
+chr1	964525	rs2465135	G	T	124.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.24;MQ=58.59;MQ0=0;OQ=621.72;QD=18.84;SB=-320.48	GT:AD:DP:GL:GQ	0/1:13,20:32:-75.10,-9.64,-38.41:99
+chr1	964757	rs3121578	C	T	344.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.81;MQ0=0;OQ=283.06;QD=10.11;SB=-156.67	GT:AD:DP:GL:GQ	0/1:18,10:26:-39.43,-7.84,-52.76:99
+chr1	964996	rs3121579	T	A	109.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.40;MQ0=0;OQ=475.63;QD=15.34;SB=-146.82	GT:AD:DP:GL:GQ	0/1:15,16:30:-59.88,-9.04,-53.03:99
+chr1	965565	rs9331224	A	G	58.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=1.21;MQ=58.67;MQ0=0;OQ=414.04;QD=11.83;SB=-233.27	GT:AD:DP:GL:GQ	0/1:19,16:32:-54.33,-9.64,-64.60:99
+chr1	967066	rs3121552	G	C	40.51	LowQual	AC=1;AF=0.50;AN=2;DB;DP=5;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;QD=8.10;SB=-43.44	GT:AD:DP:GL:GQ	0/1:3,2:4:-8.54,-1.21,-8.39:71.79
+chr1	967193	rs2799066	T	C	15.85	LowQual	AC=1;AF=0.50;AN=2;DB;DP=8;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.05;MQ0=0;QD=1.98;SB=-24.63	GT:AD:DP:GL:GQ	0/1:6,2:8:-7.27,-2.41,-22.53:48.57
+chr1	967433	rs2710876	G	A	2.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=7.34;MQ=57.29;MQ0=0;OQ=207.99;QD=8.00;SB=-101.60	GT:AD:DP:GL:GQ	0/1:14,12:21:-30.42,-6.34,-38.59:99
+chr1	967643	rs2710875	C	T	1.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=4.71;MQ=57.25;MQ0=0;OQ=665.34;QD=21.46;SB=-289.34	GT:AD:DP:GL:GQ	0/1:11,20:28:-78.26,-8.44,-23.82:99
+chr1	970323	rs3128097	G	A	1.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=9.72;MQ=59.47;MQ0=0;OQ=926.21;QD=16.84;SB=-308.84	GT:AD:DP:GL:GQ	0/1:24,31:51:-111.27,-15.36,-80.98:99
+chr1	970950	rs3128098	A	G	264.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=57.28;MQ0=0;OQ=593.17;QD=14.83;SB=-270.38	GT:AD:DP:GL:GQ	0/1:15,24:36:-73.46,-10.85,-50.98:99
+chr1	971794	rs2465128	A	G	68.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=60.00;MQ0=0;OQ=206.80;QD=7.66;SB=-83.65	GT:AD:DP:GL:GQ	0/1:13,14:23:-30.90,-6.93,-51.94:99
+chr1	972307	rs3128099	A	G	0.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=7.82;MQ=57.77;MQ0=0;OQ=622.11;QD=14.81;SB=-282.64	GT:AD:DP:GL:GQ	0/1:15,25:37:-76.65,-11.15,-58.34:99
+chr1	972325	rs3128100	T	C	8.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=4.33;MQ=57.56;MQ0=0;OQ=1298.64;QD=27.06;SB=-459.21	GT:AD:DP:GL:GQ	1/1:0,48:42:-133.49,-12.67,-0.04:99
+chr1	972376	rs3128101	T	C	10.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=5.66;MQ=56.76;MQ0=0;OQ=571.56;QD=13.94;SB=-141.55	GT:AD:DP:GL:GQ	0/1:15,25:36:-73.37,-12.93,-53.37:99
+chr1	972804	rs3128102	T	C	4.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=3.75;MQ=59.50;MQ0=0;OQ=547.08;QD=11.89;SB=-200.60	GT:AD:DP:GL:GQ	0/1:23,23:37:-69.14,-11.15,-71.89:99
+chr1	972857	rs10267	T	C	1.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=2.51;MQ=58.63;MQ0=0;OQ=633.32;QD=18.63;SB=-175.96	GT:AD:DP:GL:GQ	0/1:12,21:33:-76.56,-9.94,-48.12:99
+chr1	974010	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=20;HaplotypeScore=11.22;MQ=50.83;MQ0=0;OQ=57.83;QD=3.04;SB=2.03	GT:AD:DP:GL:GQ	0/1:15,4:17:-14.19,-5.12,-41.74:90.67
+chr1	974165	rs9442391	T	C	32.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=1.12;MQ=57.07;MQ0=0;OQ=302.47;QD=11.63;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,13:22:-40.16,-6.63,-43.34:99
+chr1	975129	rs2275813	C	T	11.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.16;MQ0=0;OQ=102.58;QD=20.52;SB=-45.66	GT:AD:DP:GL:GQ	0/1:1,4:5:-15.04,-1.51,-2.70:11.90
+chr1	975309	rs2275812	G	T	1.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=7.77;MQ=59.16;MQ0=0;OQ=108.56;QD=9.87;SB=-36.92	GT:AD:DP:GL:GQ	0/1:5,6:10:-17.15,-3.01,-16.77:99
+chr1	975312	rs56255212	G	A	0.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=7.96;MQ=57.00;MQ0=0;OQ=248.84;QD=22.62;SB=-118.97	GT:AD:DP:GL:GQ	0/1:2,9:10:-31.18,-3.01,-6.57:35.54
+chr1	976306	rs2710887	C	T	180.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=498.86;QD=13.13;SB=-206.20	GT:AD:DP:GL:GQ	0/1:21,17:37:-64.33,-11.16,-66.50:99
+chr1	977063	rs9803031	C	T	254.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.50;MQ0=0;OQ=585.89;QD=18.90;SB=-309.86	GT:AD:DP:GL:GQ	0/1:13,18:30:-70.92,-9.05,-35.55:99
+chr1	977533	rs13303287	T	G	495.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=796.56;QD=13.73;SB=-424.70	GT:AD:DP:GL:GQ	0/1:25,33:58:-100.42,-17.48,-92.24:99
+chr1	978366	rs2799071	A	T	261.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=849.34;QD=16.33;SB=-440.60	GT:AD:DP:GL:GQ	0/1:23,29:48:-102.68,-14.47,-71.41:99
+chr1	978795	rs2710871	G	C	22.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=0.83;MQ=58.33;MQ0=0;OQ=743.65;QD=17.71;SB=-370.12	GT:AD:DP:GL:GQ	0/1:18,24:36:-88.51,-10.86,-57.89:99
+chr1	980143	rs4275402	C	T	40.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=58.13;MQ0=0;OQ=896.64;QD=35.87;SB=-438.31	GT:AD:DP:GL:GQ	1/1:0,25:24:-93.26,-7.23,-0.01:72.23
+chr1	980380	rs2710872	C	T	78.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=549.92;QD=18.33;SB=-189.29	GT:AD:DP:GL:GQ	0/1:12,18:27:-66.42,-8.14,-30.90:99
+chr1	980636	rs2799072	C	T	101.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=60.00;MQ0=0;OQ=1104.80;QD=20.09;SB=-396.92	GT:AD:DP:GL:GQ	0/1:22,33:54:-130.03,-16.27,-75.12:99
+chr1	980669	rs2799073	G	A	136.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=60.00;MQ0=0;OQ=1001.06;QD=20.02;SB=-407.16	GT:AD:DP:GL:GQ	0/1:17,32:47:-117.55,-14.17,-57.43:99
+chr1	980847	rs8014	G	A	99.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=656.29;QD=17.27;SB=-261.26	GT:AD:DP:GL:GQ	0/1:18,20:38:-80.37,-11.45,-56.60:99
+chr1	981587	rs3121562	C	T	350.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.79;MQ0=0;OQ=354.87;QD=13.14;SB=-164.15	GT:AD:DP:GL:GQ	0/1:12,15:25:-46.32,-7.55,-37.60:99
+chr1	981840	rs4970400	G	A	115.33	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=38.45;MQ=54.81;MQ0=0;QD=3.04;SB=-51.02	GT:AD:DP:GL:GQ	0/1:30,8:33:-24.78,-9.96,-81.20:99
+chr1	981844	rs13303259	A	G	138.38	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=33.28;MQ=55.32;MQ0=0;QD=3.29;SB=-90.63	GT:AD:DP:GL:GQ	0/1:32,10:37:-28.28,-11.16,-110.43:99
+chr1	981845	rs2710885	T	C	325.46	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=29.31;MQ=55.32;MQ0=0;QD=7.75;SB=-95.70	GT:AD:DP:GL:GQ	0/1:24,18:34:-46.08,-10.25,-78.60:99
+chr1	981905	rs3121564	C	T	503.25	Indel	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.81;MQ=56.07;MQ0=0;QD=13.24;SB=-230.23	GT:AD:DP:GL:GQ	0/1:19,19:34:-63.86,-10.25,-57.54:99
+chr1	981947	rs2710886	T	C	139.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.81;MQ=57.30;MQ0=0;OQ=454.51;QD=9.88;SB=-191.43	GT:AD:DP:GL:GQ	0/1:25,21:45:-62.31,-13.57,-94.53:99
+chr1	981957	rs2799074	T	C	39.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=57.39;MQ0=0;OQ=362.93;QD=6.48;SB=-127.51	GT:AD:DP:GL:GQ	0/1:32,23:44:-52.84,-13.27,-101.58:99
+chr1	982190	rs2245754	C	T	115.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.93;MQ=56.87;MQ0=0;OQ=667.97;QD=12.60;SB=-322.42	GT:AD:DP:GL:GQ	0/1:29,24:49:-84.84,-14.76,-98.05:99
+chr1	982682	rs9331226	G	A	139.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=47.23;MQ0=0;OQ=1563.99;QD=20.85;SB=-791.90	GT:AD:DP:GL:GQ	0/1:29,46:74:-181.97,-22.29,-107.08:99
+chr1	983223	rs13303240	C	A	201.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.32;MQ0=0;OQ=838.66;QD=15.82;SB=-290.67	GT:AD:DP:GL:GQ	0/1:25,28:52:-102.82,-15.67,-74.49:99
+chr1	984254	rs2488991	G	T	204.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=58.59;MQ0=0;OQ=458.34;QD=13.89;SB=-201.49	GT:AD:DP:GL:GQ	0/1:13,19:30:-58.16,-9.04,-45.43:99
+chr1	985344	rs9442393	T	G	429.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=599.53;QD=14.99;SB=-298.50	GT:AD:DP:GL:GQ	0/1:18,22:39:-74.98,-11.75,-60.16:99
+chr1	987271	rs28397086	T	C	29.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.90;MQ0=0;OQ=513.69;QD=32.11;SB=-117.05	GT:AD:DP:GL:GQ	1/1:0,16:15:-54.96,-4.52,-0.01:45.13
+chr1	988258	rs7526076	A	G	181.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.56;MQ0=0;OQ=852.42;QD=16.08;SB=-332.31	GT:AD:DP:GL:GQ	0/1:24,29:52:-104.19,-15.67,-91.85:99
+chr1	988445	rs3813194	G	C	229.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.48;MQ0=0;OQ=676.17;QD=16.90;SB=-324.02	GT:AD:DP:GL:GQ	0/1:19,21:38:-82.36,-11.46,-78.97:99
+chr1	990019	rs11584349	C	T	5.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=221.74;QD=18.48;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,7:12:-29.08,-3.62,-14.98:99
+chr1	991040	rs4970401	G	C	199.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=1348.36;QD=21.75;SB=-452.37	GT:AD:DP:GL:GQ	0/1:27,35:61:-156.51,-18.39,-101.07:99
+chr1	992297	rs11260596	C	T	126.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.11;MQ0=0;OQ=235.14;QD=11.76;SB=-75.09	GT:AD:DP:GL:GQ	0/1:10,10:18:-32.23,-5.43,-30.14:99
+chr1	992795	rs4246502	C	G	1.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.20;MQ0=0;OQ=331.32;QD=25.49;SB=-10.00	GT:AD:DP:GL:GQ	0/1:3,10:12:-40.03,-3.62,-11.85:82.27
+chr1	992916	rs4074992	C	T	64.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.96;MQ0=0;OQ=236.09;QD=13.12;SB=-45.65	GT:AD:DP:GL:GQ	0/1:9,9:18:-32.32,-5.43,-28.25:99
+chr1	993492	rs4075116	C	T	510.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=697.41;QD=15.16;SB=-277.76	GT:AD:DP:GL:GQ	0/1:23,23:43:-85.98,-12.96,-73.34:99
+chr1	994820	rs4073176	G	A	10.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=141.42;QD=15.71;SB=-0.98	GT:AD:DP:GL:GQ	0/1:4,5:9:-20.14,-2.71,-13.80:99
+chr1	994843	rs4073177	G	A	1.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=225.74;QD=20.52;SB=-3.99	GT:AD:DP:GL:GQ	0/1:4,7:11:-29.17,-3.31,-13.13:98.16
+chr1	995932	rs55918415	G	A	129.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=57.98;MQ0=1;OQ=500.10;QD=13.89;SB=-124.09	GT:AD:DP:GL:GQ	0/1:20,16:33:-63.24,-9.94,-54.88:99
+chr1	996086	rs9442394	G	A	160.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=2.17;MQ=59.51;MQ0=0;OQ=685.95;QD=14.59;SB=-304.81	GT:AD:DP:GL:GQ	0/1:25,22:45:-85.44,-13.56,-78.07:99
+chr1	996853	rs4326571	G	A	22.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.32;MQ=58.90;MQ0=0;OQ=529.40;QD=13.93;SB=-35.65	GT:AD:DP:GL:GQ	0/1:21,17:38:-67.68,-11.45,-66.25:99
+chr1	999097	rs9442366	T	C	69.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.30;MQ0=0;OQ=217.52;QD=6.59;SB=-81.95	GT:AD:DP:GL:GQ	0/1:21,12:31:-34.38,-9.34,-81.07:99
+chr1	999304	.	G	A	28.33	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=57.94;MQ0=0;OQ=327.19;QD=9.62;SB=-182.19	GT:AD:DP:GL:GQ	0/1:21,13:31:-45.35,-9.34,-65.26:99
+chr1	999341	rs9442367	G	C	25.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=2;HaplotypeScore=0.81;MQ=58.59;MQ0=0;OQ=590.30;QD=17.89;SB=-256.14	GT:AD:DP:GL:GQ	0/1:14,19:30:-71.37,-9.06,-48.75:99
+chr1	1000580	rs9442368	C	T	47.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=4.96;MQ=54.71;MQ0=0;OQ=650.78;QD=15.49;SB=-262.79	GT:AD:DP:GL:GQ	0/1:21,21:39:-80.11,-11.75,-60.91:99
+chr1	1000958	rs11810785	A	G	695.93	Indel	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=6;HaplotypeScore=2.96;MQ=54.24;MQ0=1;QD=26.77;SB=-339.63	GT:AD:DP:GL:GQ	1/1:0,26:21:-73.19,-6.33,-0.01:63.17
+chr1	1001394	.	T	C	34.95	LowQual	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=41.30;MQ0=1;QD=3.88;SB=-6.99	GT:AD:DP:GL:GQ	0/1:6,3:8:-9.19,-2.41,-20.53:67.78
+chr1	1001500	.	A	T	20.13	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=16.78;MQ0=8;QD=0.81;SB=-10.00	GT:AD:DP:GL:GQ	0/1:19,5:9:-8.01,-2.72,-22.07:52.92
+chr1	1002064	.	G	C	10.08	LowQual	AC=1;AF=0.50;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.77;MQ0=0;QD=5.04;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,1:1:-4.25,-0.30,-0.00:1.76
+chr1	1002464	.	A	T	1.23	PASS	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=18.46;MQ0=3;OQ=57.47;QD=3.59;SB=-37.37	GT:AD:DP:GL:GQ	0/1:8,7:4:-10.24,-1.21,-3.80:25.95
+chr1	1002488	.	A	T	34.11	LowQual	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=7.23;MQ=19.96;MQ0=3;QD=2.27;SB=-4.00	GT:AD:DP:GL:GQ	0/1:9,6:4:-7.90,-1.21,-5.60:43.89
+chr1	1002494	.	A	T	35.11	LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=4.75;MQ=19.72;MQ0=3;QD=2.51;SB=-7.00	GT:AD:DP:GL:GQ	0/1:7,7:3:-7.70,-0.90,-3.30:23.95
+chr1	1002516	.	G	A	46.02	LowQual	AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=4.77;MQ=18.44;MQ0=1;QD=4.60;SB=-10.00	GT:AD:DP:GL:GQ	1/1:5,5:2:-8.01,-0.60,-0.00:6.02
+chr1	1002856	.	T	G	12.29	PASS	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.33;MQ0=1;OQ=106.33;QD=5.32;SB=-21.95	GT:AD:DP:GL:GQ	0/1:10,10:13:-17.84,-3.92,-27.80:99
+chr1	1003100	.	C	T	26.46	LowQual	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=39.70;MQ0=0;QD=2.65;SB=-3.99	GT:AD:DP:GL:GQ	0/1:8,2:6:-7.74,-1.81,-13.13:59.28
+chr1	1003243	.	G	C	4.11	PASS	AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=4.94;MQ=27.95;MQ0=9;OQ=330.47;QD=13.77;SB=-94.94	GT:AD:DP:GL:GQ	1/1:14,10:9:-36.64,-2.72,-0.01:27.09
+chr1	1003514	.	C	A	42.25	LowQual	AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.30;MQ0=1;QD=7.04;SB=-46.39	GT:AD:DP:GL:GQ	1/1:0,6:2:-7.63,-0.60,-0.00:6.02
+chr1	1003557	.	T	A	0.08	PASS	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=5.02;MQ=17.13;MQ0=14;OQ=71.49;QD=2.98;SB=-43.38	GT:AD:DP:GL:GQ	0/1:21,3:4:-11.64,-1.20,-3.64:24.35
+chr1	1003864	.	G	C	10.99	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=9.87;MQ=5.60;MQ0=15;QD=0.58;SB=-10.00	GT:AD:DP:GL:GQ	0/1:17,2:1:-4.35,-0.30,-0.00:1.76
+chr1	1004168	.	A	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=12.18;MQ=19.95;MQ0=11;OQ=53.86;QD=2.56;SB=-37.95	GT:AD:DP:GL:GQ	0/1:14,6:6:-10.48,-1.81,-11.22:86.70
+chr1	1004254	.	G	C	33.05	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=6.90;MQ=13.09;MQ0=11;QD=1.32;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,12:4:-7.80,-1.21,-8.59:65.89
+chr1	1004313	.	G	C	21.04	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=11.38;MQ0=14;QD=0.84;SB=-3.98	GT:AD:DP:GL:GQ	0/1:23,2:6:-7.19,-1.81,-17.58:53.84
+chr1	1004699	rs12401605	A	G	193.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=54.82;MQ0=0;OQ=256.92;QD=8.56;SB=-154.32	GT:AD:DP:GL:GQ	0/1:17,12:28:-37.42,-8.44,-63.53:99
+chr1	1004727	rs12411041	T	A	29.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=54.35;MQ0=0;OQ=225.92;QD=6.11;SB=-72.06	GT:AD:DP:GL:GQ	0/1:25,11:32:-35.52,-9.65,-76.83:99
+chr1	1004989	rs36027499	A	G	65.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=54.55;MQ0=0;OQ=184.41;QD=7.38;SB=-109.60	GT:AD:DP:GL:GQ	0/1:16,9:24:-28.96,-7.24,-58.60:99
+chr1	1005120	rs9442369	A	G	5.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.36;MQ0=0;OQ=146.76;QD=4.08;SB=-64.75	GT:AD:DP:GL:GQ	0/1:26,10:34:-28.21,-10.25,-99.59:99
+chr1	1005414	rs9442370	C	T	185.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.23;MQ0=0;OQ=413.23;QD=13.77;SB=-165.25	GT:AD:DP:GL:GQ	0/1:14,16:26:-52.45,-7.84,-38.57:99
+chr1	1005680	rs12746483	G	A	50.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=2.06;MQ=55.16;MQ0=0;OQ=462.98;QD=16.54;SB=-241.55	GT:AD:DP:GL:GQ	0/1:13,15:28:-58.02,-8.44,-44.58:99
+chr1	1007033	rs3766193	C	G	206.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=57.65;MQ0=0;OQ=606.89;QD=15.97;SB=-241.40	GT:AD:DP:GL:GQ	0/1:19,19:36:-74.82,-10.85,-77.35:99
+chr1	1007060	rs3766192	C	T	263.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=59.03;MQ0=0;OQ=740.51;QD=17.22;SB=-335.87	GT:AD:DP:GL:GQ	0/1:19,24:42:-90.01,-12.67,-54.97:99
+chr1	1007204	rs1133647	G	T	220.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.63;MQ0=0;OQ=352.30;QD=10.36;SB=-144.83	GT:AD:DP:GL:GQ	0/1:20,14:34:-48.76,-10.25,-68.42:99
+chr1	1008007	rs9442395	T	C	79.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.17;MQ=58.20;MQ0=0;OQ=515.12;QD=11.71;SB=-260.59	GT:AD:DP:GL:GQ	0/1:23,21:43:-67.76,-12.96,-87.04:99
+chr1	1008425	rs9442371	C	T	263.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=58.95;MQ0=0;OQ=629.69;QD=14.31;SB=-217.52	GT:AD:DP:GL:GQ	0/1:24,20:39:-78.01,-11.76,-59.01:99
+chr1	1008567	rs9442372	A	G	252.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.72;MQ=58.97;MQ0=0;OQ=538.45;QD=11.97;SB=-254.34	GT:AD:DP:GL:GQ	0/1:20,24:42:-69.79,-12.66,-79.04:99
+chr1	1009038	rs2298215	C	G	217.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=60.00;MQ0=0;OQ=687.91;QD=14.95;SB=-237.07	GT:AD:DP:GL:GQ	0/1:26,20:46:-85.94,-13.87,-107.64:99
+chr1	1009043	rs9442396	T	C	432.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=537.22;QD=11.94;SB=-291.59	GT:AD:DP:GL:GQ	0/1:24,21:42:-69.65,-12.65,-93.39:99
+chr1	1010269	rs9442397	T	C	3.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.96;MQ=59.38;MQ0=0;OQ=202.19;QD=5.46;SB=-53.82	GT:AD:DP:GL:GQ	0/1:25,12:35:-34.05,-10.54,-100.39:99
+chr1	1011278	rs3737728	A	G	36.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=3.58;MQ=58.01;MQ0=0;OQ=401.40;QD=7.72;SB=-209.34	GT:AD:DP:GL:GQ	0/1:32,20:49:-58.20,-14.77,-121.11:99
+chr1	1011558	rs9442398	A	G	416.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.92;MQ0=0;OQ=544.78;QD=12.67;SB=-280.28	GT:AD:DP:GL:GQ	0/1:17,25:38:-69.23,-11.47,-56.30:99
+chr1	1011900	rs6701114	C	T	240.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=59.30;MQ0=0;OQ=587.87;QD=17.81;SB=-314.84	GT:AD:DP:GL:GQ	0/1:13,20:30:-71.11,-9.04,-40.79:99
+chr1	1013307	rs9442399	C	G	25.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=338.37;QD=37.60;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,9:9:-37.42,-2.71,-0.00:27.09
+chr1	1015133	.	C	T	6.55	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.91;MQ=59.48;MQ0=0;OQ=504.60;QD=11.47;SB=-145.62	GT:AD:DP:GL:GQ	0/1:26,18:38:-65.20,-11.46,-67.24:99
+chr1	1015164	rs9442400	T	C	212.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.61;MQ0=0;OQ=1416.80;QD=29.52;SB=-594.18	GT:AD:DP:GL:GQ	1/1:0,48:47:-145.32,-14.18,-0.06:99
+chr1	1016570	rs4074137	C	A	81.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=60.00;MQ0=0;OQ=196.23;QD=6.33;SB=-112.43	GT:AD:DP:GL:GQ	0/1:22,9:30:-31.95,-9.04,-69.97:99
+chr1	1016664	rs4562563	T	A	69.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=58.99;MQ0=0;OQ=428.33;QD=18.62;SB=-222.84	GT:AD:DP:GL:GQ	0/1:8,15:23:-53.05,-6.93,-28.44:99
+chr1	1021403	rs9651273	A	G	292.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=648.57;QD=9.40;SB=-308.20	GT:AD:DP:GL:GQ	0/1:44,25:69:-88.92,-20.78,-180.93:99
+chr1	1022047	rs9651272	A	G	123.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=59.58;MQ0=0;OQ=389.06;QD=8.84;SB=-195.60	GT:AD:DP:GL:GQ	0/1:25,19:42:-54.85,-12.66,-100.05:99
+chr1	1023862	rs4970353	C	T	10.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=971.03;QD=16.18;SB=-472.48	GT:AD:DP:GL:GQ	0/1:30,30:59:-118.16,-17.77,-101.63:99
+chr1	1025668	rs12759295	G	A	84.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=59.60;MQ0=0;OQ=2089.51;QD=36.03;SB=-522.67	GT:AD:DP:GL:GQ	1/1:0,58:54:-212.56,-16.27,-0.02:99
+chr1	1026680	rs61766341	T	C	205.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=959.29;QD=13.51;SB=-415.84	GT:AD:DP:GL:GQ	0/1:32,39:68:-119.71,-20.50,-125.74:99
+chr1	1026910	rs12134754	C	T	210.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.33;MQ0=0;OQ=1080.76;QD=17.43;SB=-366.87	GT:AD:DP:GL:GQ	0/1:30,32:60:-129.44,-18.08,-89.78:99
+chr1	1027893	.	T	A	15.04	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=20;HaplotypeScore=5.87;MQ=44.25;MQ0=4;QD=0.40;SB=32.13	GT:AD:DP:GL:GQ	0/1:33,5:23:-11.70,-6.93,-76.52:47.73
+chr1	1037844	rs11584392	G	A	163.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.18;MQ=59.82;MQ0=0;OQ=608.74;QD=14.16;SB=-241.74	GT:AD:DP:GL:GQ	0/1:22,21:40:-76.22,-12.06,-65.82:99
+chr1	1043248	rs4970408	C	T	441.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.36;MQ0=0;OQ=945.52;QD=17.51;SB=-425.94	GT:AD:DP:GL:GQ	0/1:25,29:54:-114.11,-16.27,-86.23:99
+chr1	1050037	rs7548798	C	T	114.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=3.36;MQ=58.61;MQ0=0;OQ=733.89;QD=15.61;SB=-330.30	GT:AD:DP:GL:GQ	0/1:24,23:47:-90.84,-14.17,-83.86:99
+chr1	1050038	rs7556082	T	C	10.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=4;HaplotypeScore=2.36;MQ=58.61;MQ0=0;OQ=528.95;QD=11.25;SB=-283.60	GT:AD:DP:GL:GQ	0/1:24,23:46:-70.05,-13.87,-95.38:99
+chr1	1050218	rs12567855	G	C	18.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=1.10;MQ=59.48;MQ0=0;OQ=549.12;QD=15.25;SB=-150.55	GT:AD:DP:GL:GQ	0/1:19,17:33:-68.15,-9.95,-68.62:99
+chr1	1050923	.	C	G	38.31	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=7.12;MQ=59.57;MQ0=0;QD=0.71;SB=62.24	GT:AD:DP:GL:GQ	0/1:40,14:36:-17.98,-10.86,-134.66:71.15
+chr1	1051029	rs11807848	T	C	153.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.10;MQ=60.00;MQ0=0;OQ=328.64;QD=9.39;SB=-171.94	GT:AD:DP:GL:GQ	0/1:21,14:34:-46.39,-10.24,-82.90:99
+chr1	1051657	rs34530354	A	G	139.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.25;MQ0=0;OQ=341.50;QD=11.02;SB=-128.73	GT:AD:DP:GL:GQ	0/1:17,14:30:-46.47,-9.04,-63.98:99
+chr1	1051711	rs35207507	A	G	157.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=57.36;MQ0=0;OQ=232.59;QD=9.30;SB=-75.78	GT:AD:DP:GL:GQ	0/1:12,13:22:-33.17,-6.63,-47.34:99
+chr1	1051888	rs9329411	A	G	8.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=3;HaplotypeScore=0.32;MQ=58.95;MQ0=0;OQ=307.14;QD=13.96;SB=-152.31	GT:AD:DP:GL:GQ	0/1:10,12:20:-40.02,-6.03,-35.33:99
+chr1	1052501	rs9442373	C	A	218.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.03;MQ0=0;OQ=1229.67;QD=18.35;SB=-293.35	GT:AD:DP:GL:GQ	0/1:29,38:65:-145.84,-19.58,-78.11:99
+chr1	1052907	rs7545801	A	G	1.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=2.49;MQ=60.00;MQ0=0;OQ=935.67;QD=29.24;SB=-247.57	GT:AD:DP:GL:GQ	1/1:0,32:30:-97.17,-9.04,-0.02:90.21
+chr1	1053104	rs4970413	G	T	111.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.50;MQ=59.42;MQ0=0;OQ=637.82;QD=15.95;SB=-209.62	GT:AD:DP:GL:GQ	0/1:16,24:36:-77.92,-10.85,-38.08:99
+chr1	1053355	rs55945496	G	A	154.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=58.97;MQ0=0;OQ=692.26;QD=15.38;SB=-240.56	GT:AD:DP:GL:GQ	0/1:24,21:40:-84.57,-12.06,-60.15:99
+chr1	1054398	rs6682475	G	C	62.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=3.35;MQ=57.20;MQ0=0;OQ=522.88;QD=16.34;SB=-284.57	GT:AD:DP:GL:GQ	0/1:16,16:32:-65.22,-9.65,-67.94:99
+chr1	1054533	rs7547403	C	G	0.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=4;HaplotypeScore=0.79;MQ=59.42;MQ0=0;OQ=1637.77;QD=40.94;SB=-672.45	GT:AD:DP:GL:GQ	1/1:0,40:39:-167.38,-11.75,-0.02:99
+chr1	1054665	rs2298216	T	C	152.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=59.60;MQ0=0;OQ=1938.74;QD=34.01;SB=-772.11	GT:AD:DP:GL:GQ	1/1:0,57:57:-197.48,-17.17,-0.02:99
+chr1	1055159	rs4072537	T	C	138.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=51.50;MQ0=0;OQ=1817.15;QD=30.80;SB=-665.83	GT:AD:DP:GL:GQ	1/1:0,59:56:-185.34,-16.89,-0.04:99
+chr1	1055460	rs9442357	C	A	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.04;HRun=20;HaplotypeScore=17.31;MQ=48.11;MQ0=2;OQ=1123.16;QD=23.90;SB=-311.46	GT:AD:DP:GL:GQ	1/1:9,36:37:-122.62,-11.15,-6.72:44.32
+chr1	1056122	rs4072496	G	C	273.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=828.08;QD=31.85;SB=-146.57	GT:AD:DP:GL:GQ	1/1:0,26:22:-86.41,-6.64,-0.02:66.21
+chr1	1056145	rs10907181	A	G	65.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=60.00;MQ0=0;OQ=849.61;QD=28.32;SB=-350.43	GT:AD:DP:GL:GQ	1/1:0,30:29:-88.58,-8.75,-0.04:87.15
+chr1	1056266	rs10907182	T	C	152.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.47;MQ0=0;OQ=1343.61;QD=29.86;SB=-493.15	GT:AD:DP:GL:GQ	1/1:0,45:43:-137.99,-12.97,-0.04:99
+chr1	1056679	.	A	G	17.68	PASS	AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.92;MQ0=0;OQ=622.64;QD=23.06;SB=-77.91	GT:AD:DP:GL:GQ	1/1:0,27:19:-65.86,-5.72,-0.01:57.16
+chr1	1056682	rs7513297	A	G	4.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=33.92;MQ0=0;OQ=613.60;QD=22.73;SB=-73.89	GT:AD:DP:GL:GQ	1/1:0,27:19:-64.96,-5.73,-0.01:57.15
+chr1	1056691	rs7553878	C	G	182.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=38.04;MQ0=0;OQ=986.57;QD=30.83;SB=-182.68	GT:AD:DP:GL:GQ	1/1:0,32:25:-102.26,-7.54,-0.01:75.24
+chr1	1056809	rs7513404	A	G	1483.16	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=11.12;MQ=36.69;MQ0=3;QD=26.02;SB=-571.97	GT:AD:DP:GL:GQ	1/1:2,55:47:-151.94,-14.18,-0.04:99
+chr1	1056815	rs7513405	A	G	1422.20	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=12.03;MQ=35.94;MQ0=3;QD=26.83;SB=-591.02	GT:AD:DP:GL:GQ	1/1:4,49:44:-145.84,-13.27,-0.03:99
+chr1	1056816	rs7516160	T	C	1466.09	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=12.03;MQ=36.53;MQ0=3;QD=27.15;SB=-727.28	GT:AD:DP:GL:GQ	1/1:3,50:47:-150.24,-14.18,-0.04:99
+chr1	1057725	rs9442374	T	G	13.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=58.50;MQ0=0;OQ=951.55;QD=30.70;SB=-471.37	GT:AD:DP:GL:GQ	1/1:0,31:29:-98.75,-8.74,-0.01:87.23
+chr1	1057728	rs9442358	A	C	4.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=3;HaplotypeScore=0.48;MQ=58.50;MQ0=0;OQ=931.22;QD=30.04;SB=-418.04	GT:AD:DP:GL:GQ	1/1:1,30:28:-96.72,-8.44,-0.02:84.22
+chr1	1059288	rs9442375	C	A	11.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.68;MQ=37.62;MQ0=0;OQ=1307.51;QD=33.53;SB=-359.86	GT:AD:DP:GL:GQ	1/1:0,39:37:-134.35,-11.15,-0.01:99
+chr1	1059306	rs9442376	G	A	317.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=30.41;MQ0=0;OQ=1189.43;QD=32.15;SB=-404.66	GT:AD:DP:GL:GQ	1/1:0,37:31:-122.54,-9.34,-0.01:93.30
+chr1	1059314	rs9442377	G	A	1.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=4.82;MQ=29.14;MQ0=0;OQ=1298.78;QD=30.92;SB=-496.01	GT:AD:DP:GL:GQ	1/1:0,42:35:-133.48,-10.55,-0.02:99
+chr1	1059991	rs9442378	T	G	44.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=59.34;MQ0=0;OQ=1111.12;QD=31.75;SB=-500.92	GT:AD:DP:GL:GQ	1/1:0,35:33:-114.71,-9.94,-0.02:99
+chr1	1060304	rs9442379	C	T	128.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1793.65;QD=37.37;SB=-715.98	GT:AD:DP:GL:GQ	1/1:0,48:46:-182.96,-13.86,-0.01:99
+chr1	1060981	rs10907183	G	C	289	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.17;MQ=58.88;MQ0=0;OQ=1986.90;QD=34.26;SB=-998.16	GT:AD:DP:GL:GQ	1/1:0,58:51:-202.32,-15.40,-0.05:99
+chr1	1061055	rs6604971	T	C	165.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=59.35;MQ0=0;OQ=1959.28;QD=30.61;SB=-872.00	GT:AD:DP:GL:GQ	1/1:0,64:62:-199.57,-18.70,-0.06:99
+chr1	1062361	rs9442360	G	C	41.74	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.77;MQ0=0;QD=13.91;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:2:-7.58,-0.60,-0.00:6.02
+chr1	1063812	.	C	A	39.60	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=20;HaplotypeScore=10.99;MQ=49.89;MQ0=1;QD=0.94;SB=53.19	GT:AD:DP:GL:GQ	0/1:34,7:30:-16.28,-9.04,-89.71:72.44
+chr1	1064433	.	T	C	21.13	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=43.11;MQ0=1;QD=1.11;SB=5.04	GT:AD:DP:GL:GQ	0/1:14,5:14:-9.62,-4.23,-37.37:53.93
+chr1	1064508	.	A	G	48.32	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=5;HaplotypeScore=5.11;MQ=25.52;MQ0=20;QD=0.93;SB=-10.00	GT:AD:DP:GL:GQ	0/1:42,6:27:-16.25,-8.14,-83.13:81.15
+chr1	1064534	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=3;HaplotypeScore=5.91;MQ=22.24;MQ0=19;OQ=77.81;QD=1.62;SB=-10.00	GT:AD:DP:GL:GQ	0/1:26,22:23:-17.99,-6.93,-63.10:99
+chr1	1064544	.	G	A	18.70	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=9.26;MQ=23.84;MQ0=13;QD=0.45;SB=-10.00	GT:AD:DP:GL:GQ	0/1:39,3:23:-12.08,-6.93,-67.67:51.47
+chr1	1064666	.	G	A	28.24	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=17.49;MQ0=7;QD=1.34;SB=-10.00	GT:AD:DP:GL:GQ	0/1:19,2:4:-7.31,-1.21,-6.24:50.32
+chr1	1064676	.	G	A	32.25	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=15.31;MQ0=8;QD=1.61;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,4:3:-7.41,-0.90,-3.57:26.65
+chr1	1064678	.	A	G	13.68	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=15.31;MQ0=8;QD=0.68;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,5:3:-5.54,-0.90,-4.06:31.54
+chr1	1065083	.	T	G	0.75	PASS	AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=3;HaplotypeScore=1.47;MQ=13.28;MQ0=6;OQ=72.14;QD=8.02;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,7:3:-10.70,-0.90,-0.00:9.03
+chr1	1065545	.	A	T	15.58	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=6.82;MQ=15.84;MQ0=10;QD=0.78;SB=-20.32	GT:AD:DP:GL:GQ	0/1:16,4:8:-7.24,-2.41,-23.49:48.29
+chr1	1065754	.	T	G	10.50	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=26.23;MQ0=5;QD=0.50;SB=-7.00	GT:AD:DP:GL:GQ	0/1:10,11:9:-7.00,-2.71,-25.01:42.93
+chr1	1065788	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=4;HaplotypeScore=1.91;MQ=35.15;MQ0=3;OQ=426.85;QD=16.42;SB=-65.33	GT:AD:DP:GL:GQ	0/1:10,16:20:-52.00,-6.03,-21.27:99
+chr1	1065876	rs34294086	G	T	14.09	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.05;MQ=16.68;MQ0=19;QD=0.25;SB=-0.98	GT:AD:DP:GL:GQ	0/1:47,10:18:-10.10,-5.43,-46.58:46.75
+chr1	1065896	rs34976191	A	G	3.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=5.11;MQ=25.24;MQ0=16;OQ=221.06;QD=5.02;SB=-47.30	GT:AD:DP:GL:GQ	0/1:32,12:17:-30.51,-5.13,-29.81:99
+chr1	1065898	rs35853231	G	A	14.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=25.42;MQ0=15;OQ=228.24;QD=5.43;SB=-22.49	GT:AD:DP:GL:GQ	0/1:33,9:15:-30.63,-4.52,-21.87:99
+chr1	1066927	rs4970357	C	A	263.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=704.25;QD=32.01;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,22:21:-74.02,-6.32,-0.01:63.19
+chr1	1067825	rs55750860	C	T	23.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.51;MQ=58.95;MQ0=0;OQ=1494.41;QD=37.36;SB=-613.01	GT:AD:DP:GL:GQ	1/1:0,40:39:-153.04,-11.75,-0.01:99
+chr1	1070149	rs1539638	G	A	498.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1278.23;QD=37.59;SB=-657.67	GT:AD:DP:GL:GQ	1/1:0,34:33:-131.42,-9.94,-0.01:99
+chr1	1070766	.	C	G	0.10	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=47.59;MQ0=0;OQ=113.71;QD=2.58;SB=-2.32	GT:AD:DP:GL:GQ	0/1:34,9:39:-26.42,-11.76,-133.80:99
+chr1	1070768	.	C	T	0.13	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=46.93;MQ0=0;OQ=115.95;QD=2.64;SB=-32.19	GT:AD:DP:GL:GQ	0/1:34,10:38:-26.33,-11.45,-104.66:99
+chr1	1070788	rs1539637	G	C	8.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=2.86;MQ=44.98;MQ0=0;OQ=574.54;QD=14.73;SB=-154.58	GT:AD:DP:GL:GQ	0/1:22,17:37:-71.91,-11.17,-77.14:99
+chr1	1070790	rs4512588	T	C	118.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.33;MQ=44.52;MQ0=0;OQ=439.51;QD=11.57;SB=-120.73	GT:AD:DP:GL:GQ	0/1:20,18:36:-58.08,-10.85,-73.14:99
+chr1	1070804	.	T	C	317.73	Indel	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=43.50;MQ0=0;QD=8.83;SB=-125.65	GT:AD:DP:GL:GQ	0/1:20,16:34:-45.31,-10.25,-78.50:99
+chr1	1070810	.	T	C	59.59	Indel	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=42.56;MQ0=0;QD=1.92;SB=-21.88	GT:AD:DP:GL:GQ	0/1:21,10:26:-17.08,-7.83,-82.36:92.43
+chr1	1070825	.	C	T	12.15	LowQual	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=46.99;MQ0=0;QD=0.45;SB=-5.49	GT:AD:DP:GL:GQ	0/1:24,3:26:-12.31,-7.84,-75.55:44.71
+chr1	1070828	.	C	T	17.92	LowQual	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=46.99;MQ0=0;QD=0.66;SB=-11.45	GT:AD:DP:GL:GQ	0/1:24,3:24:-12.30,-7.23,-73.32:50.69
+chr1	1074807	.	T	G	14.10	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=4;HaplotypeScore=1.72;MQ=58.59;MQ0=0;QD=0.43;SB=59.21	GT:AD:DP:GL:GQ	0/1:24,8:27:-12.81,-8.13,-82.30:46.77
+chr1	1075432	.	C	T	38.87	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=57.97;MQ0=0;OQ=818.81;QD=17.80;SB=-345.86	GT:AD:DP:GL:GQ	0/1:20,26:46:-99.04,-13.88,-63.69:99
+chr1	1077546	rs9442380	T	C	202.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=2295.26;QD=29.81;SB=-1162.13	GT:AD:DP:GL:GQ	1/1:0,76:73:-233.18,-22.02,-0.07:99
+chr1	1079125	rs4970358	A	G	12.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=5.70;MQ=59.35;MQ0=0;OQ=2374.58;QD=33.44;SB=-995.95	GT:AD:DP:GL:GQ	1/1:0,69:68:-244.00,-23.26,-2.96:99
+chr1	1079873	rs9442361	C	A	5.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=3;HaplotypeScore=1.89;MQ=53.07;MQ0=0;OQ=1204.88;QD=33.47;SB=-532.76	GT:AD:DP:GL:GQ	1/1:0,36:34:-124.08,-10.24,-0.01:99
+chr1	1080440	rs6604972	A	G	531.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=1807.70;QD=30.64;SB=-735.76	GT:AD:DP:GL:GQ	1/1:0,59:56:-184.40,-16.89,-0.04:99
+chr1	1082462	rs56863140	G	C	99.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.04;MQ0=0;OQ=146.93;QD=24.49;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,6:5:-18.26,-1.52,-0.01:15.05
+chr1	1084348	rs4970360	C	T	64.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.36;MQ=58.41;MQ0=0;OQ=1613.83;QD=36.68;SB=-777.04	GT:AD:DP:GL:GQ	1/1:0,44:42:-164.99,-12.66,-0.02:99
+chr1	1084535	rs4970361	A	C	88.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=58.78;MQ0=1;OQ=1424.16;QD=32.37;SB=-688.05	GT:AD:DP:GL:GQ	1/1:1,43:41:-146.01,-12.35,-0.01:99
+chr1	1084601	rs4970362	A	G	229.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.71;MQ=59.53;MQ0=0;OQ=1464.98;QD=29.90;SB=-668.84	GT:AD:DP:GL:GQ	1/1:0,49:47:-150.13,-14.18,-0.04:99
+chr1	1084842	rs7538773	G	A	9.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.13;MQ0=0;OQ=1279.59;QD=36.56;SB=-199.76	GT:AD:DP:GL:GQ	1/1:0,33:33:-131.55,-9.94,-0.01:99
+chr1	1085246	rs6604973	G	A	85.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=59.42;MQ0=0;OQ=1511.71;QD=37.79;SB=-646.86	GT:AD:DP:GL:GQ	1/1:0,40:38:-154.76,-11.45,-0.01:99
+chr1	1085482	rs4970419	C	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=7;HaplotypeScore=2.24;MQ=59.45;MQ0=0;OQ=1670.84;QD=39.78;SB=-828.31	GT:AD:DP:GL:GQ	1/1:0,42:40:-170.69,-12.06,-0.02:99
+chr1	1085874	rs9442381	C	G	314.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.11;MQ0=0;OQ=1195.39;QD=38.56;SB=-412.65	GT:AD:DP:GL:GQ	1/1:0,31:28:-123.13,-8.44,-0.01:84.28
+chr1	1086061	rs9442382	C	T	139.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=990.01;QD=38.08;SB=-164.21	GT:AD:DP:GL:GQ	1/1:0,26:26:-102.60,-7.84,-0.01:78.25
+chr1	1086771	rs1539636	T	C	148.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=60.00;MQ0=0;OQ=1262.30;QD=33.22;SB=-642.89	GT:AD:DP:GL:GQ	1/1:0,38:37:-129.83,-11.15,-0.02:99
+chr1	1086955	rs1539635	G	A	48.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.31;MQ=56.37;MQ0=0;OQ=1687.66;QD=35.91;SB=-612.00	GT:AD:DP:GL:GQ	1/1:0,47:43:-172.36,-12.95,-0.01:99
+chr1	1086963	rs1539634	C	T	83.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.95;MQ0=0;OQ=1761.33;QD=36.69;SB=-642.86	GT:AD:DP:GL:GQ	1/1:0,48:45:-179.73,-13.56,-0.02:99
+chr1	1087150	rs9442384	T	C	36.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.26;MQ=59.81;MQ0=0;OQ=1429.90;QD=29.79;SB=-636.25	GT:AD:DP:GL:GQ	1/1:0,48:46:-146.63,-13.88,-0.05:99
+chr1	1087198	rs9442385	T	G	89.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=57.84;MQ0=0;OQ=1240.37;QD=26.39;SB=-556.87	GT:AD:DP:GL:GQ	1/1:0,47:40:-127.66,-12.06,-0.04:99
+chr1	1087800	rs1891907	A	G	2.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=57.36;MQ0=0;OQ=810.89;QD=32.44;SB=-193.80	GT:AD:DP:GL:GQ	1/1:0,25:24:-84.68,-7.23,-0.01:72.21
+chr1	1088284	rs12135382	C	T	198.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=312.05;QD=28.37;SB=-50.56	GT:AD:DP:GL:GQ	1/1:0,11:9:-34.79,-2.71,-0.00:27.09
+chr1	1088577	rs4379629	C	G	8.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=217.53;QD=24.17;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,9:7:-25.35,-2.12,-0.02:21.06
+chr1	1089205	rs9660710	A	C	62.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.52;MQ=60.00;MQ0=0;OQ=1253.07;QD=26.66;SB=-477.88	GT:AD:DP:GL:GQ	1/1:0,47:40:-128.93,-12.06,-0.03:99
+chr1	1090080	rs1891905	C	T	107.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=58.89;MQ0=0;OQ=1593.75;QD=37.95;SB=-678.31	GT:AD:DP:GL:GQ	1/1:0,42:41:-162.97,-12.35,-0.01:99
+chr1	1090182	rs1891904	C	A	413.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=739.19;QD=30.80;SB=-375.45	GT:AD:DP:GL:GQ	1/1:0,24:22:-77.51,-6.63,-0.01:66.17
+chr1	1090866	rs7549819	C	T	73.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=59.25;MQ0=0;OQ=998.72;QD=32.22;SB=-450.59	GT:AD:DP:GL:GQ	1/1:1,30:27:-103.47,-8.14,-0.02:81.25
+chr1	1091932	rs9442386	A	G	1.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=172.84;QD=21.61;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,8:7:-20.87,-2.12,-0.01:21.04
+chr1	1093405	rs7518873	T	C	57.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.77;MQ0=0;OQ=646.68;QD=30.79;SB=-268.71	GT:AD:DP:GL:GQ	1/1:0,21:20:-68.26,-6.03,-0.01:60.16
+chr1	1093821	rs7521584	T	G	116.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.95;MQ0=0;OQ=1316.49;QD=29.92;SB=-587.88	GT:AD:DP:GL:GQ	1/1:0,44:43:-135.27,-12.96,-0.04:99
+chr1	1095101	rs9442362	T	C	65.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.90;MQ=60.00;MQ0=0;OQ=375.39;QD=7.99;SB=-207.86	GT:AD:DP:GL:GQ	0/1:27,20:44:-54.09,-13.27,-100.76:99
+chr1	1095924	rs6656236	G	A	130.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=57.77;MQ0=0;OQ=609.61;QD=16.04;SB=-273.30	GT:AD:DP:GL:GQ	0/1:18,20:34:-74.49,-10.25,-50.31:99
+chr1	1096647	rs4442317	T	C	203.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=59.13;MQ0=0;OQ=506.89;QD=10.56;SB=-244.47	GT:AD:DP:GL:GQ	0/1:29,19:48:-68.44,-14.47,-111.87:99
+chr1	1114401	rs11577350	G	A	483.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=1009.34;QD=13.28;SB=-463.05	GT:AD:DP:GL:GQ	0/1:45,31:75:-126.83,-22.61,-139.35:99
+chr1	1114613	rs6702156	T	C	467.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=978.73;QD=12.23;SB=-374.99	GT:AD:DP:GL:GQ	0/1:42,38:78:-124.66,-23.50,-162.90:99
+chr1	1127805	.	C	T	17.93	LowQual	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.76;MQ=47.96;MQ0=1;QD=0.48;SB=-4.44	GT:AD:DP:GL:GQ	0/1:29,6:21:-11.40,-6.33,-63.23:50.69
+chr1	1133298	rs55945303	G	A	59.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=925.55;QD=21.52;SB=-252.58	GT:AD:DP:GL:GQ	0/1:14,29:40:-107.89,-12.05,-42.24:99
+chr1	1139524	rs35878953	C	T	131.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.33;MQ=58.24;MQ0=0;OQ=799.98;QD=18.60;SB=-423.99	GT:AD:DP:GL:GQ	0/1:17,25:37:-94.44,-11.16,-36.66:99
+chr1	1148494	rs6603781	A	G	136.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.05;MQ0=0;OQ=1330.48;QD=27.15;SB=-433.29	GT:AD:DP:GL:GQ	1/1:0,49:42:-136.66,-12.66,-0.03:99
+chr1	1149380	rs6702268	T	C	227.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.80;MQ0=0;OQ=961.17;QD=27.46;SB=-122.75	GT:AD:DP:GL:GQ	1/1:0,35:31:-99.73,-9.35,-0.03:93.18
+chr1	1152189	rs4970423	A	G	15.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=59.39;MQ0=0;OQ=1088.52;QD=28.65;SB=-378.40	GT:AD:DP:GL:GQ	1/1:0,38:34:-112.46,-10.25,-0.02:99
+chr1	1161280	rs6603782	C	T	102.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=59.00;MQ0=0;OQ=708.75;QD=16.88;SB=-201.20	GT:AD:DP:GL:GQ	0/1:20,22:40:-86.21,-12.05,-64.42:99
+chr1	1162770	rs715643	C	T	309.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.45;MQ=57.65;MQ0=0;OQ=561.34;QD=14.77;SB=-301.32	GT:AD:DP:GL:GQ	0/1:18,19:36:-70.27,-10.85,-55.47:99
+chr1	1171665	.	C	T	4.62	PASS	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.39;MQ0=0;OQ=105.76;QD=11.75;SB=-6.99	GT:AD:DP:GL:GQ	0/1:5,4:9:-16.57,-2.71,-16.65:99
+chr1	1178813	.	G	C	27.28	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=1;HaplotypeScore=10.95;MQ=55.60;MQ0=0;QD=0.43;SB=74.28	GT:AD:DP:GL:GQ	0/1:46,17:41:-18.38,-12.37,-155.87:60.10
+chr1	1182131	.	G	A	44.09	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=52;Dels=0.04;HRun=20;HaplotypeScore=11.11;MQ=50.33;MQ0=0;QD=0.85;SB=65.22	GT:AD:DP:GL:GQ	0/1:38,12:42:-20.05,-12.36,-125.30:76.92
+chr1	1183574	.	T	C	30.78	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=5;HaplotypeScore=13.00;MQ=56.93;MQ0=0;QD=0.83;SB=23.10	GT:AD:DP:GL:GQ	0/1:22,15:21:-12.69,-6.33,-67.62:63.61
+chr1	1186726	rs6659787	T	C	444.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1920.21;QD=33.11;SB=-425.81	GT:AD:DP:GL:GQ	1/1:0,58:55:-195.63,-16.57,-0.02:99
+chr1	1194535	.	A	G	16.67	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=6.08;MQ=52.52;MQ0=1;QD=0.32;SB=29.11	GT:AD:DP:GL:GQ	0/1:42,10:39:-16.70,-11.76,-128.34:49.41
+chr1	1204684	rs34258594	C	T	26.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=41.53;MQ0=1;OQ=534.60;QD=15.27;SB=-99.92	GT:AD:DP:GL:GQ	0/1:16,19:32:-66.39,-9.65,-50.26:99
+chr1	1206810	.	C	A	15.67	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=59.17;MQ0=0;QD=0.56;SB=17.05	GT:AD:DP:GL:GQ	0/1:19,7:21:-11.17,-6.33,-52.97:48.38
+chr1	1212553	.	C	T	5.74	PASS	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=5.06;MQ=57.97;MQ0=0;OQ=298.13;QD=12.96;SB=-173.70	GT:AD:DP:GL:GQ	0/1:12,11:19:-38.83,-5.73,-27.23:99
+chr1	1213523	.	A	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=15.57;MQ=33.50;MQ0=4;OQ=59.03;QD=3.28;SB=2.04	GT:AD:DP:GL:GQ	0/1:9,9:9:-11.90,-2.71,-23.47:91.86
+chr1	1213617	.	C	T	7.11	PASS	AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=3.14;MQ=18.72;MQ0=10;OQ=134.34;QD=6.72;SB=-10.00	GT:AD:DP:GL:GQ	1/1:5,15:4:-16.97,-1.20,-0.00:12.04
+chr1	1213622	.	T	C	11.33	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=2;HaplotypeScore=3.30;MQ=19.74;MQ0=10;QD=0.49;SB=-3.98	GT:AD:DP:GL:GQ	0/1:20,3:7:-6.49,-2.11,-18.92:43.83
+chr1	1213635	.	C	T	23.33	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=18.06;MQ0=13;QD=0.75;SB=-33.62	GT:AD:DP:GL:GQ	0/1:24,7:9:-8.33,-2.71,-24.32:56.15
+chr1	1213653	.	C	T	47.94	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.74;MQ=17.89;MQ0=21;QD=1.00;SB=-23.48	GT:AD:DP:GL:GQ	0/1:37,11:13:-11.99,-3.92,-35.04:80.78
+chr1	1213671	.	C	T	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=22.77;MQ0=22;OQ=90.19;QD=1.80;SB=-17.46	GT:AD:DP:GL:GQ	0/1:28,22:20:-18.33,-6.03,-51.67:99
+chr1	1213694	.	T	C	39.97	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=2;HaplotypeScore=8.39;MQ=23.73;MQ0=21;QD=0.73;SB=-15.88	GT:AD:DP:GL:GQ	0/1:51,4:21:-13.61,-6.33,-64.53:72.80
+chr1	1213750	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=7.03;MQ=25.74;MQ0=11;OQ=59.44;QD=1.56;SB=-49.23	GT:AD:DP:GL:GQ	0/1:22,16:17:-14.35,-5.12,-45.82:92.28
+chr1	1213763	.	C	T	47.85	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=26.61;MQ0=8;QD=1.65;SB=-29.61	GT:AD:DP:GL:GQ	0/1:21,8:13:-11.99,-3.92,-33.55:80.68
+chr1	1213781	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=3.20;MQ=28.82;MQ0=7;OQ=70.59;QD=2.82;SB=-20.63	GT:AD:DP:GL:GQ	0/1:21,4:13:-14.26,-3.92,-34.86:99
+chr1	1213884	.	C	T	18.32	PASS	AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=20.52;MQ0=9;OQ=123.88;QD=9.53;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,11:4:-15.92,-1.20,-0.00:12.04
+chr1	1213994	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=2;HaplotypeScore=2.99;MQ=9.42;MQ0=22;OQ=67.77;QD=1.94;SB=-42.68	GT:AD:DP:GL:GQ	0/1:31,4:4:-11.26,-1.21,-2.97:17.61
+chr1	1214386	.	C	T	18.53	PASS	AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=12.80;MQ0=7;OQ=79.89;QD=6.15;SB=-52.67	GT:AD:DP:GL:GQ	1/1:3,10:3:-11.48,-0.90,-0.00:9.03
+chr1	1214538	.	C	T	13.99	PASS	AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.76;MQ0=3;OQ=222.41;QD=22.24;SB=-119.99	GT:AD:DP:GL:GQ	1/1:1,9:7:-25.82,-2.11,-0.00:21.06
+chr1	1214556	.	C	T	78.88	PASS	AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.62;MQ0=3;OQ=125.22;QD=13.91;SB=-42.55	GT:AD:DP:GL:GQ	1/1:2,7:4:-16.06,-1.21,-0.00:12.04
+chr1	1214569	.	C	T	4.09	PASS	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=21.21;MQ0=3;OQ=121.10;QD=17.30;SB=-81.10	GT:AD:DP:GL:GQ	1/1:3,4:4:-15.65,-1.21,-0.00:12.04
+chr1	1214849	.	T	C	10.83	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=11.01;MQ0=15;QD=0.39;SB=-10.00	GT:AD:DP:GL:GQ	0/1:20,8:6:-6.14,-1.81,-16.12:43.30
+chr1	1214919	.	A	T	0.53	PASS	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=4.77;MQ=20.32;MQ0=10;OQ=98.85;QD=4.94;SB=-69.74	GT:AD:DP:GL:GQ	0/1:10,9:7:-15.28,-2.11,-10.80:86.87
+chr1	1215102	.	A	T	1.26	PASS	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.90;MQ=20.59;MQ0=9;OQ=98.25;QD=4.91;SB=-47.98	GT:AD:DP:GL:GQ	0/1:4,16:7:-15.22,-2.11,-12.20:99
+chr1	1215147	.	T	C	24.78	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=2;HaplotypeScore=5.19;MQ=18.98;MQ0=32;QD=0.28;SB=-36.82	GT:AD:DP:GL:GQ	0/1:83,7:38:-17.21,-11.45,-127.57:57.61
+chr1	1215165	.	C	T	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=3.30;MQ=20.48;MQ0=21;OQ=101.26;QD=1.35;SB=26.10	GT:AD:DP:GL:GQ	0/1:48,27:30:-22.45,-9.04,-79.18:99
+chr1	1215324	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=4.60;MQ=26.05;MQ0=19;OQ=186.49;QD=2.49;SB=8.19	GT:AD:DP:GL:GQ	0/1:60,15:45:-35.50,-13.57,-130.76:99
+chr1	1227467	rs2296475	T	C	67.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=59.44;MQ0=0;OQ=1380.81;QD=33.68;SB=-616.59	GT:AD:DP:GL:GQ	1/1:0,40:39:-141.68,-11.75,-0.01:99
+chr1	1227692	rs11586188	G	A	13.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=2.73;MQ=60.00;MQ0=0;OQ=456.88;QD=14.74;SB=-204.92	GT:AD:DP:GL:GQ	0/1:15,16:30:-58.02,-9.04,-49.24:99
+chr1	1228900	.	T	C	25.48	LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=4;HaplotypeScore=1.75;MQ=56.48;MQ0=0;QD=0.75;SB=-20.62	GT:AD:DP:GL:GQ	0/1:26,7:28:-14.27,-8.44,-89.93:58.30
+chr1	1229202	rs11260584	T	G	37.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=976.99;QD=27.91;SB=-499.87	GT:AD:DP:GL:GQ	1/1:0,35:32:-101.31,-9.64,-0.03:96.16
+chr1	1229816	rs10399878	A	G	473.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1102.82;QD=26.90;SB=-522.83	GT:AD:DP:GL:GQ	1/1:0,41:37:-113.91,-11.17,-0.05:99
+chr1	1231392	rs1536168	A	G	97.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.82;MQ0=0;OQ=1395.06;QD=27.90;SB=-606.94	GT:AD:DP:GL:GQ	1/1:0,50:45:-143.13,-13.57,-0.04:99
+chr1	1231663	rs3737720	A	G	139.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.21;MQ=58.81;MQ0=0;OQ=1690.11;QD=30.73;SB=-679.26	GT:AD:DP:GL:GQ	1/1:0,55:50:-172.62,-15.06,-0.03:99
+chr1	1231766	rs3737719	C	G	2.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=1.43;MQ=58.78;MQ0=0;OQ=1400.23;QD=36.85;SB=-370.18	GT:AD:DP:GL:GQ	1/1:0,38:34:-143.63,-10.26,-0.03:99
+chr1	1232078	rs4970431	A	G	216.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1612.70;QD=32.91;SB=-685.61	GT:AD:DP:GL:GQ	1/1:0,49:46:-164.87,-13.86,-0.01:99
+chr1	1232570	rs2274262	A	G	6.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=2.33;MQ=58.39;MQ0=0;OQ=927.22;QD=31.97;SB=-261.82	GT:AD:DP:GL:GQ	1/1:0,28:29:-99.47,-11.27,-3.16:81.12
+chr1	1232846	rs2887285	G	A	7.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=60.00;MQ0=0;OQ=156.17;QD=26.03;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,5:5:-19.18,-1.51,-0.00:15.05
+chr1	1233759	rs61766198	C	T	47.25	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;QD=23.62;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,2:2:-8.13,-0.60,-0.00:6.02
+chr1	1235231	rs11590283	G	A	557.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1461.68;QD=36.54;SB=-745.00	GT:AD:DP:GL:GQ	1/1:1,39:37:-149.76,-11.15,-0.01:99
+chr1	1235867	rs2296474	A	G	712.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.51;MQ0=0;OQ=1812.39;QD=34.20;SB=-908.32	GT:AD:DP:GL:GQ	1/1:0,53:53:-184.85,-15.97,-0.02:99
+chr1	1237357	rs12103	T	C	207.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=647.94;QD=29.45;SB=-286.45	GT:AD:DP:GL:GQ	1/1:0,22:21:-68.40,-6.33,-0.02:63.15
+chr1	1237452	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=10;HaplotypeScore=2.81;MQ=58.76;MQ0=0;OQ=54.80;QD=4.98;SB=-3.98	GT:AD:DP:GL:GQ	0/1:7,4:6:-10.58,-1.82,-11.64:87.64
+chr1	1239050	rs12142199	G	A	66.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=1.62;MQ=58.97;MQ0=0;OQ=2440.21;QD=38.73;SB=-1144.03	GT:AD:DP:GL:GQ	1/1:1,62:62:-247.62,-18.68,-0.02:99
+chr1	1239352	.	C	G	26.31	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=58.82;MQ0=0;OQ=1214.59;QD=20.59;SB=-515.28	GT:AD:DP:GL:GQ	0/1:25,34:56:-141.62,-16.88,-95.25:99
+chr1	1242263	rs55998830	C	T	160.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=57.24;MQ0=0;OQ=503.69;QD=12.29;SB=-134.60	GT:AD:DP:GL:GQ	0/1:23,18:39:-65.41,-11.76,-71.08:99
+chr1	1243999	rs4970432	G	A	36.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=2.94;MQ=58.63;MQ0=0;OQ=2692.59;QD=39.60;SB=-1179.08	GT:AD:DP:GL:GQ	1/1:0,68:67:-272.86,-20.18,-0.01:99
+chr1	1244299	rs1886773	A	G	203.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.11;MQ0=0;OQ=1463.44;QD=28.14;SB=-748.56	GT:AD:DP:GL:GQ	1/1:0,52:48:-149.98,-14.48,-0.05:99
+chr1	1244306	rs1886772	G	A	170.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=58.89;MQ0=0;OQ=2428.21;QD=38.54;SB=-1150.05	GT:AD:DP:GL:GQ	1/1:0,63:62:-246.42,-18.68,-0.02:99
+chr1	1244704	rs10907179	C	G	226.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=2474.22;QD=40.56;SB=-1116.55	GT:AD:DP:GL:GQ	1/1:0,61:58:-251.03,-17.48,-0.03:99
+chr1	1245150	rs10449892	C	T	372.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1031.28;QD=35.56;SB=-512.17	GT:AD:DP:GL:GQ	1/1:0,29:28:-106.73,-8.44,-0.02:84.26
+chr1	1247456	rs1810745	A	G	110.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=54.75;MQ0=0;OQ=1043.28;QD=28.20;SB=-313.49	GT:AD:DP:GL:GQ	1/1:0,37:33:-107.94,-9.95,-0.02:99
+chr1	1256339	rs28704486	A	G	29.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=16.01;MQ0=0;OQ=60.16;QD=4.63;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,13:3:-9.51,-0.90,-0.00:9.02
+chr1	1258710	rs307378	T	G	2.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=76.83;QD=25.61;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:3:-11.17,-0.90,-0.00:9.03
+chr1	1259417	rs307377	T	C	101.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=21.92;MQ0=3;OQ=105.39;QD=15.06;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,7:4:-14.07,-1.20,-0.00:12.04
+chr1	1260192	rs188647	A	G	29.27	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=14.64;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,2:2:-6.34,-0.60,-0.00:6.01
+chr1	1260222	rs307374	T	C	0.04	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=63.98;QD=21.33;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:3:-9.89,-0.91,-0.00:9.02
+chr1	1262360	rs307372	A	G	1.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.52;MQ=35.06;MQ0=0;OQ=290.20;QD=24.18;SB=-151.34	GT:AD:DP:GL:GQ	1/1:0,12:11:-32.62,-3.32,-0.02:33.05
+chr1	1262979	rs307371	A	G	118.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.17;MQ0=0;OQ=96.93;QD=24.23;SB=-72.91	GT:AD:DP:GL:GQ	1/1:0,4:4:-13.23,-1.21,-0.00:12.03
+chr1	1263141	rs307370	A	G	373.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.14;MQ0=0;OQ=479.19;QD=34.23;SB=-188.41	GT:AD:DP:GL:GQ	1/1:0,14:14:-51.51,-4.22,-0.00:42.13
+chr1	1265154	rs11582808	G	A	10.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=44.52;MQ0=0;OQ=273.35;QD=19.53;SB=-116.97	GT:AD:DP:GL:GQ	0/1:5,9:13:-34.54,-3.92,-12.73:88.15
+chr1	1266341	rs307364	T	G	24.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.44;MQ=22.99;MQ0=5;OQ=64.81;QD=5.40;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,10:3:-9.97,-0.90,-0.00:9.02
+chr1	1267396	rs17854636	T	C	111.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=34.81;MQ0=1;OQ=372.39;QD=23.27;SB=-142.72	GT:AD:DP:GL:GQ	1/1:0,16:13:-40.84,-3.92,-0.02:39.08
+chr1	1268100	rs307361	T	C	193.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.78;MQ0=3;OQ=449.98;QD=25.00;SB=-194.71	GT:AD:DP:GL:GQ	1/1:0,18:15:-48.59,-4.52,-0.01:45.11
+chr1	1268888	rs307360	A	G	2.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=29.77;MQ0=0;OQ=268.28;QD=26.83;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,9:9:-30.42,-2.71,-0.01:27.07
+chr1	1270382	rs307358	T	C	22.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=83.45;QD=20.86;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,4:4:-11.88,-1.21,-0.01:12.02
+chr1	1276604	.	G	C	27.05	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.66;MQ=11.97;MQ0=10;QD=1.29;SB=-10.00	GT:AD:DP:GL:GQ	0/1:9,12:4:-7.20,-1.21,-7.49:59.88
+chr1	1276657	rs35104845	C	T	49.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=2.90;MQ=23.40;MQ0=3;OQ=76.78;QD=6.98;SB=-10.00	GT:AD:DP:GL:GQ	1/1:5,5:3:-11.17,-0.90,-0.00:9.03
+chr1	1276684	rs61766214	G	C	3.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=32.46;MQ0=2;OQ=374.70;QD=28.82;SB=-82.81	GT:AD:DP:GL:GQ	1/1:1,12:10:-41.06,-3.02,-0.01:30.10
+chr1	1276760	rs34380086	G	C	256.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.61;MQ0=0;OQ=915.51;QD=35.21;SB=-194.53	GT:AD:DP:GL:GQ	1/1:0,26:24:-95.15,-7.24,-0.02:72.23
+chr1	1276990	rs56165241	G	A	0.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=23.71;MQ0=1;OQ=124.88;QD=20.81;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,6:4:-16.02,-1.20,-0.00:12.04
+chr1	1278208	rs13249	A	G	0.03	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=4;HaplotypeScore=0.79;MQ=29.00;MQ0=0;OQ=519.51;QD=34.63;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,15:15:-55.54,-4.52,-0.01:45.13
+chr1	1278334	rs3766183	C	T	70.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=12.77;MQ0=25;OQ=129.88;QD=4.48;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,29:4:-16.52,-1.20,-0.00:12.04
+chr1	1279774	rs4970365	G	A	205.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=37.02;MQ0=1;OQ=413.00;QD=27.53;SB=-81.33	GT:AD:DP:GL:GQ	1/1:0,15:12:-44.89,-3.62,-0.01:36.11
+chr1	1283627	rs34841888	G	C	242.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=17.25;MQ0=18;OQ=165.64;QD=7.20;SB=-87.83	GT:AD:DP:GL:GQ	1/1:0,23:5:-20.13,-1.51,-0.00:15.05
+chr1	1284791	rs2649608	A	G	15.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=325.53;QD=25.04;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,13:12:-36.15,-3.62,-0.02:36.07
+chr1	1285186	rs34389364	G	A	48.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=44.84;MQ0=0;OQ=775.48;QD=28.72;SB=-269.63	GT:AD:DP:GL:GQ	1/1:0,25:23:-81.16,-6.94,-0.03:69.18
+chr1	1285266	rs34876581	T	C	166.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=42.89;MQ0=0;OQ=1629.47;QD=31.95;SB=-823.96	GT:AD:DP:GL:GQ	1/1:0,51:47:-166.55,-14.16,-0.02:99
+chr1	1285545	rs61766236	A	G	14.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=53.58;MQ0=0;OQ=756.88;QD=26.10;SB=-99.85	GT:AD:DP:GL:GQ	1/1:0,29:25:-79.29,-7.54,-0.02:75.15
+chr1	1285750	.	T	C	31.55	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=14.50;MQ0=6;QD=3.94;SB=-38.95	GT:AD:DP:GL:GQ	1/1:0,8:2:-6.56,-0.60,-0.00:6.01
+chr1	1286016	rs2765027	T	G	82.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=481.12;QD=30.07;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,16:16:-51.71,-4.82,-0.01:48.07
+chr1	1286554	rs2765025	C	G	315.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=27.90;MQ0=0;OQ=1204.51;QD=36.50;SB=-193.69	GT:AD:DP:GL:GQ	1/1:0,33:29:-124.04,-8.74,-0.01:87.29
+chr1	1286681	rs2765024	C	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=715.35;QD=35.77;SB=-192.69	GT:AD:DP:GL:GQ	1/1:0,20:18:-75.13,-5.42,-0.01:54.18
+chr1	1286922	rs35056373	G	A	454.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.41;MQ0=1;OQ=1368.71;QD=34.22;SB=-459.59	GT:AD:DP:GL:GQ	1/1:0,40:36:-140.48,-10.85,-0.02:99
+chr1	1287079	rs2649611	A	G	142	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.17;MQ0=0;OQ=99.93;QD=24.98;SB=-76.36	GT:AD:DP:GL:GQ	1/1:0,4:4:-13.53,-1.21,-0.00:12.03
+chr1	1287285	rs2765021	C	T	19.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=27.13;MQ0=1;OQ=211.29;QD=26.41;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,8:6:-24.70,-1.81,-0.00:18.06
+chr1	1287346	.	G	A	32.26	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.41;MQ=19.54;MQ0=6;QD=3.23;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,5:4:-7.72,-1.21,-5.84:46.31
+chr1	1287498	rs34896744	G	A	28.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=522.90;QD=37.35;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,14:14:-55.88,-4.22,-0.00:42.14
+chr1	1288153	.	C	T	10.16	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=6.84;MQ0=17;QD=0.56;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,3:1:-4.26,-0.30,-0.00:1.76
+chr1	1288274	rs4970439	C	T	158.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.76;MQ0=1;OQ=198.94;QD=24.87;SB=-120.99	GT:AD:DP:GL:GQ	1/1:0,8:6:-23.47,-1.81,-0.00:18.06
+chr1	1288396	rs9700464	T	G	39.49	LowQual	AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.48;MQ0=3;QD=7.90;SB=-46.01	GT:AD:DP:GL:GQ	1/1:0,5:2:-7.36,-0.60,-0.00:6.02
+chr1	1288400	rs2477784	C	T	45.25	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.37;MQ0=1;QD=15.08;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:2:-7.93,-0.60,-0.00:6.02
+chr1	1288965	.	T	C	42.83	LowQual	AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=3;HaplotypeScore=1.16;MQ=15.81;MQ0=3;QD=8.57;SB=-10.00	GT:AD:DP:GL:GQ	1/1:3,2:2:-7.69,-0.60,-0.00:6.02
+chr1	1288989	.	G	A	32	LowQual	AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.68;MQ0=2;QD=8.00;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,2:2:-6.61,-0.60,-0.00:6.01
+chr1	1288993	.	G	A	39.02	LowQual	AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.68;MQ0=2;QD=9.75;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,2:2:-7.31,-0.60,-0.00:6.02
+chr1	1289038	.	G	A	46.02	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=8.33;MQ0=16;QD=2.56;SB=-10.00	GT:AD:DP:GL:GQ	1/1:16,2:2:-8.01,-0.60,-0.00:6.02
+chr1	1289229	rs28368296	C	T	48.25	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=16.08;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,2:2:-8.23,-0.60,-0.00:6.02
+chr1	1292190	.	A	C	28.74	DPFilter;HARD_TO_VALIDATE;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=31.67;MQ=32.93;MQ0=5;QD=1.44;SB=2.03	GT:AD:DP:GL:GQ	0/1:14,6:12:-9.77,-3.62,-33.18:61.57
+chr1	1292271	rs61766242	A	G	18.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=30.84;MQ0=4;OQ=1066.32;QD=26.66;SB=-193.80	GT:AD:DP:GL:GQ	1/1:0,40:32:-110.23,-9.64,-0.01:96.27
+chr1	1292418	rs3104610	C	T	418.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=45.84;MQ0=1;OQ=2220.73;QD=38.96;SB=-760.52	GT:AD:DP:GL:GQ	1/1:0,57:55:-225.67,-16.57,-0.01:99
+chr1	1297501	rs2649597	T	C	2.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.11;MQ0=4;OQ=360.28;QD=22.52;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,16:12:-39.62,-3.62,-0.01:36.08
+chr1	1298491	rs2477775	A	G	32.28	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=16.14;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,2:2:-6.64,-0.60,-0.00:6.02
+chr1	1298734	rs2649595	A	T	1.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.11;MQ0=1;OQ=88.08;QD=22.02;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,4:3:-12.30,-0.90,-0.00:9.03
+chr1	1300531	rs2242398	A	C	250.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.82;MQ0=0;OQ=470.94;QD=31.40;SB=-111.01	GT:AD:DP:GL:GQ	1/1:0,15:15:-50.69,-4.52,-0.01:45.12
+chr1	1300838	rs2649594	C	T	51.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.25;MQ0=5;OQ=315.14;QD=22.51;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,14:9:-35.10,-2.71,-0.01:27.08
+chr1	1300941	rs2649592	G	T	12.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.29;MQ0=5;OQ=256.28;QD=18.31;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,14:8:-29.21,-2.41,-0.00:24.07
+chr1	1302674	rs34582295	C	T	6.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=2;HaplotypeScore=3.06;MQ=25.59;MQ0=11;OQ=374.66;QD=16.29;SB=-144.64	GT:AD:DP:GL:GQ	1/1:0,23:11:-41.06,-3.32,-0.01:33.10
+chr1	1303447	rs11489820	G	C	2.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=7.53;MQ0=41;OQ=125.53;QD=2.73;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,46:4:-16.09,-1.21,-0.00:12.04
+chr1	1304035	rs2477777	C	T	175.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=34.74;MQ0=4;OQ=578.49;QD=28.92;SB=-248.33	GT:AD:DP:GL:GQ	1/1:0,20:15:-61.44,-4.52,-0.00:45.15
+chr1	1304333	rs2313135	T	G	34.29	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.98;MQ0=4;QD=4.90;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,2:3:-7.61,-0.90,-3.34:24.36
+chr1	1304907	rs2368566	G	A	186.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.16;MQ0=0;OQ=83.01;QD=27.67;SB=-45.55	GT:AD:DP:GL:GQ	1/1:0,3:3:-11.79,-0.90,-0.00:9.03
+chr1	1305206	rs2368565	G	A	178.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=123.88;QD=30.97;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,4:4:-15.92,-1.20,-0.00:12.04
+chr1	1305756	rs2454652	C	T	47.02	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=23.51;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,2:2:-8.11,-0.60,-0.00:6.02
+chr1	1306033	rs2649587	G	A	6.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=34.70;MQ0=1;OQ=503.12;QD=31.45;SB=-129.67	GT:AD:DP:GL:GQ	1/1:0,16:14:-53.90,-4.22,-0.01:42.13
+chr1	1306331	rs2649586	A	G	0.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=29.00;MQ0=0;OQ=293.94;QD=24.50;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,11:10:-32.98,-3.01,-0.01:30.07
+chr1	1307502	.	C	G	13.29	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=4.50;MQ0=24;QD=0.49;SB=-10.00	GT:AD:DP:GL:GQ	0/1:26,1:1:-4.59,-0.30,-0.00:1.76
+chr1	1307925	.	G	C	0.13	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=13.45;MQ0=29;OQ=83.85;QD=1.78;SB=-0.97	GT:AD:DP:GL:GQ	0/1:38,9:8:-14.08,-2.41,-22.17:99
+chr1	1307979	.	T	C	42.83	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=1;HaplotypeScore=2.20;MQ=7.67;MQ0=16;QD=2.38;SB=-10.00	GT:AD:DP:GL:GQ	1/1:13,5:2:-7.69,-0.60,-0.00:6.02
+chr1	1308095	.	C	G	10.99	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=29;Dels=0.17;HRun=1;HaplotypeScore=14.74;MQ=6.41;MQ0=25;QD=0.38;SB=-10.00	GT:AD:DP:GL:GQ	0/1:20,4:1:-4.35,-0.30,-0.00:1.76
+chr1	1321841	.	G	T	47.94	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=20;HaplotypeScore=6.03;MQ=23.98;MQ0=9;QD=1.65;SB=-0.97	GT:AD:DP:GL:GQ	0/1:18,11:6:-9.89,-1.81,-11.27:80.77
+chr1	1323299	rs1240743	C	A	6.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.08;MQ=38.33;MQ0=6;OQ=144.07;QD=3.27;SB=50.03	GT:AD:DP:GL:GQ	0/1:30,14:36:-28.54,-10.85,-84.17:99
+chr1	1332475	rs2275915	G	C	24.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=31.54;MQ0=6;OQ=92.26;QD=5.77;SB=-43.44	GT:AD:DP:GL:GQ	0/1:8,8:10:-15.53,-3.02,-24.58:99
+chr1	1346911	.	G	A	0.08	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=8.57;MQ=40.33;MQ0=2;OQ=331.50;QD=8.72;SB=-7.00	GT:AD:DP:GL:GQ	0/1:22,16:33:-46.38,-9.94,-72.87:99
+chr1	1349702	.	C	A	0.66	PASS	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=5.78;MQ=19.45;MQ0=7;OQ=297.18;QD=9.29;SB=-141.76	GT:AD:DP:GL:GQ	0/1:14,17:13:-36.92,-3.92,-7.86:39.43
+chr1	1352746	rs58304223	G	C	14.25	LowQual	AC=1;AF=0.50;AN=2;DB;DP=1;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=14.25;SB=-10.00	GT:AD:DP:GL:GQ	0/1:0,1:1:-4.69,-0.30,-0.00:1.76
+chr1	1353363	.	G	T	42.81	LowQual	AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=37.00;MQ0=0;QD=21.40;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,2:2:-7.69,-0.60,-0.00:6.02
+chr1	1355197	rs1781138	A	G	15.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=39.89;MQ0=3;OQ=305.23;QD=16.96;SB=-38.95	GT:AD:DP:GL:GQ	1/1:0,18:10:-34.11,-3.01,-0.00:30.08
+chr1	1358462	rs1240703	A	C	0.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=3;HaplotypeScore=0.32;MQ=21.92;MQ0=3;OQ=100.91;QD=14.42;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,7:4:-13.63,-1.21,-0.00:12.03
+chr1	1358648	.	C	G	24.94	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=3;HaplotypeScore=2.70;MQ=19.30;MQ0=6;QD=1.19;SB=5.05	GT:AD:DP:GL:GQ	0/1:13,8:7:-7.89,-2.11,-21.96:57.76
+chr1	1377530	rs1781144	C	G	16.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=20.51;MQ0=10;OQ=394.74;QD=19.74;SB=-103.85	GT:AD:DP:GL:GQ	1/1:0,20:10:-43.06,-3.01,-0.00:30.10
+chr1	1380491	.	G	A	10.40	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=6;HaplotypeScore=29.42;MQ=36.22;MQ0=8;QD=0.18;SB=26.07	GT:AD:DP:GL:GQ	0/1:33,26:17:-9.41,-5.13,-45.72:42.82
+chr1	1390605	rs1240723	T	C	30.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.36;MQ=30.70;MQ0=2;OQ=239.92;QD=7.06;SB=-41.82	GT:AD:DP:GL:GQ	0/1:20,14:26:-35.12,-7.84,-56.30:99
+chr1	1390829	.	C	T	33.01	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=3;HaplotypeScore=8.88;MQ=28.73;MQ0=9;QD=1.00;SB=26.10	GT:AD:DP:GL:GQ	0/1:27,6:18:-12.01,-5.42,-52.81:65.84
+chr1	1394381	.	T	G	40.77	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=20.66;MQ0=17;QD=0.91;SB=-10.00	GT:AD:DP:GL:GQ	0/1:31,13:12:-10.98,-3.61,-30.75:73.61
+chr1	1398226	.	C	T	36.49	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=10.21;MQ0=21;QD=1.46;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,13:3:-7.84,-0.90,-3.10:21.92
+chr1	1410500	rs35871802	C	T	116.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.49;MQ0=17;OQ=181.39;QD=6.05;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,18:11:-24.74,-3.31,-17.34:99
+chr1	1413144	.	G	A	12.73	PASS	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=22.29;MQ0=2;OQ=489.12;QD=14.82;SB=-131.14	GT:AD:DP:GL:GQ	0/1:17,16:30:-61.25,-9.05,-41.87:99
+chr1	1414249	.	G	C	31.95	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=2;HaplotypeScore=6.60;MQ=15.28;MQ0=13;QD=1.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:18,6:4:-7.69,-1.21,-7.60:63.89
+chr1	1423959	rs1781141	T	G	30.05	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=21.23;MQ0=4;QD=1.58;SB=5.04	GT:AD:DP:GL:GQ	0/1:13,6:14:-10.50,-4.22,-40.36:62.88
+chr1	1424829	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=20;HaplotypeScore=5.78;MQ=28.83;MQ0=9;OQ=77.31;QD=1.98;SB=59.13	GT:AD:DP:GL:GQ	0/1:32,7:28:-19.45,-8.44,-75.28:99
+chr1	1424855	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=20;HaplotypeScore=4.13;MQ=29.08;MQ0=4;OQ=54.78;QD=1.96;SB=29.12	GT:AD:DP:GL:GQ	0/1:21,7:17:-13.88,-5.12,-48.25:87.62
+chr1	1425922	rs28755011	C	T	122.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=53.56;MQ0=1;OQ=756.68;QD=16.45;SB=-222.92	GT:AD:DP:GL:GQ	0/1:21,25:43:-91.92,-12.96,-62.88:99
+chr1	1430132	rs3104609	A	G	485.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=42.69;MQ0=1;OQ=1088.71;QD=31.11;SB=-534.36	GT:AD:DP:GL:GQ	1/1:0,35:33:-112.47,-9.94,-0.02:99
+chr1	1447936	rs3118507	A	G	40.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=47.98;MQ0=0;OQ=209.16;QD=6.97;SB=-124.72	GT:AD:DP:GL:GQ	0/1:20,10:26:-32.03,-7.83,-67.04:99
+chr1	1450120	rs6603789	G	C	0.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=28.41;MQ0=9;OQ=784.91;QD=23.09;SB=-55.93	GT:AD:DP:GL:GQ	1/1:6,28:20:-82.08,-6.03,-0.01:60.20
+chr1	1450953	rs3128345	A	G	6.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=8.00;MQ=58.21;MQ0=0;OQ=533.48;QD=10.67;SB=-234.27	GT:AD:DP:GL:GQ	0/1:28,22:48:-71.10,-14.47,-106.23:99
+chr1	1457784	.	T	A	85.12	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.74;MQ0=0;OQ=950.58;QD=15.09;SB=-335.63	GT:AD:DP:GL:GQ	0/1:32,31:63:-117.32,-18.98,-122.45:99
+chr1	1458041	rs6694994	T	C	138.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=49.26;MQ0=0;OQ=499.68;QD=12.19;SB=-117.64	GT:AD:DP:GL:GQ	0/1:20,21:38:-64.71,-11.46,-68.00:99
+chr1	1459409	rs3128344	G	A	558.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.45;MQ0=0;OQ=1638.56;QD=37.24;SB=-778.68	GT:AD:DP:GL:GQ	1/1:0,43:42:-167.45,-12.65,-0.01:99
+chr1	1461502	.	A	C	42.07	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=2;HaplotypeScore=1.74;MQ=57.05;MQ0=0;QD=2.63;SB=14.06	GT:AD:DP:GL:GQ	0/1:8,8:12:-11.11,-3.62,-27.42:74.90
+chr1	1461910	rs3118505	C	T	45.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.75;MQ=58.35;MQ0=0;OQ=649.92;QD=17.57;SB=-339.91	GT:AD:DP:GL:GQ	0/1:17,20:34:-78.52,-10.25,-48.35:99
+chr1	1462403	rs1571148	T	G	289.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=414.06;QD=9.41;SB=-126.87	GT:AD:DP:GL:GQ	0/1:27,17:41:-57.04,-12.35,-89.89:99
+chr1	1462736	rs4259576	T	A	334.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.42;MQ=60.00;MQ0=0;OQ=380.45;QD=11.19;SB=-195.57	GT:AD:DP:GL:GQ	0/1:20,14:33:-51.27,-9.94,-69.97:99
+chr1	1464030	rs1571149	A	G	400.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=649.88;QD=11.01;SB=-311.08	GT:AD:DP:GL:GQ	0/1:30,29:55:-84.85,-16.58,-112.84:99
+chr1	1464167	rs1571150	C	A	91.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.52;MQ0=0;OQ=665.06;QD=17.05;SB=-221.93	GT:AD:DP:GL:GQ	0/1:16,23:39:-81.54,-11.75,-55.47:99
+chr1	1464327	rs56239289	T	C	341.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=731.44;QD=11.99;SB=-372.97	GT:AD:DP:GL:GQ	0/1:31,30:58:-93.91,-17.48,-117.75:99
+chr1	1464734	rs9439465	G	C	86.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=410.54;QD=15.21;SB=-187.22	GT:AD:DP:GL:GQ	0/1:13,14:25:-51.89,-7.55,-46.69:99
+chr1	1468557	rs55694463	C	G	72.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.11;MQ0=0;OQ=367.44;QD=14.13;SB=-116.67	GT:AD:DP:GL:GQ	0/1:13,13:22:-46.66,-6.63,-46.00:99
+chr1	1468920	rs61777888	A	T	11.23	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=40.58;MQ0=0;QD=1.12;SB=2.00	GT:AD:DP:GL:GQ	0/1:8,2:6:-6.19,-1.81,-11.86:43.73
+chr1	1471211	rs3766177	T	C	144.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.26;MQ=59.42;MQ0=0;OQ=424.79;QD=8.50;SB=-61.74	GT:AD:DP:GL:GQ	0/1:28,22:46:-59.63,-13.86,-111.57:99
+chr1	1472873	rs7517401	G	A	289.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.75;MQ=59.55;MQ0=0;OQ=742.89;QD=14.57;SB=-367.87	GT:AD:DP:GL:GQ	0/1:27,24:48:-92.05,-14.47,-78.97:99
+chr1	1474833	rs7515814	C	G	227.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.23;MQ0=0;OQ=1418.95;QD=20.87;SB=-692.35	GT:AD:DP:GL:GQ	0/1:30,38:67:-165.38,-20.20,-121.41:99
+chr1	1476697	rs3128342	C	A	175.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=1.77;MQ=59.37;MQ0=0;OQ=1038.77;QD=15.74;SB=-518.96	GT:AD:DP:GL:GQ	0/1:32,34:66:-127.04,-19.88,-111.54:99
+chr1	1478935	rs3930748	A	G	131.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=57.35;MQ0=0;OQ=678.62;QD=14.44;SB=-210.49	GT:AD:DP:GL:GQ	0/1:18,29:41:-83.51,-12.36,-58.93:99
+chr1	1479484	rs11590038	T	C	187.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.28;MQ=60.00;MQ0=0;OQ=498.05;QD=12.45;SB=-267.61	GT:AD:DP:GL:GQ	0/1:17,23:38:-64.56,-11.47,-62.93:99
+chr1	1479489	rs11588893	C	T	162.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=60.00;MQ0=0;OQ=580.48;QD=15.69;SB=-263.76	GT:AD:DP:GL:GQ	0/1:17,20:34:-71.58,-10.25,-50.12:99
+chr1	1479533	rs7531530	C	T	220.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.91;MQ=59.18;MQ0=1;OQ=444.32;QD=12.01;SB=-149.64	GT:AD:DP:GL:GQ	0/1:19,18:31:-57.07,-9.35,-49.87:99
+chr1	1479791	rs7366884	T	C	122.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=816.32;QD=13.61;SB=-418.23	GT:AD:DP:GL:GQ	0/1:30,30:57:-102.08,-17.17,-116.37:99
+chr1	1479937	rs7366635	A	G	20.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.12;MQ=59.07;MQ0=0;OQ=292.89;QD=6.51;SB=-136.53	GT:AD:DP:GL:GQ	0/1:30,15:42:-45.23,-12.66,-112.08:99
+chr1	1480024	rs3753332	A	G	36.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=1.31;MQ=59.44;MQ0=0;OQ=490.38;QD=11.96;SB=-170.97	GT:AD:DP:GL:GQ	0/1:21,20:37:-63.47,-11.15,-78.00:99
+chr1	1480095	rs3753331	T	C	462.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=783.79;QD=15.07;SB=-339.35	GT:AD:DP:GL:GQ	0/1:24,28:51:-97.03,-15.37,-89.70:99
+chr1	1480422	rs3820075	A	G	268.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.65;MQ0=0;OQ=768.88;QD=14.24;SB=-360.10	GT:AD:DP:GL:GQ	0/1:23,31:53:-96.15,-15.98,-92.13:99
+chr1	1480490	rs3753330	T	A	237.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.22;MQ0=0;OQ=615.93;QD=11.41;SB=-300.65	GT:AD:DP:GL:GQ	0/1:28,26:50:-79.94,-15.07,-101.11:99
+chr1	1480556	.	C	T	26.64	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=59.59;MQ0=0;OQ=854.85;QD=18.58;SB=-376.92	GT:AD:DP:GL:GQ	0/1:20,26:44:-102.04,-13.27,-56.58:99
+chr1	1481114	rs12048706	T	C	201.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=57.91;MQ0=0;OQ=878.58;QD=11.87;SB=-292.17	GT:AD:DP:GL:GQ	0/1:36,38:70:-112.24,-21.10,-138.24:99
+chr1	1484218	rs3118509	T	C	19.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1926.74;QD=28.76;SB=-881.49	GT:AD:DP:GL:GQ	1/1:0,67:60:-196.31,-18.09,-0.05:99
+chr1	1484946	rs6667347	G	C	188.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.64;MQ0=0;OQ=1104.15;QD=17.25;SB=-384.86	GT:AD:DP:GL:GQ	0/1:33,31:63:-132.69,-18.99,-142.09:99
+chr1	1485056	rs3118508	A	G	123.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.54;MQ0=0;OQ=1673.18;QD=28.36;SB=-768.59	GT:AD:DP:GL:GQ	1/1:0,59:54:-170.96,-16.29,-0.05:99
+chr1	1486871	rs3766170	T	C	6.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=4;HaplotypeScore=1.66;MQ=57.15;MQ0=0;OQ=440.82;QD=8.82;SB=-192.43	GT:AD:DP:GL:GQ	0/1:28,22:46:-61.23,-13.87,-105.72:99
+chr1	1488802	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=20;HaplotypeScore=27.79;MQ=52.29;MQ0=1;OQ=57.57;QD=0.82;SB=89.30	GT:AD:DP:GL:GQ	0/1:49,20:48:-23.51,-14.47,-151.88:90.40
+chr1	1489161	rs9439468	A	G	111.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=2.15;MQ=56.25;MQ0=0;OQ=911.03;QD=16.56;SB=-250.50	GT:AD:DP:GL:GQ	0/1:21,34:50:-109.45,-15.06,-75.57:99
+chr1	1490804	rs6603791	A	G	440.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=55.41;MQ0=0;OQ=778.85;QD=12.98;SB=-348.06	GT:AD:DP:GL:GQ	0/1:28,32:58:-98.65,-17.48,-110.76:99
+chr1	1490867	.	C	G	0.31	PASS	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=53.32;MQ0=0;OQ=206.00;QD=2.71;SB=-32.07	GT:AD:DP:GL:GQ	0/1:64,12:75:-46.49,-22.61,-271.24:99
+chr1	1490871	.	A	G	0.08	PASS	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=1.61;MQ=53.82;MQ0=0;OQ=220.05;QD=2.75;SB=-14.75	GT:AD:DP:GL:GQ	0/1:66,14:78:-48.79,-23.50,-263.73:99
+chr1	1490927	rs6656541	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=3;HaplotypeScore=23.59;MQ=53.32;MQ0=0;OQ=1558.39;QD=20.51;SB=-788.78	GT:AD:DP:GL:GQ	0/1:23,53:74:-181.42,-22.29,-76.04:99
+chr1	1490930	rs12730242	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=22.45;MQ=53.65;MQ0=0;OQ=417.53;QD=5.49;SB=-224.35	GT:AD:DP:GL:GQ	0/1:55,21:70:-66.13,-21.09,-238.86:99
+chr1	1490948	rs12742689	T	C	0.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=53.98;MQ0=0;OQ=96.30;QD=1.23;SB=-34.35	GT:AD:DP:GL:GQ	0/1:66,12:72:-34.61,-21.70,-240.60:99
+chr1	1490950	rs12730248	C	T	0.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=54.06;MQ0=0;OQ=172.01;QD=2.18;SB=-98.81	GT:AD:DP:GL:GQ	0/1:67,11:73:-45.59,-25.10,-225.19:99
+chr1	1491329	rs7543799	G	A	29	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=5.33;MQ=58.37;MQ0=0;OQ=592.32;QD=13.16;SB=-320.34	GT:AD:DP:GL:GQ	0/1:24,21:38:-73.97,-11.45,-67.99:99
+chr1	1492958	rs7367692	G	A	226.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=59.16;MQ0=0;OQ=759.07;QD=13.80;SB=-311.80	GT:AD:DP:GL:GQ	0/1:31,24:51:-94.56,-15.37,-89.99:99
+chr1	1492962	rs7364711	A	C	163.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=59.20;MQ0=0;OQ=581.10;QD=10.02;SB=-270.86	GT:AD:DP:GL:GQ	0/1:35,23:56:-78.26,-16.87,-122.50:99
+chr1	1493671	rs11578409	C	G	251.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=59.04;MQ0=0;OQ=1371.84;QD=13.45;SB=-443.87	GT:AD:DP:GL:GQ	0/1:57,45:96:-169.40,-28.93,-244.12:99
+chr1	1493791	rs7550471	G	A	6.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=5.83;MQ=58.91;MQ0=0;OQ=1272.31;QD=21.21;SB=-593.09	GT:AD:DP:GL:GQ	0/1:20,38:56:-150.16,-19.64,-65.04:99
+chr1	1494423	rs7552586	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=6;HaplotypeScore=3.99;MQ=59.04;MQ0=0;OQ=1025.73;QD=12.36;SB=-469.22	GT:AD:DP:GL:GQ	0/1:45,38:80:-129.96,-24.11,-158.72:99
+chr1	1494904	rs6603792	T	C	342.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=427.21;QD=9.94;SB=-158.94	GT:AD:DP:GL:GQ	0/1:24,19:43:-58.97,-12.96,-97.93:99
+chr1	1495118	rs6603793	C	T	185.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.74;MQ0=0;OQ=1162.21;QD=15.92;SB=-407.71	GT:AD:DP:GL:GQ	0/1:38,35:73:-141.49,-21.99,-140.54:99
+chr1	1495830	rs7548959	C	T	131.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=3.07;MQ=58.74;MQ0=0;OQ=1025.47;QD=14.65;SB=-444.99	GT:AD:DP:GL:GQ	0/1:38,32:69:-126.64,-20.81,-114.78:99
+chr1	1495898	rs7540231	G	A	67.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=2;HaplotypeScore=1.75;MQ=58.44;MQ0=0;OQ=3508.72;QD=37.73;SB=-1621.33	GT:AD:DP:GL:GQ	1/1:0,92:90:-349.87,-27.12,-0.03:99
+chr1	1497229	rs9439469	G	A	187.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.17;MQ0=0;OQ=210.39;QD=8.42;SB=-10.00	GT:AD:DP:GL:GQ	0/1:17,8:25:-31.85,-7.53,-57.26:99
+chr1	1497775	rs61774865	A	C	52.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=53.97;MQ0=0;OQ=260.15;QD=7.88;SB=-10.00	GT:AD:DP:GL:GQ	0/1:20,13:31:-38.64,-9.34,-70.58:99
+chr1	1498322	rs9439473	A	G	18.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=3.82;MQ=56.11;MQ0=0;OQ=610.76;QD=13.57;SB=-249.32	GT:AD:DP:GL:GQ	0/1:21,24:44:-77.63,-13.27,-79.03:99
+chr1	1498506	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=5;HaplotypeScore=2.45;MQ=50.85;MQ0=0;OQ=161.89;QD=3.37;SB=24.24	GT:AD:DP:GL:GQ	0/1:38,10:40:-31.52,-12.05,-112.23:99
+chr1	1498508	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=15;HaplotypeScore=1.82;MQ=51.05;MQ0=0;OQ=196.72;QD=4.01;SB=27.81	GT:AD:DP:GL:GQ	0/1:38,11:41:-35.31,-12.36,-104.62:99
+chr1	1498897	rs7520996	T	C	291.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=56.74;MQ0=0;OQ=1344.56;QD=17.46;SB=-662.63	GT:AD:DP:GL:GQ	0/1:31,46:75:-160.33,-22.59,-123.58:99
+chr1	1499019	rs7518083	A	G	453.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.97;MQ0=0;OQ=1144.84;QD=14.49;SB=-308.25	GT:AD:DP:GL:GQ	0/1:39,40:76:-140.66,-22.89,-155.49:99
+chr1	1499688	rs6666293	A	G	47.16	LowQual	AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=1.90;MQ=53.03;MQ0=0;QD=6.74;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,3:5:-9.51,-1.51,-8.01:65.07
+chr1	1500664	rs7519837	C	T	335.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=543.75;QD=13.59;SB=-294.78	GT:AD:DP:GL:GQ	0/1:21,19:39:-69.41,-11.75,-74.55:99
+chr1	1500967	rs7556282	G	C	209.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=56.81;MQ0=0;OQ=874.72;QD=17.85;SB=-362.79	GT:AD:DP:GL:GQ	0/1:21,27:44:-104.04,-13.28,-69.73:99
+chr1	1501107	rs4590622	G	A	74.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.06;MQ=35.43;MQ0=2;OQ=406.87;QD=8.30;SB=-78.55	GT:AD:DP:GL:GQ	0/1:30,19:38:-55.43,-11.46,-75.84:99
+chr1	1501178	rs4618908	T	C	437.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.31;MQ0=1;OQ=645.96;QD=14.68;SB=-291.48	GT:AD:DP:GL:GQ	0/1:19,25:40:-79.93,-12.05,-65.32:99
+chr1	1504046	.	C	T	7.57	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=3.52;MQ=59.17;MQ0=0;OQ=1022.24;QD=18.25;SB=-279.21	GT:AD:DP:GL:GQ	0/1:26,30:52:-121.18,-15.67,-71.09:99
+chr1	1504960	rs9331751	T	A	36.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=4.88;MQ=56.51;MQ0=1;OQ=1100.76;QD=14.11;SB=-360.40	GT:AD:DP:GL:GQ	0/1:39,39:73:-135.35,-21.99,-132.17:99
+chr1	1506133	rs9442407	C	T	139.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=35.12;MQ0=12;OQ=825.82;QD=11.16;SB=-394.16	GT:AD:DP:GL:GQ	0/1:42,32:54:-102.14,-16.28,-92.88:99
+chr1	1509564	rs9442406	T	C	136.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=56.80;MQ0=0;OQ=711.41;QD=13.42;SB=-198.20	GT:AD:DP:GL:GQ	0/1:27,26:51:-89.79,-15.37,-103.56:99
+chr1	1510588	rs28788874	C	T	634.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.10;MQ0=1;OQ=2154.00;QD=35.90;SB=-1071.35	GT:AD:DP:GL:GQ	1/1:0,60:56:-219.01,-16.88,-0.03:99
+chr1	1510832	rs6666084	A	G	27.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=29.16;MQ0=1;OQ=863.94;QD=22.15;SB=-357.32	GT:AD:DP:GL:GQ	1/1:0,34:29:-93.05,-11.63,-3.07:85.61
+chr1	1511143	rs6679999	C	T	270.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=46.32;MQ0=0;OQ=967.03;QD=37.19;SB=-287.88	GT:AD:DP:GL:GQ	1/1:0,26:25:-100.30,-7.53,-0.01:75.24
+chr1	1511216	.	T	A	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=2;HaplotypeScore=0.79;MQ=40.83;MQ0=0;OQ=921.95;QD=25.61;SB=-124.48	GT:AD:DP:GL:GQ	0/1:7,29:35:-106.02,-10.55,-27.02:99
+chr1	1511668	rs4648786	A	G	87.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=58.14;MQ0=0;OQ=1843.13;QD=31.78;SB=-498.18	GT:AD:DP:GL:GQ	1/1:0,58:57:-187.94,-17.18,-0.05:99
+chr1	1511869	rs4648787	C	T	29.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.56;MQ=56.20;MQ0=1;OQ=2155.57;QD=37.82;SB=-1079.94	GT:AD:DP:GL:GQ	1/1:1,56:55:-219.17,-16.58,-0.02:99
+chr1	1511922	rs4648612	C	T	25.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=42.53;MQ0=1;OQ=1102.46;QD=35.56;SB=-299.68	GT:AD:DP:GL:GQ	1/1:1,30:28:-113.84,-8.43,-0.01:84.28
+chr1	1512199	rs4648613	T	C	554.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.33;MQ0=0;OQ=1584.81;QD=33.02;SB=-688.28	GT:AD:DP:GL:GQ	1/1:0,48:45:-162.08,-13.55,-0.01:99
+chr1	1512230	rs28809773	G	A	465.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=52.87;MQ0=0;OQ=1755.99;QD=36.58;SB=-748.51	GT:AD:DP:GL:GQ	1/1:0,48:45:-179.20,-13.56,-0.01:99
+chr1	1512325	.	G	A	85.65	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.80;MQ=55.47;MQ0=0;OQ=776.49;QD=14.65;SB=-378.86	GT:AD:DP:GL:GQ	0/1:28,24:51:-96.30,-15.37,-89.39:99
+chr1	1512595	rs4366263	A	G	19.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=3.13;MQ=56.40;MQ0=0;OQ=1310.46;QD=34.49;SB=-610.36	GT:AD:DP:GL:GQ	1/1:0,38:38:-134.64,-11.45,-0.01:99
+chr1	1512656	rs28778974	C	T	131.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=49.50;MQ0=1;OQ=1426.66;QD=34.80;SB=-730.49	GT:AD:DP:GL:GQ	1/1:1,40:37:-146.26,-11.15,-0.01:99
+chr1	1512790	rs61774869	C	T	40.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=48.67;MQ0=1;OQ=1682.46;QD=36.58;SB=-840.63	GT:AD:DP:GL:GQ	1/1:2,44:43:-171.84,-12.95,-0.01:99
+chr1	1513302	rs9725077	G	A	148.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=48.17;MQ0=1;OQ=1464.10;QD=34.05;SB=-687.33	GT:AD:DP:GL:GQ	1/1:1,42:38:-150.01,-11.45,-0.01:99
+chr1	1514300	rs9442423	T	C	34.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.59;MQ0=0;OQ=266.23;QD=6.83;SB=-0.97	GT:AD:DP:GL:GQ	0/1:24,15:34:-40.16,-10.25,-85.89:99
+chr1	1514394	.	C	T	901.86	Indel	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.65;MQ0=0;QD=14.78;SB=-128.11	GT:AD:DP:GL:GQ	0/1:33,28:59:-111.26,-17.79,-98.57:99
+chr1	1514734	rs9442403	A	G	0.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=12.23;MQ=53.49;MQ0=0;OQ=367.70;QD=7.99;SB=-54.31	GT:AD:DP:GL:GQ	0/1:25,19:37:-51.21,-11.16,-85.57:99
+chr1	1514861	.	A	T	164.64	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.34;MQ0=0;OQ=646.82;QD=13.76;SB=-331.07	GT:AD:DP:GL:GQ	0/1:25,22:46:-81.82,-13.86,-91.60:99
+chr1	1515925	rs6681422	T	C	152.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=56.53;MQ0=0;OQ=534.97;QD=11.15;SB=-174.52	GT:AD:DP:GL:GQ	0/1:23,25:43:-69.74,-12.96,-84.05:99
+chr1	1516662	rs12735276	A	G	21.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.05;MQ=57.32;MQ0=1;OQ=2133.75;QD=30.05;SB=-1092.47	GT:AD:DP:GL:GQ	1/1:2,69:66:-217.02,-19.91,-0.06:99
+chr1	1516946	rs10157140	T	C	503.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.65;MQ0=0;OQ=1116.09;QD=14.69;SB=-475.23	GT:AD:DP:GL:GQ	0/1:37,39:76:-137.79,-22.90,-145.96:99
+chr1	1517815	.	T	C	151.98	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.19;MQ0=0;OQ=718.93;QD=11.41;SB=-330.87	GT:AD:DP:GL:GQ	0/1:32,31:61:-93.57,-18.39,-126.83:99
+chr1	1518089	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=19;HaplotypeScore=19.37;MQ=53.15;MQ0=1;OQ=397.54;QD=5.76;SB=50.30	GT:AD:DP:GL:GQ	0/1:45,23:60:-60.81,-17.78,-147.22:99
+chr1	1518109	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=82;Dels=0.01;HRun=19;HaplotypeScore=9.39;MQ=51.76;MQ0=1;OQ=216.06;QD=2.63;SB=62.19	GT:AD:DP:GL:GQ	0/1:54,27:58:-42.07,-17.18,-142.92:99
+chr1	1518112	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=77;Dels=0.01;HRun=4;HaplotypeScore=9.55;MQ=51.62;MQ0=1;OQ=92.02;QD=1.20;SB=65.18	GT:AD:DP:GL:GQ	0/1:56,20:51:-27.56,-15.07,-144.06:99
+chr1	1518863	rs12725297	G	C	139.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=58.84;MQ0=0;OQ=1568.02;QD=18.67;SB=-365.83	GT:AD:DP:GL:GQ	0/1:39,45:81:-184.49,-24.41,-167.76:99
+chr1	1518975	rs12725449	G	C	178.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.97;MQ0=0;OQ=2276.77;QD=38.59;SB=-1002.01	GT:AD:DP:GL:GQ	1/1:0,59:56:-231.29,-16.89,-0.03:99
+chr1	1519320	rs28566709	T	C	64.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=4.25;MQ=59.59;MQ0=0;OQ=477.78;QD=8.53;SB=-190.61	GT:AD:DP:GL:GQ	0/1:33,23:51:-66.44,-15.38,-114.90:99
+chr1	1519374	rs28662991	T	C	77.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=59.56;MQ0=0;OQ=635.95;QD=12.23;SB=-285.60	GT:AD:DP:GL:GQ	0/1:29,23:51:-82.25,-15.37,-108.55:99
+chr1	1519813	rs28503881	A	G	211.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.02;MQ0=0;OQ=531.98;QD=8.58;SB=-234.91	GT:AD:DP:GL:GQ	0/1:35,27:58:-73.97,-17.49,-134.84:99
+chr1	1519842	rs4648788	T	C	59.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=56.83;MQ0=0;OQ=1829.71;QD=27.72;SB=-554.05	GT:AD:DP:GL:GQ	1/1:0,66:57:-186.60,-17.18,-0.04:99
+chr1	1519857	.	G	C	3.15	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=1;HaplotypeScore=5.53;MQ=56.98;MQ0=0;OQ=985.46;QD=15.64;SB=-338.06	GT:AD:DP:GL:GQ	0/1:28,35:57:-119.03,-17.20,-116.72:99
+chr1	1519861	rs28689700	C	G	213.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=56.88;MQ0=0;OQ=841.97;QD=13.80;SB=-287.94	GT:AD:DP:GL:GQ	0/1:30,31:57:-104.69,-17.21,-125.41:99
+chr1	1520060	rs4648789	A	C	15.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=4;HaplotypeScore=1.27;MQ=50.71;MQ0=0;OQ=838.47;QD=14.46;SB=-329.82	GT:AD:DP:GL:GQ	0/1:26,32:54:-103.41,-16.28,-79.25:99
+chr1	1520063	rs4648790	C	T	336.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=51.65;MQ0=0;OQ=926.60;QD=15.19;SB=-418.36	GT:AD:DP:GL:GQ	0/1:30,31:60:-114.03,-18.08,-107.59:99
+chr1	1520195	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=113;Dels=0.02;HRun=0;HaplotypeScore=46.04;MQ=50.13;MQ0=3;OQ=55.61;QD=0.49;SB=110.40	GT:AD:DP:GL:GQ	0/1:96,14:92:-36.27,-27.42,-356.52:88.45
+chr1	1520222	.	G	A	94.09	SnpCluster	AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=77.51;MQ=46.35;MQ0=0;QD=0.80;SB=-48.89	GT:AD:DP:GL:GQ	0/1:102,15:106:-44.62,-31.93,-348.40:99
+chr1	1520225	.	G	C	344.68	SnpCluster	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=69.75;MQ=44.94;MQ0=0;QD=2.92;SB=-153.13	GT:AD:DP:GL:GQ	0/1:100,18:110:-70.90,-33.15,-412.65:99
+chr1	1520229	.	C	G	412.05	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=121;Dels=0.00;HRun=0;HaplotypeScore=94.26;MQ=43.35;MQ0=0;QD=3.41;SB=-151.44	GT:AD:DP:GL:GQ	0/1:103,18:106:-76.44,-31.95,-372.75:99
+chr1	1520237	.	G	C	91.10	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=128;Dels=0.05;HRun=0;HaplotypeScore=131.86;MQ=42.98;MQ0=0;QD=0.71;SB=13.51	GT:AD:DP:GL:GQ	0/1:106,16:113:-45.55,-33.15,-430.26:99
+chr1	1520238	rs61774873	T	A	718.56	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.05;HRun=0;HaplotypeScore=125.70;MQ=43.01;MQ0=0;QD=5.75;SB=-75.62	GT:AD:DP:GL:GQ	0/1:71,41:100:-122.71,-47.57,-247.49:99
+chr1	1520243	.	C	G	225.05	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=0;HaplotypeScore=118.32;MQ=42.36;MQ0=0;QD=1.77;SB=107.39	GT:AD:DP:GL:GQ	0/1:107,20:111:-59.26,-33.47,-404.28:99
+chr1	1520250	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=130;Dels=0.03;HRun=1;HaplotypeScore=70.65;MQ=43.20;MQ0=0;OQ=629.57;QD=4.84;SB=-297.59	GT:AD:DP:GL:GQ	0/1:85,37:107:-98.49,-32.25,-308.33:99
+chr1	1520281	rs61774874	G	C	511.99	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=95.68;MQ=43.19;MQ0=0;QD=4.13;SB=-246.08	GT:AD:DP:GL:GQ	0/1:99,25:103:-85.52,-31.04,-362.79:99
+chr1	1520285	.	G	C	387.17	SnpCluster	AC=1;AF=0.50;AN=2;DP=119;Dels=0.01;HRun=0;HaplotypeScore=65.61;MQ=43.42;MQ0=0;QD=3.25;SB=-155.15	GT:AD:DP:GL:GQ	0/1:98,20:100:-71.84,-29.84,-355.29:99
+chr1	1520289	rs62642589	C	G	93.31	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=121;Dels=0.01;HRun=0;HaplotypeScore=35.98;MQ=43.17;MQ0=0;QD=0.77;SB=134.48	GT:AD:DP:GL:GQ	0/1:107,13:109:-45.17,-32.56,-411.19:99
+chr1	1520331	rs28654137	C	G	48.96	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.01;HRun=0;HaplotypeScore=27.98;MQ=47.63;MQ0=0;QD=0.60;SB=18.43	GT:AD:DP:GL:GQ	0/1:72,9:75:-30.78,-22.60,-290.44:81.79
+chr1	1520344	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=73;Dels=0.01;HRun=0;HaplotypeScore=35.55;MQ=46.62;MQ0=0;OQ=147.13;QD=2.02;SB=-55.25	GT:AD:DP:GL:GQ	0/1:57,14:62:-36.39,-18.39,-179.58:99
+chr1	1520377	.	C	G	26.02	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=20.54;MQ=46.26;MQ0=1;QD=0.42;SB=59.22	GT:AD:DP:GL:GQ	0/1:52,10:48:-20.35,-14.47,-182.03:58.84
+chr1	1520381	rs28593368	C	G	11.70	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=9.32;MQ=47.21;MQ0=1;QD=0.18;SB=37.38	GT:AD:DP:GL:GQ	0/1:58,8:56:-21.30,-16.87,-217.45:44.23
+chr1	1520469	rs11488585	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.01;HRun=0;HaplotypeScore=36.86;MQ=43.53;MQ0=4;OQ=2355.10;QD=23.55;SB=-1049.66	GT:AD:DP:GL:GQ	0/1:35,63:89:-265.31,-26.51,-115.33:99
+chr1	1520498	.	G	A	0.22	PASS	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=42.41;MQ0=4;OQ=313.12;QD=3.48;SB=-164.48	GT:AD:DP:GL:GQ	0/1:71,19:76:-57.51,-22.91,-206.14:99
+chr1	1520609	.	G	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=16.97;MQ=45.11;MQ0=1;OQ=1017.74;QD=9.51;SB=-327.71	GT:AD:DP:GL:GQ	0/1:72,34:94:-133.38,-28.32,-275.79:99
+chr1	1520627	.	T	C	0.10	PASS	AC=2;AF=1.00;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=10.65;MQ=46.29;MQ0=2;OQ=3224.03;QD=30.42;SB=-1396.99	GT:AD:DP:GL:GQ	1/1:0,101:93:-329.81,-30.68,-3.83:99
+chr1	1520757	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=47.64;MQ0=6;OQ=89.81;QD=0.88;SB=110.39	GT:AD:DP:GL:GQ	0/1:91,11:89:-39.08,-26.81,-310.80:99
+chr1	1520774	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=99;Dels=0.01;HRun=0;HaplotypeScore=56.31;MQ=48.08;MQ0=6;OQ=62.24;QD=0.63;SB=110.34	GT:AD:DP:GL:GQ	0/1:89,9:83:-34.23,-24.72,-231.51:95.08
+chr1	1520787	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=96;Dels=0.04;HRun=0;HaplotypeScore=27.20;MQ=49.95;MQ0=4;OQ=173.92;QD=1.81;SB=77.51	GT:AD:DP:GL:GQ	0/1:78,14:87:-45.69,-25.01,-305.10:99
+chr1	1520821	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=37.97;MQ=51.43;MQ0=1;OQ=216.93;QD=2.55;SB=101.36	GT:AD:DP:GL:GQ	0/1:69,16:80:-49.07,-24.10,-269.00:99
+chr1	1520848	.	G	A	0.20	PASS	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=2.89;MQ=50.21;MQ0=2;OQ=302.35;QD=3.44;SB=74.15	GT:AD:DP:GL:GQ	0/1:72,16:76:-56.43,-22.92,-203.92:99
+chr1	1520892	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=1;HaplotypeScore=71.05;MQ=51.39;MQ0=2;OQ=950.76;QD=9.51;SB=-387.75	GT:AD:DP:GL:GQ	0/1:63,37:86:-124.27,-25.91,-211.22:99
+chr1	1520953	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=74;Dels=0.01;HRun=0;HaplotypeScore=47.85;MQ=52.80;MQ0=2;OQ=265.98;QD=3.59;SB=-146.32	GT:AD:DP:GL:GQ	0/1:59,14:61:-47.97,-18.09,-205.99:99
+chr1	1520957	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=21.78;MQ=53.36;MQ0=2;OQ=105.70;QD=1.55;SB=-47.11	GT:AD:DP:GL:GQ	0/1:59,9:55:-30.43,-16.57,-209.84:99
+chr1	1520979	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=45.80;MQ=49.11;MQ0=2;OQ=234.58;QD=3.72;SB=-118.04	GT:AD:DP:GL:GQ	0/1:53,10:50:-41.81,-15.07,-172.68:99
+chr1	1521029	.	C	G	208.12	Indel	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=31.42;MQ=47.45;MQ0=1;QD=3.20;SB=-33.62	GT:AD:DP:GL:GQ	0/1:53,12:61:-42.48,-18.38,-218.36:99
+chr1	1521111	.	C	G	34.71	LowQual	AC=1;AF=0.50;AN=2;DP=75;Dels=0.05;HRun=0;HaplotypeScore=51.94;MQ=49.50;MQ0=5;QD=0.46;SB=-34.07	GT:AD:DP:GL:GQ	0/1:62,9:60:-24.84,-18.09,-231.30:67.54
+chr1	1521139	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=19.29;MQ=49.73;MQ0=4;OQ=471.32;QD=8.42;SB=-237.06	GT:AD:DP:GL:GQ	0/1:38,18:43:-63.38,-12.96,-121.81:99
+chr1	1521149	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=50;Dels=0.04;HRun=0;HaplotypeScore=25.97;MQ=51.25;MQ0=5;OQ=94.80;QD=1.90;SB=0.71	GT:AD:DP:GL:GQ	0/1:42,6:42:-25.43,-12.66,-151.77:99
+chr1	1521416	.	G	A	908.87	Indel	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=49.66;MQ0=7;QD=12.12;SB=-403.37	GT:AD:DP:GL:GQ	0/1:47,28:66:-114.05,-19.88,-141.06:99
+chr1	1521692	.	G	A	0.94	PASS	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=9.14;MQ=58.40;MQ0=0;OQ=1252.37;QD=15.27;SB=-600.00	GT:AD:DP:GL:GQ	0/1:41,41:79:-152.32,-23.80,-150.35:99
+chr1	1521772	rs36210710	A	G	0.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=15.96;MQ=57.04;MQ0=1;OQ=875.12;QD=13.46;SB=-359.37	GT:AD:DP:GL:GQ	0/1:32,33:57:-107.96,-17.17,-110.70:99
+chr1	1522125	rs28569178	A	G	2.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=5.24;MQ=53.41;MQ0=0;OQ=1519.29;QD=31.65;SB=-783.99	GT:AD:DP:GL:GQ	1/1:0,48:43:-155.53,-12.95,-0.01:99
+chr1	1522142	rs35051391	A	C	34.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=4.14;MQ=53.19;MQ0=0;OQ=509.94;QD=11.86;SB=-251.92	GT:AD:DP:GL:GQ	0/1:20,23:38:-65.73,-11.45,-61.61:99
+chr1	1522705	.	C	T	4.71	PASS	AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=50.65;MQ0=0;OQ=133.19;QD=16.65;SB=-79.09	GT:AD:DP:GL:GQ	0/1:3,5:8:-19.01,-2.41,-10.59:81.80
+chr1	1524477	rs11552172	T	C	56.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.17;MQ0=0;OQ=436.12;QD=15.58;SB=-113.68	GT:AD:DP:GL:GQ	0/1:12,16:28:-55.34,-8.44,-45.31:99
+chr1	1527039	rs4075469	A	C	248.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.34;MQ0=0;OQ=696.22;QD=16.58;SB=-340.88	GT:AD:DP:GL:GQ	0/1:16,26:40:-84.95,-12.05,-59.28:99
+chr1	1527300	rs7554569	C	T	296.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=424.42;QD=8.16;SB=-236.55	GT:AD:DP:GL:GQ	0/1:35,17:46:-59.60,-13.87,-96.44:99
+chr1	1527750	.	C	A	254.99	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.50;MQ0=0;OQ=986.18;QD=16.71;SB=-374.21	GT:AD:DP:GL:GQ	0/1:26,33:55:-118.47,-16.57,-69.65:99
+chr1	1527909	.	G	A	103.61	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.52;MQ0=0;OQ=783.03;QD=16.31;SB=-358.36	GT:AD:DP:GL:GQ	0/1:23,25:47:-95.76,-14.17,-71.60:99
+chr1	1528300	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=3;HaplotypeScore=10.61;MQ=58.05;MQ0=0;OQ=286.83;QD=5.98;SB=62.19	GT:AD:DP:GL:GQ	0/1:26,22:41:-44.32,-12.35,-90.74:99
+chr1	1529232	rs6656591	T	C	65.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.39;MQ=56.33;MQ0=0;OQ=1005.79;QD=17.65;SB=-491.70	GT:AD:DP:GL:GQ	0/1:23,34:55:-120.43,-16.57,-83.35:99
+chr1	1529445	rs6691649	G	A	161.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=59.46;MQ0=0;OQ=1057.94;QD=19.59;SB=-480.07	GT:AD:DP:GL:GQ	0/1:20,34:51:-124.45,-15.37,-67.92:99
+chr1	1529817	rs4075275	G	C	15.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=2.13;MQ=58.35;MQ0=0;OQ=1607.65;QD=30.92;SB=-720.33	GT:AD:DP:GL:GQ	1/1:0,52:40:-164.38,-12.07,-0.03:99
+chr1	1530590	.	C	T	27.41	PASS	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=55.36;MQ0=0;OQ=363.07;QD=13.45;SB=-133.59	GT:AD:DP:GL:GQ	0/1:14,13:26:-47.43,-7.84,-42.81:99
+chr1	1530910	.	G	C	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=6.92;MQ=37.58;MQ0=2;OQ=79.86;QD=5.32;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,8:5:-12.78,-1.51,-7.90:63.88
+chr1	1530912	.	C	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=2;HaplotypeScore=4.15;MQ=38.11;MQ0=2;OQ=71.50;QD=5.11;SB=-6.99	GT:AD:DP:GL:GQ	0/1:4,10:6:-12.24,-1.81,-12.03:99
+chr1	1530952	.	G	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=8.79;MQ=42.16;MQ0=2;OQ=53.35;QD=3.33;SB=-39.44	GT:AD:DP:GL:GQ	0/1:11,5:9:-11.33,-2.71,-25.48:86.19
+chr1	1530975	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=5.18;MQ=46.58;MQ0=0;OQ=57.06;QD=3.57;SB=5.04	GT:AD:DP:GL:GQ	0/1:12,4:12:-12.60,-3.61,-32.43:89.90
+chr1	1531008	.	C	G	10.82	LowQual	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=2;HaplotypeScore=6.64;MQ=46.16;MQ0=1;QD=0.52;SB=-26.85	GT:AD:DP:GL:GQ	0/1:16,5:11:-7.66,-3.33,-32.36:43.28
+chr1	1531060	.	A	C	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=9.36;MQ=36.61;MQ0=1;OQ=116.93;QD=7.31;SB=-3.99	GT:AD:DP:GL:GQ	0/1:5,10:9:-17.69,-2.71,-12.57:98.57
+chr1	1531096	.	C	T	31.46	LowQual	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=8.94;MQ=35.04;MQ0=1;QD=3.15;SB=-6.99	GT:AD:DP:GL:GQ	0/1:5,5:4:-7.64,-1.21,-6.67:54.60
+chr1	1531214	.	C	T	12.58	LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=48.08;MQ0=0;QD=0.90;SB=-28.53	GT:AD:DP:GL:GQ	0/1:11,2:10:-7.53,-3.02,-23.43:45.17
+chr1	1531255	.	G	A	2.13	PASS	AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=54.60;MQ0=0;OQ=208.62;QD=17.39;SB=-121.64	GT:AD:DP:GL:GQ	0/1:2,10:8:-26.44,-2.41,-2.60:1.87
+chr1	1531316	.	A	T	48.17	LowQual	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=3.10;MQ=48.85;MQ0=0;QD=2.01;SB=-30.94	GT:AD:DP:GL:GQ	0/1:15,8:14:-12.32,-4.22,-35.65:81.01
+chr1	1531334	.	C	T	13.43	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=4.16;MQ=45.60;MQ0=1;QD=0.56;SB=5.01	GT:AD:DP:GL:GQ	0/1:15,7:11:-7.93,-3.32,-25.96:46.07
+chr1	1531359	.	G	A	17.07	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=4.20;MQ=46.76;MQ0=1;QD=0.74;SB=11.04	GT:AD:DP:GL:GQ	0/1:19,4:19:-10.71,-5.73,-55.15:49.82
+chr1	1531380	.	C	G	42.65	LowQual	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=3;HaplotypeScore=7.66;MQ=46.38;MQ0=2;QD=1.42;SB=-45.68	GT:AD:DP:GL:GQ	0/1:23,7:24:-14.78,-7.24,-85.75:75.49
+chr1	1531419	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=2;HaplotypeScore=5.63;MQ=45.92;MQ0=1;OQ=63.73;QD=3.03;SB=23.10	GT:AD:DP:GL:GQ	0/1:16,5:18:-15.09,-5.43,-50.86:96.57
+chr1	1531527	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=2;HaplotypeScore=3.70;MQ=32.41;MQ0=1;OQ=75.08;QD=3.75;SB=-44.95	GT:AD:DP:GL:GQ	0/1:9,10:9:-13.51,-2.71,-17.78:99
+chr1	1531545	.	G	C	27.47	LowQual	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=8.08;MQ=36.24;MQ0=1;QD=1.37;SB=-32.85	GT:AD:DP:GL:GQ	0/1:18,2:9:-8.74,-2.71,-27.23:60.30
+chr1	1531547	.	C	G	25.49	LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=2;HaplotypeScore=8.42;MQ=36.81;MQ0=1;QD=1.34;SB=-27.40	GT:AD:DP:GL:GQ	0/1:14,5:6:-7.64,-1.81,-15.17:58.31
+chr1	1532873	rs9442420	T	C	73.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.50;MQ0=0;OQ=1279.49;QD=27.81;SB=-597.57	GT:AD:DP:GL:GQ	1/1:0,46:41:-131.57,-12.37,-0.04:99
+chr1	1533487	rs61774903	T	C	6.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=59.07;MQ0=0;OQ=267.71;QD=10.71;SB=-22.90	GT:AD:DP:GL:GQ	0/1:12,13:23:-36.99,-6.93,-45.73:99
+chr1	1533846	.	C	A	150.54	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=607.30;QD=13.20;SB=-294.38	GT:AD:DP:GL:GQ	0/1:23,23:45:-77.57,-13.56,-81.22:99
+chr1	1534313	.	G	A	286.31	PASS	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.20;MQ0=0;OQ=679.07;QD=15.09;SB=-355.53	GT:AD:DP:GL:GQ	0/1:22,23:43:-84.16,-12.97,-66.20:99
+chr1	1535152	rs6671612	G	T	108.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=2.91;MQ=57.71;MQ0=0;OQ=838.64;QD=11.98;SB=-304.64	GT:AD:DP:GL:GQ	0/1:41,29:64:-106.43,-19.29,-110.69:99
+chr1	1536167	rs11492279	C	T	248.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=60.00;MQ0=0;OQ=1040.79;QD=15.31;SB=-440.43	GT:AD:DP:GL:GQ	0/1:36,32:64:-126.65,-19.29,-102.67:99
+chr1	1536812	rs4612573	T	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.03;HRun=1;HaplotypeScore=39.15;MQ=49.08;MQ0=0;OQ=1478.03;QD=23.09;SB=-556.56	GT:AD:DP:GL:GQ	1/1:5,57:50:-162.89,-15.07,-11.50:35.64
+chr1	1537429	rs4369171	A	G	1.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=7.54;MQ=57.32;MQ0=0;OQ=2121.87;QD=33.68;SB=-744.31	GT:AD:DP:GL:GQ	1/1:0,62:59:-215.79,-17.77,-0.02:99
+chr1	1537803	.	G	T	52.70	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=13;HaplotypeScore=28.28;MQ=58.09;MQ0=1;QD=0.71;SB=63.90	GT:AD:DP:GL:GQ	0/1:60,13:55:-25.14,-16.58,-155.96:85.54
+chr1	1537805	.	T	C	135.64	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=41.12;MQ=58.24;MQ0=1;QD=2.02;SB=15.89	GT:AD:DP:GL:GQ	0/1:57,10:56:-33.73,-16.88,-176.73:99
+chr1	1538333	.	A	G	136.38	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=58.86;MQ0=0;OQ=748.93;QD=13.87;SB=-356.58	GT:AD:DP:GL:GQ	0/1:27,27:53:-94.15,-15.98,-99.69:99
+chr1	1538565	rs9442431	T	C	829.64	Indel	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=7.58;MQ=50.06;MQ0=1;QD=21.83;SB=-151.73	GT:AD:DP:GL:GQ	1/1:0,37:28:-86.58,-8.45,-0.03:84.18
+chr1	1538664	rs9442430	T	C	1.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.01;HRun=1;HaplotypeScore=8.39;MQ=59.12;MQ0=0;OQ=2182.53;QD=31.63;SB=-555.08	GT:AD:DP:GL:GQ	1/1:0,68:67:-221.88,-20.20,-0.05:99
+chr1	1539012	rs34501155	C	T	24.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=2;HaplotypeScore=0.10;MQ=59.44;MQ0=0;OQ=1523.49;QD=20.31;SB=-698.38	GT:AD:DP:GL:GQ	0/1:29,46:74:-177.93,-22.30,-104.96:99
+chr1	1539217	rs12066	G	A	112.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2269.66;QD=38.47;SB=-1077.37	GT:AD:DP:GL:GQ	1/1:0,59:57:-230.57,-17.17,-0.02:99
+chr1	1539583	.	C	T	13.58	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.17;MQ=59.69;MQ0=0;OQ=849.58;QD=14.16;SB=-408.41	GT:AD:DP:GL:GQ	0/1:34,26:60:-106.31,-18.07,-125.62:99
+chr1	1540565	rs4648611	A	G	1.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=2;HaplotypeScore=4.13;MQ=58.95;MQ0=0;OQ=632.46;QD=28.75;SB=-329.75	GT:AD:DP:GL:GQ	1/1:0,22:20:-66.85,-6.03,-0.02:60.13
+chr1	1541790	rs7418389	T	C	9.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=60.00;MQ0=0;OQ=644.37;QD=28.02;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,23:21:-68.04,-6.33,-0.01:63.14
+chr1	1542618	rs6604985	T	C	187.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.49;MQ0=0;OQ=2789.66;QD=34.02;SB=-860.05	GT:AD:DP:GL:GQ	1/1:0,82:81:-282.58,-24.40,-0.03:99
+chr1	1543361	rs28546565	G	A	262.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.46;MQ0=0;OQ=627.76;QD=14.60;SB=-285.20	GT:AD:DP:GL:GQ	0/1:20,23:40:-78.11,-12.05,-70.94:99
+chr1	1543456	rs28623434	C	G	8.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=2.93;MQ=59.20;MQ0=0;OQ=2332.23;QD=40.21;SB=-1030.14	GT:AD:DP:GL:GQ	1/1:0,58:55:-236.83,-16.57,-0.02:99
+chr1	1543533	rs9442410	G	C	82.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=2713.47;QD=43.07;SB=-1108.14	GT:AD:DP:GL:GQ	1/1:0,63:62:-274.95,-18.68,-0.02:99
+chr1	1544225	rs9442425	G	A	33.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.11;MQ=59.22;MQ0=0;OQ=1855.01;QD=38.65;SB=-869.17	GT:AD:DP:GL:GQ	1/1:0,48:47:-189.10,-14.16,-0.01:99
+chr1	1545229	rs9329576	T	C	4.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=2.58;MQ=60.00;MQ0=0;OQ=1266.55;QD=28.15;SB=-625.18	GT:AD:DP:GL:GQ	1/1:0,45:39:-130.27,-11.76,-0.03:99
+chr1	1545852	rs7543265	G	A	8.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=6.32;MQ=58.20;MQ0=0;OQ=611.29;QD=15.67;SB=-238.27	GT:AD:DP:GL:GQ	0/1:17,20:35:-74.97,-10.56,-46.23:99
+chr1	1546595	rs34983251	G	A	45.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=59.23;MQ0=0;OQ=349.98;QD=11.67;SB=-133.57	GT:AD:DP:GL:GQ	0/1:16,14:26:-46.12,-7.83,-51.50:99
+chr1	1547538	rs28710339	G	C	59.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=3.45;MQ=58.50;MQ0=0;OQ=866.08;QD=15.47;SB=-347.43	GT:AD:DP:GL:GQ	0/1:31,25:53:-105.89,-16.00,-107.63:99
+chr1	1547753	.	C	T	52.88	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.60;MQ0=0;OQ=1139.64;QD=19.99;SB=-512.06	GT:AD:DP:GL:GQ	0/1:22,35:54:-133.53,-16.28,-63.46:99
+chr1	1548655	rs12755088	T	C	97.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=439.27;QD=24.40;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,18:16:-47.54,-4.84,-0.03:48.08
+chr1	1548983	.	C	G	40.73	LowQual	AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=5;HaplotypeScore=1.58;MQ=47.12;MQ0=0;QD=6.79;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,5:2:-7.48,-0.61,-0.00:6.02
+chr1	1549329	rs28617190	G	A	97.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=1.74;MQ=57.37;MQ0=0;OQ=547.08;QD=16.09;SB=-253.53	GT:AD:DP:GL:GQ	0/1:16,18:32:-67.63,-9.64,-54.05:99
+chr1	1549834	rs12748433	C	T	442.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.23;MQ0=0;OQ=1400.65;QD=37.86;SB=-569.32	GT:AD:DP:GL:GQ	1/1:0,37:36:-143.66,-10.85,-0.01:99
+chr1	1549963	rs28441650	G	A	319.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.05;MQ0=0;OQ=739.99;QD=15.10;SB=-342.91	GT:AD:DP:GL:GQ	0/1:25,24:48:-91.75,-14.47,-81.34:99
+chr1	1551048	.	G	A	13.72	PASS	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=55.20;MQ0=0;OQ=331.40;QD=13.81;SB=-96.94	GT:AD:DP:GL:GQ	0/1:12,12:21:-42.75,-6.33,-33.17:99
+chr1	1551194	.	G	A	9.75	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=59.45;MQ0=0;OQ=497.08;QD=14.62;SB=-108.95	GT:AD:DP:GL:GQ	0/1:18,16:33:-62.94,-9.95,-55.65:99
+chr1	1552758	rs12735861	C	T	11.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=56.58;MQ0=0;OQ=143.44;QD=15.94;SB=-6.99	GT:AD:DP:GL:GQ	0/1:3,6:8:-20.04,-2.41,-9.16:67.50
+chr1	1553652	.	C	A	57.28	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=59.52;MQ0=0;OQ=736.76;QD=15.35;SB=-347.43	GT:AD:DP:GL:GQ	0/1:23,25:44:-90.22,-13.26,-60.84:99
+chr1	1554057	rs3935032	C	T	0.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=59.31;MQ0=0;OQ=580.92;QD=21.52;SB=-104.60	GT:AD:DP:GL:GQ	0/1:9,18:26:-69.21,-7.83,-32.29:99
+chr1	1555931	rs28730454	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=7;HaplotypeScore=0.32;MQ=55.21;MQ0=0;OQ=59.16;QD=11.83;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,5:3:-9.41,-0.90,-0.00:9.02
+chr1	1556023	rs28464684	T	C	13.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=73.72;QD=24.57;SB=-40.68	GT:AD:DP:GL:GQ	1/1:0,3:3:-10.86,-0.90,-0.00:9.03
+chr1	1556952	rs28451771	T	C	12.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=601.05;QD=31.63;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,19:19:-63.70,-5.72,-0.01:57.14
+chr1	1561503	rs61774909	G	T	0.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=9.65;MQ0=29;OQ=78.96;QD=2.47;SB=-10.00	GT:AD:DP:GL:GQ	1/1:16,16:3:-11.38,-0.90,-0.00:9.03
+chr1	1563882	rs61774911	A	G	1.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=39.06;MQ0=5;OQ=124.38;QD=2.76;SB=-85.66	GT:AD:DP:GL:GQ	0/1:34,10:35:-26.27,-10.55,-104.24:99
+chr1	1563939	rs9442413	G	A	8.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=40.26;MQ0=2;OQ=315.22;QD=4.50;SB=-153.56	GT:AD:DP:GL:GQ	0/1:51,19:59:-52.60,-17.79,-143.72:99
+chr1	1564183	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=20;HaplotypeScore=14.98;MQ=46.49;MQ0=5;OQ=64.66;QD=1.80;SB=35.13	GT:AD:DP:GL:GQ	0/1:31,5:28:-18.18,-8.44,-79.86:97.49
+chr1	1564572	rs28401288	T	G	29.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=41.92;MQ0=1;OQ=1158.48;QD=27.58;SB=-476.97	GT:AD:DP:GL:GQ	1/1:0,42:35:-119.45,-10.55,-0.02:99
+chr1	1565479	rs28394074	T	C	98.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=12.86;MQ0=16;OQ=207.25;QD=7.68;SB=-36.94	GT:AD:DP:GL:GQ	1/1:0,27:7:-24.31,-2.11,-0.00:21.06
+chr1	1565699	.	C	G	5.41	PASS	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=1;HaplotypeScore=2.34;MQ=26.47;MQ0=10;OQ=657.44;QD=8.65;SB=-346.42	GT:AD:DP:GL:GQ	0/1:55,21:62:-87.73,-18.71,-164.80:99
+chr1	1566499	rs3765908	G	A	18.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.75;MQ=37.81;MQ0=3;OQ=1730.84;QD=29.34;SB=-752.15	GT:AD:DP:GL:GQ	1/1:8,51:54:-192.27,-16.27,-15.84:4.30
+chr1	1566866	rs3819995	C	T	33.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=17.30;MQ0=34;OQ=418.63;QD=7.34;SB=-10.00	GT:AD:DP:GL:GQ	0/1:21,36:18:-50.57,-5.43,-18.99:99
+chr1	1567043	rs1137001	C	T	0.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=9.65;MQ0=38;OQ=66.77;QD=1.34;SB=-10.00	GT:AD:DP:GL:GQ	0/1:35,15:6:-11.77,-1.81,-10.91:90.99
+chr1	1569585	rs61774912	C	T	0.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=8.98;MQ=13.84;MQ0=43;OQ=132.92;QD=1.51;SB=-3.99	GT:AD:DP:GL:GQ	0/1:64,24:26:-24.41,-7.83,-74.67:99
+chr1	1569917	rs6688326	C	A	0.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=2.45;MQ=26.34;MQ0=26;OQ=227.69;QD=3.04;SB=-87.75	GT:AD:DP:GL:GQ	0/1:58,17:44:-39.31,-13.26,-117.30:99
+chr1	1570601	rs4648767	T	A	243.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=24.85;MQ0=18;OQ=1006.84;QD=11.57;SB=-380.53	GT:AD:DP:GL:GQ	0/1:42,45:58:-121.45,-17.48,-87.58:99
+chr1	1570928	.	G	C	0.90	PASS	AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=0;HaplotypeScore=3.62;MQ=32.27;MQ0=14;OQ=845.01;QD=5.52;SB=-333.79	GT:AD:DP:GL:GQ	0/1:113,40:123:-124.85,-37.07,-408.45:99
+chr1	1570959	.	C	T	0.27	PASS	AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=2;HaplotypeScore=4.89;MQ=34.90;MQ0=12;OQ=2272.40;QD=13.77;SB=-727.55	GT:AD:DP:GL:GQ	0/1:85,80:144:-273.90,-43.38,-268.43:99
+chr1	1571421	rs61774913	C	T	442.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.06;MQ0=31;OQ=744.27;QD=14.31;SB=-218.78	GT:AD:DP:GL:GQ	1/1:0,52:19:-78.02,-5.72,-0.00:57.19
+chr1	1571449	rs61774914	T	C	385.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=19.48;MQ0=37;OQ=993.50;QD=14.19;SB=-324.14	GT:AD:DP:GL:GQ	1/1:0,70:28:-102.94,-8.43,-0.01:84.26
+chr1	1571467	.	G	A	0.11	PASS	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=5.46;MQ=31.83;MQ0=25;OQ=330.51;QD=3.76;SB=-146.19	GT:AD:DP:GL:GQ	0/1:69,19:55:-52.91,-16.58,-135.58:99
+chr1	1571576	.	A	C	50.03	PASS	AC=2;AF=1.00;AN=2;DP=93;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=35.58;MQ0=13;OQ=1974.59;QD=21.23;SB=-847.56	GT:AD:DP:GL:GQ	1/1:0,61:79:-282.59,-90.56,-81.54:90.13
+chr1	1571744	rs61774916	T	C	0.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=43.65;MQ0=18;OQ=618.53;QD=4.99;SB=-195.46	GT:AD:DP:GL:GQ	0/1:91,33:103:-96.17,-31.03,-294.76:99
+chr1	1571789	rs61774917	G	T	99.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=114;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=40.38;MQ0=17;OQ=858.73;QD=7.53;SB=-166.41	GT:AD:DP:GL:GQ	0/1:66,48:94:-117.47,-28.31,-223.12:99
+chr1	1571821	rs4279785	T	C	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=33.09;MQ0=22;OQ=74.70;QD=0.60;SB=13.40	GT:AD:DP:GL:GQ	0/1:103,22:85:-36.35,-25.60,-306.33:99
+chr1	1571969	rs4648753	T	C	252.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.21;MQ0=23;OQ=2308.47;QD=23.08;SB=-928.73	GT:AD:DP:GL:GQ	1/1:1,99:73:-234.50,-22.02,-0.07:99
+chr1	1572065	rs61774918	C	T	271.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=40.98;MQ0=5;OQ=1993.46;QD=16.08;SB=-715.20	GT:AD:DP:GL:GQ	0/1:57,67:116:-237.58,-34.95,-201.11:99
+chr1	1572318	rs61774919	G	A	28.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=173;Dels=0.00;HRun=0;HaplotypeScore=4.27;MQ=26.57;MQ0=15;OQ=1639.76;QD=9.48;SB=-550.56	GT:AD:DP:GL:GQ	0/1:104,69:121:-203.75,-36.49,-222.67:99
+chr1	1572479	.	T	C	0.14	PASS	AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=45.14;MQ0=0;OQ=1750.04;QD=12.24;SB=-888.87	GT:AD:DP:GL:GQ	0/1:83,60:141:-220.76,-42.47,-332.08:99
+chr1	1572504	.	T	C	0.71	PASS	AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=42.33;MQ0=3;OQ=1049.29;QD=7.72;SB=-546.16	GT:AD:DP:GL:GQ	0/1:84,52:129:-147.09,-38.88,-337.66:99
+chr1	1572657	rs4648754	C	A	97.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=39.40;MQ0=0;OQ=4131.60;QD=35.01;SB=-1448.13	GT:AD:DP:GL:GQ	1/1:1,117:114:-412.16,-34.34,-0.04:99
+chr1	1572704	rs61774920	A	G	0.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=29.04;MQ0=13;OQ=131.71;QD=1.78;SB=23.25	GT:AD:DP:GL:GQ	0/1:54,20:56:-33.33,-16.87,-184.69:99
+chr1	1572707	rs61774921	G	T	0.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=28.52;MQ0=13;OQ=177.56;QD=2.50;SB=-37.61	GT:AD:DP:GL:GQ	0/1:52,19:55:-37.61,-16.57,-159.55:99
+chr1	1572743	rs3820000	G	C	38.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=26.84;MQ0=19;OQ=650.68;QD=7.75;SB=38.16	GT:AD:DP:GL:GQ	0/1:50,34:58:-85.85,-17.49,-156.24:99
+chr1	1572824	rs3820001	G	C	184.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=41.82;MQ0=4;OQ=1359.68;QD=17.43;SB=-597.25	GT:AD:DP:GL:GQ	0/1:31,47:67:-159.47,-20.22,-110.10:99
+chr1	1572866	rs61776849	C	T	39.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=4.48;MQ=49.73;MQ0=0;OQ=1155.72;QD=12.70;SB=-351.36	GT:AD:DP:GL:GQ	0/1:50,41:84:-144.17,-25.32,-161.47:99
+chr1	1572951	.	A	G	0.08	PASS	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=47.33;MQ0=7;OQ=238.29;QD=2.91;SB=26.27	GT:AD:DP:GL:GQ	0/1:60,22:73:-49.11,-21.99,-235.06:99
+chr1	1573358	rs61774952	T	C	32.21	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=47.33;MQ0=8;QD=0.37;SB=67.42	GT:AD:DP:GL:GQ	0/1:70,16:71:-27.89,-21.39,-252.84:65.04
+chr1	1573532	.	C	T	35.47	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=10.41;MQ0=15;QD=1.97;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,3:3:-7.73,-0.90,-3.80:28.93
+chr1	1573550	.	T	C	24.36	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=33.97;MQ0=17;QD=0.72;SB=-17.89	GT:AD:DP:GL:GQ	0/1:23,11:14:-9.94,-4.22,-42.08:57.18
+chr1	1573618	.	C	T	2.54	PASS	AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=5.35;MQ=45.15;MQ0=15;OQ=814.16;QD=7.75;SB=-232.64	GT:AD:DP:GL:GQ	0/1:66,38:82:-109.43,-24.73,-173.93:99
+chr1	1573625	.	G	A	3.56	PASS	AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=45.17;MQ0=14;OQ=654.74;QD=6.18;SB=-207.09	GT:AD:DP:GL:GQ	0/1:70,36:84:-94.09,-25.34,-189.03:99
+chr1	1573865	rs6691927	A	G	0.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=13.93;MQ=47.63;MQ0=8;OQ=1026.45;QD=17.40;SB=-411.69	GT:AD:DP:GL:GQ	0/1:13,46:46:-119.80,-13.87,-37.07:99
+chr1	1573965	rs28525262	G	A	126.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=48.13;MQ0=7;OQ=3091.70;QD=33.97;SB=-1505.87	GT:AD:DP:GL:GQ	1/1:7,83:80:-316.25,-24.10,-3.49:99
+chr1	1573980	rs4648756	G	C	18.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=4.39;MQ=47.15;MQ0=6;OQ=3392.36;QD=38.99;SB=-1642.01	GT:AD:DP:GL:GQ	1/1:0,87:79:-338.24,-23.81,-0.03:99
+chr1	1574055	rs4648606	G	A	59.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=37.73;MQ0=7;OQ=2424.32;QD=33.21;SB=-1231.00	GT:AD:DP:GL:GQ	1/1:0,72:61:-246.03,-18.38,-0.02:99
+chr1	1574081	rs4648607	T	C	84.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=40.76;MQ0=4;OQ=2240.23;QD=31.55;SB=-1072.45	GT:AD:DP:GL:GQ	1/1:0,71:63:-227.63,-18.98,-0.02:99
+chr1	1574087	rs4648757	G	C	98.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=43.14;MQ0=1;OQ=2791.35;QD=39.31;SB=-1268.99	GT:AD:DP:GL:GQ	1/1:0,71:65:-282.74,-19.59,-0.02:99
+chr1	1574123	.	A	C	149.77	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=169.77;MQ=39.72;MQ0=1;QD=1.63;SB=83.29	GT:AD:DP:GL:GQ	0/1:79,13:73:-40.25,-21.99,-225.95:99
+chr1	1574124	.	A	G	50.98	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=0;HaplotypeScore=170.51;MQ=39.99;MQ0=1;QD=0.55;SB=86.31	GT:AD:DP:GL:GQ	0/1:80,13:72:-30.08,-21.70,-250.90:83.81
+chr1	1574131	.	A	G	472.59	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=2;HaplotypeScore=66.93;MQ=41.08;MQ0=1;QD=5.25;SB=86.31	GT:AD:DP:GL:GQ	0/1:61,29:78:-74.04,-23.50,-234.93:99
+chr1	1574135	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=78.57;MQ=41.20;MQ0=1;OQ=155.65;QD=1.75;SB=86.32	GT:AD:DP:GL:GQ	0/1:76,13:71:-40.23,-21.39,-240.65:99
+chr1	1574143	.	A	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=43.74;MQ0=1;OQ=78.06;QD=1.07;SB=89.31	GT:AD:DP:GL:GQ	0/1:60,13:65:-30.68,-19.59,-219.52:99
+chr1	1574152	.	C	T	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=43.30;MQ0=0;OQ=130.78;QD=1.92;SB=41.52	GT:AD:DP:GL:GQ	0/1:58,10:59:-34.15,-17.79,-160.93:99
+chr1	1574339	.	T	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=12.88;MQ=42.39;MQ0=0;OQ=429.14;QD=5.50;SB=104.35	GT:AD:DP:GL:GQ	0/1:59,19:76:-69.09,-22.90,-217.44:99
+chr1	1574367	rs12749208	C	T	7.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=36.29;MQ0=0;OQ=733.94;QD=10.48;SB=80.18	GT:AD:DP:GL:GQ	0/1:43,27:66:-96.58,-19.90,-132.61:99
+chr1	1574398	rs12756960	A	G	17.43	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=34.26;MQ0=0;QD=0.28;SB=39.57	GT:AD:DP:GL:GQ	0/1:29,33:32:-14.67,-9.65,-103.72:50.18
+chr1	1574404	rs12756961	A	T	204.46	Indel	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=35.46;MQ0=0;QD=3.01;SB=-19.65	GT:AD:DP:GL:GQ	0/1:32,36:41:-36.08,-12.35,-112.04:99
+chr1	1574410	rs12749336	C	G	884.89	Indel	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=10.32;MQ=35.72;MQ0=0;QD=12.82;SB=-17.81	GT:AD:DP:GL:GQ	0/1:40,29:35:-102.33,-10.56,-39.37:99
+chr1	1574434	rs61774954	A	C	428.65	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=8.25;MQ=34.95;MQ0=1;QD=6.30;SB=56.20	GT:AD:DP:GL:GQ	0/1:39,29:57:-63.32,-17.18,-124.62:99
+chr1	1574437	rs61774955	A	C	431.78	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=7.93;MQ=34.95;MQ0=1;QD=6.35;SB=56.19	GT:AD:DP:GL:GQ	0/1:38,30:51:-61.82,-15.36,-118.50:99
+chr1	1574456	rs12749364	C	A	1380.74	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=20.46;MQ=37.20;MQ0=1;QD=17.26;SB=-577.01	GT:AD:DP:GL:GQ	1/1:30,50:46:-152.08,-13.86,-10.42:34.36
+chr1	1574458	.	G	C	45.27	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=79;Dels=0.01;HRun=0;HaplotypeScore=10.44;MQ=37.76;MQ0=1;QD=0.57;SB=71.27	GT:AD:DP:GL:GQ	0/1:52,26:51:-22.87,-15.06,-200.14:78.10
+chr1	1574459	.	G	A	19.52	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=78;Dels=0.01;HRun=1;HaplotypeScore=9.38;MQ=37.85;MQ0=1;QD=0.25;SB=68.24	GT:AD:DP:GL:GQ	0/1:50,27:51:-20.29,-15.06,-165.60:52.31
+chr1	1574490	.	C	T	446.32	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=13.97;MQ=40.46;MQ0=1;QD=6.11;SB=62.20	GT:AD:DP:GL:GQ	0/1:48,25:59:-65.69,-17.77,-151.07:99
+chr1	1574491	.	A	G	363.54	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=14.98;MQ=40.79;MQ0=1;QD=4.91;SB=65.24	GT:AD:DP:GL:GQ	0/1:48,26:58:-57.11,-17.48,-164.32:99
+chr1	1574495	.	G	A	435.54	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=16.96;MQ=40.97;MQ0=1;QD=5.73;SB=65.16	GT:AD:DP:GL:GQ	0/1:50,26:61:-65.23,-18.39,-146.68:99
+chr1	1574611	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=41.66;MQ0=2;OQ=80.08;QD=1.13;SB=68.24	GT:AD:DP:GL:GQ	0/1:54,17:60:-29.38,-18.09,-195.87:99
+chr1	1574622	.	G	A	0.30	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=40.91;MQ0=2;OQ=251.34;QD=3.44;SB=59.11	GT:AD:DP:GL:GQ	0/1:55,18:61:-46.81,-18.39,-160.50:99
+chr1	1574627	.	C	T	0.19	PASS	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.69;MQ=42.21;MQ0=2;OQ=221.98;QD=2.88;SB=74.24	GT:AD:DP:GL:GQ	0/1:61,16:67:-45.68,-20.20,-184.31:99
+chr1	1574705	rs12753686	C	T	533.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=47.26;MQ0=1;OQ=2577.15;QD=38.46;SB=-1301.71	GT:AD:DP:GL:GQ	1/1:1,66:64:-261.31,-19.28,-0.01:99
+chr1	1574781	rs12753729	C	T	0.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=7.51;MQ=55.74;MQ0=0;OQ=2039.46;QD=37.77;SB=-910.24	GT:AD:DP:GL:GQ	1/1:1,53:52:-207.55,-15.67,-0.02:99
+chr1	1575120	rs4648758	A	G	435.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.79;MQ0=0;OQ=1070.30;QD=28.93;SB=-511.19	GT:AD:DP:GL:GQ	1/1:0,37:35:-110.65,-10.56,-0.04:99
+chr1	1575210	rs4648760	T	C	43.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=63.90;MQ0=0;OQ=1693.31;QD=34.56;SB=-784.12	GT:AD:DP:GL:GQ	1/1:0,49:49:-172.94,-14.76,-0.02:99
+chr1	1575251	rs4648761	A	G	5.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=60.80;MQ0=0;OQ=1436.67;QD=28.17;SB=-671.85	GT:AD:DP:GL:GQ	1/1:0,51:45:-147.29,-13.57,-0.04:99
+chr1	1575460	rs7531938	A	G	536.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.20;MQ0=0;OQ=2059.81;QD=30.29;SB=-875.65	GT:AD:DP:GL:GQ	1/1:0,68:66:-209.63,-19.91,-0.06:99
+chr1	1575505	rs3936009	G	T	209.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=57.75;MQ0=0;OQ=2310.00;QD=35.54;SB=-1127.37	GT:AD:DP:GL:GQ	1/1:0,65:65:-234.60,-19.58,-0.02:99
+chr1	1576615	rs11486023	T	C	106.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=57.19;MQ0=0;OQ=1526.39;QD=31.15;SB=-484.14	GT:AD:DP:GL:GQ	1/1:0,49:47:-156.26,-14.17,-0.04:99
+chr1	1577178	rs4648762	A	G	161.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=54.74;MQ0=0;OQ=2251.82;QD=30.85;SB=-761.70	GT:AD:DP:GL:GQ	1/1:0,72:69:-228.82,-20.80,-0.05:99
+chr1	1578533	rs61774958	G	A	209.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=136;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.20;MQ0=11;OQ=1051.54;QD=7.73;SB=-56.39	GT:AD:DP:GL:GQ	0/1:86,50:122:-145.19,-36.75,-299.83:99
+chr1	1578580	rs61774959	G	A	15.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=42.73;MQ0=4;OQ=297.29;QD=2.89;SB=-52.85	GT:AD:DP:GL:GQ	0/1:73,30:83:-58.01,-25.00,-251.41:99
+chr1	1578600	rs61776760	C	T	0.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=43.98;MQ0=2;OQ=158.49;QD=1.69;SB=-47.28	GT:AD:DP:GL:GQ	0/1:69,25:74:-41.42,-22.29,-233.46:99
+chr1	1579194	rs28530622	C	G	155.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.72;MQ0=1;OQ=430.39;QD=33.11;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,13:10:-46.62,-3.01,-0.00:30.10
+chr1	1579428	rs61776762	A	G	153.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.52;MQ0=1;OQ=97.37;QD=13.91;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,7:4:-13.27,-1.21,-0.00:12.02
+chr1	1580015	rs11486024	G	A	46.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=22.93;MQ0=7;OQ=160.84;QD=5.96;SB=11.04	GT:AD:DP:GL:GQ	0/1:15,12:15:-23.90,-4.53,-24.75:99
+chr1	1580190	rs7547516	A	G	298.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.87;MQ0=6;OQ=291.00;QD=13.23;SB=-79.37	GT:AD:DP:GL:GQ	1/1:0,22:11:-32.70,-3.32,-0.02:33.05
+chr1	1580389	rs9329573	G	C	27.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=38.23;MQ0=0;OQ=1419.74;QD=36.40;SB=-378.04	GT:AD:DP:GL:GQ	1/1:0,39:37:-145.59,-11.17,-0.03:99
+chr1	1580438	rs9661285	G	A	38.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=39.42;MQ0=4;OQ=1274.78;QD=31.87;SB=-484.63	GT:AD:DP:GL:GQ	1/1:2,38:33:-131.07,-9.94,-0.01:99
+chr1	1580544	rs9661500	G	A	46.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=56.47;MQ0=0;OQ=1331.19;QD=35.03;SB=-445.09	GT:AD:DP:GL:GQ	1/1:0,38:35:-136.72,-10.55,-0.02:99
+chr1	1581642	.	C	T	0.06	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.20;MQ=10.78;MQ0=31;OQ=96.64;QD=2.06;SB=-42.54	GT:AD:DP:GL:GQ	0/1:28,19:6:-14.76,-1.81,-6.20:43.86
+chr1	1581652	rs61776763	A	G	3.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=2.07;MQ=12.19;MQ0=23;OQ=234.90;QD=5.87;SB=-48.96	GT:AD:DP:GL:GQ	1/1:0,40:8:-27.08,-2.41,-0.00:24.06
+chr1	1581732	.	C	T	10.55	PASS	AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.72;MQ0=12;OQ=388.23;QD=16.18;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,24:11:-42.41,-3.31,-0.00:33.10
+chr1	1581758	rs61776764	C	G	0.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=4.17;MQ=24.63;MQ0=12;OQ=1218.98;QD=26.50;SB=-184.87	GT:AD:DP:GL:GQ	1/1:2,44:29:-125.50,-8.74,-0.02:87.29
+chr1	1582007	rs28625763	T	C	180.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.96;MQ0=0;OQ=1011.19;QD=29.74;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,34:31:-104.72,-9.34,-0.02:93.23
+chr1	1582130	rs4648770	T	G	609.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=44.32;MQ0=0;OQ=2027.74;QD=33.24;SB=-1018.12	GT:AD:DP:GL:GQ	1/1:1,60:58:-206.38,-17.47,-0.02:99
+chr1	1582744	rs4648774	A	C	3.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=4.26;MQ=37.79;MQ0=0;OQ=1971.73;QD=29.87;SB=-941.08	GT:AD:DP:GL:GQ	1/1:1,65:56:-200.78,-16.87,-0.02:99
+chr1	1582886	rs1062088	G	C	0.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=28.33;MQ0=1;OQ=872.58;QD=39.66;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,22:20:-90.85,-6.03,-0.01:60.20
+chr1	1584178	rs1061892	C	T	196.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=53.48;MQ0=0;OQ=3220.76;QD=38.34;SB=-1363.82	GT:AD:DP:GL:GQ	1/1:0,84:80:-325.67,-24.10,-0.02:99
+chr1	1584256	rs6659270	T	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=6;HaplotypeScore=1.24;MQ=50.39;MQ0=3;OQ=904.07;QD=12.05;SB=-396.42	GT:AD:DP:GL:GQ	0/1:40,35:71:-115.08,-21.39,-150.96:99
+chr1	1584361	rs7416520	C	T	137.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=54.09;MQ0=1;OQ=651.60;QD=13.86;SB=-179.69	GT:AD:DP:GL:GQ	0/1:25,22:41:-80.80,-12.36,-66.61:99
+chr1	1585061	rs4307513	A	G	66.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=51.44;MQ0=9;OQ=1311.89;QD=23.85;SB=-662.93	GT:AD:DP:GL:GQ	1/1:0,55:42:-134.81,-12.67,-0.04:99
+chr1	1585263	rs4313339	A	G	2.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=25.65;MQ0=5;OQ=594.23;QD=25.84;SB=-123.88	GT:AD:DP:GL:GQ	1/1:0,23:18:-63.01,-5.42,-0.01:54.15
+chr1	1585730	rs4443835	C	A	38.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=31.44;MQ0=8;OQ=878.16;QD=23.73;SB=-366.86	GT:AD:DP:GL:GQ	1/1:0,37:25:-91.41,-7.53,-0.01:75.22
+chr1	1586059	rs1109644	C	T	45.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=26.30;MQ0=10;OQ=1336.40;QD=26.73;SB=-334.34	GT:AD:DP:GL:GQ	1/1:3,47:35:-137.24,-10.55,-0.01:99
+chr1	1586167	rs1109645	G	A	15.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=25.64;MQ0=10;OQ=920.81;QD=25.58;SB=-127.66	GT:AD:DP:GL:GQ	1/1:5,31:24:-95.67,-7.23,-0.01:72.23
+chr1	1586837	rs4074020	C	T	96.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=59.56;MQ0=0;OQ=1972.50;QD=37.93;SB=-886.69	GT:AD:DP:GL:GQ	1/1:0,52:51:-200.86,-15.37,-0.02:99
+chr1	1588296	.	A	C	37.76	DPFilter;Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=3.93;MQ=44.22;MQ0=1;QD=2.36;SB=20.08	GT:AD:DP:GL:GQ	0/1:12,4:13:-10.98,-3.92,-35.85:70.59
+chr1	1588297	.	C	T	55.71	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=2;HaplotypeScore=3.93;MQ=44.22;MQ0=1;QD=3.48;SB=17.08	GT:AD:DP:GL:GQ	0/1:12,4:12:-12.47,-3.61,-34.17:88.55
+chr1	1588300	.	G	T	70.59	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=2;HaplotypeScore=3.93;MQ=44.22;MQ0=1;QD=4.41;SB=-0.98	GT:AD:DP:GL:GQ	0/1:12,4:13:-14.26,-3.92,-32.75:99
+chr1	1588313	.	A	G	0.48	PASS	AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=34.54;MQ0=0;OQ=106.39;QD=17.73;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,6:4:-14.17,-1.20,-0.00:12.04
+chr1	1588430	.	A	C	41.05	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=1;HaplotypeScore=7.96;MQ=16.51;MQ0=4;QD=5.86;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,5:2:-7.51,-0.60,-0.00:6.02
+chr1	1588435	.	G	A	88.13	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=3.96;MQ=17.24;MQ0=5;QD=8.81;SB=-10.00	GT:AD:DP:GL:GQ	1/1:5,5:3:-12.30,-0.90,-0.00:9.03
+chr1	1588436	.	C	T	85.79	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=17.47;MQ0=5;QD=9.53;SB=-10.00	GT:AD:DP:GL:GQ	1/1:4,5:3:-12.07,-0.90,-0.00:9.03
+chr1	1588443	.	T	A	229.32	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=32.72;MQ0=5;QD=15.29;SB=-115.17	GT:AD:DP:GL:GQ	1/1:5,10:7:-26.51,-2.11,-0.00:21.07
+chr1	1589024	rs6604981	A	G	620.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.22;MQ0=0;OQ=1995.26;QD=35.00;SB=-949.98	GT:AD:DP:GL:GQ	1/1:0,57:56:-203.13,-16.87,-0.02:99
+chr1	1589224	rs6662227	A	G	24.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=48.28;MQ0=4;OQ=837.14;QD=23.92;SB=-301.43	GT:AD:DP:GL:GQ	1/1:0,35:27:-87.33,-8.14,-0.03:81.18
+chr1	1589250	.	A	G	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=2;HaplotypeScore=3.35;MQ=44.60;MQ0=6;OQ=197.93;QD=4.95;SB=-12.85	GT:AD:DP:GL:GQ	0/1:24,16:34:-33.32,-10.25,-92.46:99
+chr1	1589410	rs12725286	C	T	1.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=10.99;MQ=39.64;MQ0=8;OQ=1191.02;QD=13.38;SB=-569.58	GT:AD:DP:GL:GQ	0/1:50,39:71:-143.77,-21.38,-134.51:99
+chr1	1589675	rs12729295	C	T	309.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.48;MQ0=3;OQ=671.60;QD=8.72;SB=-350.30	GT:AD:DP:GL:GQ	0/1:53,24:68:-90.94,-20.50,-145.90:99
+chr1	1589751	rs2072923	A	G	247.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=29.67;MQ0=6;OQ=1186.35;QD=17.98;SB=-547.83	GT:AD:DP:GL:GQ	0/1:14,52:56:-138.81,-16.89,-48.69:99
+chr1	1589844	.	C	T	0.07	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=10.53;MQ=52.48;MQ0=3;OQ=898.69;QD=17.28;SB=-297.81	GT:AD:DP:GL:GQ	0/1:24,28:47:-107.32,-14.16,-70.31:99
+chr1	1589914	.	C	G	0.11	PASS	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=2;HaplotypeScore=0.33;MQ=46.80;MQ0=0;OQ=573.53;QD=6.52;SB=39.39	GT:AD:DP:GL:GQ	0/1:67,21:88:-87.20,-26.56,-264.39:99
+chr1	1589924	.	G	A	1.33	PASS	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=1;HaplotypeScore=0.49;MQ=46.92;MQ0=0;OQ=633.71;QD=6.67;SB=49.65	GT:AD:DP:GL:GQ	0/1:70,25:92:-94.37,-27.71,-247.48:99
+chr1	1590019	.	C	G	30.30	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=49.37;MQ0=3;OQ=641.05;QD=9.29;SB=-314.06	GT:AD:DP:GL:GQ	0/1:47,21:64:-90.20,-22.81,-187.56:99
+chr1	1590023	.	C	T	0.46	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=8.72;MQ=48.76;MQ0=3;OQ=551.31;QD=8.89;SB=-275.75	GT:AD:DP:GL:GQ	0/1:40,22:54:-74.68,-16.27,-125.00:99
+chr1	1590878	.	G	A	29.06	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=58.63;MQ0=0;OQ=418.19;QD=12.30;SB=-160.22	GT:AD:DP:GL:GQ	0/1:18,16:32:-54.75,-9.64,-59.96:99
+chr1	1590915	.	G	A	47.89	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.20;MQ0=0;OQ=322.06;QD=8.26;SB=-141.18	GT:AD:DP:GL:GQ	0/1:27,12:38:-46.95,-11.46,-84.40:99
+chr1	1592399	rs4648609	G	C	54.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=906.62;QD=20.60;SB=-310.97	GT:AD:DP:GL:GQ	0/1:19,25:42:-106.61,-12.66,-75.02:99
+chr1	1592450	rs4233029	C	T	90.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.31;MQ=60.00;MQ0=0;OQ=849.63;QD=19.76;SB=-437.98	GT:AD:DP:GL:GQ	0/1:15,28:37:-99.40,-11.15,-39.71:99
+chr1	1592650	rs4639697	G	T	61.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=1.87;MQ=58.92;MQ0=0;OQ=2757.17;QD=35.35;SB=-1369.99	GT:AD:DP:GL:GQ	1/1:1,77:76:-279.32,-22.89,-0.02:99
+chr1	1593099	rs11523819	G	A	285.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.60;MQ0=0;OQ=1010.41;QD=14.43;SB=-280.29	GT:AD:DP:GL:GQ	0/1:39,31:68:-124.83,-20.51,-114.09:99
+chr1	1593297	rs6699975	G	T	40.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=6.04;MQ=58.42;MQ0=0;OQ=872.27;QD=15.58;SB=-424.16	GT:AD:DP:GL:GQ	0/1:24,32:48:-104.97,-14.46,-59.27:99
+chr1	1594362	rs36048328	G	A	212.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=53.76;MQ0=0;OQ=936.15;QD=14.86;SB=-437.40	GT:AD:DP:GL:GQ	0/1:33,30:61:-115.28,-18.38,-109.00:99
+chr1	1595120	rs12736155	A	C	482.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=48.94;MQ0=1;OQ=857.21;QD=13.61;SB=-454.19	GT:AD:DP:GL:GQ	0/1:31,32:60:-107.08,-18.07,-108.87:99
+chr1	1595458	.	A	G	4.92	PASS	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=5.30;MQ=27.16;MQ0=16;OQ=685.03;QD=9.01;SB=-336.52	GT:AD:DP:GL:GQ	0/1:42,34:52:-87.45,-15.67,-106.28:99
+chr1	1595935	.	C	A	13.79	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=13;HaplotypeScore=5.11;MQ=47.25;MQ0=0;QD=0.27;SB=44.14	GT:AD:DP:GL:GQ	0/1:44,8:42:-17.30,-12.66,-119.04:46.44
+chr1	1596150	rs28678861	G	C	0.01	FDRtranche2.00to10.00	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=6;HaplotypeScore=0.16;MQ=35.71;MQ0=1;OQ=1428.28;QD=37.59;SB=-739.75	GT:AD:DP:GL:GQ	1/1:0,38:34:-146.42,-10.25,-0.01:99
+chr1	1596170	rs61776786	G	A	218.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.46;MQ=33.82;MQ0=1;OQ=367.66;QD=11.86;SB=-172.25	GT:AD:DP:GL:GQ	0/1:17,14:26:-47.89,-7.84,-41.82:99
+chr1	1596393	.	A	G	1.96	PASS	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=2;HaplotypeScore=1.79;MQ=38.63;MQ0=2;OQ=223.84;QD=8.95;SB=-123.74	GT:AD:DP:GL:GQ	0/1:13,12:22:-32.30,-6.64,-46.25:99
+chr1	1596434	rs61776787	A	G	239.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=27.74;MQ0=11;OQ=461.68;QD=12.82;SB=-213.08	GT:AD:DP:GL:GQ	1/1:0,36:16:-49.77,-4.83,-0.02:48.10
+chr1	1598092	rs61776790	C	T	85.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=16.88;MQ0=18;OQ=268.46;QD=6.88;SB=-142.62	GT:AD:DP:GL:GQ	0/1:27,12:20:-36.16,-6.04,-33.65:99
+chr1	1599022	rs12724172	T	G	248.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=48.86;MQ0=1;OQ=792.00;QD=12.00;SB=-236.82	GT:AD:DP:GL:GQ	0/1:30,36:59:-100.27,-17.78,-99.33:99
+chr1	1599028	rs12757736	A	T	344.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=49.16;MQ0=1;OQ=842.96;QD=13.82;SB=-342.44	GT:AD:DP:GL:GQ	0/1:27,34:53:-103.55,-15.97,-87.26:99
+chr1	1600387	rs7544851	T	C	182.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=59.17;MQ0=0;OQ=618.77;QD=11.05;SB=-250.34	GT:AD:DP:GL:GQ	0/1:28,28:48:-79.63,-14.47,-94.46:99
+chr1	1601295	rs6700884	A	G	128.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=57.79;MQ0=0;OQ=747.49;QD=15.90;SB=-253.32	GT:AD:DP:GL:GQ	0/1:21,26:46:-91.89,-13.86,-83.83:99
+chr1	1601516	rs6695303	T	C	234.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.59;MQ=57.63;MQ0=0;OQ=837.86;QD=14.45;SB=-344.58	GT:AD:DP:GL:GQ	0/1:27,31:54:-103.34,-16.27,-95.10:99
+chr1	1601858	rs4074196	A	G	175.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=56.26;MQ0=0;OQ=386.06;QD=8.39;SB=-209.64	GT:AD:DP:GL:GQ	0/1:26,20:39:-53.65,-11.76,-84.70:99
+chr1	1601974	rs4074197	C	T	305.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.98;MQ0=0;OQ=818.07;QD=17.41;SB=-411.47	GT:AD:DP:GL:GQ	0/1:22,25:46:-98.95,-13.86,-71.35:99
+chr1	1602466	rs4074198	G	A	258.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.07;MQ0=0;OQ=1998.12;QD=19.98;SB=-732.09	GT:AD:DP:GL:GQ	0/1:43,57:99:-232.92,-29.82,-143.69:99
+chr1	1602672	rs4076580	T	G	4.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=6.99;MQ=58.71;MQ0=0;OQ=379.11;QD=10.53;SB=-115.90	GT:AD:DP:GL:GQ	0/1:20,16:35:-51.74,-10.54,-71.19:99
+chr1	1603230	.	C	A	105.90	PASS	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.30;MQ0=0;OQ=439.60;QD=13.32;SB=-227.94	GT:AD:DP:GL:GQ	0/1:17,16:31:-56.59,-9.34,-45.91:99
+chr1	1605211	rs7520934	A	C	437.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=732.80;QD=12.42;SB=-285.83	GT:AD:DP:GL:GQ	0/1:28,31:56:-93.43,-16.87,-99.80:99
+chr1	1605568	rs28774670	T	C	204.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.50;MQ0=0;OQ=582.27;QD=9.87;SB=-203.22	GT:AD:DP:GL:GQ	0/1:33,26:57:-78.69,-17.18,-127.49:99
+chr1	1605610	rs28435953	G	C	130.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.47;MQ=58.73;MQ0=0;OQ=779.25;QD=14.17;SB=-322.40	GT:AD:DP:GL:GQ	0/1:29,26:52:-96.88,-15.68,-122.76:99
+chr1	1605921	rs28464677	G	A	40.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=6.09;MQ=58.05;MQ0=1;OQ=855.32;QD=14.50;SB=-377.37	GT:AD:DP:GL:GQ	0/1:31,28:56:-105.70,-16.88,-92.60:99
+chr1	1606119	rs61776792	G	C	0.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=15.64;MQ=49.02;MQ0=1;OQ=469.22;QD=9.02;SB=-238.10	GT:AD:DP:GL:GQ	0/1:28,21:33:-60.17,-9.96,-72.09:99
+chr1	1606735	.	G	A	20.16	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=18;HaplotypeScore=5.53;MQ=52.51;MQ0=0;QD=0.29;SB=62.21	GT:AD:DP:GL:GQ	0/1:55,14:41:-17.65,-12.36,-123.60:52.96
+chr1	1607449	rs28736713	T	G	133.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.99;MQ=58.63;MQ0=0;OQ=1023.89;QD=16.00;SB=-507.80	GT:AD:DP:GL:GQ	0/1:29,35:64:-124.95,-19.28,-105.76:99
+chr1	1607623	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=18;HaplotypeScore=7.66;MQ=51.83;MQ0=1;OQ=52.14;QD=1.00;SB=0.53	GT:AD:DP:GL:GQ	0/1:41,11:37:-19.66,-11.16,-103.64:84.98
+chr1	1608184	rs28367203	T	C	304.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.41;MQ0=0;OQ=680.60;QD=12.15;SB=-333.30	GT:AD:DP:GL:GQ	0/1:31,25:55:-87.91,-16.57,-127.27:99
+chr1	1608363	rs28463291	C	T	163.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1453.08;QD=22.02;SB=-689.01	GT:AD:DP:GL:GQ	0/1:22,44:66:-168.48,-19.89,-77.76:99
+chr1	1608455	rs28366981	A	G	89.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=1.13;MQ=57.97;MQ0=0;OQ=661.92;QD=12.98;SB=-317.10	GT:AD:DP:GL:GQ	0/1:21,30:45:-83.04,-13.57,-76.52:99
+chr1	1608461	rs28561498	G	T	18.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=3.73;MQ=57.75;MQ0=0;OQ=745.42;QD=16.20;SB=-317.33	GT:AD:DP:GL:GQ	0/1:20,26:44:-91.08,-13.26,-59.03:99
+chr1	1608538	rs28541555	T	G	156.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=57.89;MQ0=0;OQ=606.69;QD=12.91;SB=-204.78	GT:AD:DP:GL:GQ	0/1:20,27:44:-77.21,-13.26,-75.77:99
+chr1	1608823	rs4648780	T	C	124.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=58.99;MQ0=0;OQ=1965.86;QD=28.49;SB=-779.58	GT:AD:DP:GL:GQ	1/1:0,69:63:-200.23,-19.00,-0.06:99
+chr1	1608945	rs7524863	G	A	246.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=57.51;MQ0=0;OQ=796.58;QD=15.03;SB=-348.35	GT:AD:DP:GL:GQ	0/1:28,25:52:-98.61,-15.67,-100.29:99
+chr1	1609404	rs28487995	G	A	270.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=56.05;MQ0=0;OQ=943.08;QD=14.97;SB=-428.82	GT:AD:DP:GL:GQ	0/1:34,29:58:-115.07,-17.48,-93.42:99
+chr1	1609630	rs9442411	T	C	340.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.02;MQ0=2;OQ=562.05;QD=9.37;SB=-254.95	GT:AD:DP:GL:GQ	0/1:29,31:53:-75.47,-15.98,-117.16:99
+chr1	1609711	rs61776794	G	C	177	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=50.27;MQ0=2;OQ=557.29;QD=11.15;SB=-303.13	GT:AD:DP:GL:GQ	0/1:25,25:40:-71.08,-12.07,-91.96:99
+chr1	1609833	.	C	T	8.33	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.64;MQ=46.17;MQ0=4;OQ=546.56;QD=9.42;SB=-24.96	GT:AD:DP:GL:GQ	0/1:34,24:50:-73.01,-15.07,-102.31:99
+chr1	1609872	.	T	A	2.74	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=43.11;MQ0=2;OQ=308.49;QD=7.17;SB=35.14	GT:AD:DP:GL:GQ	0/1:26,17:38:-45.58,-11.45,-97.07:99
+chr1	1609888	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=6.91;MQ=43.11;MQ0=0;OQ=145.44;QD=3.93;SB=26.10	GT:AD:DP:GL:GQ	0/1:23,14:31:-27.18,-9.35,-84.75:99
+chr1	1609946	.	A	G	0.35	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=42.17;MQ0=4;OQ=138.81;QD=3.39;SB=-12.69	GT:AD:DP:GL:GQ	0/1:29,12:37:-28.31,-11.14,-120.75:99
+chr1	1610085	rs61776797	A	G	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=4;HaplotypeScore=1.23;MQ=52.83;MQ0=0;OQ=168.50;QD=4.32;SB=29.12	GT:AD:DP:GL:GQ	0/1:29,10:36:-30.98,-10.85,-111.33:99
+chr1	1610720	rs3737622	A	G	151.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=52.83;MQ0=0;OQ=742.56;QD=16.14;SB=-328.41	GT:AD:DP:GL:GQ	0/1:21,25:45:-91.09,-13.55,-80.03:99
+chr1	1610745	rs3737623	C	T	272.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=54.47;MQ0=0;OQ=1103.20;QD=18.09;SB=-448.99	GT:AD:DP:GL:GQ	0/1:28,33:59:-131.40,-17.79,-81.29:99
+chr1	1610764	rs3737624	G	A	559.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.35;MQ0=0;OQ=1181.67;QD=16.88;SB=-410.16	GT:AD:DP:GL:GQ	0/1:34,36:69:-142.24,-20.78,-119.02:99
+chr1	1612040	.	T	A	0.13	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=3;HaplotypeScore=1.10;MQ=42.64;MQ0=1;OQ=306.88;QD=6.39;SB=17.08	GT:AD:DP:GL:GQ	0/1:34,14:39:-45.73,-11.76,-89.73:99
+chr1	1612676	rs1855706	C	T	48.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=4.57;MQ=18.63;MQ0=42;OQ=747.37;QD=8.59;SB=-370.40	GT:AD:DP:GL:GQ	0/1:52,35:41:-90.38,-12.36,-60.67:99
+chr1	1612716	rs61776798	T	C	0.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=7.54;MQ0=54;OQ=87.83;QD=1.39;SB=-10.00	GT:AD:DP:GL:GQ	0/1:40,23:6:-13.87,-1.81,-8.21:64.05
+chr1	1613585	rs7542306	C	A	20.92	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=15.32;MQ0=21;QD=0.67;SB=-10.00	GT:AD:DP:GL:GQ	0/1:18,13:6:-7.18,-1.81,-14.53:53.72
+chr1	1614256	rs368915	T	G	26.47	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=20.52;MQ0=9;QD=2.04;SB=-32.98	GT:AD:DP:GL:GQ	1/1:0,13:2:-6.06,-0.60,-0.00:6
+chr1	1614726	rs4648651	G	A	96.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.04;MQ0=5;OQ=94.30;QD=5.55;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,5:9:-15.42,-2.71,-17.14:99
+chr1	1615466	rs35947799	G	A	107.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=52.41;MQ0=0;OQ=601.60;QD=18.23;SB=-258.27	GT:AD:DP:GL:GQ	0/1:13,20:32:-73.09,-9.64,-46.27:99
+chr1	1616758	rs28587348	A	G	239	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=22.66;MQ0=5;OQ=648.18;QD=9.53;SB=-227.25	GT:AD:DP:GL:GQ	0/1:39,28:59:-88.06,-19.96,-129.14:99
+chr1	1617046	rs1932228	C	T	15.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=15.02;MQ0=16;OQ=210.38;QD=4.29;SB=-111.61	GT:AD:DP:GL:GQ	0/1:30,19:14:-28.54,-4.22,-22.09:99
+chr1	1617416	rs61776801	G	A	266.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=37.27;MQ0=15;OQ=982.95;QD=15.60;SB=-353.39	GT:AD:DP:GL:GQ	0/1:28,35:47:-115.75,-14.17,-56.63:99
+chr1	1617665	rs601141	A	C	373.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=54.30;MQ0=0;OQ=987.22;QD=15.19;SB=-461.24	GT:AD:DP:GL:GQ	0/1:31,34:63:-120.98,-18.98,-104.99:99
+chr1	1618057	rs61776802	A	G	60.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=53.96;MQ0=1;OQ=690.37;QD=9.86;SB=-238.28	GT:AD:DP:GL:GQ	0/1:36,33:62:-91.01,-18.69,-134.09:99
+chr1	1618313	rs61776803	G	T	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=3;HaplotypeScore=2.46;MQ=39.85;MQ0=11;OQ=285.62;QD=3.97;SB=-133.03	GT:AD:DP:GL:GQ	0/1:51,21:59:-49.62,-17.77,-159.76:99
+chr1	1618571	rs12081891	G	A	12.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=28.69;MQ0=14;OQ=348.19;QD=5.36;SB=-177.80	GT:AD:DP:GL:GQ	0/1:47,18:38:-49.56,-11.46,-83.32:99
+chr1	1618766	rs61776804	G	A	86.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=43.94;MQ0=0;OQ=732.16;QD=19.27;SB=-352.49	GT:AD:DP:GL:GQ	0/1:16,22:37:-87.65,-11.15,-51.61:99
+chr1	1619321	rs4648621	G	A	136.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=27.57;MQ0=5;OQ=508.21;QD=13.37;SB=-144.61	GT:AD:DP:GL:GQ	0/1:18,20:30:-63.15,-9.04,-45.60:99
+chr1	1619347	rs34716550	T	C	0.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=6.10;MQ=29.73;MQ0=3;OQ=380.00;QD=9.05;SB=-24.63	GT:AD:DP:GL:GQ	0/1:23,19:33:-51.24,-9.95,-72.01:99
+chr1	1624864	rs874516	T	C	339.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=46.52;MQ0=1;OQ=784.43;QD=15.38;SB=-383.28	GT:AD:DP:GL:GQ	0/1:22,29:49:-96.49,-14.76,-89.37:99
+chr1	1625479	rs2076329	T	C	1.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=3.63;MQ=58.85;MQ0=0;OQ=346.77;QD=7.08;SB=-173.37	GT:AD:DP:GL:GQ	0/1:30,19:42:-50.63,-12.67,-103.10:99
+chr1	1625609	rs1136997	C	A	28.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.88;MQ=49.57;MQ0=0;OQ=129.32;QD=4.62;SB=-74.73	GT:AD:DP:GL:GQ	0/1:19,9:24:-23.45,-7.23,-57.11:99
+chr1	1625904	rs1059822	G	A	133.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=49.02;MQ0=1;OQ=290.88;QD=7.65;SB=-88.57	GT:AD:DP:GL:GQ	0/1:22,16:33:-42.33,-9.95,-69.30:99
+chr1	1626134	rs2179381	C	T	246.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=42.93;MQ0=0;OQ=354.22;QD=9.84;SB=-190.16	GT:AD:DP:GL:GQ	0/1:22,14:30:-47.74,-9.04,-64.17:99
+chr1	1626190	.	G	A	71.25	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=48.48;MQ0=0;OQ=619.32;QD=15.48;SB=-321.82	GT:AD:DP:GL:GQ	0/1:21,19:40:-77.26,-12.05,-77.19:99
+chr1	1627098	rs61774911	A	G	6.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.86;MQ0=3;OQ=57.73;QD=2.14;SB=17.07	GT:AD:DP:GL:GQ	0/1:19,8:19:-14.79,-5.73,-53.94:90.57
+chr1	1627115	rs9439480	A	G	25.79	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=40.42;MQ0=0;QD=1.07;SB=26.10	GT:AD:DP:GL:GQ	0/1:18,5:21:-12.19,-6.33,-66.21:58.62
+chr1	1627865	rs17162876	G	C	61.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=50.90;MQ0=0;OQ=596.59;QD=13.56;SB=-287.98	GT:AD:DP:GL:GQ	0/1:25,19:41:-75.32,-12.38,-88.05:99
+chr1	1628397	.	C	T	6.47	PASS	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=17.03;MQ0=21;OQ=258.72;QD=7.19;SB=-86.31	GT:AD:DP:GL:GQ	0/1:19,17:11:-32.47,-3.31,-10.93:76.22
+chr1	1628516	.	G	A	0.42	PASS	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=23.14;MQ0=15;OQ=161.97;QD=3.60;SB=-32.64	GT:AD:DP:GL:GQ	0/1:32,13:24:-26.72,-7.23,-54.65:99
+chr1	1629661	.	T	C	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=34.50;MQ0=9;OQ=82.09;QD=2.22;SB=-48.26	GT:AD:DP:GL:GQ	0/1:21,16:24:-18.73,-7.24,-70.81:99
+chr1	1631887	rs61776845	C	T	226.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.12;MQ0=0;OQ=487.31;QD=34.81;SB=-143.63	GT:AD:DP:GL:GQ	1/1:0,14:14:-52.32,-4.22,-0.01:42.13
+chr1	1633129	rs6688326	C	A	4.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=11.56;MQ0=25;OQ=150.41;QD=4.30;SB=-10.00	GT:AD:DP:GL:GQ	0/1:25,10:8:-20.73,-2.41,-7.32:49.07
+chr1	1634432	rs2143105	A	G	2.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=3.86;MQ=24.63;MQ0=4;OQ=286.53;QD=16.85;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,17:11:-32.26,-3.33,-0.02:33.05
+chr1	1634696	rs2179382	G	A	8.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=3.64;MQ=32.34;MQ0=16;OQ=279.13;QD=3.58;SB=-95.45	GT:AD:DP:GL:GQ	0/1:61,16:59:-48.98,-17.78,-155.91:99
+chr1	1634768	rs2179383	C	T	205.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=11.72;MQ0=13;OQ=127.00;QD=6.35;SB=-51.67	GT:AD:DP:GL:GQ	1/1:0,20:4:-16.23,-1.20,-0.00:12.04
+chr1	1634910	.	C	T	73.11	PASS	AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=12.98;MQ0=22;OQ=295.97;QD=9.25;SB=-135.01	GT:AD:DP:GL:GQ	1/1:0,32:8:-33.18,-2.41,-0.00:24.08
+chr1	1634953	.	C	T	62.81	PASS	AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.86;MQ0=18;OQ=384.85;QD=13.27;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,29:10:-42.07,-3.01,-0.00:30.10
+chr1	1634973	.	T	C	4.22	PASS	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.05;MQ0=18;OQ=118.84;QD=3.71;SB=-10.00	GT:AD:DP:GL:GQ	0/1:22,10:13:-19.08,-3.92,-33.24:99
+chr1	1634975	.	C	T	14.66	PASS	AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.05;MQ0=18;OQ=504.84;QD=15.78;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,32:13:-54.07,-3.92,-0.00:39.13
+chr1	1635050	rs4279785	T	C	293.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=22.94;MQ0=12;OQ=364.98;QD=8.90;SB=-161.33	GT:AD:DP:GL:GQ	0/1:23,18:28:-48.21,-8.43,-62.26:99
+chr1	1635547	rs61774919	G	A	162.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=14.59;MQ0=11;OQ=173.64;QD=7.55;SB=-50.56	GT:AD:DP:GL:GQ	1/1:6,17:5:-20.92,-1.51,-0.00:15.05
+chr1	1635860	rs3819996	T	C	34.28	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=13.67;MQ0=7;QD=3.81;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,9:2:-6.84,-0.60,-0.00:6.02
+chr1	1635866	rs3819997	A	G	27.83	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=14.50;MQ0=6;QD=3.48;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,8:2:-6.19,-0.60,-0.00:6.01
+chr1	1635934	rs3819998	A	G	17.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=5.04;MQ=31.93;MQ0=9;OQ=462.29;QD=12.84;SB=-95.99	GT:AD:DP:GL:GQ	0/1:9,27:21:-55.85,-6.34,-11.59:52.52
+chr1	1635937	rs3819999	G	T	0.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=5.04;MQ=31.93;MQ0=9;OQ=663.10;QD=18.42;SB=-104.11	GT:AD:DP:GL:GQ	0/1:9,26:24:-76.82,-7.23,-11.28:40.49
+chr1	1635973	rs3820000	G	C	54.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.49;MQ0=15;OQ=883.63;QD=21.55;SB=-127.19	GT:AD:DP:GL:GQ	1/1:8,33:25:-95.91,-7.54,-3.96:35.78
+chr1	1636091	rs3820002	T	C	108.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.55;MQ0=2;OQ=418.10;QD=27.87;SB=-161.84	GT:AD:DP:GL:GQ	1/1:0,15:13:-45.40,-3.92,-0.01:39.10
+chr1	1636096	rs61776849	C	T	171.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.06;MQ0=2;OQ=513.34;QD=30.20;SB=-178.68	GT:AD:DP:GL:GQ	1/1:0,17:14:-54.92,-4.22,-0.01:42.13
+chr1	1636231	rs61776850	G	T	45.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=2.84;MQ=41.85;MQ0=7;OQ=641.89;QD=13.95;SB=-342.30	GT:AD:DP:GL:GQ	0/1:20,26:39:-79.22,-11.75,-58.73:99
+chr1	1636287	rs61776851	T	G	219.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=36.80;MQ0=8;OQ=1107.10;QD=20.13;SB=-508.74	GT:AD:DP:GL:GQ	1/1:4,51:37:-114.34,-11.16,-0.05:99
+chr1	1636310	rs3820004	G	A	84.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=34.50;MQ0=11;OQ=1585.10;QD=27.33;SB=-811.33	GT:AD:DP:GL:GQ	1/1:6,52:41:-162.11,-12.35,-0.01:99
+chr1	1636434	rs56030177	T	C	84.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=28.90;MQ0=10;OQ=1324.64;QD=27.60;SB=-500.48	GT:AD:DP:GL:GQ	1/1:0,48:38:-136.06,-11.45,-0.01:99
+chr1	1636517	rs760926	T	C	66.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=26.90;MQ0=7;OQ=976.98;QD=25.05;SB=-384.56	GT:AD:DP:GL:GQ	1/1:1,38:28:-101.29,-8.43,-0.01:84.25
+chr1	1636649	rs760927	T	C	127.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.47;MQ0=5;OQ=898.10;QD=25.66;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,35:25:-93.41,-7.53,-0.01:75.22
+chr1	1636735	.	C	G	66.44	PASS	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=39.28;MQ0=9;OQ=1254.01;QD=12.80;SB=-309.31	GT:AD:DP:GL:GQ	0/1:56,42:83:-153.70,-25.01,-208.71:99
+chr1	1636777	.	C	T	31.32	PASS	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=38.96;MQ0=9;OQ=1301.14;QD=13.41;SB=-647.75	GT:AD:DP:GL:GQ	0/1:49,48:84:-158.72,-25.32,-141.36:99
+chr1	1636840	rs61776853	A	C	1.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=3;HaplotypeScore=0.97;MQ=31.48;MQ0=5;OQ=997.06;QD=27.70;SB=-256.95	GT:AD:DP:GL:GQ	1/1:0,36:30:-103.31,-9.04,-0.02:90.22
+chr1	1636845	rs61776854	C	T	13.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=31.12;MQ0=5;OQ=595.02;QD=17.50;SB=-27.62	GT:AD:DP:GL:GQ	0/1:11,23:28:-71.23,-8.44,-30.58:99
+chr1	1636852	rs35642458	G	A	71.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.10;MQ0=4;OQ=612.21;QD=24.49;SB=-39.52	GT:AD:DP:GL:GQ	0/1:3,22:20:-70.53,-6.02,-10.71:46.85
+chr1	1637044	rs61073446	G	A	19.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=5.47;MQ=48.10;MQ0=1;OQ=604.36;QD=8.06;SB=-316.73	GT:AD:DP:GL:GQ	0/1:54,21:68:-84.21,-20.50,-156.95:99
+chr1	1637060	.	G	C	0.16	PASS	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=1;HaplotypeScore=3.23;MQ=46.92;MQ0=1;OQ=770.35;QD=8.37;SB=83.29	GT:AD:DP:GL:GQ	0/1:66,26:89:-107.18,-26.86,-257.87:99
+chr1	1637092	.	A	G	13.80	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=45.24;MQ0=3;OQ=524.47;QD=7.09;SB=62.24	GT:AD:DP:GL:GQ	0/1:50,24:71:-77.11,-21.38,-201.71:99
+chr1	1637137	rs4437818	C	T	70.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.48;MQ=37.21;MQ0=3;OQ=419.91;QD=7.63;SB=-236.03	GT:AD:DP:GL:GQ	0/1:38,17:49:-60.03,-14.76,-127.40:99
+chr1	1637159	rs760928	C	T	610.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.78;MQ0=3;OQ=1773.57;QD=35.47;SB=-891.67	GT:AD:DP:GL:GQ	1/1:0,50:45:-180.95,-13.56,-0.01:99
+chr1	1637161	rs760929	G	A	499.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=39.49;MQ0=3;OQ=1819.83;QD=36.40;SB=-852.64	GT:AD:DP:GL:GQ	1/1:0,50:45:-185.58,-13.55,-0.01:99
+chr1	1637349	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=1;HaplotypeScore=12.15;MQ=53.21;MQ0=0;OQ=258.06;QD=3.04;SB=74.27	GT:AD:DP:GL:GQ	0/1:68,17:73:-51.13,-22.04,-238.97:99
+chr1	1637350	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=13.99;MQ=53.21;MQ0=0;OQ=156.60;QD=1.84;SB=74.27	GT:AD:DP:GL:GQ	0/1:68,16:78:-42.44,-23.50,-258.99:99
+chr1	1637384	rs760930	C	T	155.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=57.38;MQ0=0;OQ=2369.71;QD=38.22;SB=-867.02	GT:AD:DP:GL:GQ	1/1:0,62:60:-240.58,-18.08,-0.02:99
+chr1	1637388	rs760931	G	C	174.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=56.72;MQ0=0;OQ=2115.79;QD=36.48;SB=-781.25	GT:AD:DP:GL:GQ	1/1:0,58:53:-215.20,-15.99,-0.03:99
+chr1	1637546	rs56081394	A	C	94.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=52.34;MQ0=0;OQ=2774.94;QD=32.65;SB=-1180.71	GT:AD:DP:GL:GQ	1/1:0,85:81:-281.12,-24.40,-0.04:99
+chr1	1637613	.	C	T	21.89	LowQual	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=3;HaplotypeScore=1.05;MQ=50.67;MQ0=0;QD=0.27;SB=-29.39	GT:AD:DP:GL:GQ	0/1:68,12:72:-27.16,-21.69,-231.62:54.70
+chr1	1637638	.	C	G	0.51	PASS	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=4.82;MQ=47.75;MQ0=0;OQ=459.74;QD=4.84;SB=-189.88	GT:AD:DP:GL:GQ	0/1:65,30:83:-74.29,-25.03,-272.64:99
+chr1	1637674	.	T	C	96.11	PASS	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.42;MQ0=0;OQ=794.87;QD=7.87;SB=-336.87	GT:AD:DP:GL:GQ	0/1:55,46:82:-107.47,-24.70,-217.72:99
+chr1	1637731	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=1;HaplotypeScore=1.79;MQ=47.58;MQ0=0;OQ=197.23;QD=2.38;SB=-124.83	GT:AD:DP:GL:GQ	0/1:61,22:74:-45.30,-22.29,-250.27:99
+chr1	1637788	rs1883424	A	G	452.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.70;MQ0=0;OQ=1180.37;QD=13.26;SB=-539.57	GT:AD:DP:GL:GQ	0/1:48,41:89:-148.13,-26.81,-196.69:99
+chr1	1637887	rs61776857	T	C	8.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=37.62;MQ0=3;OQ=1207.11;QD=23.21;SB=-211.69	GT:AD:DP:GL:GQ	1/1:2,49:41:-124.35,-12.38,-0.05:99
+chr1	1638000	.	G	C	4.04	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=49.72;MQ0=1;OQ=363.96;QD=6.17;SB=-28.72	GT:AD:DP:GL:GQ	0/1:37,21:48:-56.87,-17.19,-155.52:99
+chr1	1638008	.	G	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=51.97;MQ0=1;OQ=62.73;QD=1.08;SB=29.80	GT:AD:DP:GL:GQ	0/1:41,17:44:-22.82,-13.26,-168.23:95.57
+chr1	1638068	rs61776858	C	T	414.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.78;MQ0=0;OQ=1645.34;QD=38.26;SB=-705.35	GT:AD:DP:GL:GQ	1/1:1,42:42:-168.13,-12.65,-0.01:99
+chr1	1638095	rs28722732	A	C	115.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=48.13;MQ0=1;OQ=1285.24;QD=32.95;SB=-522.05	GT:AD:DP:GL:GQ	1/1:1,38:38:-132.12,-11.45,-0.02:99
+chr1	1638236	.	G	A	17.91	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=2;HaplotypeScore=8.77;MQ=38.97;MQ0=0;QD=0.34;SB=23.08	GT:AD:DP:GL:GQ	0/1:43,6:25:-15.81,-10.75,-74.55:50.67
+chr1	1638252	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=56.73;MQ=41.68;MQ0=0;OQ=220.25;QD=3.86;SB=17.08	GT:AD:DP:GL:GQ	0/1:43,13:37:-36.47,-11.16,-97.19:99
+chr1	1638265	rs28669101	A	G	1.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=5.08;MQ=44.94;MQ0=1;OQ=1841.80;QD=27.49;SB=-530.20	GT:AD:DP:GL:GQ	1/1:1,66:52:-187.79,-15.67,-0.02:99
+chr1	1638282	.	T	C	372.16	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=2;HaplotypeScore=20.32;MQ=48.81;MQ0=1;QD=5.64;SB=53.20	GT:AD:DP:GL:GQ	0/1:48,18:62:-59.18,-18.68,-176.85:99
+chr1	1638285	.	G	A	362.16	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=22.88;MQ=49.05;MQ0=1;QD=5.57;SB=50.16	GT:AD:DP:GL:GQ	0/1:45,17:60:-57.59,-18.09,-158.00:99
+chr1	1638291	.	G	T	350.74	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=1;HaplotypeScore=36.28;MQ=47.79;MQ0=1;QD=5.48;SB=47.16	GT:AD:DP:GL:GQ	0/1:46,17:57:-55.53,-17.18,-142.31:99
+chr1	1638353	.	T	C	4.41	PASS	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=49.10;MQ0=0;OQ=579.45;QD=7.24;SB=-118.38	GT:AD:DP:GL:GQ	0/1:52,28:75:-83.82,-22.59,-209.22:99
+chr1	1638397	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=103;Dels=0.02;HRun=4;HaplotypeScore=13.77;MQ=49.39;MQ0=0;OQ=1251.99;QD=12.16;SB=-214.10	GT:AD:DP:GL:GQ	0/1:54,47:95:-156.50,-28.02,-195.84:99
+chr1	1638484	rs61776859	C	A	0.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=1;HaplotypeScore=3.66;MQ=44.01;MQ0=0;OQ=2573.54;QD=19.06;SB=-1062.18	GT:AD:DP:GL:GQ	0/1:54,81:126:-298.59,-37.95,-167.48:99
+chr1	1638485	.	A	G	2.65	PASS	AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=2.76;MQ=44.20;MQ0=0;OQ=954.08;QD=7.07;SB=27.40	GT:AD:DP:GL:GQ	0/1:81,54:124:-136.06,-37.37,-329.92:99
+chr1	1638496	.	A	C	4.42	PASS	AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=43.37;MQ0=0;OQ=1281.45;QD=9.42;SB=-10.58	GT:AD:DP:GL:GQ	0/1:80,56:126:-169.38,-37.95,-296.59:99
+chr1	1638502	.	T	C	3.56	PASS	AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=44.49;MQ0=0;OQ=1373.44;QD=10.25;SB=-79.40	GT:AD:DP:GL:GQ	0/1:76,58:123:-177.67,-37.05,-300.79:99
+chr1	1638544	.	C	T	171.39	PASS	AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=48.39;MQ0=0;OQ=1993.39;QD=14.44;SB=-439.97	GT:AD:DP:GL:GQ	0/1:62,76:123:-239.68,-37.06,-213.30:99
+chr1	1638628	.	C	T	21.95	PASS	AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=49.90;MQ0=0;OQ=1604.78;QD=15.14;SB=-725.65	GT:AD:DP:GL:GQ	0/1:52,53:100:-193.90,-30.14,-170.77:99
+chr1	1638640	.	A	C	22.88	PASS	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=47.54;MQ0=0;OQ=1027.76;QD=10.18;SB=-470.68	GT:AD:DP:GL:GQ	0/1:56,45:93:-134.07,-28.01,-207.58:99
+chr1	1638645	.	G	C	1.18	PASS	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=6.44;MQ=47.94;MQ0=0;OQ=1189.28;QD=12.14;SB=-604.90	GT:AD:DP:GL:GQ	0/1:56,42:91:-149.63,-27.42,-247.05:99
+chr1	1638691	rs61777460	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=113;Dels=0.00;HRun=1;HaplotypeScore=70.95;MQ=45.55;MQ0=0;OQ=1598.01;QD=14.14;SB=-702.52	GT:AD:DP:GL:GQ	0/1:53,60:107:-195.32,-32.23,-214.62:99
+chr1	1638728	.	T	A	0.06	PASS	AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=48.71;MQ0=0;OQ=2481.89;QD=16.22;SB=-1020.86	GT:AD:DP:GL:GQ	0/1:71,82:150:-296.65,-45.18,-270.24:99
+chr1	1638806	rs909824	T	C	0.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=154;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=50.30;MQ0=0;OQ=2209.99;QD=14.35;SB=-996.92	GT:AD:DP:GL:GQ	0/1:79,75:150:-269.47,-45.19,-301.46:99
+chr1	1638825	rs61777461	C	T	0.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=143;Dels=0.00;HRun=1;HaplotypeScore=2.68;MQ=50.48;MQ0=0;OQ=2137.82;QD=14.95;SB=-1070.06	GT:AD:DP:GL:GQ	0/1:71,72:135:-257.74,-40.67,-255.42:99
+chr1	1638946	.	C	T	467.64	SnpCluster	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=32.37;MQ=43.71;MQ0=5;QD=7.19;SB=-205.68	GT:AD:DP:GL:GQ	0/1:44,21:47:-64.21,-14.16,-108.79:99
+chr1	1638954	.	T	C	736.34	SnpCluster	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=21.87;MQ=42.89;MQ0=5;QD=12.70;SB=-358.18	GT:AD:DP:GL:GQ	0/1:23,35:42:-89.58,-12.66,-57.09:99
+chr1	1638955	.	G	A	193.46	SnpCluster	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=28.88;MQ=42.53;MQ0=5;QD=3.39;SB=-66.48	GT:AD:DP:GL:GQ	0/1:44,13:42:-35.29,-12.66,-112.58:99
+chr1	1638965	rs61777464	A	G	0.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=17.05;MQ=41.40;MQ0=5;OQ=280.02;QD=5.83;SB=-138.25	GT:AD:DP:GL:GQ	0/1:30,18:32:-40.93,-9.64,-84.27:99
+chr1	1638997	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=10.71;MQ=41.45;MQ0=4;OQ=154.17;QD=3.08;SB=35.12	GT:AD:DP:GL:GQ	0/1:37,12:37:-29.85,-11.15,-98.68:99
+chr1	1639030	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=25.29;MQ=40.65;MQ0=7;OQ=247.09;QD=2.75;SB=50.20	GT:AD:DP:GL:GQ	0/1:68,21:63:-46.97,-18.98,-193.46:99
+chr1	1639109	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=25.12;MQ=46.53;MQ0=4;OQ=115.22;QD=1.05;SB=83.25	GT:AD:DP:GL:GQ	0/1:96,13:84:-40.14,-25.34,-234.06:99
+chr1	1639113	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=24.12;MQ=46.66;MQ0=4;OQ=396.71;QD=3.64;SB=8.10	GT:AD:DP:GL:GQ	0/1:82,27:87:-69.20,-26.24,-219.98:99
+chr1	1639145	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=1;HaplotypeScore=44.81;MQ=46.42;MQ0=3;OQ=230.67;QD=1.94;SB=-28.38	GT:AD:DP:GL:GQ	0/1:92,27:94:-54.66,-28.31,-297.41:99
+chr1	1639152	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=23.68;MQ=46.30;MQ0=1;OQ=1088.67;QD=9.07;SB=-62.94	GT:AD:DP:GL:GQ	0/1:69,50:95:-140.79,-28.64,-195.69:99
+chr1	1639166	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=19.38;MQ=46.56;MQ0=1;OQ=479.08;QD=3.89;SB=-121.97	GT:AD:DP:GL:GQ	0/1:92,31:101:-81.65,-30.45,-258.17:99
+chr1	1639203	.	C	T	59.61	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=106;Dels=0.01;HRun=4;HaplotypeScore=28.93;MQ=49.66;MQ0=0;QD=0.56;SB=37.04	GT:AD:DP:GL:GQ	0/1:84,20:85:-34.85,-25.61,-268.94:92.45
+chr1	1639204	.	A	G	88.80	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=34.26;MQ=50.07;MQ0=0;QD=0.81;SB=122.42	GT:AD:DP:GL:GQ	0/1:87,23:90:-39.28,-27.11,-316.10:99
+chr1	1639210	.	T	G	106.61	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=1;HaplotypeScore=109.94;MQ=48.22;MQ0=0;QD=0.90;SB=107.36	GT:AD:DP:GL:GQ	0/1:99,20:91:-41.35,-27.41,-290.49:99
+chr1	1639221	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=0;HaplotypeScore=51.18;MQ=48.34;MQ0=0;OQ=110.59;QD=0.87;SB=-36.37	GT:AD:DP:GL:GQ	0/1:109,18:89:-41.16,-26.82,-305.73:99
+chr1	1639227	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=3;HaplotypeScore=53.65;MQ=47.85;MQ0=2;OQ=61.26;QD=0.48;SB=63.76	GT:AD:DP:GL:GQ	0/1:90,38:88:-35.92,-26.51,-284.90:94.09
+chr1	1639237	.	A	T	220.03	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=2;HaplotypeScore=39.50;MQ=47.38;MQ0=3;QD=1.53;SB=98.34	GT:AD:DP:GL:GQ	0/1:108,36:102:-56.01,-30.73,-323.39:99
+chr1	1639238	.	T	C	363.43	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=40.62;MQ=46.99;MQ0=4;QD=2.51;SB=-35.37	GT:AD:DP:GL:GQ	0/1:115,29:91:-67.04,-27.41,-296.52:99
+chr1	1639239	.	T	G	307.74	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=40.46;MQ=46.55;MQ0=5;QD=2.08;SB=5.35	GT:AD:DP:GL:GQ	0/1:110,36:106:-65.98,-31.93,-325.39:99
+chr1	1639244	.	C	G	433.01	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=151;Dels=0.00;HRun=0;HaplotypeScore=72.81;MQ=46.68;MQ0=6;QD=2.87;SB=-83.32	GT:AD:DP:GL:GQ	0/1:112,37:109:-82.29,-35.70,-402.49:99
+chr1	1639252	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=2;HaplotypeScore=45.12;MQ=45.10;MQ0=7;OQ=932.16;QD=6.13;SB=-397.36	GT:AD:DP:GL:GQ	0/1:117,33:103:-127.53,-31.03,-261.51:99
+chr1	1639301	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=21.56;MQ=40.71;MQ0=20;OQ=622.52;QD=6.35;SB=-215.64	GT:AD:DP:GL:GQ	0/1:52,46:51:-80.90,-15.37,-137.71:99
+chr1	1639318	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=38.28;MQ=34.31;MQ0=28;OQ=125.27;QD=1.35;SB=-14.91	GT:AD:DP:GL:GQ	0/1:76,17:35:-26.35,-10.54,-101.55:99
+chr1	1639325	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=5.46;MQ=33.52;MQ0=28;OQ=116.93;QD=1.38;SB=23.07	GT:AD:DP:GL:GQ	0/1:73,12:33:-24.93,-9.95,-86.29:99
+chr1	1639374	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=1;HaplotypeScore=20.02;MQ=34.37;MQ0=20;OQ=192.31;QD=2.19;SB=-88.00	GT:AD:DP:GL:GQ	0/1:73,15:45:-36.07,-13.55,-128.18:99
+chr1	1639407	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=10.99;MQ=42.54;MQ0=9;OQ=114.05;QD=1.02;SB=-8.75	GT:AD:DP:GL:GQ	0/1:85,19:71:-46.36,-31.67,-236.26:99
+chr1	1639417	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=4;HaplotypeScore=17.30;MQ=43.78;MQ0=5;OQ=74.87;QD=0.61;SB=-8.76	GT:AD:DP:GL:GQ	0/1:106,16:83:-35.80,-25.03,-240.05:99
+chr1	1639441	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=3;HaplotypeScore=5.23;MQ=45.90;MQ0=8;OQ=109.77;QD=0.77;SB=-10.15	GT:AD:DP:GL:GQ	0/1:120,22:103:-45.28,-31.02,-334.31:99
+chr1	1639479	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=26.42;MQ=48.72;MQ0=12;OQ=76.35;QD=0.64;SB=70.54	GT:AD:DP:GL:GQ	0/1:100,20:90:-38.04,-27.12,-310.60:99
+chr1	1639492	.	C	T	15.20	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=3;HaplotypeScore=52.40;MQ=48.82;MQ0=15;QD=0.14;SB=67.73	GT:AD:DP:GL:GQ	0/1:90,22:79:-28.59,-23.80,-254.17:47.90
+chr1	1639499	rs36141200	G	A	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=107;Dels=0.01;HRun=0;HaplotypeScore=32.74;MQ=48.53;MQ0=15;OQ=2982.80;QD=27.88;SB=-1344.29	GT:AD:DP:GL:GQ	1/1:0,106:74:-301.88,-22.29,-0.02:99
+chr1	1639600	rs36135823	C	T	0.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=3;HaplotypeScore=14.31;MQ=43.93;MQ0=12;OQ=2247.07;QD=26.44;SB=-416.38	GT:AD:DP:GL:GQ	1/1:10,75:60:-232.21,-18.08,-3.91:99
+chr1	1639610	rs34963151	A	T	0.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=15.64;MQ=43.34;MQ0=11;OQ=1936.12;QD=25.14;SB=-344.48	GT:AD:DP:GL:GQ	1/1:5,72:55:-200.25,-16.56,-3.05:99
+chr1	1639612	rs36137888	T	G	0.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=11.64;MQ=43.34;MQ0=11;OQ=1831.08;QD=23.78;SB=-311.74	GT:AD:DP:GL:GQ	1/1:2,72:55:-190.04,-16.56,-3.35:99
+chr1	1639702	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=132;Dels=0.00;HRun=0;HaplotypeScore=34.54;MQ=35.32;MQ0=37;OQ=98.37;QD=0.75;SB=39.28	GT:AD:DP:GL:GQ	0/1:59,72:53:-29.08,-15.96,-156.59:99
+chr1	1639726	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=70.45;MQ=36.36;MQ0=39;OQ=52.18;QD=0.37;SB=48.69	GT:AD:DP:GL:GQ	0/1:67,74:65:-28.09,-19.58,-201.69:85.02
+chr1	1639861	.	C	T	25.55	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=57.75;MQ=41.48;MQ0=14;QD=0.18;SB=-23.37	GT:AD:DP:GL:GQ	0/1:90,50:90:-32.98,-27.15,-260.27:58.37
+chr1	1639867	.	C	T	19.37	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=3;HaplotypeScore=75.47;MQ=41.18;MQ0=14;QD=0.14;SB=-17.32	GT:AD:DP:GL:GQ	0/1:97,46:92:-32.93,-27.71,-303.81:52.16
+chr1	1639892	rs61777469	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=134;Dels=0.04;HRun=2;HaplotypeScore=74.14;MQ=41.98;MQ0=12;OQ=2469.47;QD=18.43;SB=-1178.56	GT:AD:DP:GL:GQ	0/1:25,104:86:-276.13,-25.90,-32.75:68.49
+chr1	1639893	rs61777470	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=134;Dels=0.00;HRun=0;HaplotypeScore=137.24;MQ=41.98;MQ0=12;OQ=2615.52;QD=19.52;SB=-1204.51	GT:AD:DP:GL:GQ	0/1:44,90:89:-291.64,-26.81,-37.18:99
+chr1	1639911	.	G	A	14.93	LowQual	AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=0;HaplotypeScore=26.42;MQ=45.76;MQ0=10;QD=0.13;SB=-12.75	GT:AD:DP:GL:GQ	0/1:81,37:78:-28.28,-23.52,-231.19:47.63
+chr1	1639962	rs61777471	C	T	260.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=54.09;MQ0=1;OQ=1805.36;QD=37.61;SB=-829.34	GT:AD:DP:GL:GQ	1/1:0,48:47:-184.14,-14.16,-0.02:99
+chr1	1640060	rs1969650	A	C	38.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=47.36;MQ0=0;OQ=1283.12;QD=25.66;SB=-659.19	GT:AD:DP:GL:GQ	1/1:0,50:43:-131.95,-12.97,-0.05:99
+chr1	1640123	rs1967676	G	T	619.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.68;MQ0=0;OQ=2013.64;QD=35.33;SB=-938.04	GT:AD:DP:GL:GQ	1/1:0,57:55:-204.96,-16.56,-0.01:99
+chr1	1640270	rs1967677	T	C	0.01	FDRtranche2.00to10.00	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=23.68;MQ=51.29;MQ0=1;OQ=2260.88;QD=25.69;SB=-1076.20	GT:AD:DP:GL:GQ	1/1:7,81:78:-241.90,-23.52,-12.23:99
+chr1	1640284	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=21.65;MQ=49.80;MQ0=1;OQ=283.77;QD=2.56;SB=107.23	GT:AD:DP:GL:GQ	0/1:95,16:94:-60.00,-28.34,-253.49:99
+chr1	1640321	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=250.42;MQ=48.13;MQ0=0;OQ=561.76;QD=3.98;SB=122.35	GT:AD:DP:GL:GQ	0/1:98,27:119:-99.13,-39.67,-333.17:99
+chr1	1640332	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=158;Dels=0.00;HRun=0;HaplotypeScore=133.26;MQ=46.63;MQ0=0;OQ=950.96;QD=6.02;SB=119.36	GT:AD:DP:GL:GQ	0/1:94,64:124:-135.74,-37.36,-315.76:99
+chr1	1640347	.	T	C	550.46	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=23.57;MQ=45.32;MQ0=0;QD=3.72;SB=95.35	GT:AD:DP:GL:GQ	0/1:118,30:114:-92.67,-34.34,-350.75:99
+chr1	1640368	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=1;HaplotypeScore=38.96;MQ=45.47;MQ0=0;OQ=414.73;QD=2.94;SB=65.22	GT:AD:DP:GL:GQ	0/1:119,22:108:-77.29,-32.53,-317.79:99
+chr1	1640378	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=4;HaplotypeScore=21.61;MQ=45.56;MQ0=0;OQ=227.10;QD=1.77;SB=59.14	GT:AD:DP:GL:GQ	0/1:110,18:98:-55.53,-29.53,-284.49:99
+chr1	1640389	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=23.69;MQ=45.00;MQ0=0;OQ=372.62;QD=3.11;SB=38.14	GT:AD:DP:GL:GQ	0/1:83,37:73:-62.56,-22.01,-186.44:99
+chr1	1640393	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=31.49;MQ=46.43;MQ0=0;OQ=193.70;QD=1.67;SB=47.18	GT:AD:DP:GL:GQ	0/1:63,52:78:-46.16,-23.50,-255.92:99
+chr1	1640402	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=3;HaplotypeScore=44.61;MQ=47.57;MQ0=0;OQ=589.53;QD=5.51;SB=47.18	GT:AD:DP:GL:GQ	0/1:71,36:90:-89.34,-27.11,-243.28:99
+chr1	1640405	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=32.67;MQ=47.67;MQ0=0;OQ=576.56;QD=5.54;SB=44.17	GT:AD:DP:GL:GQ	0/1:79,25:85:-86.54,-25.60,-227.82:99
+chr1	1640428	.	C	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=1;HaplotypeScore=12.31;MQ=51.68;MQ0=0;OQ=687.66;QD=7.47;SB=59.21	GT:AD:DP:GL:GQ	0/1:63,29:86:-97.95,-25.90,-226.28:99
+chr1	1640435	.	T	C	0.39	PASS	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=52.41;MQ0=0;OQ=479.95;QD=4.95;SB=65.24	GT:AD:DP:GL:GQ	0/1:69,28:91:-78.69,-27.41,-274.97:99
+chr1	1640479	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=10.56;MQ=53.01;MQ0=0;OQ=125.57;QD=1.23;SB=55.33	GT:AD:DP:GL:GQ	0/1:77,25:89:-42.65,-26.81,-277.44:99
+chr1	1640500	.	C	A	40.46	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=1;HaplotypeScore=5.00;MQ=52.43;MQ0=0;QD=0.42;SB=79.01	GT:AD:DP:GL:GQ	0/1:71,25:78:-30.82,-23.49,-254.06:73.30
+chr1	1640502	.	T	G	39.38	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=52.41;MQ0=0;QD=0.40;SB=58.40	GT:AD:DP:GL:GQ	0/1:73,26:82:-31.92,-24.69,-274.53:72.21
+chr1	1640517	.	C	G	1.85	PASS	AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=50.82;MQ0=0;OQ=540.14;QD=4.54;SB=-210.84	GT:AD:DP:GL:GQ	0/1:81,38:99:-87.13,-29.83,-340.31:99
+chr1	1640647	rs17845218	T	C	5.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=139;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=46.16;MQ0=1;OQ=829.41;QD=5.97;SB=-392.09	GT:AD:DP:GL:GQ	0/1:85,54:124:-123.60,-37.37,-339.83:99
+chr1	1640657	rs1059830	A	G	689.07	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=136;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=46.01;MQ0=1;QD=5.07;SB=-273.97	GT:AD:DP:GL:GQ	0/1:84,52:114:-106.55,-34.36,-315.05:99
+chr1	1640661	rs1137004	T	C	924.56	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=137;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=45.08;MQ0=1;QD=6.75;SB=-478.80	GT:AD:DP:GL:GQ	0/1:82,55:116:-130.68,-34.94,-330.64:99
+chr1	1640667	rs3200657	T	C	2206.14	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=133;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=43.98;MQ0=1;QD=16.59;SB=-708.39	GT:AD:DP:GL:GQ	0/1:59,73:112:-259.82,-35.92,-162.90:99
+chr1	1640692	.	A	G	15.57	PASS	AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=41.55;MQ0=0;OQ=1129.49;QD=8.89;SB=-491.78	GT:AD:DP:GL:GQ	0/1:59,68:99:-146.06,-29.83,-231.81:99
+chr1	1640705	rs1059831	G	A	307.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=41.79;MQ0=0;OQ=1854.51;QD=15.72;SB=-686.99	GT:AD:DP:GL:GQ	0/1:63,55:86:-214.65,-25.92,-105.31:99
+chr1	1640780	rs36191908	G	A	2.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=50.84;MQ0=0;OQ=222.00;QD=2.52;SB=-69.38	GT:AD:DP:GL:GQ	0/1:66,22:78:-49.00,-23.51,-215.31:99
+chr1	1640799	.	G	A	26.24	LowQual	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=54.16;MQ0=0;QD=0.29;SB=-18.77	GT:AD:DP:GL:GQ	0/1:79,12:87:-32.13,-26.22,-265.70:59.07
+chr1	1640856	.	T	C	1.18	PASS	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=51.06;MQ0=0;OQ=537.04;QD=4.84;SB=42.60	GT:AD:DP:GL:GQ	0/1:73,38:93:-85.00,-28.02,-284.38:99
+chr1	1640863	.	G	A	0.15	PASS	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=2;HaplotypeScore=0.93;MQ=50.41;MQ0=0;OQ=682.37;QD=6.20;SB=40.52	GT:AD:DP:GL:GQ	0/1:69,41:93:-99.55,-28.03,-223.44:99
+chr1	1640907	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=91;Dels=0.01;HRun=2;HaplotypeScore=10.49;MQ=48.20;MQ0=0;OQ=731.52;QD=8.04;SB=71.23	GT:AD:DP:GL:GQ	0/1:53,37:73:-98.42,-21.99,-174.07:99
+chr1	1640923	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=64.78;MQ=43.84;MQ0=1;OQ=272.78;QD=3.17;SB=56.20	GT:AD:DP:GL:GQ	0/1:67,19:80:-54.67,-24.11,-250.01:99
+chr1	1640931	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=98.55;MQ=40.13;MQ0=1;OQ=147.14;QD=2.16;SB=38.15	GT:AD:DP:GL:GQ	0/1:57,11:64:-37.28,-19.28,-217.64:99
+chr1	1640986	.	A	C	0.64	PASS	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.69;MQ=43.40;MQ0=0;OQ=371.72;QD=5.81;SB=77.22	GT:AD:DP:GL:GQ	0/1:47,17:62:-59.13,-18.68,-158.05:99
+chr1	1640996	.	C	T	0.49	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=45.56;MQ0=0;OQ=291.78;QD=4.63;SB=80.17	GT:AD:DP:GL:GQ	0/1:49,14:56:-49.34,-16.88,-145.60:99
+chr1	1641016	.	C	T	53.74	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=51.28;MQ0=0;QD=0.87;SB=74.21	GT:AD:DP:GL:GQ	0/1:47,15:50:-23.72,-15.06,-152.06:86.58
+chr1	1641017	.	A	G	257.15	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=51.43;MQ0=0;QD=4.08;SB=80.28	GT:AD:DP:GL:GQ	0/1:48,15:61:-47.39,-18.39,-179.46:99
+chr1	1641026	.	C	T	369.95	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=52.99;MQ0=0;QD=5.97;SB=74.25	GT:AD:DP:GL:GQ	0/1:47,15:60:-58.35,-18.07,-168.55:99
+chr1	1641040	.	G	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.80;MQ=51.94;MQ0=0;OQ=253.54;QD=4.23;SB=74.26	GT:AD:DP:GL:GQ	0/1:44,15:55:-45.26,-16.62,-168.61:99
+chr1	1641126	rs12137617	A	G	24.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.12;MQ=54.87;MQ0=0;OQ=1275.18;QD=31.10;SB=-536.43	GT:AD:DP:GL:GQ	1/1:0,41:37:-131.12,-11.15,-0.02:99
+chr1	1641482	rs11260627	C	T	34.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=55.33;MQ0=0;OQ=1435.98;QD=36.82;SB=-496.00	GT:AD:DP:GL:GQ	1/1:0,39:37:-147.19,-11.15,-0.01:99
+chr1	1641491	rs12135951	T	G	20.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=56.50;MQ0=0;OQ=197.57;QD=5.20;SB=-66.56	GT:AD:DP:GL:GQ	0/1:25,13:35:-33.59,-10.55,-90.46:99
+chr1	1641587	rs12044811	G	A	0.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=15.92;MQ=55.20;MQ0=1;OQ=1462.24;QD=35.66;SB=-578.76	GT:AD:DP:GL:GQ	1/1:1,40:37:-149.82,-11.15,-0.01:99
+chr1	1641608	rs12044814	G	C	398.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.85;MQ0=0;OQ=998.26;QD=30.25;SB=-358.22	GT:AD:DP:GL:GQ	1/1:1,32:26:-103.43,-7.84,-0.02:78.25
+chr1	1641675	rs4648768	T	C	52.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.85;MQ=49.39;MQ0=0;OQ=640.24;QD=18.29;SB=-205.57	GT:AD:DP:GL:GQ	1/1:0,32:21:-67.63,-6.34,-0.02:63.13
+chr1	1641761	rs4648772	T	C	503.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.21;MQ0=0;OQ=1369.78;QD=30.44;SB=-625.00	GT:AD:DP:GL:GQ	1/1:0,45:43:-140.60,-12.97,-0.03:99
+chr1	1641771	rs4648773	C	A	18.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=2.41;MQ=54.78;MQ0=0;OQ=1559.28;QD=33.90;SB=-751.90	GT:AD:DP:GL:GQ	1/1:0,46:44:-159.53,-13.25,-0.02:99
+chr1	1641797	rs4648775	G	A	91.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=54.06;MQ0=0;OQ=1591.86;QD=36.18;SB=-734.99	GT:AD:DP:GL:GQ	1/1:0,44:41:-162.79,-12.35,-0.01:99
+chr1	1641822	rs4648776	G	A	529.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.06;MQ0=0;OQ=1730.65;QD=38.46;SB=-774.66	GT:AD:DP:GL:GQ	1/1:0,45:44:-176.66,-13.26,-0.01:99
+chr1	1642086	rs4648777	A	G	238.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.56;MQ0=1;OQ=1172.89;QD=24.44;SB=-406.15	GT:AD:DP:GL:GQ	1/1:1,47:39:-120.92,-11.77,-0.04:99
+chr1	1642864	rs36039898	T	C	113.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=54.55;MQ0=0;OQ=2211.83;QD=36.26;SB=-727.29	GT:AD:DP:GL:GQ	1/1:0,61:61:-224.79,-18.37,-0.02:99
+chr1	1642888	rs16825265	C	T	105.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=54.90;MQ0=0;OQ=2464.17;QD=40.40;SB=-985.30	GT:AD:DP:GL:GQ	1/1:0,61:61:-250.01,-18.37,-0.01:99
+chr1	1643163	rs35548050	T	C	620.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.02;MQ0=0;OQ=2383.87;QD=34.06;SB=-1115.83	GT:AD:DP:GL:GQ	1/1:0,70:67:-241.99,-20.18,-0.02:99
+chr1	1643221	rs2206307	C	T	629.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.40;MQ0=0;OQ=2196.71;QD=34.87;SB=-1116.03	GT:AD:DP:GL:GQ	1/1:0,63:57:-223.28,-17.18,-0.02:99
+chr1	1643274	rs2206308	C	T	615.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.68;MQ0=0;OQ=2077.20;QD=37.77;SB=-1010.04	GT:AD:DP:GL:GQ	1/1:0,55:53:-211.32,-15.97,-0.02:99
+chr1	1643659	rs2223485	C	T	454.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.70;MQ0=1;OQ=1724.40;QD=36.69;SB=-535.21	GT:AD:DP:GL:GQ	1/1:0,47:43:-176.03,-12.95,-0.01:99
+chr1	1643745	rs61777493	C	A	268.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=53.15;MQ0=3;OQ=2449.58;QD=34.50;SB=-1240.29	GT:AD:DP:GL:GQ	1/1:3,68:66:-248.56,-19.87,-0.01:99
+chr1	1643867	.	A	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=19.40;MQ0=14;OQ=84.98;QD=3.04;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,15:12:-15.40,-3.61,-30.71:99
+chr1	1643873	.	C	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=27;Dels=0.41;HRun=0;HaplotypeScore=83.92;MQ=18.34;MQ0=14;OQ=350.65;QD=12.99;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,15:10:-42.29,-6.54,-3.64:28.97
+chr1	1643898	rs61777494	G	A	157	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.17;MQ0=2;OQ=461.81;QD=27.17;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,16:12:-49.77,-3.61,-0.00:36.12
+chr1	1643918	rs61777495	C	T	757.85	Indel	AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.37;MQ0=1;QD=31.58;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,23:19:-79.37,-5.72,-0.00:57.19
+chr1	1643924	.	A	T	950.73	Indel	AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.62;MQ0=1;QD=30.67;SB=-180.94	GT:AD:DP:GL:GQ	1/1:1,30:26:-98.67,-7.83,-0.01:78.24
+chr1	1644591	rs61777496	G	A	138.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.34;MQ0=0;OQ=130.88;QD=26.18;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,5:4:-16.62,-1.20,-0.00:12.04
+chr1	1644813	rs2056977	A	G	170.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=26.65;MQ0=9;OQ=292.06;QD=7.69;SB=-147.83	GT:AD:DP:GL:GQ	1/1:7,31:10:-32.80,-3.01,-0.01:30.08
+chr1	1645334	rs11486024	G	A	35.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=22.46;MQ0=10;OQ=345.89;QD=5.67;SB=32.11	GT:AD:DP:GL:GQ	0/1:46,15:32:-47.52,-9.65,-66.64:99
+chr1	1645788	rs28649027	G	C	26.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=2.58;MQ=53.44;MQ0=0;OQ=593.92;QD=15.23;SB=-280.31	GT:AD:DP:GL:GQ	0/1:20,19:36:-73.54,-10.87,-73.49:99
+chr1	1646881	rs61777497	T	C	0.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=11.68;MQ0=43;OQ=71.62;QD=1.23;SB=-32.65	GT:AD:DP:GL:GQ	0/1:40,18:10:-13.46,-3.01,-23.67:99
+chr1	1646928	.	C	T	0.40	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=15.38;MQ0=21;OQ=97.42;QD=2.87;SB=-39.65	GT:AD:DP:GL:GQ	0/1:20,14:7:-15.13,-2.11,-10.71:85.98
+chr1	1646938	rs61776763	A	G	17.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=2.10;MQ=17.28;MQ0=15;OQ=266.90;QD=8.34;SB=-88.98	GT:AD:DP:GL:GQ	1/1:0,32:9:-30.28,-2.71,-0.01:27.04
+chr1	1646996	rs4648783	T	C	206.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=31.62;MQ0=1;OQ=494.82;QD=9.00;SB=-214.36	GT:AD:DP:GL:GQ	0/1:25,30:43:-65.73,-12.96,-90.44:99
+chr1	1647044	rs4648784	C	G	2.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=1.82;MQ=32.49;MQ0=8;OQ=1818.45;QD=23.93;SB=-827.04	GT:AD:DP:GL:GQ	0/1:14,62:58:-202.62,-17.49,-37.52:99
+chr1	1647352	rs9439501	G	C	210.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=45.38;MQ0=4;OQ=1643.24;QD=34.96;SB=-614.99	GT:AD:DP:GL:GQ	1/1:0,47:39:-167.92,-11.75,-0.01:99
+chr1	1647425	rs11576302	G	A	125.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=52.45;MQ0=0;OQ=868.24;QD=17.72;SB=-259.77	GT:AD:DP:GL:GQ	0/1:23,26:49:-104.87,-14.76,-83.38:99
+chr1	1647461	rs11589282	T	C	44.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=0.94;MQ=51.71;MQ0=1;OQ=1927.78;QD=33.24;SB=-715.12	GT:AD:DP:GL:GQ	1/1:0,58:56:-196.39,-16.87,-0.02:99
+chr1	1648203	rs4648785	T	C	8.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=3.12;MQ=39.29;MQ0=4;OQ=1376.56;QD=30.59;SB=-396.50	GT:AD:DP:GL:GQ	1/1:0,45:38:-141.25,-11.44,-0.01:99
+chr1	1648805	rs1062057	T	C	6.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=1;HaplotypeScore=3.69;MQ=25.80;MQ0=25;OQ=1469.54;QD=13.86;SB=-734.60	GT:AD:DP:GL:GQ	0/1:45,61:78:-173.74,-23.50,-116.68:99
+chr1	1649970	rs1801781	C	A	600.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.53;MQ0=0;OQ=2075.47;QD=36.41;SB=-874.83	GT:AD:DP:GL:GQ	1/1:0,57:57:-211.15,-17.17,-0.01:99
+chr1	1650495	rs2377220	T	G	497.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.20;MQ0=1;OQ=1908.80;QD=31.81;SB=-547.03	GT:AD:DP:GL:GQ	1/1:0,60:54:-194.48,-16.27,-0.02:99
+chr1	1650579	.	G	C	24.29	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=1;HaplotypeScore=9.52;MQ=48.11;MQ0=12;QD=0.34;SB=80.30	GT:AD:DP:GL:GQ	0/1:60,12:43:-18.68,-12.97,-167.36:57.11
+chr1	1650586	rs28662997	T	C	0.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=7.30;MQ=48.54;MQ0=13;OQ=175.02;QD=2.22;SB=-47.44	GT:AD:DP:GL:GQ	0/1:53,26:60:-38.86,-18.08,-194.29:99
+chr1	1650595	rs1061883	T	C	0.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=3.64;MQ=49.38;MQ0=13;OQ=60.20;QD=0.69;SB=-8.74	GT:AD:DP:GL:GQ	0/1:58,29:65:-28.90,-19.59,-216.78:93.04
+chr1	1651158	rs1546882	A	G	91.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=1.86;MQ=36.24;MQ0=1;OQ=1126.99;QD=14.09;SB=-474.67	GT:AD:DP:GL:GQ	0/1:32,48:73:-138.00,-22.01,-116.79:99
+chr1	1651704	rs61777505	G	C	26.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.62;MQ=32.64;MQ0=2;OQ=1226.35;QD=32.27;SB=-479.52	GT:AD:DP:GL:GQ	1/1:4,34:33:-134.22,-9.95,-8.01:19.39
+chr1	1652175	.	C	G	107.65	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.31;MQ0=18;OQ=446.15;QD=8.42;SB=-112.32	GT:AD:DP:GL:GQ	0/1:32,21:35:-58.45,-10.56,-85.98:99
+chr1	1652288	rs2281171	A	G	55.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.68;MQ=47.07;MQ0=0;OQ=1046.84;QD=33.77;SB=-483.46	GT:AD:DP:GL:GQ	1/1:0,31:31:-108.28,-9.34,-0.01:93.26
+chr1	1652674	rs61777506	T	C	260.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.10;MQ0=0;OQ=1515.24;QD=32.94;SB=-289.56	GT:AD:DP:GL:GQ	1/1:0,46:45:-155.13,-13.56,-0.02:99
+chr1	1652697	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=17;HaplotypeScore=26.60;MQ=53.41;MQ0=0;OQ=216.45;QD=3.80;SB=47.16	GT:AD:DP:GL:GQ	0/1:42,15:40:-36.99,-12.06,-92.34:99
+chr1	1652700	.	G	A	48.19	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=2;HaplotypeScore=19.75;MQ=52.95;MQ0=0;QD=0.96;SB=53.18	GT:AD:DP:GL:GQ	0/1:40,10:33:-18.05,-9.95,-95.61:81.03
+chr1	1652755	rs61777507	A	G	615.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=1969.12;QD=34.55;SB=-927.86	GT:AD:DP:GL:GQ	1/1:0,57:57:-200.52,-17.17,-0.03:99
+chr1	1653262	rs34298494	A	C	3.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=4.92;MQ=57.93;MQ0=0;OQ=1820.14;QD=28.89;SB=-933.22	GT:AD:DP:GL:GQ	1/1:0,63:59:-185.65,-17.78,-0.05:99
+chr1	1653465	.	A	G	0.67	PASS	AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;HRun=3;HaplotypeScore=0.82;MQ=58.69;MQ0=0;OQ=1218.77;QD=28.34;SB=-585.02	GT:AD:DP:GL:GQ	1/1:0,43:39:-125.50,-11.76,-0.03:99
+chr1	1653691	rs3817856	C	T	262.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=59.21;MQ0=0;OQ=2006.29;QD=37.85;SB=-990.80	GT:AD:DP:GL:GQ	1/1:0,53:51:-204.23,-15.37,-0.02:99
+chr1	1653879	rs2294488	T	C	118.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=52.10;MQ0=0;OQ=1419.75;QD=28.40;SB=-681.96	GT:AD:DP:GL:GQ	1/1:0,49:45:-145.60,-13.57,-0.04:99
+chr1	1653984	rs2294489	T	C	14.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=3;HaplotypeScore=0.63;MQ=58.58;MQ0=0;OQ=1353.88;QD=31.49;SB=-691.09	GT:AD:DP:GL:GQ	1/1:0,43:40:-138.99,-12.05,-0.02:99
+chr1	1655431	rs61777508	T	G	492.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.47;MQ0=3;OQ=2585.92;QD=31.92;SB=-532.88	GT:AD:DP:GL:GQ	1/1:0,81:75:-262.21,-22.59,-0.04:99
+chr1	1655473	rs4648764	A	G	513.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.46;MQ0=4;OQ=2874.97;QD=29.64;SB=-827.61	GT:AD:DP:GL:GQ	1/1:1,96:86:-291.13,-25.92,-0.05:99
+chr1	1655600	rs2281176	T	C	43.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=43.78;MQ0=0;OQ=2374.61;QD=30.44;SB=-588.04	GT:AD:DP:GL:GQ	1/1:0,78:71:-241.09,-21.40,-0.04:99
+chr1	1655607	rs2281177	T	C	16.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=43.12;MQ0=0;OQ=1801.45;QD=22.24;SB=-550.84	GT:AD:DP:GL:GQ	0/1:17,64:75:-206.03,-22.60,-57.34:99
+chr1	1656111	.	G	A	19.94	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=24.98;MQ0=9;OQ=1269.10;QD=20.14;SB=-363.89	GT:AD:DP:GL:GQ	0/1:20,43:51:-145.56,-15.37,-46.93:99
+chr1	1656198	rs2072924	G	A	130.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=29.23;MQ0=3;OQ=1510.31;QD=34.33;SB=-636.84	GT:AD:DP:GL:GQ	1/1:0,44:39:-154.63,-11.75,-0.02:99
+chr1	1656202	rs2072925	A	G	35.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=31.20;MQ0=3;OQ=1130.90;QD=24.58;SB=-545.87	GT:AD:DP:GL:GQ	1/1:0,46:37:-116.71,-11.16,-0.04:99
+chr1	1656475	rs2076325	C	T	114.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=50.53;MQ0=0;OQ=1787.32;QD=37.24;SB=-867.16	GT:AD:DP:GL:GQ	1/1:0,48:46:-182.33,-13.86,-0.01:99
+chr1	1657113	rs1474648	T	C	589.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.20;MQ0=0;OQ=2447.49;QD=32.63;SB=-1145.82	GT:AD:DP:GL:GQ	1/1:0,75:68:-248.35,-20.48,-0.02:99
+chr1	1657231	rs1474649	A	G	31.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=49.42;MQ0=0;OQ=1497.15;QD=33.27;SB=-642.31	GT:AD:DP:GL:GQ	1/1:0,45:43:-153.31,-12.95,-0.02:99
+chr1	1657279	rs2377208	A	C	135.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=44.04;MQ0=1;OQ=1645.48;QD=30.47;SB=-668.23	GT:AD:DP:GL:GQ	1/1:0,54:48:-168.15,-14.46,-0.02:99
+chr1	1658028	rs28718827	G	T	1.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=10.14;MQ=51.62;MQ0=0;OQ=1872.10;QD=31.73;SB=-828.68	GT:AD:DP:GL:GQ	1/1:2,57:55:-190.82,-16.57,-0.03:99
+chr1	1658119	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=69;Dels=0.03;HRun=18;HaplotypeScore=24.79;MQ=51.46;MQ0=0;OQ=102.87;QD=1.49;SB=-23.99	GT:AD:DP:GL:GQ	0/1:55,12:49:-28.05,-14.47,-131.71:99
+chr1	1658135	rs2889577	A	G	0.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=15.54;MQ=53.86;MQ0=0;OQ=1611.78;QD=21.78;SB=-529.45	GT:AD:DP:GL:GQ	1/1:8,66:53:-172.54,-15.98,-7.77:82.05
+chr1	1658803	rs28537345	A	C	60.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.02;HRun=1;HaplotypeScore=0.16;MQ=51.80;MQ0=0;OQ=1884.76;QD=31.95;SB=-820.50	GT:AD:DP:GL:GQ	1/1:0,58:56:-192.08,-16.57,-0.02:99
+chr1	1659088	rs11485870	T	C	2.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=5.25;MQ=48.74;MQ0=0;OQ=1314.03;QD=25.77;SB=-582.00	GT:AD:DP:GL:GQ	1/1:2,49:46:-142.54,-13.87,-7.55:63.21
+chr1	1659426	rs9442408	C	T	56.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=38.94;MQ0=1;OQ=469.40;QD=7.96;SB=-62.79	GT:AD:DP:GL:GQ	0/1:41,18:57:-67.39,-17.17,-141.22:99
+chr1	1659594	rs61777512	G	T	329.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.52;MQ0=1;OQ=761.00;QD=27.18;SB=-349.52	GT:AD:DP:GL:GQ	1/1:2,26:23:-79.70,-6.93,-0.01:69.17
+chr1	1659896	.	C	A	16.91	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=18.32;MQ0=25;OQ=324.85;QD=7.55;SB=-33.35	GT:AD:DP:GL:GQ	0/1:14,29:14:-39.99,-4.22,-11.38:71.59
+chr1	1659905	.	C	T	19.49	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=18.62;MQ0=24;OQ=356.25;QD=8.28;SB=-31.52	GT:AD:DP:GL:GQ	0/1:14,29:15:-43.43,-4.52,-12.58:80.58
+chr1	1661214	rs2005995	G	A	408.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=11.78;MQ0=23;OQ=327.72;QD=9.93;SB=-165.22	GT:AD:DP:GL:GQ	1/1:16,17:9:-36.36,-2.71,-0.00:27.09
+chr1	1661590	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=3.96;MQ=36.56;MQ0=3;OQ=54.36;QD=1.05;SB=68.26	GT:AD:DP:GL:GQ	0/1:38,14:35:-19.28,-10.56,-129.90:87.20
+chr1	1661642	rs4648793	C	T	457.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.04;MQ0=0;OQ=1470.76;QD=37.71;SB=-587.27	GT:AD:DP:GL:GQ	1/1:0,39:38:-150.68,-11.45,-0.01:99
+chr1	1661726	rs7364986	A	T	4.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=5.15;MQ=47.34;MQ0=1;OQ=2656.76;QD=33.63;SB=-1106.52	GT:AD:DP:GL:GQ	1/1:0,79:72:-269.28,-21.69,-0.02:99
+chr1	1662002	.	C	T	0.16	PASS	AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=5.72;MQ=52.52;MQ0=1;OQ=1857.08;QD=37.14;SB=-705.36	GT:AD:DP:GL:GQ	1/1:0,50:47:-189.31,-14.16,-0.02:99
+chr1	1662772	.	C	T	43.11	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=50.80;MQ0=2;QD=0.70;SB=83.20	GT:AD:DP:GL:GQ	0/1:53,9:53:-23.58,-15.98,-150.38:75.94
+chr1	1663032	.	T	C	46.58	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=53.54;MQ0=2;QD=0.93;SB=38.12	GT:AD:DP:GL:GQ	0/1:38,9:34:-18.20,-10.26,-102.10:79.41
+chr1	1663379	rs35790103	T	C	8.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=-0.24;MQ=57.22;MQ0=0;OQ=1409.71;QD=33.56;SB=-634.30	GT:AD:DP:GL:GQ	1/1:0,42:41:-144.58,-12.35,-0.02:99
+chr1	1663767	rs35678883	G	C	8.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=2.38;MQ=50.72;MQ0=2;OQ=2425.38;QD=39.12;SB=-647.42	GT:AD:DP:GL:GQ	1/1:0,62:56:-246.15,-16.88,-0.03:99
+chr1	1663886	rs36050429	G	C	377.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.29;MQ0=3;OQ=1259.11;QD=34.03;SB=-328.71	GT:AD:DP:GL:GQ	1/1:0,37:30:-129.51,-9.04,-0.01:90.30
+chr1	1664767	.	G	C	282.90	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.97;MQ0=0;OQ=606.08;QD=13.77;SB=-320.01	GT:AD:DP:GL:GQ	0/1:24,20:40:-75.96,-12.06,-88.71:99
+chr1	1664855	.	A	G	129.97	Indel	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=9.28;MQ=43.11;MQ0=1;QD=4.06;SB=-24.89	GT:AD:DP:GL:GQ	0/1:24,8:26:-24.12,-7.84,-71.93:99
+chr1	1664856	.	G	A	433.28	Indel	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=12;HaplotypeScore=9.83;MQ=42.77;MQ0=1;QD=12.74;SB=-25.59	GT:AD:DP:GL:GQ	0/1:18,16:29:-55.35,-8.74,-47.19:99
+chr1	1665027	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=13;HaplotypeScore=3.74;MQ=53.18;MQ0=0;OQ=78.07;QD=1.28;SB=0.76	GT:AD:DP:GL:GQ	0/1:47,14:45:-24.65,-13.56,-131.48:99
+chr1	1665395	.	C	T	17.70	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.53;MQ=22.06;MQ0=30;QD=0.34;SB=14.07	GT:AD:DP:GL:GQ	0/1:42,10:21:-11.37,-6.32,-66.25:50.46
+chr1	1667416	rs16824474	G	C	10.38	LowQual	AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=47.86;MQ0=3;QD=0.61;SB=-0.97	GT:AD:DP:GL:GQ	0/1:12,5:14:-8.50,-4.22,-50.97:42.79
+chr1	1670869	.	G	C	14.33	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=45.06;MQ0=4;QD=0.19;SB=74.28	GT:AD:DP:GL:GQ	0/1:64,12:62:-23.39,-18.69,-239.55:47
+chr1	1670881	.	G	C	19.24	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=4.38;MQ=42.81;MQ0=4;QD=0.27;SB=74.28	GT:AD:DP:GL:GQ	0/1:59,12:59:-22.99,-17.79,-226.11:52.02
+chr1	1670904	.	C	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=38.22;MQ0=4;OQ=63.86;QD=0.91;SB=56.13	GT:AD:DP:GL:GQ	0/1:50,20:51:-25.06,-15.39,-141.72:96.69
+chr1	1670928	.	G	A	848.58	HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=30.83;MQ0=10;QD=13.91;SB=-297.25	GT:AD:DP:GL:GQ	0/1:30,31:35:-98.68,-10.54,-33.99:99
+chr1	1670936	.	G	T	255.10	DPFilter;HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=3;HaplotypeScore=4.00;MQ=28.80;MQ0=12;QD=3.99;SB=20.07	GT:AD:DP:GL:GQ	0/1:33,31:36:-39.64,-10.84,-86.07:99
+chr1	1671525	rs35301881	C	T	26.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=43.35;MQ0=4;OQ=980.88;QD=30.65;SB=-483.00	GT:AD:DP:GL:GQ	1/1:4,28:26:-101.68,-7.83,-0.01:78.25
+chr1	1672234	rs4648812	G	A	127.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=26.23;MQ0=1;OQ=275.04;QD=7.86;SB=-150.63	GT:AD:DP:GL:GQ	0/1:24,11:30:-39.83,-9.05,-63.69:99
+chr1	1673187	rs14390	C	T	78.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=730.68;QD=36.53;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,20:19:-76.66,-5.72,-0.00:57.19
+chr1	1673425	rs12588	G	A	34.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=30.14;MQ0=16;OQ=466.02;QD=6.66;SB=-83.01	GT:AD:DP:GL:GQ	0/1:47,23:47:-64.06,-14.17,-100.00:99
+chr1	1675073	rs2072928	C	G	44.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.71;MQ=59.55;MQ0=0;OQ=1934.62;QD=37.93;SB=-835.43	GT:AD:DP:GL:GQ	1/1:0,51:47:-197.07,-14.17,-0.02:99
+chr1	1675900	rs4751	G	T	24.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=1.42;MQ=59.65;MQ0=0;OQ=1889.22;QD=34.99;SB=-617.91	GT:AD:DP:GL:GQ	1/1:0,54:52:-192.52,-15.66,-0.02:99
+chr1	1676803	rs2072929	T	C	69.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=1256.22;QD=28.55;SB=-491.53	GT:AD:DP:GL:GQ	1/1:0,44:41:-129.26,-12.37,-0.05:99
+chr1	1676822	rs2076327	C	T	34.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=58.97;MQ0=0;OQ=1637.49;QD=36.39;SB=-774.03	GT:AD:DP:GL:GQ	1/1:0,45:43:-167.35,-12.96,-0.02:99
+chr1	1677485	rs34306661	T	C	77.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.61;MQ=60.00;MQ0=0;OQ=1787.88;QD=27.94;SB=-566.94	GT:AD:DP:GL:GQ	1/1:0,64:57:-182.43,-17.19,-0.05:99
+chr1	1677651	.	C	T	157.32	PASS	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.08;MQ0=0;OQ=1381.04;QD=20.92;SB=-549.37	GT:AD:DP:GL:GQ	0/1:23,43:64:-160.68,-19.29,-80.55:99
+chr1	1677956	.	C	T	7.81	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.35;MQ=59.68;MQ0=0;OQ=1209.30;QD=20.50;SB=-531.10	GT:AD:DP:GL:GQ	0/1:22,37:56:-141.09,-16.88,-73.03:99
+chr1	1678052	rs2281173	A	G	576.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1215.40;QD=30.39;SB=-536.99	GT:AD:DP:GL:GQ	1/1:0,40:39:-125.17,-11.77,-0.04:99
+chr1	1678329	rs4648623	C	G	0.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=58.16;MQ0=0;OQ=844.68;QD=36.73;SB=-124.74	GT:AD:DP:GL:GQ	1/1:0,23:22:-88.07,-6.64,-0.02:66.21
+chr1	1678373	rs4648624	G	T	1.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=58.84;MQ0=0;OQ=639.15;QD=31.96;SB=-120.84	GT:AD:DP:GL:GQ	1/1:0,20:19:-67.51,-5.72,-0.01:57.16
+chr1	1679024	rs2235536	C	T	173.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.47;MQ0=0;OQ=2302.66;QD=39.70;SB=-1126.49	GT:AD:DP:GL:GQ	1/1:0,58:58:-233.87,-17.47,-0.02:99
+chr1	1679622	rs2235537	T	C	108.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=59.56;MQ0=0;OQ=1772.95;QD=33.45;SB=-589.32	GT:AD:DP:GL:GQ	1/1:0,53:52:-180.90,-15.67,-0.02:99
+chr1	1681624	.	G	A	66.45	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=58.28;MQ0=0;OQ=379.97;QD=10.00;SB=-141.64	GT:AD:DP:GL:GQ	0/1:24,13:33:-51.23,-9.94,-69.72:99
+chr1	1682181	rs1107910	T	C	610.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1733.17;QD=30.41;SB=-652.94	GT:AD:DP:GL:GQ	1/1:0,57:55:-176.95,-16.58,-0.05:99
+chr1	1683963	rs2011384	A	G	3.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=4.20;MQ=58.55;MQ0=0;OQ=1546.21;QD=34.36;SB=-525.21	GT:AD:DP:GL:GQ	1/1:0,45:43:-158.22,-12.95,-0.01:99
+chr1	1684111	.	C	T	6.27	PASS	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=0;HaplotypeScore=5.81;MQ=58.90;MQ0=0;OQ=1337.84;QD=16.12;SB=-601.14	GT:AD:DP:GL:GQ	0/1:40,41:79:-160.90,-23.83,-119.77:99
+chr1	1685322	rs4648629	C	A	210.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.13;MQ0=0;OQ=2599.96;QD=34.67;SB=-1123.97	GT:AD:DP:GL:GQ	1/1:0,75:71:-263.60,-21.38,-0.02:99
+chr1	1685434	rs876029	G	T	83.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1202.21;QD=31.64;SB=-492.27	GT:AD:DP:GL:GQ	1/1:0,38:36:-123.83,-10.85,-0.02:99
+chr1	1685691	rs63093560	C	T	514.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.49;MQ0=0;OQ=1899.13;QD=37.98;SB=-713.35	GT:AD:DP:GL:GQ	1/1:0,50:49:-193.52,-14.77,-0.02:99
+chr1	1686194	rs35270315	A	C	13.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=3.38;MQ=58.28;MQ0=0;OQ=2324.40;QD=30.19;SB=-1042.79	GT:AD:DP:GL:GQ	1/1:0,77:73:-236.08,-22.00,-0.06:99
+chr1	1686519	.	A	G	162.43	PASS	AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=1839.98;QD=29.21;SB=-784.98	GT:AD:DP:GL:GQ	1/1:0,63:60:-187.66,-18.11,-0.08:99
+chr1	1687967	rs35086222	C	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=6;HaplotypeScore=6.25;MQ=58.18;MQ0=0;OQ=2341.51;QD=37.77;SB=-1078.61	GT:AD:DP:GL:GQ	1/1:1,61:60:-237.76,-18.08,-0.02:99
+chr1	1688667	rs4648826	C	G	14.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.45;MQ=58.62;MQ0=0;OQ=2540.02;QD=41.64;SB=-864.78	GT:AD:DP:GL:GQ	1/1:0,61:58:-257.61,-17.48,-0.02:99
+chr1	1689061	rs4648827	C	A	174	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2030.67;QD=34.42;SB=-1001.13	GT:AD:DP:GL:GQ	1/1:1,58:58:-206.68,-17.47,-0.02:99
+chr1	1692374	rs6658139	T	C	285.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.82;MQ0=0;OQ=1093.26;QD=29.55;SB=-273.03	GT:AD:DP:GL:GQ	0/1:3,34:37:-123.62,-11.15,-11.29:1.44
+chr1	1694514	rs61774982	C	A	248.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.73;MQ0=0;OQ=726.51;QD=34.60;SB=-285.07	GT:AD:DP:GL:GQ	1/1:0,21:21:-76.24,-6.33,-0.01:63.18
+chr1	1695016	.	T	A	11.74	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=37;Dels=0.03;HRun=0;HaplotypeScore=27.67;MQ=32.06;MQ0=0;QD=0.32;SB=-25.92	GT:AD:DP:GL:GQ	0/1:10,26:10:-7.44,-3.01,-29.53:44.28
+chr1	1695024	.	T	A	13.63	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=9.62;MQ=29.68;MQ0=0;QD=0.39;SB=-25.92	GT:AD:DP:GL:GQ	0/1:9,26:10:-7.64,-3.01,-29.53:46.28
+chr1	1695026	.	T	A	81.80	SnpCluster	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=32.06;MQ0=0;QD=2.21;SB=-59.89	GT:AD:DP:GL:GQ	0/1:8,29:12:-15.08,-3.61,-28.63:99
+chr1	1695028	.	T	A	128.81	SnpCluster	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.66;MQ=32.06;MQ0=0;QD=3.48;SB=-77.75	GT:AD:DP:GL:GQ	0/1:7,30:9:-18.88,-2.71,-13.92:99
+chr1	1695464	rs61774983	A	G	565.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.28;MQ0=0;OQ=1675.23;QD=34.19;SB=-712.27	GT:AD:DP:GL:GQ	1/1:0,49:49:-171.13,-14.76,-0.02:99
+chr1	1695607	rs6603809	G	A	610.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.73;MQ0=0;OQ=1827.34;QD=36.55;SB=-919.23	GT:AD:DP:GL:GQ	1/1:0,50:48:-186.34,-14.47,-0.02:99
+chr1	1695633	rs6603810	A	G	70.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.63;MQ0=1;OQ=1141.91;QD=27.85;SB=-557.89	GT:AD:DP:GL:GQ	1/1:0,41:37:-117.81,-11.16,-0.04:99
+chr1	1695996	rs6603811	T	C	513.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1134.00;QD=29.08;SB=-433.18	GT:AD:DP:GL:GQ	1/1:0,39:37:-117.03,-11.17,-0.04:99
+chr1	1696020	rs7531583	A	G	565.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1293.98;QD=28.76;SB=-649.94	GT:AD:DP:GL:GQ	1/1:0,45:43:-133.03,-12.97,-0.04:99
+chr1	1697600	rs12041925	T	G	3.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=58.61;MQ0=0;OQ=1724.62;QD=29.73;SB=-619.85	GT:AD:DP:GL:GQ	1/1:0,58:53:-176.09,-15.97,-0.04:99
+chr1	1702090	rs10907194	C	T	0.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=5.73;MQ=57.94;MQ0=0;OQ=1197.78;QD=35.23;SB=-529.68	GT:AD:DP:GL:GQ	1/1:1,33:31:-123.37,-9.34,-0.01:93.30
+chr1	1703208	rs10907195	C	T	76.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.55;MQ0=0;OQ=1814.27;QD=37.80;SB=-686.40	GT:AD:DP:GL:GQ	1/1:0,48:45:-185.02,-13.55,-0.01:99
+chr1	1703574	rs454577	T	G	67.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=652.72;QD=31.08;SB=-294.53	GT:AD:DP:GL:GQ	1/1:0,21:20:-68.87,-6.03,-0.01:60.16
+chr1	1703729	rs7534617	T	G	38.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=59.38;MQ0=0;OQ=1200.11;QD=32.44;SB=-519.95	GT:AD:DP:GL:GQ	1/1:0,37:36:-123.61,-10.85,-0.02:99
+chr1	1704871	rs742359	C	A	251.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.49;MQ0=0;OQ=1398.04;QD=31.07;SB=-698.80	GT:AD:DP:GL:GQ	1/1:0,45:41:-143.41,-12.36,-0.02:99
+chr1	1706848	.	G	A	26.61	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=2;HaplotypeScore=3.11;MQ=59.44;MQ0=0;QD=0.65;SB=62.22	GT:AD:DP:GL:GQ	0/1:33,8:34:-16.19,-10.25,-103.26:59.43
+chr1	1709327	.	C	A	45.07	LowQual	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=18;HaplotypeScore=15.97;MQ=51.18;MQ0=0;QD=1.07;SB=-1.26	GT:AD:DP:GL:GQ	0/1:34,8:30:-16.83,-9.04,-86.61:77.90
+chr1	1710980	.	G	C	20.70	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.37;MQ=53.66;MQ0=1;QD=0.48;SB=38.15	GT:AD:DP:GL:GQ	0/1:38,5:37:-16.51,-11.16,-138.32:53.50
+chr1	1712688	rs3737627	G	A	389.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1534.00;QD=37.41;SB=-461.61	GT:AD:DP:GL:GQ	1/1:0,41:41:-157.01,-12.36,-0.03:99
+chr1	1715121	rs7545812	A	G	362.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=2055.38;QD=33.69;SB=-1042.38	GT:AD:DP:GL:GQ	1/1:0,61:58:-209.15,-17.47,-0.02:99
+chr1	1715620	rs6690956	C	T	11.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=5.08;MQ=58.81;MQ0=0;OQ=2937.89;QD=37.67;SB=-1197.36	GT:AD:DP:GL:GQ	1/1:0,77:75:-297.40,-22.60,-0.03:99
+chr1	1716741	.	G	A	184.26	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=52.39;MQ0=0;OQ=1148.50;QD=16.18;SB=-579.64	GT:AD:DP:GL:GQ	0/1:37,34:69:-138.94,-20.80,-109.67:99
+chr1	1718547	rs6603794	C	G	73.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.81;MQ=57.85;MQ0=0;OQ=2921.36;QD=42.96;SB=-1363.94	GT:AD:DP:GL:GQ	1/1:0,68:67:-295.74,-20.18,-0.02:99
+chr1	1722071	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=84;Dels=0.01;HRun=18;HaplotypeScore=24.45;MQ=58.30;MQ0=0;OQ=60.55;QD=0.72;SB=155.39	GT:AD:DP:GL:GQ	0/1:70,13:70:-30.14,-20.80,-197.36:93.38
+chr1	1724830	rs12077553	C	T	351.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.34;MQ0=0;OQ=2450.74;QD=39.53;SB=-952.27	GT:AD:DP:GL:GQ	1/1:0,62:62:-248.68,-18.68,-0.02:99
+chr1	1726513	rs12134783	T	G	35.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=59.11;MQ0=0;OQ=1936.28;QD=28.47;SB=-959.69	GT:AD:DP:GL:GQ	1/1:0,68:64:-197.28,-19.30,-0.07:99
+chr1	1726715	rs11260613	A	G	12.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=55.98;MQ0=0;OQ=727.27;QD=23.46;SB=-220.64	GT:AD:DP:GL:GQ	1/1:0,31:24:-76.34,-7.24,-0.02:72.14
+chr1	1728231	rs11585349	C	T	444.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.78;MQ0=0;OQ=853.44;QD=13.13;SB=-325.29	GT:AD:DP:GL:GQ	0/1:37,28:63:-107.61,-18.98,-131.07:99
+chr1	1728793	.	C	A	11.24	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=87;Dels=0.01;HRun=20;HaplotypeScore=12.66;MQ=49.01;MQ0=7;QD=0.13;SB=83.42	GT:AD:DP:GL:GQ	0/1:67,19:60:-22.45,-18.07,-182.40:43.74
+chr1	1731385	rs12407008	A	G	570.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=1462.68;QD=34.02;SB=-730.24	GT:AD:DP:GL:GQ	1/1:0,43:43:-149.87,-12.95,-0.02:99
+chr1	1733337	rs4648725	G	C	64.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=54.96;MQ0=0;OQ=2515.07;QD=40.57;SB=-1047.66	GT:AD:DP:GL:GQ	1/1:0,62:59:-255.12,-17.78,-0.02:99
+chr1	1733967	rs6603795	T	C	231.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.62;MQ0=0;OQ=1265.69;QD=28.77;SB=-184.41	GT:AD:DP:GL:GQ	1/1:0,44:42:-130.20,-12.68,-0.05:99
+chr1	1736016	rs12408690	A	G	634.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1961.02;QD=35.02;SB=-638.31	GT:AD:DP:GL:GQ	1/1:0,56:56:-199.70,-16.87,-0.02:99
+chr1	1736120	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=20;HaplotypeScore=11.72;MQ=42.99;MQ0=2;OQ=648.30;QD=8.64;SB=8.14	GT:AD:DP:GL:GQ	0/1:44,31:58:-85.60,-17.49,-115.79:99
+chr1	1737932	.	A	T	32.39	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=5;HaplotypeScore=48.11;MQ=56.04;MQ0=0;QD=0.40;SB=116.40	GT:AD:DP:GL:GQ	0/1:65,15:66:-26.41,-19.89,-217.38:65.23
+chr1	1737943	.	C	T	27.67	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=20;HaplotypeScore=10.01;MQ=51.69;MQ0=1;QD=0.36;SB=101.33	GT:AD:DP:GL:GQ	0/1:61,16:52:-21.72,-15.67,-162.40:60.50
+chr1	1739272	.	T	G	33.88	PASS	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=1;HaplotypeScore=2.35;MQ=58.21;MQ0=0;OQ=1071.30;QD=13.56;SB=-555.72	GT:AD:DP:GL:GQ	0/1:40,39:77:-133.61,-23.19,-145.75:99
+chr1	1741546	rs12140085	T	C	459.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.38;MQ0=0;OQ=960.01;QD=14.12;SB=-398.30	GT:AD:DP:GL:GQ	0/1:32,36:66:-119.17,-19.88,-129.12:99
+chr1	1741636	rs11260615	A	G	471.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.06;MQ0=1;OQ=1308.14;QD=29.07;SB=-638.27	GT:AD:DP:GL:GQ	1/1:1,44:42:-134.44,-12.67,-0.04:99
+chr1	1742815	rs4648726	C	T	274.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=3089.56;QD=40.12;SB=-1427.40	GT:AD:DP:GL:GQ	1/1:0,77:77:-312.56,-23.19,-0.02:99
+chr1	1743224	rs7542340	T	C	171.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=3;HaplotypeScore=-0.06;MQ=58.50;MQ0=0;OQ=2101.69;QD=35.62;SB=-1028.76	GT:AD:DP:GL:GQ	1/1:0,59:59:-213.77,-17.77,-0.02:99
+chr1	1744541	.	G	A	32.03	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=61;Dels=0.03;HRun=20;HaplotypeScore=23.82;MQ=51.57;MQ0=1;QD=0.53;SB=71.26	GT:AD:DP:GL:GQ	0/1:45,13:49:-20.64,-14.16,-151.56:64.87
+chr1	1748886	rs9786963	T	C	652.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1920.23;QD=32.55;SB=-686.89	GT:AD:DP:GL:GQ	1/1:0,59:59:-195.65,-17.79,-0.04:99
+chr1	1748914	rs10907187	G	A	586.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2397.92;QD=36.89;SB=-817.09	GT:AD:DP:GL:GQ	1/1:0,65:65:-243.43,-19.61,-0.05:99
+chr1	1750849	rs12568603	A	C	141.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=1462.88;QD=34.02;SB=-618.64	GT:AD:DP:GL:GQ	1/1:0,43:43:-149.89,-12.95,-0.02:99
+chr1	1751196	rs1999704	A	C	13.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=2.14;MQ=56.69;MQ0=1;OQ=2047.05;QD=32.49;SB=-593.04	GT:AD:DP:GL:GQ	1/1:1,62:59:-208.31,-17.77,-0.02:99
+chr1	1751865	rs11260616	A	T	0.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=6;HaplotypeScore=1.13;MQ=59.11;MQ0=0;OQ=1852.12;QD=35.62;SB=-771.53	GT:AD:DP:GL:GQ	1/1:0,52:52:-188.82,-15.67,-0.02:99
+chr1	1751874	rs7553640	T	C	711.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1893.02;QD=35.06;SB=-889.04	GT:AD:DP:GL:GQ	1/1:0,54:53:-192.90,-15.97,-0.02:99
+chr1	1752558	rs6603796	T	C	171.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.20;MQ0=0;OQ=1646.02;QD=32.27;SB=-583.16	GT:AD:DP:GL:GQ	1/1:0,51:48:-168.22,-14.47,-0.03:99
+chr1	1755443	rs6603797	T	C	720.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=2694.93;QD=35.46;SB=-935.73	GT:AD:DP:GL:GQ	1/1:0,76:74:-273.10,-22.29,-0.02:99
+chr1	1755954	rs6663586	A	C	220.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.45;MQ0=0;OQ=1370.69;QD=32.64;SB=-604.02	GT:AD:DP:GL:GQ	1/1:0,42:40:-140.67,-12.05,-0.02:99
+chr1	1756219	rs6603798	A	G	29.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=55.51;MQ0=2;OQ=1475.64;QD=28.38;SB=-669.92	GT:AD:DP:GL:GQ	1/1:2,50:47:-151.19,-14.18,-0.04:99
+chr1	1757221	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=20;HaplotypeScore=10.23;MQ=53.30;MQ0=1;OQ=618.88;QD=9.67;SB=31.58	GT:AD:DP:GL:GQ	0/1:38,25:58:-82.66,-17.49,-122.37:99
+chr1	1758520	rs10752417	C	G	0.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=106;Dels=0.00;HRun=1;HaplotypeScore=5.58;MQ=57.83;MQ0=0;OQ=4550.45;QD=42.93;SB=-2086.29	GT:AD:DP:GL:GQ	1/1:0,106:103:-454.04,-31.03,-0.03:99
+chr1	1758754	rs10907188	C	T	32.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=2.66;MQ=58.85;MQ0=1;OQ=2558.37;QD=38.18;SB=-882.18	GT:AD:DP:GL:GQ	1/1:1,66:64:-259.44,-19.28,-0.02:99
+chr1	1759918	rs6603799	T	C	1.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=10.20;MQ=56.09;MQ0=0;OQ=1988.53;QD=33.14;SB=-981.94	GT:AD:DP:GL:GQ	1/1:1,59:56:-202.45,-16.87,-0.02:99
+chr1	1760648	rs6657357	C	G	301.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.38;MQ0=0;OQ=2954.84;QD=38.37;SB=-1347.06	GT:AD:DP:GL:GQ	1/1:0,77:74:-299.12,-22.32,-0.05:99
+chr1	1760649	rs6665287	T	A	112.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=59.39;MQ0=0;OQ=2934.49;QD=37.15;SB=-1492.41	GT:AD:DP:GL:GQ	1/1:0,79:78:-297.05,-23.49,-0.02:99
+chr1	1762348	rs6603800	T	G	88.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=59.54;MQ0=0;OQ=1401.85;QD=28.04;SB=-481.90	GT:AD:DP:GL:GQ	1/1:0,50:43:-143.80,-12.96,-0.03:99
+chr1	1762595	rs10907189	T	C	215.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.73;MQ0=1;OQ=2558.08;QD=35.53;SB=-1178.50	GT:AD:DP:GL:GQ	1/1:1,71:71:-259.41,-21.39,-0.02:99
+chr1	1763512	rs11260618	A	G	251.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=34.24;MQ0=0;OQ=1296.92;QD=19.36;SB=-537.23	GT:AD:DP:GL:GQ	1/1:0,67:42:-133.32,-12.67,-0.05:99
+chr1	1763520	rs11260619	C	G	204.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=32.31;MQ0=0;OQ=1789.21;QD=27.11;SB=-722.93	GT:AD:DP:GL:GQ	1/1:0,66:41:-182.52,-12.35,-0.01:99
+chr1	1763525	rs11260620	T	C	490.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.33;MQ0=0;OQ=1197.40;QD=18.42;SB=-469.25	GT:AD:DP:GL:GQ	1/1:0,65:37:-123.35,-11.15,-0.02:99
+chr1	1763536	rs11260621	T	C	53.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=2.15;MQ=32.77;MQ0=1;OQ=1342.11;QD=19.74;SB=-614.98	GT:AD:DP:GL:GQ	1/1:1,67:42:-137.83,-12.66,-0.03:99
+chr1	1763632	rs10907190	G	A	500.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=2342.36;QD=38.40;SB=-955.26	GT:AD:DP:GL:GQ	1/1:0,61:60:-237.85,-18.08,-0.03:99
+chr1	1765035	rs11260622	A	G	3.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=4.83;MQ=58.68;MQ0=1;OQ=1949.34;QD=28.25;SB=-876.43	GT:AD:DP:GL:GQ	1/1:0,68:61:-198.58,-18.40,-0.06:99
+chr1	1766129	rs4648727	C	A	222.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.39;MQ0=0;OQ=2474.83;QD=35.87;SB=-1254.46	GT:AD:DP:GL:GQ	1/1:0,69:68:-251.09,-20.48,-0.02:99
+chr1	1768896	rs6692959	T	C	606.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=2761.38;QD=31.74;SB=-1372.68	GT:AD:DP:GL:GQ	1/1:0,87:87:-279.80,-26.24,-0.08:99
+chr1	1769657	.	A	T	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=45;Dels=0.02;HRun=0;HaplotypeScore=8.89;MQ=56.00;MQ0=1;OQ=229.76;QD=5.11;SB=-125.76	GT:AD:DP:GL:GQ	0/1:24,18:27:-34.10,-7.84,-57.21:99
+chr1	1770738	rs6603801	T	C	614.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1986.61;QD=34.85;SB=-910.02	GT:AD:DP:GL:GQ	1/1:0,57:57:-202.27,-17.17,-0.02:99
+chr1	1771205	rs6664578	G	A	696.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=3186.74;QD=38.39;SB=-1518.58	GT:AD:DP:GL:GQ	1/1:0,83:81:-322.28,-24.40,-0.02:99
+chr1	1772480	rs12066667	C	T	200.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.77;MQ0=0;OQ=1986.28;QD=37.48;SB=-1001.85	GT:AD:DP:GL:GQ	1/1:0,53:51:-202.23,-15.37,-0.02:99
+chr1	1773061	rs12402876	G	A	282.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=57.70;MQ0=0;OQ=2522.68;QD=37.10;SB=-929.21	GT:AD:DP:GL:GQ	1/1:0,68:65:-255.88,-19.59,-0.03:99
+chr1	1773444	rs7526236	G	A	531.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=1822.31;QD=37.96;SB=-748.50	GT:AD:DP:GL:GQ	1/1:0,48:47:-185.83,-14.16,-0.02:99
+chr1	1782409	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=18;HaplotypeScore=10.25;MQ=50.63;MQ0=2;OQ=451.92;QD=7.66;SB=-97.66	GT:AD:DP:GL:GQ	0/1:39,20:52:-64.14,-15.67,-118.24:99
+chr1	1782428	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=65;Dels=0.02;HRun=18;HaplotypeScore=18.34;MQ=52.25;MQ0=1;OQ=88.42;QD=1.36;SB=56.19	GT:AD:DP:GL:GQ	0/1:56,8:49:-26.89,-14.77,-145.13:99
+chr1	1782863	rs1889678	A	G	536.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.83;MQ0=0;OQ=1352.43;QD=28.18;SB=-598.57	GT:AD:DP:GL:GQ	1/1:0,48:43:-138.86,-12.97,-0.04:99
+chr1	1782931	rs12076620	A	G	575.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=1635.06;QD=34.79;SB=-754.18	GT:AD:DP:GL:GQ	1/1:0,47:46:-167.10,-13.85,-0.01:99
+chr1	1782971	rs10907192	A	G	594.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=1599.36;QD=34.03;SB=-532.43	GT:AD:DP:GL:GQ	1/1:0,47:46:-163.54,-13.86,-0.02:99
+chr1	1783646	rs7511905	A	C	266.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1582.35;QD=31.65;SB=-751.07	GT:AD:DP:GL:GQ	1/1:0,50:47:-161.84,-14.16,-0.02:99
+chr1	1785347	rs6660452	A	C	506.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.51;MQ0=0;OQ=1748.60;QD=30.15;SB=-666.84	GT:AD:DP:GL:GQ	1/1:0,58:55:-178.49,-16.58,-0.04:99
+chr1	1785613	.	C	A	22.53	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=20;HaplotypeScore=2.54;MQ=46.56;MQ0=0;QD=0.48;SB=89.31	GT:AD:DP:GL:GQ	0/1:40,7:41:-17.88,-12.35,-133.39:55.34
+chr1	1785636	rs6697311	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.01;HRun=20;HaplotypeScore=31.36;MQ=43.36;MQ0=1;OQ=989.12;QD=9.79;SB=-44.45	GT:AD:DP:GL:GQ	0/1:50,49:75:-124.51,-22.31,-136.94:99
+chr1	1785639	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=98;Dels=0.01;HRun=4;HaplotypeScore=41.45;MQ=42.87;MQ0=1;OQ=381.85;QD=3.90;SB=86.26	GT:AD:DP:GL:GQ	0/1:59,38:65:-60.76,-19.29,-163.75:99
+chr1	1785649	rs12036384	C	T	5.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=10.21;MQ=50.24;MQ0=1;OQ=2105.43;QD=30.96;SB=-932.26	GT:AD:DP:GL:GQ	1/1:2,63:54:-214.14,-16.27,-0.02:99
+chr1	1786577	rs12134553	A	C	2.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=7.76;MQ=57.97;MQ0=1;OQ=1915.32;QD=26.98;SB=-959.05	GT:AD:DP:GL:GQ	1/1:3,68:63:-201.59,-18.99,-6.48:99
+chr1	1787250	rs6670246	T	A	192	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.78;MQ0=0;OQ=2864.46;QD=33.70;SB=-1257.90	GT:AD:DP:GL:GQ	1/1:2,83:84:-296.95,-25.31,-6.91:99
+chr1	1789560	rs4648591	T	C	58.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=47.68;MQ0=0;OQ=1563.80;QD=30.66;SB=-605.93	GT:AD:DP:GL:GQ	1/1:0,51:49:-160.01,-14.78,-0.04:99
+chr1	1789813	rs7516995	T	C	114.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.57;MQ0=0;OQ=1801.38;QD=30.53;SB=-555.03	GT:AD:DP:GL:GQ	1/1:0,59:55:-183.76,-16.58,-0.04:99
+chr1	1790511	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=100;Dels=0.02;HRun=20;HaplotypeScore=40.13;MQ=50.15;MQ0=2;OQ=70.47;QD=0.70;SB=149.46	GT:AD:DP:GL:GQ	0/1:69,28:73:-32.03,-21.69,-222.30:99
+chr1	1790894	rs4648592	G	A	598.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.49;MQ0=0;OQ=2599.64;QD=38.23;SB=-928.70	GT:AD:DP:GL:GQ	1/1:0,68:65:-263.57,-19.58,-0.02:99
+chr1	1792032	rs6666068	A	G	457.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2160.60;QD=28.43;SB=-673.85	GT:AD:DP:GL:GQ	1/1:0,76:67:-219.70,-20.20,-0.05:99
+chr1	1794162	rs3855951	C	T	52.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=2.26;MQ=59.71;MQ0=0;OQ=3179.43;QD=39.74;SB=-1555.57	GT:AD:DP:GL:GQ	1/1:0,80:79:-321.55,-23.80,-0.02:99
+chr1	1795251	rs10907193	G	A	266.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=60.00;MQ0=0;OQ=1860.92;QD=32.65;SB=-731.44	GT:AD:DP:GL:GQ	1/1:0,56:50:-189.71,-15.08,-0.03:99
+chr1	1796166	rs10399762	A	G	54.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=58.73;MQ0=0;OQ=1409.98;QD=25.64;SB=-484.50	GT:AD:DP:GL:GQ	1/1:0,55:46:-144.64,-13.88,-0.05:99
+chr1	1798609	.	A	T	162.96	SnpCluster	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=74.10;MQ=46.50;MQ0=2;QD=4.29;SB=-81.05	GT:AD:DP:GL:GQ	0/1:27,11:32:-29.22,-9.64,-87.24:99
+chr1	1798611	.	A	T	632.57	SnpCluster	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=43.92;MQ=46.08;MQ0=2;QD=17.10;SB=-306.76	GT:AD:DP:GL:GQ	0/1:10,25:30:-75.58,-9.04,-33.08:99
+chr1	1798613	rs57488553	A	T	825.28	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=35.29;MQ=45.64;MQ0=2;QD=22.92;SB=-393.55	GT:AD:DP:GL:GQ	0/1:7,29:31:-95.15,-9.34,-18.41:90.67
+chr1	1798615	rs58263709	A	T	846.29	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=33.82;MQ=45.64;MQ0=2;QD=23.51;SB=-402.56	GT:AD:DP:GL:GQ	0/1:6,30:30:-96.95,-9.04,-14.67:56.29
+chr1	1799369	rs11260624	C	T	198.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.40;MQ0=0;OQ=2735.01;QD=39.07;SB=-1363.94	GT:AD:DP:GL:GQ	1/1:0,69:70:-279.86,-23.72,-2.77:99
+chr1	1799950	rs7525092	C	T	160.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=59.72;MQ0=0;OQ=3051.79;QD=36.77;SB=-1420.35	GT:AD:DP:GL:GQ	1/1:0,83:79:-308.79,-23.80,-0.03:99
+chr1	1800981	rs12133865	G	A	87.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=56.12;MQ0=0;OQ=1844.69;QD=38.43;SB=-730.97	GT:AD:DP:GL:GQ	1/1:0,48:48:-188.07,-14.47,-0.02:99
+chr1	1802311	.	A	G	78.46	Indel	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=3;HaplotypeScore=2.28;MQ=57.45;MQ0=0;QD=1.09;SB=-6.51	GT:AD:DP:GL:GQ	0/1:62,10:70:-32.22,-21.09,-246.49:99
+chr1	1802688	rs6670776	G	A	560.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=2301.44;QD=40.38;SB=-996.99	GT:AD:DP:GL:GQ	1/1:0,57:57:-233.74,-17.17,-0.01:99
+chr1	1805482	rs12138152	G	A	76.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.49;MQ0=0;OQ=2306.96;QD=39.10;SB=-1138.66	GT:AD:DP:GL:GQ	1/1:0,59:59:-234.30,-17.78,-0.02:99
+chr1	1807030	rs10796396	G	A	291.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.36;MQ0=0;OQ=1090.79;QD=38.96;SB=-403.67	GT:AD:DP:GL:GQ	1/1:0,28:28:-112.67,-8.43,-0.01:84.28
+chr1	1809238	rs6603804	T	C	659.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2030.11;QD=33.84;SB=-689.61	GT:AD:DP:GL:GQ	1/1:0,60:59:-206.62,-17.78,-0.03:99
+chr1	1809966	rs28608797	A	C	520.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.00;MQ0=0;OQ=1235.99;QD=32.53;SB=-595.06	GT:AD:DP:GL:GQ	1/1:1,37:36:-127.20,-10.84,-0.01:99
+chr1	1813782	rs6688000	A	G	233.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=58.61;MQ0=0;OQ=1439.33;QD=30.62;SB=-681.87	GT:AD:DP:GL:GQ	1/1:0,46:46:-147.56,-13.87,-0.04:99
+chr1	1818624	rs12045595	G	A	59.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=59.53;MQ0=0;OQ=1836.38;QD=37.48;SB=-594.97	GT:AD:DP:GL:GQ	1/1:0,49:48:-187.24,-14.46,-0.02:99
+chr1	1821118	rs6603808	A	G	79.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=60.00;MQ0=0;OQ=1052.30;QD=28.44;SB=-413.55	GT:AD:DP:GL:GQ	1/1:0,37:31:-108.83,-9.34,-0.01:93.27
+chr1	1822217	rs941531	G	A	113.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=58.68;MQ0=0;OQ=2643.63;QD=39.46;SB=-1073.33	GT:AD:DP:GL:GQ	1/1:0,67:66:-267.97,-19.88,-0.02:99
+chr1	1822410	.	A	G	49.96	LowQual	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.13;MQ0=0;QD=0.89;SB=-35.78	GT:AD:DP:GL:GQ	0/1:49,7:55:-24.85,-16.57,-195.12:82.80
+chr1	1822442	rs4996032	G	A	113.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.02;HRun=2;HaplotypeScore=1.09;MQ=59.55;MQ0=0;OQ=884.12;QD=14.03;SB=-419.83	GT:AD:DP:GL:GQ	0/1:35,27:62:-110.37,-18.67,-127.42:99
+chr1	1822448	rs4996031	A	G	133.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.02;MQ=59.08;MQ0=1;OQ=897.87;QD=14.03;SB=-423.51	GT:AD:DP:GL:GQ	0/1:31,33:61:-111.45,-18.38,-115.75:99
+chr1	1823355	rs10454464	G	A	100.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=57.95;MQ0=0;OQ=1113.42;QD=34.79;SB=-534.62	GT:AD:DP:GL:GQ	1/1:0,31:31:-117.34,-11.71,-2.42:92.95
+chr1	1824608	rs4648731	A	G	30.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=54.33;MQ0=0;OQ=891.08;QD=28.74;SB=-233.75	GT:AD:DP:GL:GQ	1/1:0,31:26:-92.71,-7.84,-0.01:78.21
+chr1	1824902	rs11260625	G	A	47.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=46.58;MQ0=0;OQ=814.82;QD=27.16;SB=-295.36	GT:AD:DP:GL:GQ	1/1:0,25:22:-85.08,-6.64,-0.02:66.19
+chr1	1824916	rs11260626	C	T	92.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=48.72;MQ0=0;OQ=1289.62;QD=36.85;SB=-588.96	GT:AD:DP:GL:GQ	1/1:0,35:34:-132.56,-10.25,-0.01:99
+chr1	1825136	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=16;HaplotypeScore=8.80;MQ=56.14;MQ0=0;OQ=163.77;QD=3.72;SB=41.15	GT:AD:DP:GL:GQ	0/1:27,17:32:-29.31,-9.65,-83.86:99
+chr1	1826546	rs2748989	C	G	308.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.60;MQ0=0;OQ=2438.44;QD=41.33;SB=-736.72	GT:AD:DP:GL:GQ	1/1:0,59:58:-247.45,-17.48,-0.02:99
+chr1	1827738	rs4648732	C	T	470.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=1741.59;QD=38.70;SB=-666.40	GT:AD:DP:GL:GQ	1/1:0,45:44:-177.75,-13.25,-0.01:99
+chr1	1828376	rs2377037	C	A	189.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=1605.71;QD=33.45;SB=-826.68	GT:AD:DP:GL:GQ	1/1:1,47:46:-164.17,-13.86,-0.02:99
+chr1	1828498	rs28672079	A	G	314.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=1270.30;QD=29.54;SB=-594.88	GT:AD:DP:GL:GQ	1/1:0,43:41:-130.66,-12.37,-0.05:99
+chr1	1829551	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=17.55;MQ=56.35;MQ0=0;OQ=57.59;QD=1.48;SB=26.11	GT:AD:DP:GL:GQ	0/1:19,19:17:-14.19,-5.14,-50.87:90.43
+chr1	1829898	rs2474461	T	C	40.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=579.60;QD=34.09;SB=-105.03	GT:AD:DP:GL:GQ	1/1:0,17:17:-61.55,-5.12,-0.01:51.14
+chr1	1830536	rs28384316	G	T	112.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=125.10;QD=25.02;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,5:5:-16.07,-1.51,-0.01:15.03
+chr1	1832651	.	A	G	0.32	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=3;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=742.60;QD=18.11;SB=-247.32	GT:AD:DP:GL:GQ	0/1:17,24:40:-89.59,-12.05,-62.50:99
+chr1	1834219	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=20;HaplotypeScore=9.36;MQ=53.72;MQ0=0;OQ=93.63;QD=2.46;SB=11.06	GT:AD:DP:GL:GQ	0/1:25,13:25:-20.18,-7.53,-63.71:99
+chr1	1834282	.	T	C	14.27	PASS	AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=417.56;QD=26.10;SB=-221.65	GT:AD:DP:GL:GQ	1/1:0,16:14:-45.35,-4.22,-0.01:42.10
+chr1	1834553	rs28842562	C	T	275.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.51;MQ0=1;OQ=892.93;QD=34.34;SB=-192.75	GT:AD:DP:GL:GQ	1/1:0,26:23:-92.88,-6.93,-0.01:69.22
+chr1	1836321	rs41306992	C	T	57.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.24;MQ0=0;OQ=2100.54;QD=38.19;SB=-756.01	GT:AD:DP:GL:GQ	1/1:0,55:53:-213.65,-15.97,-0.01:99
+chr1	1836442	rs2748987	A	G	431.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=1604.85;QD=34.15;SB=-631.28	GT:AD:DP:GL:GQ	1/1:0,47:47:-164.09,-14.16,-0.02:99
+chr1	1838594	rs941532	A	G	20.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=58.71;MQ0=0;OQ=477.15;QD=26.51;SB=-129.69	GT:AD:DP:GL:GQ	1/1:0,18:17:-51.32,-5.13,-0.02:51.08
+chr1	1839996	rs2295364	C	T	1.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.59;MQ0=0;OQ=1245.14;QD=37.73;SB=-117.65	GT:AD:DP:GL:GQ	1/1:0,33:32:-128.11,-9.64,-0.01:96.31
+chr1	1841796	rs2474458	C	A	22.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=3.16;MQ=58.78;MQ0=0;OQ=1243.51;QD=32.72;SB=-630.04	GT:AD:DP:GL:GQ	1/1:0,38:36:-127.95,-10.85,-0.01:99
+chr1	1842344	rs28508199	A	G	34.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=58.67;MQ0=0;OQ=1404.62;QD=28.67;SB=-672.87	GT:AD:DP:GL:GQ	1/1:0,49:45:-144.09,-13.57,-0.04:99
+chr1	1843148	rs1884454	G	T	340.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=56.74;MQ0=0;OQ=831.99;QD=14.34;SB=-322.02	GT:AD:DP:GL:GQ	0/1:28,30:55:-103.05,-16.57,-95.32:99
+chr1	1844181	rs2250833	A	G	20.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=995.90;QD=27.66;SB=-313.46	GT:AD:DP:GL:GQ	1/1:0,36:31:-103.20,-9.35,-0.02:93.22
+chr1	1845310	rs28423370	A	G	170.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=608.06;QD=32.00;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,19:19:-64.40,-5.72,-0.01:57.14
+chr1	1845407	.	C	A	46.94	LowQual	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=55.21;MQ0=0;QD=9.39;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,3:5:-9.49,-1.51,-6.80:52.97
+chr1	1845958	rs752965	C	T	17.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.17;MQ0=0;OQ=985.76;QD=35.21;SB=-88.34	GT:AD:DP:GL:GQ	1/1:0,28:26:-102.17,-7.83,-0.01:78.25
+chr1	1846560	rs2092922	C	T	67.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.95;MQ0=0;OQ=1561.86;QD=36.32;SB=-529.71	GT:AD:DP:GL:GQ	1/1:0,43:41:-159.79,-12.36,-0.02:99
+chr1	1848991	rs4648734	C	T	0.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=7.13;MQ=58.00;MQ0=0;OQ=1973.99;QD=36.56;SB=-772.04	GT:AD:DP:GL:GQ	1/1:0,53:53:-203.45,-18.19,-2.47:99
+chr1	1849418	rs28670388	T	C	0.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=3;HaplotypeScore=7.22;MQ=55.28;MQ0=2;OQ=1025.15;QD=29.29;SB=-496.47	GT:AD:DP:GL:GQ	1/1:3,32:30:-106.11,-9.04,-0.01:90.24
+chr1	1850605	rs28685049	C	T	18.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=778.38;QD=38.92;SB=-47.56	GT:AD:DP:GL:GQ	1/1:0,20:20:-81.43,-6.03,-0.01:60.20
+chr1	1850678	.	T	A	0.69	PASS	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=41.96;MQ0=0;OQ=61.03;QD=6.78;SB=5.04	GT:AD:DP:GL:GQ	0/1:6,3:9:-12.10,-2.71,-21.43:93.87
+chr1	1850683	.	G	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=10.93;MQ=35.14;MQ0=0;OQ=63.11;QD=9.02;SB=-3.99	GT:AD:DP:GL:GQ	0/1:4,3:6:-11.40,-1.81,-10.53:87.27
+chr1	1851012	rs55825112	G	A	257.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.15;MQ0=0;OQ=1284.14;QD=38.91;SB=-355.97	GT:AD:DP:GL:GQ	1/1:0,33:33:-132.01,-9.94,-0.01:99
+chr1	1852535	rs2474449	C	T	115.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=42.11;MQ0=1;OQ=2050.54;QD=37.28;SB=-856.64	GT:AD:DP:GL:GQ	1/1:1,54:53:-211.75,-15.96,-3.11:99
+chr1	1852731	.	T	A	22.37	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=63;Dels=0.05;HRun=20;HaplotypeScore=13.90;MQ=48.22;MQ0=0;QD=0.36;SB=16.21	GT:AD:DP:GL:GQ	0/1:42,18:40:-16.96,-11.45,-121.97:55.18
+chr1	1852818	rs4648595	A	G	3.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.78;MQ=50.34;MQ0=1;OQ=917.27;QD=25.48;SB=-127.78	GT:AD:DP:GL:GQ	1/1:1,35:28:-95.33,-8.44,-0.02:84.22
+chr1	1853042	.	C	A	10.89	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=20;HaplotypeScore=9.56;MQ=49.02;MQ0=4;QD=0.19;SB=86.27	GT:AD:DP:GL:GQ	0/1:51,7:42:-16.99,-12.66,-132.54:43.35
+chr1	1853068	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=2;HaplotypeScore=13.43;MQ=48.98;MQ0=4;OQ=94.12;QD=1.00;SB=104.36	GT:AD:DP:GL:GQ	0/1:70,24:65:-32.29,-19.60,-195.03:99
+chr1	1853265	rs60147457	T	C	26.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=56.17;MQ0=0;OQ=1299.21;QD=28.24;SB=-640.40	GT:AD:DP:GL:GQ	1/1:1,45:44:-136.91,-13.28,-3.40:98.74
+chr1	1855559	.	C	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=1;HaplotypeScore=1.77;MQ=58.15;MQ0=0;OQ=143.93;QD=1.87;SB=17.18	GT:AD:DP:GL:GQ	0/1:67,10:76:-40.57,-22.90,-237.26:99
+chr1	1855612	rs2748968	C	T	224.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=53.49;MQ0=2;OQ=1207.94;QD=15.10;SB=-597.02	GT:AD:DP:GL:GQ	0/1:40,40:73:-146.08,-22.00,-120.30:99
+chr1	1855646	.	T	C	0.93	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=9.48;MQ=53.45;MQ0=2;OQ=1049.44;QD=14.78;SB=-537.98	GT:AD:DP:GL:GQ	0/1:31,40:66:-128.11,-19.89,-114.90:99
+chr1	1855674	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=15.63;MQ=50.86;MQ0=1;OQ=126.19;QD=2.25;SB=-24.71	GT:AD:DP:GL:GQ	0/1:49,7:53:-31.88,-15.98,-189.82:99
+chr1	1855675	.	A	G	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=14.63;MQ=50.86;MQ0=1;OQ=886.43;QD=15.83;SB=-281.60	GT:AD:DP:GL:GQ	0/1:21,35:52:-107.60,-15.67,-76.26:99
+chr1	1856033	rs34454803	C	G	2.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=4.56;MQ=48.03;MQ0=9;OQ=1928.44;QD=26.78;SB=-825.04	GT:AD:DP:GL:GQ	1/1:9,62:49:-203.74,-17.80,-7.31:99
+chr1	1856195	rs61775027	C	T	136.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=55.46;MQ0=1;OQ=2158.57;QD=29.98;SB=-1089.45	GT:AD:DP:GL:GQ	1/1:8,64:59:-222.77,-17.79,-3.33:99
+chr1	1856465	rs34793596	C	G	37.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=2.87;MQ=54.29;MQ0=1;OQ=3153.75;QD=39.92;SB=-1439.03	GT:AD:DP:GL:GQ	1/1:3,76:75:-323.13,-22.60,-4.17:99
+chr1	1856473	rs35531706	C	G	44.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=2.23;MQ=55.29;MQ0=1;OQ=2974.48;QD=40.20;SB=-1193.83	GT:AD:DP:GL:GQ	1/1:1,73:71:-301.06,-21.40,-0.03:99
+chr1	1858345	rs28658236	G	A	98.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.98;MQ=60.00;MQ0=0;OQ=1111.27;QD=16.34;SB=-403.37	GT:AD:DP:GL:GQ	0/1:35,33:68:-134.91,-20.49,-114.02:99
+chr1	1859106	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=2;HaplotypeScore=6.59;MQ=57.30;MQ0=0;OQ=100.83;QD=1.80;SB=56.18	GT:AD:DP:GL:GQ	0/1:31,25:39:-25.12,-11.75,-106.73:99
+chr1	1859766	rs28592294	C	T	2.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=5.60;MQ=57.03;MQ0=0;OQ=2783.58;QD=37.62;SB=-907.72	GT:AD:DP:GL:GQ	1/1:1,72:73:-285.26,-22.00,-3.32:99
+chr1	1860070	rs2803323	G	A	91.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=58.89;MQ0=0;OQ=1564.69;QD=37.25;SB=-659.28	GT:AD:DP:GL:GQ	1/1:0,42:41:-160.07,-12.36,-0.02:99
+chr1	1861277	rs2803324	T	C	62.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=848.26;QD=30.30;SB=-320.13	GT:AD:DP:GL:GQ	1/1:0,28:28:-88.44,-8.45,-0.03:84.18
+chr1	1863485	rs12758705	G	A	595.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2263.21;QD=38.36;SB=-926.70	GT:AD:DP:GL:GQ	1/1:0,59:57:-229.92,-17.17,-0.01:99
+chr1	1864441	rs2803329	A	G	280.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1008.85;QD=27.27;SB=-491.17	GT:AD:DP:GL:GQ	1/1:0,37:33:-104.50,-9.95,-0.03:99
+chr1	1864697	rs2803330	A	G	60.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.49;MQ0=0;OQ=756.37;QD=30.25;SB=-313.68	GT:AD:DP:GL:GQ	1/1:0,25:22:-79.23,-6.63,-0.01:66.20
+chr1	1865005	rs2803331	C	T	233.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=58.84;MQ0=0;OQ=1354.55;QD=33.86;SB=-668.39	GT:AD:DP:GL:GQ	1/1:0,37:37:-139.06,-11.16,-0.02:99
+chr1	1865127	rs2262190	A	G	525.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=948.06;QD=30.58;SB=-404.33	GT:AD:DP:GL:GQ	1/1:0,31:30:-98.41,-9.05,-0.02:90.22
+chr1	1867098	rs2748978	T	G	544.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.39;MQ0=0;OQ=1416.47;QD=34.55;SB=-657.23	GT:AD:DP:GL:GQ	1/1:0,41:41:-145.24,-12.35,-0.01:99
+chr1	1867212	rs2803339	T	C	83.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=54.90;MQ0=0;OQ=1104.15;QD=27.60;SB=-492.17	GT:AD:DP:GL:GQ	1/1:1,39:37:-114.04,-11.17,-0.04:99
+chr1	1868944	rs2490543	C	T	282.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=58.05;MQ0=0;OQ=849.11;QD=14.15;SB=-315.86	GT:AD:DP:GL:GQ	0/1:33,27:55:-104.77,-16.57,-95.97:99
+chr1	1868947	rs28573337	G	A	161.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=57.95;MQ0=0;OQ=983.65;QD=17.26;SB=-292.79	GT:AD:DP:GL:GQ	0/1:26,31:55:-118.23,-16.58,-80.47:99
+chr1	1869420	rs28498068	T	G	172.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=56.75;MQ0=0;OQ=395.95;QD=11.31;SB=-182.88	GT:AD:DP:GL:GQ	0/1:18,17:34:-53.12,-10.25,-61.66:99
+chr1	1869908	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=14;HaplotypeScore=14.65;MQ=46.99;MQ0=0;OQ=127.58;QD=2.90;SB=11.06	GT:AD:DP:GL:GQ	0/1:29,15:29:-24.78,-8.74,-71.11:99
+chr1	1870211	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=105;Dels=0.02;HRun=2;HaplotypeScore=156.21;MQ=37.45;MQ0=0;OQ=89.02;QD=0.85;SB=-10.74	GT:AD:DP:GL:GQ	0/1:91,12:93:-39.61,-27.42,-314.70:99
+chr1	1870216	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.13;HRun=3;HaplotypeScore=129.57;MQ=35.88;MQ0=0;OQ=216.82;QD=2.28;SB=-71.49	GT:AD:DP:GL:GQ	0/1:69,14:77:-47.26,-22.30,-241.64:99
+chr1	1870237	.	C	T	350.17	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=136.82;MQ=33.84;MQ0=0;QD=4.38;SB=-96.57	GT:AD:DP:GL:GQ	0/1:64,16:68:-58.79,-20.48,-197.51:99
+chr1	1870241	.	T	C	795.72	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=2;HaplotypeScore=105.65;MQ=33.28;MQ0=0;QD=10.33;SB=-171.98	GT:AD:DP:GL:GQ	0/1:49,28:68:-103.35,-20.49,-158.12:99
+chr1	1870246	.	T	C	783.37	SnpCluster	AC=1;AF=0.50;AN=2;DP=75;Dels=0.01;HRun=3;HaplotypeScore=106.17;MQ=32.28;MQ0=0;QD=10.44;SB=-190.65	GT:AD:DP:GL:GQ	0/1:44,29:65:-101.22,-19.60,-139.10:99
+chr1	1870249	rs28490251	C	T	536.49	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=65.25;MQ=33.25;MQ0=0;QD=8.01;SB=-19.48	GT:AD:DP:GL:GQ	0/1:45,22:60:-75.01,-18.07,-158.51:99
+chr1	1870263	.	T	C	67.37	SnpCluster	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=2;HaplotypeScore=102.33;MQ=35.77;MQ0=0;QD=1.07;SB=-0.98	GT:AD:DP:GL:GQ	0/1:55,8:53:-25.99,-15.97,-184.95:99
+chr1	1870272	.	C	T	96.33	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=2;HaplotypeScore=53.42;MQ=40.73;MQ0=0;QD=1.55;SB=5.03	GT:AD:DP:GL:GQ	0/1:52,10:55:-29.48,-16.57,-180.28:99
+chr1	1870273	.	T	C	72.37	SnpCluster	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=2;HaplotypeScore=53.42;MQ=40.73;MQ0=0;QD=1.17;SB=-0.98	GT:AD:DP:GL:GQ	0/1:55,7:53:-26.49,-15.97,-188.35:99
+chr1	1870281	.	C	T	187.69	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=96.79;MQ=44.56;MQ0=0;QD=3.24;SB=5.04	GT:AD:DP:GL:GQ	0/1:46,12:51:-37.41,-15.36,-160.10:99
+chr1	1870294	.	T	C	11.65	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=10.99;MQ=47.97;MQ0=0;QD=0.19;SB=8.05	GT:AD:DP:GL:GQ	0/1:55,6:59:-22.20,-17.78,-213.89:44.18
+chr1	1870405	.	C	A	16.24	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=38.44;MQ0=0;OQ=457.23;QD=8.97;SB=-4.29	GT:AD:DP:GL:GQ	0/1:33,18:50:-64.07,-15.06,-117.59:99
+chr1	1870410	.	T	C	0.86	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=38.95;MQ0=0;OQ=422.51;QD=8.80;SB=-31.25	GT:AD:DP:GL:GQ	0/1:31,17:47:-59.69,-14.16,-126.57:99
+chr1	1870428	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=1;HaplotypeScore=20.35;MQ=41.74;MQ0=0;OQ=75.20;QD=2.15;SB=23.10	GT:AD:DP:GL:GQ	0/1:27,8:31:-20.14,-9.34,-96.20:99
+chr1	1870432	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=16.08;MQ=42.82;MQ0=0;OQ=52.58;QD=1.81;SB=29.11	GT:AD:DP:GL:GQ	0/1:24,5:28:-16.98,-8.43,-86.35:85.42
+chr1	1870446	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=25;Dels=0.04;HRun=2;HaplotypeScore=17.65;MQ=47.45;MQ0=0;OQ=105.58;QD=4.22;SB=-62.85	GT:AD:DP:GL:GQ	0/1:18,6:24:-20.77,-6.93,-68.32:99
+chr1	1871370	rs2490541	C	A	191.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.38;MQ0=1;OQ=2594.06;QD=33.69;SB=-1155.38	GT:AD:DP:GL:GQ	1/1:0,76:73:-263.01,-21.99,-0.02:99
+chr1	1872147	rs2490540	A	G	201.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.87;MQ0=0;OQ=2121.33;QD=34.22;SB=-1028.42	GT:AD:DP:GL:GQ	1/1:0,62:60:-215.74,-18.07,-0.02:99
+chr1	1872797	rs28754760	C	T	596.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.63;MQ0=0;OQ=2762.82;QD=40.63;SB=-1367.30	GT:AD:DP:GL:GQ	1/1:0,68:68:-279.88,-20.48,-0.01:99
+chr1	1872809	rs2490564	A	G	614.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.49;MQ0=0;OQ=2664.00;QD=34.60;SB=-1257.66	GT:AD:DP:GL:GQ	1/1:0,77:76:-270.02,-22.89,-0.03:99
+chr1	1872820	rs2490563	C	A	537.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.73;MQ0=0;OQ=2673.37;QD=36.62;SB=-1103.59	GT:AD:DP:GL:GQ	1/1:0,73:73:-270.94,-21.99,-0.02:99
+chr1	1872941	rs28505085	C	T	182.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.70;MQ0=0;OQ=3049.13;QD=40.12;SB=-1406.71	GT:AD:DP:GL:GQ	1/1:0,76:76:-308.51,-22.89,-0.02:99
+chr1	1873219	rs2490562	A	G	659.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=2029.90;QD=31.23;SB=-828.58	GT:AD:DP:GL:GQ	1/1:0,65:64:-206.63,-19.30,-0.05:99
+chr1	1874915	rs2474455	C	T	626.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2935.86;QD=37.64;SB=-1349.01	GT:AD:DP:GL:GQ	1/1:0,78:74:-297.19,-22.29,-0.02:99
+chr1	1876080	rs4648738	C	T	622.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.86;MQ0=0;OQ=2172.76;QD=36.21;SB=-969.30	GT:AD:DP:GL:GQ	1/1:0,60:56:-220.88,-16.87,-0.02:99
+chr1	1876082	rs2803287	T	G	577.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.86;MQ0=0;OQ=1927.37;QD=32.12;SB=-839.09	GT:AD:DP:GL:GQ	1/1:0,60:56:-196.35,-16.87,-0.02:99
+chr1	1876206	.	G	A	152.24	Indel	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=32.79;MQ=48.52;MQ0=0;QD=4.91;SB=-65.27	GT:AD:DP:GL:GQ	0/1:20,7:27:-34.54,-16.03,-70.20:99
+chr1	1876245	rs2803286	T	C	61.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=51.77;MQ0=0;OQ=999.35;QD=27.76;SB=-355.43	GT:AD:DP:GL:GQ	1/1:0,36:34:-103.57,-10.26,-0.05:99
+chr1	1876361	rs2748976	C	A	113.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=45.22;MQ0=0;OQ=179.32;QD=6.90;SB=-106.45	GT:AD:DP:GL:GQ	0/1:18,8:25:-28.75,-7.53,-52.51:99
+chr1	1876371	.	C	A	48.69	LowQual	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=43.76;MQ0=0;QD=2.03;SB=-50.67	GT:AD:DP:GL:GQ	0/1:20,4:23:-15.08,-6.93,-60.82:81.52
+chr1	1876379	rs2748975	C	A	111.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=47.73;MQ0=0;OQ=820.31;QD=34.18;SB=-360.86	GT:AD:DP:GL:GQ	1/1:0,24:23:-85.62,-6.93,-0.01:69.21
+chr1	1876719	rs3795290	C	T	341.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.08;MQ0=0;OQ=1064.55;QD=38.02;SB=-422.06	GT:AD:DP:GL:GQ	1/1:0,28:28:-110.05,-8.44,-0.01:84.27
+chr1	1876879	rs28548017	A	G	12.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=3.36;MQ=59.09;MQ0=0;OQ=1547.11;QD=33.63;SB=-748.91	GT:AD:DP:GL:GQ	1/1:0,45:45:-158.32,-13.56,-0.02:99
+chr1	1877105	rs28575980	G	A	126.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=58.88;MQ0=0;OQ=2123.64;QD=39.33;SB=-940.36	GT:AD:DP:GL:GQ	1/1:0,54:54:-215.96,-16.27,-0.02:99
+chr1	1878053	rs3820011	C	A	596.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1358.01;QD=33.95;SB=-534.23	GT:AD:DP:GL:GQ	1/1:0,40:39:-139.40,-11.75,-0.01:99
+chr1	1878190	rs28535696	C	T	4.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=5.27;MQ=59.60;MQ0=0;OQ=1961.78;QD=33.82;SB=-651.37	GT:AD:DP:GL:GQ	1/1:0,56:52:-199.79,-15.68,-0.03:99
+chr1	1878229	rs2803285	A	G	106.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.79;MQ=60.00;MQ0=0;OQ=1952.57;QD=31.49;SB=-789.62	GT:AD:DP:GL:GQ	1/1:0,62:61:-198.90,-18.40,-0.05:99
+chr1	1878313	rs28549710	G	A	560.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=1883.77;QD=38.44;SB=-852.64	GT:AD:DP:GL:GQ	1/1:0,49:48:-191.98,-14.46,-0.02:99
+chr1	1878885	rs2748974	A	G	5.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.37;MQ=58.15;MQ0=0;OQ=1276.90;QD=26.60;SB=-511.07	GT:AD:DP:GL:GQ	1/1:1,47:40:-131.31,-12.06,-0.03:99
+chr1	1878935	rs941533	C	T	78.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.81;MQ0=0;OQ=1331.51;QD=34.14;SB=-642.34	GT:AD:DP:GL:GQ	1/1:0,39:35:-136.75,-10.55,-0.02:99
+chr1	1879652	rs2748973	A	T	145.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1566.33;QD=34.81;SB=-658.70	GT:AD:DP:GL:GQ	1/1:0,44:44:-160.23,-13.26,-0.02:99
+chr1	1881908	rs2803292	G	C	343.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=1280.73;QD=16.85;SB=-445.74	GT:AD:DP:GL:GQ	0/1:41,35:73:-153.35,-22.00,-166.87:99
+chr1	1882185	rs2803291	T	C	583.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1616.58;QD=28.87;SB=-749.95	GT:AD:DP:GL:GQ	1/1:0,56:52:-165.29,-15.68,-0.05:99
+chr1	1883521	rs9777849	T	C	52.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=1.11;MQ=58.55;MQ0=0;OQ=2600.99;QD=33.78;SB=-793.15	GT:AD:DP:GL:GQ	1/1:0,77:75:-263.71,-22.59,-0.03:99
+chr1	1883775	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=18;HaplotypeScore=34.55;MQ=54.67;MQ0=0;OQ=115.46;QD=1.72;SB=60.06	GT:AD:DP:GL:GQ	0/1:50,15:53:-37.44,-22.61,-153.19:99
+chr1	1884144	rs4648739	T	C	265.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=56.66;MQ0=0;OQ=1089.11;QD=12.10;SB=-234.30	GT:AD:DP:GL:GQ	0/1:41,48:84:-137.52,-25.33,-160.93:99
+chr1	1884622	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=7.50;MQ=53.07;MQ0=0;OQ=108.82;QD=2.02;SB=71.24	GT:AD:DP:GL:GQ	0/1:31,23:39:-25.91,-11.75,-106.64:99
+chr1	1884705	rs9697615	G	A	136.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=58.71;MQ0=0;OQ=608.41;QD=12.94;SB=-170.23	GT:AD:DP:GL:GQ	0/1:24,22:44:-77.39,-13.26,-79.80:99
+chr1	1884754	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=43.50;MQ=52.44;MQ0=1;OQ=107.17;QD=1.76;SB=65.22	GT:AD:DP:GL:GQ	0/1:47,13:52:-29.66,-15.66,-164.16:99
+chr1	1884755	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=20;HaplotypeScore=45.92;MQ=52.41;MQ0=1;OQ=326.78;QD=5.11;SB=65.23	GT:AD:DP:GL:GQ	0/1:48,16:59:-53.73,-17.77,-157.95:99
+chr1	1884837	rs35817970	T	C	556.60	Indel	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=55.91;MQ0=0;QD=10.91;SB=-219.26	GT:AD:DP:GL:GQ	0/1:29,21:48:-73.41,-14.46,-106.68:99
+chr1	1885037	rs7523728	C	T	495.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.35;MQ0=0;OQ=754.75;QD=13.98;SB=-403.19	GT:AD:DP:GL:GQ	0/1:30,24:50:-93.83,-15.07,-88.75:99
+chr1	1885400	rs28561741	A	G	4.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=3;HaplotypeScore=1.47;MQ=59.52;MQ0=0;OQ=350.23;QD=7.30;SB=-137.55	GT:AD:DP:GL:GQ	0/1:31,17:46:-52.17,-13.87,-117.69:99
+chr1	1885962	rs13302978	G	A	113.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.25;MQ=53.12;MQ0=0;OQ=689.28;QD=12.53;SB=-222.75	GT:AD:DP:GL:GQ	0/1:26,26:49:-87.00,-14.79,-79.84:99
+chr1	1886045	rs13303324	T	C	252.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.41;MQ0=0;OQ=434.96;QD=11.15;SB=-181.59	GT:AD:DP:GL:GQ	0/1:18,21:37:-57.94,-11.16,-71.83:99
+chr1	1886083	rs13303202	C	T	406.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=730.31;QD=16.98;SB=-346.33	GT:AD:DP:GL:GQ	0/1:21,22:43:-89.27,-12.95,-73.96:99
+chr1	1886300	rs16824585	G	A	23.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=56.05;MQ0=0;OQ=933.53;QD=20.75;SB=-382.89	GT:AD:DP:GL:GQ	0/1:18,27:45:-110.19,-13.56,-62.00:99
+chr1	1886413	rs28625839	C	T	106.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.20;MQ0=0;OQ=181.47;QD=6.98;SB=-69.07	GT:AD:DP:GL:GQ	0/1:17,9:21:-27.77,-6.34,-42.14:99
+chr1	1887329	rs28523363	A	G	314.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=60.00;MQ0=0;OQ=843.98;QD=13.40;SB=-333.92	GT:AD:DP:GL:GQ	0/1:32,31:62:-106.36,-18.68,-128.89:99
+chr1	1887451	rs4648599	C	T	245.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=58.01;MQ0=0;OQ=690.92;QD=14.70;SB=-275.28	GT:AD:DP:GL:GQ	0/1:24,23:44:-85.64,-13.26,-73.07:99
+chr1	1887613	rs4648600	C	G	12.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=4.38;MQ=58.99;MQ0=0;OQ=734.25;QD=15.96;SB=-239.38	GT:AD:DP:GL:GQ	0/1:23,23:42:-89.37,-12.66,-89.33:99
+chr1	1887905	rs28712827	G	A	21.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=6.31;MQ=57.89;MQ0=0;OQ=502.21;QD=13.22;SB=-250.22	GT:AD:DP:GL:GQ	0/1:20,17:35:-64.07,-10.57,-52.53:99
+chr1	1888209	rs28414188	C	T	21.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.66;MQ=59.03;MQ0=0;OQ=593.85;QD=13.81;SB=-128.12	GT:AD:DP:GL:GQ	0/1:24,19:42:-75.32,-12.65,-82.23:99
+chr1	1888229	rs28629936	G	A	50.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.95;MQ0=0;OQ=708.17;QD=17.70;SB=-204.21	GT:AD:DP:GL:GQ	0/1:19,21:39:-85.85,-11.75,-58.81:99
+chr1	1888545	rs17715950	T	C	188.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=392.93;QD=12.68;SB=-143.27	GT:AD:DP:GL:GQ	0/1:16,15:29:-51.31,-8.74,-58.30:99
+chr1	1888637	rs34506333	G	C	174.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.80;MQ=57.85;MQ0=0;OQ=1081.48;QD=18.97;SB=-492.64	GT:AD:DP:GL:GQ	0/1:26,30:56:-128.32,-16.89,-103.04:99
+chr1	1888639	rs35698161	C	A	246.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.80;MQ=57.81;MQ0=0;OQ=901.53;QD=16.10;SB=-413.05	GT:AD:DP:GL:GQ	0/1:26,30:56:-110.30,-16.87,-89.43:99
+chr1	1888688	rs34824947	T	C	245.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.71;MQ0=0;OQ=584.90;QD=12.44;SB=-198.60	GT:AD:DP:GL:GQ	0/1:25,22:46:-75.63,-13.86,-99.35:99
+chr1	1888695	rs34586002	C	A	280.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.48;MQ0=0;OQ=561.20;QD=12.75;SB=-230.89	GT:AD:DP:GL:GQ	0/1:24,20:42:-72.05,-12.65,-79.10:99
+chr1	1888719	rs35031992	G	A	261.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=534.91;QD=11.38;SB=-199.88	GT:AD:DP:GL:GQ	0/1:28,19:46:-70.65,-13.87,-88.35:99
+chr1	1888794	rs35186797	T	C	29.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.78;MQ=57.65;MQ0=0;OQ=525.33;QD=10.94;SB=-267.94	GT:AD:DP:GL:GQ	0/1:23,25:43:-68.78,-12.96,-87.05:99
+chr1	1888798	rs13303138	G	A	173.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=57.75;MQ0=0;OQ=779.95;QD=15.60;SB=-266.18	GT:AD:DP:GL:GQ	0/1:24,26:46:-95.14,-13.87,-72.15:99
+chr1	1888835	rs34940616	G	A	9.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.88;MQ0=0;OQ=741.91;QD=23.93;SB=-335.86	GT:AD:DP:GL:GQ	0/1:9,22:29:-86.21,-8.74,-25.83:99
+chr1	1889024	rs17778128	G	C	179.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=57.35;MQ0=0;OQ=668.72;QD=10.79;SB=-360.78	GT:AD:DP:GL:GQ	0/1:38,24:59:-87.94,-17.79,-162.55:99
+chr1	1889139	rs61775058	A	T	458.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.25;MQ0=0;OQ=787.44;QD=13.58;SB=-299.67	GT:AD:DP:GL:GQ	0/1:31,27:58:-99.50,-17.47,-121.67:99
+chr1	1889179	rs61775059	T	C	275.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.27;MQ0=0;OQ=765.16;QD=11.42;SB=-328.14	GT:AD:DP:GL:GQ	0/1:35,32:66:-99.69,-19.89,-140.70:99
+chr1	1889260	rs13303007	G	A	42.33	Indel;LowQual	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=6.98;MQ=52.93;MQ0=0;QD=0.73;SB=-30.38	GT:AD:DP:GL:GQ	0/1:52,6:58:-24.99,-17.47,-182.54:75.16
+chr1	1889721	rs4648601	C	T	94.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=56.35;MQ0=0;OQ=530.41;QD=10.20;SB=-77.51	GT:AD:DP:GL:GQ	0/1:33,19:47:-70.50,-14.17,-95.11:99
+chr1	1890092	rs16824588	T	C	13.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=57.02;MQ0=0;OQ=150.77;QD=3.97;SB=-54.71	GT:AD:DP:GL:GQ	0/1:26,12:35:-28.91,-10.55,-104.30:99
+chr1	1890192	rs55709963	A	G	31.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=56.20;MQ0=0;OQ=293.66;QD=11.75;SB=-65.87	GT:AD:DP:GL:GQ	0/1:12,13:24:-39.88,-7.23,-45.12:99
+chr1	1890199	rs56126097	A	G	24.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=55.86;MQ0=0;OQ=270.97;QD=11.78;SB=-47.83	GT:AD:DP:GL:GQ	0/1:11,12:22:-37.01,-6.63,-43.67:99
+chr1	1890235	rs55676322	G	A	36.70	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.45;MQ0=0;QD=2.82;SB=-3.98	GT:AD:DP:GL:GQ	0/1:10,3:12:-10.57,-3.62,-30.38:69.54
+chr1	1890236	.	C	T	56.05	SnpCluster	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.03;MQ0=0;QD=4.00;SB=-3.98	GT:AD:DP:GL:GQ	0/1:11,3:13:-12.81,-3.92,-36.41:88.89
+chr1	1890241	rs55784504	G	A	37.70	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=53.95;MQ0=0;QD=2.36;SB=-0.97	GT:AD:DP:GL:GQ	0/1:13,3:15:-11.57,-4.52,-40.91:70.54
+chr1	1890268	rs61776961	A	G	12.56	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=53.61;MQ0=0;QD=0.66;SB=-31.93	GT:AD:DP:GL:GQ	0/1:15,4:17:-9.64,-5.12,-56.10:45.15
+chr1	1890270	rs61776962	C	T	67.49	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=53.03;MQ0=0;QD=3.21;SB=-45.25	GT:AD:DP:GL:GQ	0/1:16,5:19:-15.77,-5.74,-45.89:99
+chr1	1890274	rs61776963	T	C	59.17	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=2;HaplotypeScore=2.43;MQ=51.33;MQ0=0;QD=2.96;SB=-53.70	GT:AD:DP:GL:GQ	0/1:14,6:19:-14.93,-5.73,-56.51:92.01
+chr1	1890292	rs61776964	T	G	172.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=50.53;MQ0=0;OQ=263.44;QD=9.08;SB=-95.94	GT:AD:DP:GL:GQ	0/1:17,12:28:-38.07,-8.44,-56.66:99
+chr1	1890305	rs61776965	C	T	161.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=1.46;MQ=50.32;MQ0=0;OQ=365.34;QD=11.79;SB=-175.70	GT:AD:DP:GL:GQ	0/1:18,13:27:-47.95,-8.13,-56.49:99
+chr1	1890314	rs6681749	A	G	143.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=50.65;MQ0=0;OQ=306.18;QD=9.57;SB=-129.77	GT:AD:DP:GL:GQ	0/1:17,15:29:-42.64,-8.74,-64.98:99
+chr1	1890507	.	T	C	42.73	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=2;HaplotypeScore=3.92;MQ=54.77;MQ0=0;QD=1.86;SB=14.07	GT:AD:DP:GL:GQ	0/1:16,7:17:-12.68,-5.13,-48.62:75.57
+chr1	1890548	.	A	T	8.30	PASS	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=60.00;MQ0=0;OQ=79.81;QD=7.98;SB=-57.71	GT:AD:DP:GL:GQ	0/1:6,4:10:-14.28,-3.01,-22.53:99
+chr1	1890778	rs28707401	G	A	84.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.74;MQ=58.33;MQ0=0;OQ=401.02;QD=14.32;SB=-129.13	GT:AD:DP:GL:GQ	0/1:13,14:24:-53.53,-10.14,-35.22:99
+chr1	1892326	.	A	C	112.36	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.24;MQ0=0;OQ=852.28;QD=15.50;SB=-429.85	GT:AD:DP:GL:GQ	0/1:26,29:52:-104.18,-15.67,-81.22:99
+chr1	1892422	rs7367171	A	G	220.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.60;MQ0=0;OQ=514.17;QD=9.02;SB=-267.96	GT:AD:DP:GL:GQ	0/1:32,25:54:-70.98,-16.28,-126.05:99
+chr1	1892426	rs7367879	G	A	251.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=59.60;MQ0=0;OQ=832.91;QD=14.36;SB=-352.38	GT:AD:DP:GL:GQ	0/1:32,26:52:-102.26,-15.68,-81.39:99
+chr1	1892733	rs7366028	C	T	234.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.35;MQ0=0;OQ=1086.69;QD=15.31;SB=-535.37	GT:AD:DP:GL:GQ	0/1:36,35:67:-132.15,-20.20,-106.68:99
+chr1	1893163	rs4648603	C	T	25.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=59.48;MQ0=0;OQ=261.75;QD=5.95;SB=-111.10	GT:AD:DP:GL:GQ	0/1:32,12:41:-41.83,-12.38,-90.87:99
+chr1	1893572	rs13303201	C	A	360.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=57.58;MQ0=0;OQ=726.40;QD=15.46;SB=-340.06	GT:AD:DP:GL:GQ	0/1:22,25:44:-89.18,-13.26,-62.88:99
+chr1	1895166	rs56313717	C	A	171.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=635.59;QD=15.13;SB=-197.47	GT:AD:DP:GL:GQ	0/1:18,24:41:-79.20,-12.35,-61.36:99
+chr1	1897772	rs7528894	C	T	135.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=58.63;MQ0=0;OQ=607.52;QD=11.91;SB=-152.65	GT:AD:DP:GL:GQ	0/1:30,21:44:-77.30,-13.26,-84.20:99
+chr1	1897865	rs7536087	T	C	25.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=54.74;MQ0=0;OQ=378.78;QD=5.83;SB=-147.48	GT:AD:DP:GL:GQ	0/1:38,27:56:-58.05,-16.88,-148.17:99
+chr1	1897872	rs28588807	T	C	29.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.38;MQ=53.22;MQ0=0;OQ=367.97;QD=6.24;SB=-166.50	GT:AD:DP:GL:GQ	0/1:36,23:50:-55.16,-15.08,-127.98:99
+chr1	1897899	rs4388640	C	T	188.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=52.25;MQ0=0;OQ=499.97;QD=8.20;SB=-247.55	GT:AD:DP:GL:GQ	0/1:39,22:51:-68.65,-15.37,-112.84:99
+chr1	1897945	rs28410799	A	G	3.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.71;MQ=54.36;MQ0=0;OQ=341.23;QD=5.59;SB=-142.90	GT:AD:DP:GL:GQ	0/1:39,21:52:-53.08,-15.68,-138.70:99
+chr1	1897960	rs28789409	G	T	236.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=55.27;MQ0=0;OQ=569.89;QD=9.19;SB=-286.60	GT:AD:DP:GL:GQ	0/1:38,24:59:-78.04,-17.77,-137.70:99
+chr1	1898245	rs13303203	C	T	367.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.47;MQ0=0;OQ=546.46;QD=10.31;SB=-185.87	GT:AD:DP:GL:GQ	0/1:33,20:47:-72.10,-14.17,-90.13:99
+chr1	1898289	rs28545809	T	C	170.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=55.94;MQ0=0;OQ=320.54;QD=7.82;SB=-173.95	GT:AD:DP:GL:GQ	0/1:24,16:37:-46.49,-11.16,-87.43:99
+chr1	1898563	rs4233027	C	G	427.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.18;MQ0=0;OQ=977.32;QD=15.27;SB=-297.92	GT:AD:DP:GL:GQ	0/1:36,28:63:-120.00,-18.99,-153.02:99
+chr1	1899064	rs35953639	A	G	134.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=58.52;MQ0=0;OQ=901.65;QD=15.82;SB=-439.15	GT:AD:DP:GL:GQ	0/1:25,32:55:-110.02,-16.57,-94.81:99
+chr1	1899178	rs61776976	G	A	36.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.28;MQ=59.15;MQ0=0;OQ=1106.44;QD=22.13;SB=-371.92	GT:AD:DP:GL:GQ	0/1:16,34:48:-128.39,-14.47,-53.19:99
+chr1	1899305	rs55863117	A	G	206.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.24;MQ0=0;OQ=872.61;QD=14.31;SB=-340.17	GT:AD:DP:GL:GQ	0/1:25,35:57:-107.73,-17.18,-95.38:99
+chr1	1899354	rs28716654	C	T	202.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=59.30;MQ0=0;OQ=1176.35;QD=17.82;SB=-612.15	GT:AD:DP:GL:GQ	0/1:31,35:62:-139.59,-18.67,-102.07:99
+chr1	1899413	rs28680595	T	A	360.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.29;MQ0=0;OQ=1036.44;QD=15.95;SB=-464.88	GT:AD:DP:GL:GQ	0/1:30,35:63:-125.91,-18.98,-108.28:99
+chr1	1899561	rs28613404	C	T	21.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=5.89;MQ=58.07;MQ0=0;OQ=742.01;QD=16.13;SB=-312.34	GT:AD:DP:GL:GQ	0/1:20,25:42:-90.15,-12.66,-60.03:99
+chr1	1899593	rs28491083	G	T	384.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=572.46;QD=14.31;SB=-222.49	GT:AD:DP:GL:GQ	0/1:17,23:37:-71.67,-11.14,-60.73:99
+chr1	1899703	rs28433557	C	T	153.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.28;MQ0=0;OQ=695.04;QD=16.55;SB=-241.74	GT:AD:DP:GL:GQ	0/1:19,23:39:-84.54,-11.75,-59.04:99
+chr1	1899714	rs28448395	G	A	59.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=57.87;MQ0=0;OQ=975.55;QD=21.68;SB=-411.21	GT:AD:DP:GL:GQ	0/1:16,29:43:-113.79,-12.96,-49.10:99
+chr1	1899728	rs28539219	G	A	22.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=58.50;MQ0=0;OQ=1039.92;QD=21.66;SB=-531.16	GT:AD:DP:GL:GQ	0/1:16,32:45:-120.83,-13.56,-54.90:99
+chr1	1899861	rs28468541	C	G	2.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=9.03;MQ=56.76;MQ0=0;OQ=898.89;QD=17.63;SB=-410.04	GT:AD:DP:GL:GQ	0/1:24,26:48:-107.64,-14.46,-99.37:99
+chr1	1899872	rs28588737	T	C	12.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=3.04;MQ=57.56;MQ0=0;OQ=448.65;QD=9.35;SB=-239.28	GT:AD:DP:GL:GQ	0/1:25,23:43:-61.11,-12.96,-97.10:99
+chr1	1899946	rs28645949	G	T	144.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=60.00;MQ0=0;OQ=332.80;QD=10.40;SB=-155.69	GT:AD:DP:GL:GQ	0/1:19,13:30:-45.61,-9.04,-50.81:99
+chr1	1900096	rs28651716	T	C	225.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=54.90;MQ0=0;OQ=686.40;QD=12.71;SB=-338.36	GT:AD:DP:GL:GQ	0/1:28,26:53:-87.90,-15.97,-105.41:99
+chr1	1900231	rs28642304	G	A	31.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=5.35;MQ=52.67;MQ0=2;OQ=686.17;QD=14.00;SB=-341.85	GT:AD:DP:GL:GQ	0/1:25,24:43:-84.86,-12.96,-72.07:99
+chr1	1900342	.	C	G	14.82	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=12.94;MQ=53.14;MQ0=2;QD=0.37;SB=26.12	GT:AD:DP:GL:GQ	0/1:35,5:34:-15.00,-10.25,-129.63:47.51
+chr1	1900344	.	T	C	47.56	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=13.10;MQ=54.07;MQ0=2;QD=1.16;SB=26.11	GT:AD:DP:GL:GQ	0/1:32,9:34:-18.29,-10.25,-109.75:80.39
+chr1	1900366	.	T	C	19.64	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=56.14;MQ0=0;QD=0.48;SB=17.08	GT:AD:DP:GL:GQ	0/1:34,7:35:-15.79,-10.55,-116.81:52.43
+chr1	1900466	rs7550407	A	G	75.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=45.89;MQ0=2;OQ=380.59;QD=19.03;SB=-189.68	GT:AD:DP:GL:GQ	1/1:0,20:13:-41.66,-3.92,-0.01:39.09
+chr1	1900518	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=10.99;MQ=35.59;MQ0=6;OQ=55.62;QD=1.29;SB=-13.87	GT:AD:DP:GL:GQ	0/1:29,14:19:-14.57,-5.73,-56.56:88.46
+chr1	1900571	.	C	T	45.32	LowQual	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=19.95;MQ=36.93;MQ0=3;QD=0.91;SB=-24.62	GT:AD:DP:GL:GQ	0/1:41,9:25:-15.36,-7.54,-65.46:78.16
+chr1	1900816	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=6.83;MQ=47.18;MQ0=2;OQ=71.50;QD=1.79;SB=-42.78	GT:AD:DP:GL:GQ	0/1:30,10:31:-19.78,-9.34,-96.64:99
+chr1	1900861	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=8.07;MQ=42.04;MQ0=5;OQ=136.19;QD=2.67;SB=-39.59	GT:AD:DP:GL:GQ	0/1:31,18:36:-30.43,-13.53,-101.33:99
+chr1	1900880	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=21.93;MQ=42.64;MQ0=5;OQ=81.77;QD=1.99;SB=26.03	GT:AD:DP:GL:GQ	0/1:32,9:28:-19.91,-8.45,-71.11:99
+chr1	1900981	.	G	A	32.02	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=14.77;MQ=47.97;MQ0=0;QD=1.07;SB=20.08	GT:AD:DP:GL:GQ	0/1:27,3:20:-12.51,-6.03,-56.06:64.85
+chr1	1900982	.	C	T	11.94	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=14.77;MQ=47.50;MQ0=0;QD=0.41;SB=35.07	GT:AD:DP:GL:GQ	0/1:26,3:25:-11.99,-7.54,-69.22:44.49
+chr1	1900987	.	C	G	179.53	SnpCluster	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=1;HaplotypeScore=15.25;MQ=49.14;MQ0=0;QD=5.79;SB=-106.68	GT:AD:DP:GL:GQ	0/1:23,8:22:-27.88,-6.64,-59.47:99
+chr1	1901007	.	A	G	17.82	PASS	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=50.60;MQ0=0;OQ=269.42;QD=8.42;SB=-129.64	GT:AD:DP:GL:GQ	0/1:19,13:29:-38.97,-8.74,-66.56:99
+chr1	1901025	.	T	C	1.37	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=50.85;MQ0=0;OQ=146.63;QD=3.67;SB=-63.91	GT:AD:DP:GL:GQ	0/1:26,13:31:-27.31,-9.36,-79.17:99
+chr1	1901036	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=7.09;MQ=51.49;MQ0=1;OQ=87.37;QD=1.99;SB=-8.61	GT:AD:DP:GL:GQ	0/1:38,6:38:-23.49,-11.46,-98.15:99
+chr1	1901053	.	T	C	11.36	LowQual	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=52.41;MQ0=1;QD=0.25;SB=-25.22	GT:AD:DP:GL:GQ	0/1:37,8:38:-15.84,-11.45,-126.44:43.87
+chr1	1901418	rs28645431	C	T	0.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=3.95;MQ=41.39;MQ0=1;OQ=172.22;QD=4.53;SB=-89.91	GT:AD:DP:GL:GQ	0/1:29,9:21:-26.84,-6.33,-42.67:99
+chr1	1901574	rs13303001	G	A	41.49	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=7.68;MQ=10.86;MQ0=15;QD=1.66;SB=-10.00	GT:AD:DP:GL:GQ	0/1:20,5:3:-8.34,-0.90,-3.10:21.92
+chr1	1901637	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=16.41;MQ=17.84;MQ0=13;OQ=157.79;QD=2.87;SB=-10.00	GT:AD:DP:GL:GQ	0/1:44,10:26:-26.90,-7.83,-65.70:99
+chr1	1901664	.	G	A	34.02	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.20;MQ=18.33;MQ0=14;QD=0.67;SB=-10.00	GT:AD:DP:GL:GQ	0/1:42,9:17:-11.81,-5.13,-50.35:66.86
+chr1	1901668	.	G	A	0.06	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.04;MQ=18.51;MQ0=13;OQ=99.32;QD=2.03;SB=-7.00	GT:AD:DP:GL:GQ	0/1:40,9:16:-18.04,-4.83,-38.64:99
+chr1	1901732	rs13303290	T	C	12.82	LowQual	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.55;MQ0=0;QD=0.64;SB=-24.62	GT:AD:DP:GL:GQ	0/1:15,5:16:-9.37,-4.82,-51.21:45.43
+chr1	1901798	rs4648740	A	G	153	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=48.72;MQ0=0;OQ=495.24;QD=14.15;SB=-240.44	GT:AD:DP:GL:GQ	0/1:16,19:34:-63.06,-10.25,-57.72:99
+chr1	1901828	rs4648741	T	A	223.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=49.47;MQ0=0;OQ=518.42;QD=14.01;SB=-218.56	GT:AD:DP:GL:GQ	0/1:16,21:33:-65.07,-9.94,-58.68:99
+chr1	1902252	rs35209771	G	A	29.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.72;MQ=59.38;MQ0=0;OQ=570.39;QD=15.42;SB=-188.28	GT:AD:DP:GL:GQ	0/1:17,20:31:-69.66,-9.34,-43.55:99
+chr1	1902361	rs35032062	A	G	8.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=3;HaplotypeScore=1.19;MQ=56.62;MQ0=0;OQ=288.56;QD=9.31;SB=-81.77	GT:AD:DP:GL:GQ	0/1:15,16:27:-40.29,-8.15,-49.29:99
+chr1	1902443	rs4648742	T	G	2.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=3;HaplotypeScore=1.88;MQ=52.64;MQ0=0;OQ=307.57;QD=13.98;SB=-102.98	GT:AD:DP:GL:GQ	0/1:8,14:19:-39.76,-5.72,-27.07:99
+chr1	1902590	rs34957887	A	G	5.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=54.60;MQ0=0;OQ=111.21;QD=3.83;SB=-42.82	GT:AD:DP:GL:GQ	0/1:21,8:27:-22.55,-8.14,-76.38:99
+chr1	1902594	rs34699657	T	C	6.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=55.30;MQ0=0;OQ=114.19;QD=4.08;SB=-28.64	GT:AD:DP:GL:GQ	0/1:19,9:26:-22.55,-7.85,-71.28:99
+chr1	1902618	rs13302917	G	C	80.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=55.30;MQ0=0;OQ=235.26;QD=8.40;SB=8.06	GT:AD:DP:GL:GQ	0/1:18,10:26:-34.65,-7.84,-76.52:99
+chr1	1902752	.	G	A	16.41	LowQual	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=23.04;MQ0=3;QD=0.82;SB=-30.52	GT:AD:DP:GL:GQ	0/1:17,3:9:-7.63,-2.71,-23.66:49.15
+chr1	1902780	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=12.84;MQ=20.15;MQ0=3;OQ=68.78;QD=3.62;SB=-7.00	GT:AD:DP:GL:GQ	0/1:14,5:6:-11.97,-1.81,-9.13:73.25
+chr1	1902787	.	G	A	0.55	PASS	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=20.15;MQ0=3;OQ=103.65;QD=5.46;SB=-46.55	GT:AD:DP:GL:GQ	0/1:13,6:5:-15.16,-1.51,-3.80:22.92
+chr1	1902803	.	A	G	0.43	PASS	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=19.89;MQ0=3;OQ=59.98;QD=3.75;SB=-6.99	GT:AD:DP:GL:GQ	0/1:11,5:6:-11.09,-1.81,-11.69:92.82
+chr1	1902817	.	T	C	41.42	LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=9.95;MQ=22.02;MQ0=2;QD=2.96;SB=-35.94	GT:AD:DP:GL:GQ	0/1:9,4:6:-9.23,-1.81,-11.87:74.25
+chr1	1902835	rs61776983	A	C	26.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=1.55;MQ=20.97;MQ0=2;OQ=78.83;QD=5.63;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,12:3:-11.37,-0.90,-0.00:9.03
+chr1	1903052	.	G	A	0.07	PASS	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=10.18;MQ=21.19;MQ0=5;OQ=185.24;QD=7.12;SB=-114.97	GT:AD:DP:GL:GQ	0/1:13,13:10:-24.83,-3.02,-9.74:67.23
+chr1	1903096	.	C	T	19.36	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=27.09;MQ=29.12;MQ0=4;QD=0.84;SB=-32.50	GT:AD:DP:GL:GQ	0/1:20,3:10:-8.23,-3.01,-26.23:52.14
+chr1	1903103	.	G	A	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=11.25;MQ=32.31;MQ0=4;OQ=203.36;QD=8.13;SB=-108.63	GT:AD:DP:GL:GQ	0/1:11,14:13:-27.54,-3.92,-21.98:99
+chr1	1903122	.	G	A	1.51	PASS	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=5.86;MQ=37.50;MQ0=2;OQ=277.72;QD=11.11;SB=-116.63	GT:AD:DP:GL:GQ	0/1:11,14:14:-35.28,-4.22,-14.88:99
+chr1	1903133	.	C	T	26.70	DPFilter;HARD_TO_VALIDATE;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=14.79;MQ=33.51;MQ0=4;QD=0.92;SB=2.00	GT:AD:DP:GL:GQ	0/1:25,3:16:-10.78,-4.83,-41.60:59.53
+chr1	1903194	.	G	A	0.17	PASS	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=22.60;MQ0=6;OQ=59.87;QD=3.15;SB=-29.63	GT:AD:DP:GL:GQ	0/1:15,4:8:-11.68,-2.41,-15.55:92.71
+chr1	1903256	rs56273126	A	C	0.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=9.88;MQ=34.34;MQ0=2;OQ=157.91;QD=8.77;SB=-43.00	GT:AD:DP:GL:GQ	0/1:8,10:11:-22.39,-3.31,-17.60:99
+chr1	1903263	rs56067355	C	T	0.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=9.27;MQ=35.40;MQ0=1;OQ=103.77;QD=4.72;SB=-3.99	GT:AD:DP:GL:GQ	0/1:16,6:17:-18.78,-5.12,-41.68:99
+chr1	1903283	.	G	A	8.07	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.95;MQ=39.68;MQ0=0;OQ=372.77;QD=10.96;SB=-73.09	GT:AD:DP:GL:GQ	0/1:17,16:22:-47.20,-6.63,-29.71:99
+chr1	1903404	.	C	T	39.84	LowQual	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=6.15;MQ=48.13;MQ0=1;QD=1.73;SB=-35.65	GT:AD:DP:GL:GQ	0/1:19,4:16:-12.09,-4.83,-40.40:72.68
+chr1	1903423	rs58434854	A	G	0.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=7.95;MQ=46.73;MQ0=3;OQ=182.58;QD=6.30;SB=-71.95	GT:AD:DP:GL:GQ	0/1:18,11:23:-28.48,-6.94,-51.85:99
+chr1	1903439	rs58923167	C	T	0.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=17.53;MQ=42.29;MQ0=6;OQ=136.42;QD=4.01;SB=-25.62	GT:AD:DP:GL:GQ	0/1:26,8:22:-23.56,-6.63,-53.26:99
+chr1	1903440	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=17.53;MQ=42.29;MQ0=6;OQ=187.84;QD=5.52;SB=-110.54	GT:AD:DP:GL:GQ	0/1:26,8:23:-29.00,-6.94,-48.31:99
+chr1	1903458	rs55879512	A	G	0.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=7.35;MQ=44.38;MQ0=5;OQ=75.85;QD=1.85;SB=-63.75	GT:AD:DP:GL:GQ	0/1:26,14:24:-18.11,-7.24,-65.52:99
+chr1	1903493	.	G	A	1.04	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=47.31;MQ0=2;OQ=168.07;QD=4.31;SB=-57.28	GT:AD:DP:GL:GQ	0/1:31,8:25:-27.63,-7.54,-58.38:99
+chr1	1903509	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=11.62;MQ=39.25;MQ0=5;OQ=92.69;QD=2.73;SB=5.04	GT:AD:DP:GL:GQ	0/1:25,9:18:-17.98,-5.43,-46.46:99
+chr1	1903540	.	G	A	33.23	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=27.81;MQ=22.93;MQ0=9;QD=1.15;SB=-3.98	GT:AD:DP:GL:GQ	0/1:26,3:5:-8.11,-1.51,-11.06:66.06
+chr1	1903547	.	T	A	34.51	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=29.76;MQ=15.81;MQ0=9;QD=1.33;SB=-42.38	GT:AD:DP:GL:GQ	0/1:19,6:3:-7.64,-0.90,-3.64:27.36
+chr1	1903587	rs4648605	C	T	0.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=14.50;MQ=19.08;MQ0=11;OQ=79.27;QD=1.98;SB=-3.99	GT:AD:DP:GL:GQ	0/1:27,13:10:-14.23,-3.02,-19.87:99
+chr1	1904125	rs4648745	T	C	247.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=59.25;MQ0=0;OQ=694.34;QD=11.20;SB=-245.29	GT:AD:DP:GL:GQ	0/1:33,29:61:-91.10,-18.39,-129.32:99
+chr1	1904347	rs4648746	A	G	176.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.39;MQ0=0;OQ=338.48;QD=8.91;SB=-150.90	GT:AD:DP:GL:GQ	0/1:21,17:36:-47.98,-10.85,-82.55:99
+chr1	1904465	rs28737396	A	T	328.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1094.85;QD=18.56;SB=-354.42	GT:AD:DP:GL:GQ	0/1:24,35:59:-130.54,-17.77,-93.43:99
+chr1	1904806	rs61776990	C	T	103.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=56.91;MQ0=0;OQ=639.60;QD=17.29;SB=-221.92	GT:AD:DP:GL:GQ	0/1:15,22:35:-77.80,-10.56,-46.60:99
+chr1	1905885	rs4648747	G	A	213.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=54.80;MQ0=0;OQ=758.00;QD=15.16;SB=-295.79	GT:AD:DP:GL:GQ	0/1:26,24:49:-93.85,-14.76,-88.23:99
+chr1	1905894	rs13303091	C	T	219.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=53.79;MQ0=0;OQ=656.87;QD=13.14;SB=-261.28	GT:AD:DP:GL:GQ	0/1:27,22:45:-82.54,-13.57,-75.64:99
+chr1	1905900	rs13302998	T	C	119.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=54.88;MQ0=0;OQ=405.99;QD=8.83;SB=-193.60	GT:AD:DP:GL:GQ	0/1:27,19:44:-57.15,-13.26,-102.12:99
+chr1	1906158	rs13302999	C	T	171.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=58.63;MQ0=0;OQ=813.49;QD=15.95;SB=-262.17	GT:AD:DP:GL:GQ	0/1:25,26:49:-99.40,-14.77,-77.74:99
+chr1	1906389	rs3795284	C	T	21.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=2.33;MQ=60.00;MQ0=0;OQ=758.20;QD=14.04;SB=-278.28	GT:AD:DP:GL:GQ	0/1:28,26:52:-94.77,-15.67,-93.68:99
+chr1	1906447	rs3795283	G	T	377.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=60.00;MQ0=0;OQ=998.45;QD=16.37;SB=-378.14	GT:AD:DP:GL:GQ	0/1:26,35:60:-121.20,-18.07,-93.96:99
+chr1	1906750	rs3795280	C	T	425.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=568.99;QD=13.55;SB=-250.75	GT:AD:DP:GL:GQ	0/1:24,18:42:-72.83,-12.65,-87.72:99
+chr1	1906918	rs34331632	A	G	117.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=58.45;MQ0=0;OQ=396.71;QD=8.82;SB=-212.27	GT:AD:DP:GL:GQ	0/1:26,19:41:-55.32,-12.36,-92.05:99
+chr1	1907309	rs34567059	T	G	9.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=3;HaplotypeScore=0.99;MQ=59.28;MQ0=0;OQ=266.80;QD=8.34;SB=-138.72	GT:AD:DP:GL:GQ	0/1:18,13:26:-37.80,-7.84,-51.38:99
+chr1	1907332	rs13303173	G	A	219.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=59.50;MQ0=0;OQ=402.42;QD=8.75;SB=-215.71	GT:AD:DP:GL:GQ	0/1:30,16:41:-55.89,-12.37,-85.41:99
+chr1	1907475	rs13302992	A	T	11.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=5.57;MQ=54.24;MQ0=0;OQ=373.16;QD=8.88;SB=-86.42	GT:AD:DP:GL:GQ	0/1:20,21:33:-50.55,-9.95,-63.90:99
+chr1	1907510	rs13302993	T	C	10.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=3.38;MQ=53.93;MQ0=0;OQ=691.42;QD=12.35;SB=-327.29	GT:AD:DP:GL:GQ	0/1:24,32:51:-87.80,-15.38,-95.79:99
+chr1	1907689	rs4648748	T	G	25.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.34;MQ=60.00;MQ0=0;OQ=189.73;QD=5.93;SB=-95.86	GT:AD:DP:GL:GQ	0/1:21,11:31:-31.60,-9.34,-75.09:99
+chr1	1907731	rs4648749	T	A	88.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=58.55;MQ0=0;OQ=1056.82;QD=33.03;SB=-482.74	GT:AD:DP:GL:GQ	1/1:0,32:31:-109.29,-9.34,-0.02:93.25
+chr1	1907768	rs4648750	A	C	41.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=58.69;MQ0=0;OQ=501.71;QD=15.68;SB=-178.91	GT:AD:DP:GL:GQ	0/1:13,18:31:-62.79,-9.34,-46.86:99
+chr1	1908051	rs4233028	A	G	0.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=11.36;MQ=58.24;MQ0=0;OQ=590.53;QD=10.36;SB=-318.09	GT:AD:DP:GL:GQ	0/1:28,29:51:-77.71,-15.37,-108.19:99
+chr1	1908348	rs4350140	A	G	295.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=483.27;QD=11.51;SB=-249.48	GT:AD:DP:GL:GQ	0/1:22,19:40:-63.66,-12.05,-87.28:99
+chr1	1908395	rs4535948	A	T	243.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=60.00;MQ0=0;OQ=561.16;QD=14.03;SB=-291.34	GT:AD:DP:GL:GQ	0/1:20,20:38:-70.85,-11.45,-68.83:99
+chr1	1908444	rs4603072	C	T	95.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.91;MQ=59.00;MQ0=0;OQ=825.49;QD=16.19;SB=-274.16	GT:AD:DP:GL:GQ	0/1:24,27:46:-99.69,-13.86,-72.18:99
+chr1	1908455	rs4466593	G	A	154	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=59.00;MQ0=0;OQ=749.94;QD=14.70;SB=-209.69	GT:AD:DP:GL:GQ	0/1:25,26:47:-92.45,-14.17,-73.64:99
+chr1	1910822	rs13303020	T	C	316	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.07;MQ0=0;OQ=856.90;QD=15.30;SB=-348.06	GT:AD:DP:GL:GQ	0/1:22,34:54:-105.26,-16.29,-79.82:99
+chr1	1912163	rs13303195	C	T	281.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.42;MQ0=0;OQ=1071.80;QD=15.76;SB=-460.45	GT:AD:DP:GL:GQ	0/1:35,33:67:-130.66,-20.19,-113.97:99
+chr1	1912512	rs13303233	T	C	59.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=5.24;MQ=56.21;MQ0=1;OQ=632.02;QD=12.15;SB=-238.92	GT:AD:DP:GL:GQ	0/1:24,28:49:-81.26,-14.77,-90.12:99
+chr1	1912694	rs6605075	T	C	195.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=97;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.81;MQ0=0;OQ=3518.98;QD=36.28;SB=-1667.64	GT:AD:DP:GL:GQ	1/1:0,97:97:-350.90,-29.22,-0.04:99
+chr1	1912989	rs13303332	A	G	477.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.92;MQ0=0;OQ=1063.77;QD=12.66;SB=-392.88	GT:AD:DP:GL:GQ	0/1:42,42:74:-131.95,-22.29,-145.18:99
+chr1	1913060	rs13303315	T	C	275.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=55.32;MQ0=0;OQ=932.62;QD=13.14;SB=-432.88	GT:AD:DP:GL:GQ	0/1:32,39:67:-116.74,-20.20,-124.71:99
+chr1	1913077	rs7529662	A	G	28.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=4.09;MQ=51.94;MQ0=0;OQ=415.73;QD=6.60;SB=-158.33	GT:AD:DP:GL:GQ	0/1:37,26:55:-61.45,-16.59,-136.84:99
+chr1	1913121	rs6605076	G	A	18.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=2.95;MQ=38.45;MQ0=0;OQ=1375.58;QD=22.55;SB=-647.86	GT:AD:DP:GL:GQ	1/1:0,60:36:-143.81,-13.38,-2.67:99
+chr1	1913134	rs6662056	C	T	90.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=31.19;MQ0=0;OQ=470.14;QD=8.11;SB=-253.79	GT:AD:DP:GL:GQ	0/1:33,25:32:-59.95,-9.65,-52.35:99
+chr1	1913140	rs6605077	T	C	265.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=26.77;MQ0=0;OQ=931.68;QD=17.25;SB=-415.14	GT:AD:DP:GL:GQ	1/1:0,54:27:-96.76,-8.13,-0.01:81.23
+chr1	1913166	rs6605078	A	G	225.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=29.40;MQ0=0;OQ=379.61;QD=9.73;SB=-193.70	GT:AD:DP:GL:GQ	1/1:0,39:13:-41.56,-3.92,-0.01:39.09
+chr1	1913525	rs13303140	A	G	349.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.90;MQ0=0;OQ=337.35;QD=9.92;SB=-170.51	GT:AD:DP:GL:GQ	0/1:16,18:26:-44.86,-7.84,-45.87:99
+chr1	1913541	rs6675865	A	G	238.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=54.81;MQ0=0;OQ=476.22;QD=12.53;SB=-203.64	GT:AD:DP:GL:GQ	0/1:19,19:32:-60.55,-9.64,-59.13:99
+chr1	1914266	rs35822535	A	G	10.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=4.48;MQ=52.01;MQ0=0;OQ=172.60;QD=5.57;SB=-106.80	GT:AD:DP:GL:GQ	0/1:17,12:25:-30.72,-10.17,-62.92:99
+chr1	1914406	rs28674034	C	A	137.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.38;MQ=56.09;MQ0=0;OQ=479.30;QD=11.15;SB=-93.09	GT:AD:DP:GL:GQ	0/1:24,19:37:-62.36,-11.14,-73.40:99
+chr1	1914407	.	C	G	17.06	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.38;MQ=56.18;MQ0=0;OQ=578.11;QD=13.14;SB=-126.71	GT:AD:DP:GL:GQ	0/1:24,20:35:-71.66,-10.56,-69.93:99
+chr1	1914645	rs58504758	G	A	76.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=56.31;MQ0=0;OQ=649.38;QD=14.43;SB=-87.56	GT:AD:DP:GL:GQ	0/1:23,22:44:-81.48,-13.26,-81.33:99
+chr1	1914669	rs57460771	C	G	59.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=52.90;MQ0=0;OQ=635.24;QD=15.88;SB=-152.79	GT:AD:DP:GL:GQ	0/1:17,23:37:-77.97,-11.16,-71.80:99
+chr1	1915019	rs5021356	C	T	38.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=38.83;MQ0=0;OQ=299.26;QD=5.16;SB=-51.25	GT:AD:DP:GL:GQ	0/1:26,32:29:-41.96,-8.75,-54.57:99
+chr1	1915025	rs5021357	C	T	0.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=37.79;MQ0=0;OQ=104.46;QD=1.66;SB=-36.16	GT:AD:DP:GL:GQ	0/1:31,32:32:-23.37,-9.64,-89.65:99
+chr1	1915153	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=18.97;MQ=41.21;MQ0=1;OQ=317.64;QD=7.56;SB=-31.63	GT:AD:DP:GL:GQ	0/1:23,16:24:-42.29,-7.24,-39.07:99
+chr1	1915186	rs2377036	C	A	0.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=2.46;MQ=38.80;MQ0=2;OQ=789.31;QD=23.22;SB=-127.84	GT:AD:DP:GL:GQ	1/1:3,31:25:-82.54,-7.54,-0.02:75.13
+chr1	1915197	.	C	T	2.41	PASS	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=35.96;MQ0=2;OQ=151.83;QD=4.34;SB=2.02	GT:AD:DP:GL:GQ	0/1:24,11:24:-25.70,-7.23,-56.48:99
+chr1	1915324	rs2889540	C	T	459.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.97;MQ0=0;OQ=2370.24;QD=35.38;SB=-497.01	GT:AD:DP:GL:GQ	1/1:1,66:63:-240.64,-18.99,-0.03:99
+chr1	1915581	rs6691182	G	A	155.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=58.09;MQ0=0;OQ=1565.00;QD=18.20;SB=-799.86	GT:AD:DP:GL:GQ	0/1:40,46:84:-185.10,-25.32,-125.47:99
+chr1	1915947	rs6661597	T	C	434.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=753.37;QD=11.59;SB=-273.59	GT:AD:DP:GL:GQ	0/1:32,33:62:-97.31,-18.69,-126.97:99
+chr1	1915962	rs6675751	G	C	346.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1124.09;QD=17.56;SB=-315.97	GT:AD:DP:GL:GQ	0/1:34,30:64:-134.99,-19.30,-134.99:99
+chr1	1916138	rs6667687	A	T	24.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=5.93;MQ=59.44;MQ0=0;OQ=1046.27;QD=14.14;SB=-543.64	GT:AD:DP:GL:GQ	0/1:37,36:71:-129.30,-21.39,-135.06:99
+chr1	1917124	rs13302991	A	G	77.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=48.19;MQ0=0;OQ=664.15;QD=15.09;SB=-132.68	GT:AD:DP:GL:GQ	0/1:17,27:41:-82.05,-12.36,-62.14:99
+chr1	1918235	rs58325500	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.01;HRun=15;HaplotypeScore=12.28;MQ=47.41;MQ0=2;OQ=54.80;QD=0.68;SB=8.48	GT:AD:DP:GL:GQ	0/1:66,14:56:-25.35,-16.59,-150.42:87.64
+chr1	1918448	rs28827857	G	A	289.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=57.61;MQ0=0;OQ=1091.40;QD=15.82;SB=-363.89	GT:AD:DP:GL:GQ	0/1:36,33:66:-132.32,-19.90,-105.59:99
+chr1	1918459	rs28770275	C	T	156.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.33;MQ0=0;OQ=990.70;QD=15.98;SB=-272.19	GT:AD:DP:GL:GQ	0/1:31,31:62:-121.04,-18.69,-98.12:99
+chr1	1919267	rs6672175	T	C	222.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=3.35;MQ=59.22;MQ0=0;OQ=1139.84;QD=14.61;SB=-513.90	GT:AD:DP:GL:GQ	0/1:38,40:77:-140.46,-23.19,-152.92:99
+chr1	1919526	rs7532409	A	G	229.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.27;MQ0=0;OQ=832.47;QD=13.21;SB=-385.03	GT:AD:DP:GL:GQ	0/1:26,37:58:-104.01,-17.48,-104.69:99
+chr1	1919694	rs7532529	A	C	228.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=57.10;MQ0=0;OQ=714.32;QD=14.58;SB=-265.84	GT:AD:DP:GL:GQ	0/1:24,25:47:-88.87,-14.15,-84.13:99
+chr1	1919719	rs7527169	T	C	335.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.16;MQ0=0;OQ=729.87;QD=16.59;SB=-259.34	GT:AD:DP:GL:GQ	0/1:16,28:43:-89.23,-12.96,-64.51:99
+chr1	1919737	rs7520124	C	A	233.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.52;MQ0=0;OQ=916.99;QD=20.84;SB=-414.85	GT:AD:DP:GL:GQ	0/1:15,29:44:-108.24,-13.26,-45.66:99
+chr1	1919954	rs7542825	G	A	154.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=58.01;MQ0=0;OQ=805.39;QD=15.79;SB=-224.54	GT:AD:DP:GL:GQ	0/1:26,25:50:-98.90,-15.08,-78.21:99
+chr1	1920251	rs6605079	C	G	333.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=1146.24;QD=15.08;SB=-200.61	GT:AD:DP:GL:GQ	0/1:45,31:76:-140.81,-22.90,-188.17:99
+chr1	1920372	rs6605080	A	G	234.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=57.79;MQ0=0;OQ=682.29;QD=12.87;SB=-281.00	GT:AD:DP:GL:GQ	0/1:25,28:47:-85.67,-14.16,-99.05:99
+chr1	1920614	rs6605081	C	T	426.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=58.39;MQ0=0;OQ=1403.83;QD=17.12;SB=-667.29	GT:AD:DP:GL:GQ	0/1:39,43:80:-167.77,-24.10,-135.75:99
+chr1	1920665	rs6605082	G	C	238.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=58.49;MQ0=0;OQ=1324.95;QD=16.99;SB=-669.29	GT:AD:DP:GL:GQ	0/1:42,36:76:-158.70,-22.92,-158.25:99
+chr1	1920803	rs13303035	C	T	159	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=59.45;MQ0=0;OQ=1062.14;QD=13.98;SB=-530.37	GT:AD:DP:GL:GQ	0/1:41,35:73:-131.51,-22.01,-125.50:99
+chr1	1920841	rs13303352	T	C	445.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.82;MQ0=0;OQ=837.48;QD=11.63;SB=-306.06	GT:AD:DP:GL:GQ	0/1:38,34:70:-108.13,-21.10,-146.79:99
+chr1	1921055	rs13303031	G	T	88.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=1.13;MQ=58.92;MQ0=0;OQ=786.34;QD=15.12;SB=-342.30	GT:AD:DP:GL:GQ	0/1:26,26:52:-97.58,-15.66,-91.48:99
+chr1	1921356	rs6685055	A	G	17.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=2.97;MQ=59.49;MQ0=0;OQ=448.41;QD=9.96;SB=-237.28	GT:AD:DP:GL:GQ	0/1:26,19:44:-61.39,-13.26,-100.60:99
+chr1	1921389	rs6679335	T	G	83.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=1.67;MQ=59.13;MQ0=0;OQ=685.03;QD=12.93;SB=-353.06	GT:AD:DP:GL:GQ	0/1:29,24:52:-87.45,-15.66,-100.08:99
+chr1	1922327	rs28588769	G	A	183.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.89;MQ0=1;OQ=778.96;QD=15.58;SB=-259.18	GT:AD:DP:GL:GQ	0/1:25,25:47:-95.35,-14.17,-73.16:99
+chr1	1922868	rs2376808	G	A	157.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=59.34;MQ0=0;OQ=723.69;QD=10.34;SB=-347.08	GT:AD:DP:GL:GQ	0/1:45,25:64:-94.96,-19.30,-123.08:99
+chr1	1922895	rs2376807	G	A	266.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=58.98;MQ0=0;OQ=1217.48;QD=13.99;SB=-488.00	GT:AD:DP:GL:GQ	0/1:49,38:84:-150.33,-25.30,-168.79:99
+chr1	1923727	rs4434797	T	C	63.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.46;MQ0=0;OQ=1150.76;QD=28.77;SB=-542.44	GT:AD:DP:GL:GQ	1/1:1,39:35:-118.68,-10.55,-0.02:99
+chr1	1923976	rs2376806	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=7;HaplotypeScore=3.79;MQ=59.30;MQ0=0;OQ=886.58;QD=14.78;SB=-242.95	GT:AD:DP:GL:GQ	0/1:31,29:60:-110.01,-18.07,-107.98:99
+chr1	1924507	rs6682175	C	G	459.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1286.38;QD=16.93;SB=-654.00	GT:AD:DP:GL:GQ	0/1:39,37:74:-154.22,-22.30,-163.90:99
+chr1	1925440	.	A	C	17.47	PASS	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=54.31;MQ0=0;OQ=233.12;QD=9.71;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,12:20:-32.62,-6.03,-38.03:99
+chr1	1925994	rs13303219	G	A	173.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.24;MQ0=0;OQ=2130.07;QD=38.04;SB=-927.23	GT:AD:DP:GL:GQ	1/1:0,56:55:-216.61,-16.57,-0.02:99
+chr1	1927245	.	C	A	6.32	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.74;MQ=50.81;MQ0=0;OQ=1490.54;QD=26.15;SB=-627.15	GT:AD:DP:GL:GQ	0/1:11,46:54:-168.60,-16.27,-27.03:99
+chr1	1929194	.	G	A	93.04	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=54.76;MQ0=0;OQ=934.74;QD=16.40;SB=-478.51	GT:AD:DP:GL:GQ	0/1:29,28:56:-113.63,-16.87,-101.37:99
+chr1	1929934	.	G	A	0.59	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=6.95;MQ=58.36;MQ0=1;OQ=902.25;QD=19.20;SB=-435.95	GT:AD:DP:GL:GQ	0/1:20,27:46:-107.37,-13.86,-69.60:99
+chr1	1931518	rs6605072	C	T	176.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.65;MQ0=0;OQ=1960.94;QD=37.71;SB=-913.32	GT:AD:DP:GL:GQ	1/1:0,52:51:-199.70,-15.37,-0.02:99
+chr1	1931688	rs13303071	T	C	1556.10	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.24;MQ0=0;QD=27.79;SB=-792.66	GT:AD:DP:GL:GQ	1/1:0,56:50:-159.24,-15.08,-0.05:99
+chr1	1931693	.	A	G	1848.16	SnpCluster	AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.03;MQ0=0;QD=33.60;SB=-934.96	GT:AD:DP:GL:GQ	1/1:0,55:53:-188.42,-15.97,-0.02:99
+chr1	1931694	.	T	A	1917.61	SnpCluster	AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=49.24;MQ0=0;QD=35.51;SB=-952.61	GT:AD:DP:GL:GQ	1/1:0,54:52:-195.36,-15.66,-0.02:99
+chr1	1931789	rs6656398	G	A	540.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.77;MQ0=0;OQ=2040.90;QD=38.51;SB=-804.04	GT:AD:DP:GL:GQ	1/1:0,53:51:-207.69,-15.36,-0.01:99
+chr1	1931893	rs13303124	C	A	616.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.54;MQ0=0;OQ=2901.26;QD=36.72;SB=-1390.14	GT:AD:DP:GL:GQ	1/1:0,79:79:-293.73,-23.79,-0.02:99
+chr1	1933151	rs6672254	C	T	447.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=1292.37;QD=33.14;SB=-431.53	GT:AD:DP:GL:GQ	1/1:0,39:34:-132.84,-10.25,-0.02:99
+chr1	1933961	rs6605073	C	G	112.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=54.93;MQ0=0;OQ=3433.93;QD=42.39;SB=-1558.19	GT:AD:DP:GL:GQ	1/1:0,81:81:-342.39,-24.42,-0.04:99
+chr1	1936451	rs13303016	G	A	86.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=58.88;MQ0=0;OQ=2221.58;QD=38.30;SB=-691.42	GT:AD:DP:GL:GQ	1/1:0,56:56:-225.76,-16.87,-0.02:99
+chr1	1936669	rs4648752	C	T	217.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=2508.96;QD=37.45;SB=-1210.99	GT:AD:DP:GL:GQ	1/1:0,67:64:-254.50,-19.28,-0.02:99
+chr1	1937615	rs2376804	C	A	568.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.26;MQ0=0;OQ=1581.66;QD=34.38;SB=-723.87	GT:AD:DP:GL:GQ	1/1:0,46:45:-161.77,-13.56,-0.02:99
+chr1	1938260	rs13303344	C	A	671.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.98;MQ0=0;OQ=1865.08;QD=33.91;SB=-728.87	GT:AD:DP:GL:GQ	1/1:0,55:54:-190.12,-16.27,-0.02:99
+chr1	1938665	rs4481796	T	C	1.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=7.00;MQ=59.19;MQ0=0;OQ=1999.82;QD=33.90;SB=-790.00	GT:AD:DP:GL:GQ	1/1:1,58:55:-203.58,-16.56,-0.01:99
+chr1	1939404	rs3121818	G	T	55.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=4.13;MQ=57.70;MQ0=0;OQ=2038.83;QD=32.88;SB=-977.56	GT:AD:DP:GL:GQ	1/1:1,61:60:-210.75,-18.07,-3.28:99
+chr1	1940481	rs28603108	G	A	85.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=244.10;QD=30.51;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,8:7:-27.99,-2.11,-0.00:21.07
+chr1	1941687	rs3121819	A	G	228.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2020.01;QD=32.58;SB=-994.40	GT:AD:DP:GL:GQ	1/1:0,62:62:-205.63,-18.69,-0.05:99
+chr1	1942465	rs28502222	T	C	371.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=1719.40;QD=30.16;SB=-855.54	GT:AD:DP:GL:GQ	1/1:0,57:54:-175.57,-16.29,-0.05:99
+chr1	1942470	rs28407473	T	C	563.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=1937.81;QD=31.25;SB=-894.53	GT:AD:DP:GL:GQ	1/1:0,62:60:-197.41,-18.09,-0.05:99
+chr1	1942642	rs3128318	C	A	368.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=1363.24;QD=34.95;SB=-493.39	GT:AD:DP:GL:GQ	1/1:0,39:38:-139.92,-11.45,-0.01:99
+chr1	1943112	rs3128321	T	C	309.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.60;MQ0=0;OQ=865.40;QD=28.85;SB=-224.64	GT:AD:DP:GL:GQ	1/1:0,30:27:-90.14,-8.14,-0.02:81.21
+chr1	1943436	rs28595482	G	A	148.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.62;MQ0=0;OQ=1902.67;QD=38.83;SB=-885.18	GT:AD:DP:GL:GQ	1/1:0,49:48:-193.87,-14.46,-0.01:99
+chr1	1943672	rs4648614	C	T	198.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.32;MQ0=0;OQ=2028.99;QD=36.89;SB=-959.37	GT:AD:DP:GL:GQ	1/1:0,55:53:-206.51,-15.97,-0.03:99
+chr1	1944296	rs3128322	G	A	216.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=59.01;MQ0=0;OQ=2427.18;QD=36.78;SB=-1173.08	GT:AD:DP:GL:GQ	1/1:0,65:64:-246.33,-19.29,-0.03:99
+chr1	1944940	rs3128323	G	A	20.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=59.13;MQ0=0;OQ=1516.55;QD=28.61;SB=-577.76	GT:AD:DP:GL:GQ	1/1:0,53:41:-155.26,-12.36,-0.02:99
+chr1	1945844	rs2889475	C	T	626.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.31;MQ0=0;OQ=2161.84;QD=35.44;SB=-988.03	GT:AD:DP:GL:GQ	1/1:0,61:56:-219.79,-16.87,-0.02:99
+chr1	1946222	rs2376805	G	A	202.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.86;MQ0=0;OQ=2273.19;QD=37.27;SB=-1064.36	GT:AD:DP:GL:GQ	1/1:0,61:58:-230.92,-17.47,-0.02:99
+chr1	1946897	rs2229110	T	C	11.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=58.29;MQ0=0;OQ=1169.00;QD=28.51;SB=-410.54	GT:AD:DP:GL:GQ	1/1:1,40:35:-120.50,-10.54,-0.02:99
+chr1	1947159	rs3820007	C	T	19.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=59.17;MQ0=0;OQ=557.21;QD=19.90;SB=-159.09	GT:AD:DP:GL:GQ	1/1:0,24:17:-62.02,-7.79,-2.71:50.81
+chr1	1949121	rs28574670	A	G	500.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1666.55;QD=35.46;SB=-850.35	GT:AD:DP:GL:GQ	1/1:0,47:47:-170.25,-14.16,-0.02:99
+chr1	1949838	rs28409373	C	T	14.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.07;MQ0=0;OQ=1034.54;QD=34.48;SB=-177.68	GT:AD:DP:GL:GQ	1/1:0,30:29:-107.06,-8.75,-0.02:87.26
+chr1	1950786	rs28581504	T	C	332.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.64;MQ0=0;OQ=1013.22;QD=32.68;SB=-423.78	GT:AD:DP:GL:GQ	1/1:0,31:30:-104.92,-9.04,-0.02:90.23
+chr1	1953035	rs13302932	A	G	11.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.55;MQ=60.00;MQ0=0;OQ=905.11;QD=24.46;SB=-434.83	GT:AD:DP:GL:GQ	1/1:0,37:30:-94.12,-9.05,-0.03:90.20
+chr1	1953275	rs17715203	A	G	438.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1126.75;QD=30.45;SB=-438.29	GT:AD:DP:GL:GQ	1/1:0,37:35:-116.28,-10.55,-0.02:99
+chr1	1955750	.	G	C	30.56	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=3;HaplotypeScore=5.70;MQ=42.68;MQ0=2;QD=0.27;SB=83.98	GT:AD:DP:GL:GQ	0/1:64,50:68:-26.83,-20.49,-269.17:63.39
+chr1	1955789	.	C	G	28.79	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=3.29;MQ=41.60;MQ0=2;QD=0.26;SB=62.45	GT:AD:DP:GL:GQ	0/1:60,50:64:-25.45,-19.29,-247.08:61.62
+chr1	1956476	rs3128311	A	G	7.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=2.79;MQ=58.13;MQ0=0;OQ=1189.30;QD=33.98;SB=-560.89	GT:AD:DP:GL:GQ	1/1:0,35:34:-122.53,-10.24,-0.01:99
+chr1	1956519	rs3128312	A	G	0.03	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=5;HaplotypeScore=2.16;MQ=57.85;MQ0=0;OQ=1010.92;QD=30.63;SB=-251.77	GT:AD:DP:GL:GQ	1/1:0,33:30:-104.69,-9.04,-0.02:90.25
+chr1	1956874	.	G	A	318.30	PASS	AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=1884.66;QD=38.46;SB=-687.34	GT:AD:DP:GL:GQ	1/1:0,49:48:-192.06,-14.46,-0.01:99
+chr1	1957814	rs2376803	C	T	3.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=5.41;MQ=59.46;MQ0=0;OQ=1636.24;QD=38.05;SB=-662.40	GT:AD:DP:GL:GQ	1/1:0,43:42:-167.22,-12.65,-0.01:99
+chr1	1958691	rs9442614	A	G	93.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.19;MQ0=0;OQ=1548.19;QD=27.16;SB=-690.61	GT:AD:DP:GL:GQ	1/1:0,57:50:-158.45,-15.08,-0.05:99
+chr1	1958819	rs13303086	G	A	42.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.38;MQ0=0;OQ=1355.91;QD=36.65;SB=-559.75	GT:AD:DP:GL:GQ	1/1:0,37:35:-139.19,-10.54,-0.01:99
+chr1	1961249	rs3121820	G	C	348.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.98;MQ0=0;OQ=1964.71;QD=40.10;SB=-703.68	GT:AD:DP:GL:GQ	1/1:0,49:48:-200.08,-14.47,-0.02:99
+chr1	1964088	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=20;HaplotypeScore=27.35;MQ=45.54;MQ0=0;OQ=216.77;QD=4.93;SB=-12.47	GT:AD:DP:GL:GQ	0/1:28,16:30:-34.00,-9.04,-73.59:99
+chr1	1966711	rs28394674	G	T	70.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.59;MQ=58.47;MQ0=0;OQ=2068.09;QD=33.90;SB=-496.39	GT:AD:DP:GL:GQ	1/1:0,60:58:-210.42,-17.47,-0.02:99
+chr1	1974087	rs3128319	C	T	215.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=59.66;MQ0=0;OQ=974.85;QD=17.72;SB=-353.37	GT:AD:DP:GL:GQ	0/1:25,30:52:-116.43,-15.67,-87.00:99
+chr1	1974552	rs3121826	A	G	92.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.67;MQ0=0;OQ=1020.08;QD=29.15;SB=-506.02	GT:AD:DP:GL:GQ	1/1:0,35:33:-105.63,-9.96,-0.04:99
+chr1	1974671	rs3121827	G	T	491.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.58;MQ0=0;OQ=1710.64;QD=34.91;SB=-820.86	GT:AD:DP:GL:GQ	1/1:0,49:48:-174.66,-14.46,-0.02:99
+chr1	1975030	rs35020387	G	A	113.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.07;MQ=60.00;MQ0=0;OQ=1769.06;QD=36.10;SB=-889.65	GT:AD:DP:GL:GQ	1/1:0,49:46:-180.51,-13.86,-0.02:99
+chr1	1982066	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=56.20;MQ0=0;OQ=60.60;QD=2.42;SB=35.14	GT:AD:DP:GL:GQ	0/1:18,7:19:-15.09,-5.75,-56.99:93.44
+chr1	1982837	rs17777295	G	T	2.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=4.79;MQ=57.88;MQ0=0;OQ=1411.52;QD=35.29;SB=-620.56	GT:AD:DP:GL:GQ	1/1:0,40:39:-144.75,-11.75,-0.01:99
+chr1	1987331	rs56136180	A	G	202.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=1.52;MQ=55.14;MQ0=0;OQ=1346.89;QD=15.85;SB=-685.93	GT:AD:DP:GL:GQ	0/1:38,47:81:-162.37,-24.40,-147.70:99
+chr1	1989540	rs28479788	G	A	186.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=58.66;MQ0=0;OQ=851.87;QD=16.38;SB=-358.89	GT:AD:DP:GL:GQ	0/1:25,27:48:-102.94,-14.47,-69.44:99
+chr1	1995600	rs2459986	T	C	313.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.14;MQ0=0;OQ=733.38;QD=27.16;SB=-310.12	GT:AD:DP:GL:GQ	1/1:0,27:25:-76.96,-7.55,-0.03:75.14
+chr1	1996588	rs2678943	T	C	52.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.08;MQ0=0;OQ=1052.54;QD=26.99;SB=-491.16	GT:AD:DP:GL:GQ	1/1:0,38:34:-108.87,-10.26,-0.03:99
+chr1	1997534	rs2803307	A	G	10.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.74;MQ=59.13;MQ0=0;OQ=1580.39;QD=29.82;SB=-788.60	GT:AD:DP:GL:GQ	1/1:0,53:50:-161.67,-15.08,-0.05:99
+chr1	1999411	.	C	T	1.67	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=5.65;MQ=58.95;MQ0=0;OQ=1145.66;QD=18.48;SB=-378.12	GT:AD:DP:GL:GQ	0/1:25,36:58:-135.32,-17.47,-87.50:99
+chr1	2004056	rs28436686	G	A	119.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=59.61;MQ0=0;OQ=2326.78;QD=39.44;SB=-1079.37	GT:AD:DP:GL:GQ	1/1:0,59:59:-236.28,-17.77,-0.01:99
+chr1	2014367	rs9729600	T	C	414.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=1723.74;QD=27.36;SB=-655.55	GT:AD:DP:GL:GQ	1/1:0,63:57:-176.03,-17.20,-0.07:99
+chr1	2015467	rs61775405	G	A	154	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=3.51;MQ=57.06;MQ0=0;OQ=444.57;QD=10.84;SB=-245.22	GT:AD:DP:GL:GQ	0/1:23,18:37:-58.92,-11.18,-62.94:99
+chr1	2015957	.	T	A	20.13	LowQual	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.77;MQ0=3;QD=0.75;SB=-6.99	GT:AD:DP:GL:GQ	0/1:17,10:5:-6.80,-1.51,-8.98:52.92
+chr1	2015991	.	G	T	43.95	LowQual	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=23.36;MQ0=2;QD=1.19;SB=-6.99	GT:AD:DP:GL:GQ	0/1:34,3:8:-10.09,-2.41,-13.96:76.78
+chr1	2017284	rs12123775	G	A	100.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=256.85;QD=11.17;SB=-34.51	GT:AD:DP:GL:GQ	0/1:14,9:22:-35.60,-6.63,-46.44:99
+chr1	2019252	rs3128329	T	C	18.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=2.93;MQ=58.39;MQ0=0;OQ=1634.16;QD=29.71;SB=-754.64	GT:AD:DP:GL:GQ	1/1:0,55:52:-167.05,-15.69,-0.05:99
+chr1	2019320	.	T	G	18.93	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=4;HaplotypeScore=7.98;MQ=58.04;MQ0=0;QD=0.34;SB=68.22	GT:AD:DP:GL:GQ	0/1:29,26:34:-15.41,-10.24,-102.90:51.71
+chr1	2019693	.	T	G	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=2;HaplotypeScore=1.11;MQ=51.54;MQ0=0;OQ=164.91;QD=4.34;SB=47.17	GT:AD:DP:GL:GQ	0/1:19,19:29:-28.51,-8.74,-68.55:99
+chr1	2023899	rs7521371	A	G	276.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.14;MQ0=0;OQ=762.93;QD=15.26;SB=-284.46	GT:AD:DP:GL:GQ	0/1:23,27:49:-94.34,-14.76,-92.20:99
+chr1	2025239	rs10910029	A	G	201.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.60;MQ0=0;OQ=1376.71;QD=29.29;SB=-649.94	GT:AD:DP:GL:GQ	1/1:0,47:44:-141.29,-13.27,-0.04:99
+chr1	2025544	rs10910030	C	T	525.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1279.25;QD=36.55;SB=-479.12	GT:AD:DP:GL:GQ	1/1:0,35:34:-131.53,-10.25,-0.02:99
+chr1	2025659	rs10752741	G	A	653.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2163.55;QD=37.96;SB=-800.07	GT:AD:DP:GL:GQ	1/1:0,57:55:-219.96,-16.57,-0.02:99
+chr1	2025837	rs10752742	G	T	4.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=6.39;MQ=58.92;MQ0=0;OQ=1340.29;QD=31.17;SB=-640.07	GT:AD:DP:GL:GQ	1/1:0,43:38:-137.63,-11.45,-0.01:99
+chr1	2026123	rs10797413	G	A	219.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.78;MQ0=0;OQ=1381.00;QD=36.34;SB=-700.35	GT:AD:DP:GL:GQ	1/1:0,38:36:-141.70,-10.85,-0.01:99
+chr1	2026457	rs3128332	G	T	494.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=1536.71;QD=35.74;SB=-400.25	GT:AD:DP:GL:GQ	1/1:0,43:42:-157.27,-12.65,-0.01:99
+chr1	2027806	.	A	G	242.28	HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=33.01;MQ0=5;QD=9.69;SB=-135.79	GT:AD:DP:GL:GQ	0/1:9,16:13:-31.43,-3.92,-15.54:99
+chr1	2027817	.	A	G	86.37	HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=28.31;MQ0=5;QD=5.08;SB=-66.32	GT:AD:DP:GL:GQ	0/1:7,10:8:-14.33,-2.41,-15.43:99
+chr1	2027825	rs7364595	T	C	235.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=23.06;MQ0=5;OQ=93.65;QD=7.80;SB=-40.95	GT:AD:DP:GL:GQ	1/1:0,12:4:-12.90,-1.21,-0.00:12.03
+chr1	2027884	.	A	G	40.99	LowQual	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=37.48;MQ0=2;QD=4.10;SB=-10.00	GT:AD:DP:GL:GQ	0/1:3,7:4:-8.59,-1.21,-3.37:21.64
+chr1	2027902	.	C	T	0.78	PASS	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=45.01;MQ0=2;OQ=55.77;QD=3.49;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,3:11:-12.18,-3.32,-23.75:88.60
+chr1	2027903	.	A	G	47.94	LowQual	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=45.01;MQ0=2;QD=3.00;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,4:11:-11.39,-3.31,-30.54:80.77
+chr1	2027922	rs61775410	A	G	254.38	Indel	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=10.71;MQ=52.34;MQ0=2;QD=12.11;SB=-40.68	GT:AD:DP:GL:GQ	0/1:8,13:15:-33.24,-4.52,-21.40:99
+chr1	2027961	rs12745429	G	A	0.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=3.42;MQ=51.66;MQ0=4;OQ=50.47;QD=1.58;SB=-46.03	GT:AD:DP:GL:GQ	0/1:27,5:21:-14.67,-6.34,-51.74:83.30
+chr1	2027962	rs12723086	T	C	0.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=3.42;MQ=51.66;MQ0=4;OQ=55.89;QD=1.75;SB=-41.82	GT:AD:DP:GL:GQ	0/1:25,7:25:-16.41,-7.54,-72.40:88.73
+chr1	2027980	.	A	G	0.42	PASS	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=49.52;MQ0=4;OQ=96.12;QD=2.75;SB=-41.28	GT:AD:DP:GL:GQ	0/1:27,8:28:-21.34,-8.45,-80.79:99
+chr1	2027991	.	A	G	34.81	PASS	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.55;MQ=51.01;MQ0=3;OQ=431.23;QD=9.58;SB=-194.62	GT:AD:DP:GL:GQ	0/1:24,21:36:-57.25,-10.85,-78.85:99
+chr1	2028038	rs7349084	A	G	0.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=50.77;MQ0=1;OQ=115.20;QD=1.99;SB=-64.54	GT:AD:DP:GL:GQ	0/1:47,10:48:-29.27,-14.47,-151.97:99
+chr1	2028049	rs12133181	A	G	36.56	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=65.95;MQ=50.10;MQ0=2;QD=0.48;SB=17.41	GT:AD:DP:GL:GQ	0/1:60,12:63:-25.92,-18.99,-218.94:69.39
+chr1	2028057	rs7514664	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=1;HaplotypeScore=92.07;MQ=50.08;MQ0=4;OQ=1734.98;QD=17.53;SB=-712.36	GT:AD:DP:GL:GQ	0/1:13,84:69:-197.59,-20.81,-27.48:66.63
+chr1	2028096	rs7349113	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=144;Dels=0.00;HRun=1;HaplotypeScore=338.66;MQ=50.60;MQ0=2;OQ=249.31;QD=1.73;SB=17.40	GT:AD:DP:GL:GQ	0/1:107,21:99:-60.23,-32.01,-282.27:99
+chr1	2028116	rs61775411	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=130;Dels=0.00;HRun=1;HaplotypeScore=156.17;MQ=50.22;MQ0=2;OQ=1368.71;QD=10.53;SB=-489.55	GT:AD:DP:GL:GQ	0/1:47,78:82:-164.90,-24.74,-105.56:99
+chr1	2028135	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=77.77;MQ=49.84;MQ0=2;OQ=170.97;QD=2.04;SB=-24.42	GT:AD:DP:GL:GQ	0/1:67,11:63:-39.37,-18.98,-181.92:99
+chr1	2028136	rs12080420	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=76.98;MQ=49.85;MQ0=2;OQ=157.43;QD=1.94;SB=-74.46	GT:AD:DP:GL:GQ	0/1:62,16:61:-37.41,-18.38,-198.10:99
+chr1	2028154	rs3753241	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=33.73;MQ=52.95;MQ0=1;OQ=379.95;QD=7.31;SB=-7.96	GT:AD:DP:GL:GQ	0/1:34,16:44:-54.55,-13.27,-93.77:99
+chr1	2028522	rs3128334	G	A	30.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=59.44;MQ0=0;OQ=1539.70;QD=37.55;SB=-534.21	GT:AD:DP:GL:GQ	1/1:0,39:39:-157.57,-11.75,-0.01:99
+chr1	2028753	rs908744	G	A	89.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.73;MQ=58.80;MQ0=0;OQ=1922.45;QD=33.15;SB=-549.87	GT:AD:DP:GL:GQ	1/1:0,58:52:-195.86,-15.68,-0.03:99
+chr1	2029096	rs1040231	G	T	78.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.23;MQ=58.48;MQ0=0;OQ=1527.94;QD=33.22;SB=-620.05	GT:AD:DP:GL:GQ	1/1:1,45:45:-156.40,-13.56,-0.02:99
+chr1	2029381	rs16824792	G	T	92.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.28;MQ0=0;OQ=1106.74;QD=34.59;SB=-441.64	GT:AD:DP:GL:GQ	1/1:0,32:31:-114.27,-9.34,-0.01:93.28
+chr1	2029579	rs1878752	G	A	107.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.58;MQ0=0;OQ=1364.65;QD=36.88;SB=-510.18	GT:AD:DP:GL:GQ	1/1:0,37:36:-140.06,-10.85,-0.01:99
+chr1	2029956	rs6666117	T	C	57.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=967.27;QD=27.64;SB=-467.25	GT:AD:DP:GL:GQ	1/1:0,35:31:-100.34,-9.35,-0.03:93.22
+chr1	2030248	rs6683011	G	A	365.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.46;MQ0=0;OQ=938.15;QD=36.08;SB=-369.99	GT:AD:DP:GL:GQ	1/1:0,26:24:-97.41,-7.23,-0.01:72.24
+chr1	2030623	rs4648805	G	A	629.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=1690.17;QD=38.41;SB=-769.01	GT:AD:DP:GL:GQ	1/1:0,44:44:-172.62,-13.26,-0.02:99
+chr1	2030637	rs4648806	C	T	94.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=56.04;MQ0=0;OQ=1691.52;QD=35.24;SB=-723.01	GT:AD:DP:GL:GQ	1/1:0,48:44:-172.75,-13.26,-0.02:99
+chr1	2030645	rs6674878	A	G	54.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=55.66;MQ0=0;OQ=1170.82;QD=26.61;SB=-567.76	GT:AD:DP:GL:GQ	1/1:0,44:39:-120.72,-11.78,-0.06:99
+chr1	2030758	rs4648807	T	C	223.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.74;MQ=59.17;MQ0=0;OQ=1628.83;QD=29.09;SB=-733.30	GT:AD:DP:GL:GQ	1/1:0,56:52:-166.52,-15.69,-0.05:99
+chr1	2030796	rs4648808	T	C	215.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.65;MQ0=0;OQ=1868.75;QD=28.75;SB=-846.52	GT:AD:DP:GL:GQ	1/1:0,65:59:-190.51,-17.80,-0.05:99
+chr1	2031015	rs10910046	C	T	236.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.92;MQ0=0;OQ=619.66;QD=30.98;SB=-276.86	GT:AD:DP:GL:GQ	1/1:0,20:17:-65.56,-5.12,-0.01:51.16
+chr1	2031321	rs12059660	C	T	236.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.27;MQ0=0;OQ=1048.92;QD=38.85;SB=-437.08	GT:AD:DP:GL:GQ	1/1:0,27:27:-108.48,-8.13,-0.01:81.26
+chr1	2032403	rs11584491	A	G	58.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=59.38;MQ0=0;OQ=893.06;QD=29.77;SB=-424.80	GT:AD:DP:GL:GQ	1/1:0,30:30:-92.92,-9.05,-0.03:90.18
+chr1	2032854	rs3128336	C	G	73.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=59.29;MQ0=0;OQ=1394.69;QD=35.76;SB=-622.82	GT:AD:DP:GL:GQ	1/1:0,39:35:-143.08,-10.56,-0.03:99
+chr1	2033844	rs3107141	C	T	92.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=4.37;MQ=59.25;MQ0=0;OQ=2275.40;QD=36.70;SB=-1025.90	GT:AD:DP:GL:GQ	1/1:0,62:59:-231.15,-17.78,-0.02:99
+chr1	2033897	rs925905	T	C	149.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.07;MQ0=0;OQ=2152.92;QD=34.17;SB=-821.32	GT:AD:DP:GL:GQ	1/1:0,63:61:-218.90,-18.38,-0.02:99
+chr1	2033914	rs925906	A	C	279.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.02;HRun=0;HaplotypeScore=0.48;MQ=59.34;MQ0=0;OQ=1986.91;QD=33.12;SB=-865.63	GT:AD:DP:GL:GQ	1/1:0,59:59:-202.29,-17.47,-0.02:99
+chr1	2034402	rs3107142	T	C	2.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=862.83;QD=28.76;SB=-292.45	GT:AD:DP:GL:GQ	1/1:0,30:25:-89.88,-7.54,-0.02:75.20
+chr1	2035025	rs1467217	G	A	101.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=58.81;MQ0=0;OQ=1215.26;QD=31.16;SB=-472.57	GT:AD:DP:GL:GQ	1/1:2,37:32:-125.13,-9.65,-0.02:96.30
+chr1	2035232	rs3107143	G	C	1383.32	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=3;HaplotypeScore=1.46;MQ=53.42;MQ0=0;QD=40.69;SB=-202.29	GT:AD:DP:GL:GQ	1/1:0,34:32:-141.93,-9.65,-0.01:96.32
+chr1	2035236	rs61775448	A	G	957.24	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=52.98;MQ0=0;QD=29.91;SB=-159.74	GT:AD:DP:GL:GQ	1/1:0,32:29:-99.32,-8.74,-0.01:87.24
+chr1	2035240	rs3107144	C	A	1108.98	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=53.21;MQ0=0;QD=33.61;SB=-288.09	GT:AD:DP:GL:GQ	1/1:0,33:31:-114.49,-9.34,-0.01:93.28
+chr1	2035742	rs3128337	A	G	495.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.14;MQ0=0;OQ=2084.14;QD=30.20;SB=-613.59	GT:AD:DP:GL:GQ	1/1:0,69:67:-212.07,-20.22,-0.07:99
+chr1	2036646	rs3128338	G	A	633.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2283.85;QD=36.84;SB=-1084.46	GT:AD:DP:GL:GQ	1/1:0,61:60:-232.00,-18.09,-0.03:99
+chr1	2036798	rs3128339	G	T	418.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.44;MQ0=0;OQ=1615.06;QD=33.65;SB=-604.54	GT:AD:DP:GL:GQ	1/1:0,48:46:-165.11,-13.86,-0.02:99
+chr1	2037356	rs3128340	C	G	20.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=1.21;MQ=59.34;MQ0=0;OQ=2469.41;QD=39.20;SB=-820.16	GT:AD:DP:GL:GQ	1/1:0,63:62:-250.56,-18.70,-0.04:99
+chr1	2037407	rs3107145	G	A	220.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.18;MQ=59.05;MQ0=0;OQ=2392.58;QD=37.38;SB=-1173.71	GT:AD:DP:GL:GQ	1/1:0,64:62:-242.87,-18.68,-0.02:99
+chr1	2037444	rs3107146	T	C	445.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=1708.25;QD=30.50;SB=-576.98	GT:AD:DP:GL:GQ	1/1:0,56:53:-174.45,-15.98,-0.04:99
+chr1	2038589	rs3107147	G	A	179.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.78;MQ0=0;OQ=3375.92;QD=40.19;SB=-1379.05	GT:AD:DP:GL:GQ	1/1:0,83:83:-336.59,-25.00,-0.02:99
+chr1	2039293	.	A	T	534.23	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=3;HaplotypeScore=26.93;MQ=46.16;MQ0=1;QD=5.40;SB=50.36	GT:AD:DP:GL:GQ	0/1:64,35:82:-81.41,-24.70,-228.25:99
+chr1	2039297	.	C	T	849.12	Indel	AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=16;HaplotypeScore=37.86;MQ=45.71;MQ0=2;QD=8.01;SB=-44.28	GT:AD:DP:GL:GQ	0/1:72,34:90:-115.31,-27.11,-215.41:99
+chr1	2039368	rs3128290	G	T	199.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=57.68;MQ0=0;OQ=1893.89;QD=32.65;SB=-943.62	GT:AD:DP:GL:GQ	1/1:0,58:54:-193.00,-16.27,-0.02:99
+chr1	2039459	rs3107148	T	C	580.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=1837.96;QD=36.04;SB=-792.00	GT:AD:DP:GL:GQ	1/1:0,51:51:-187.40,-15.36,-0.01:99
+chr1	2040055	rs3107149	A	T	0.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=7.05;MQ=47.19;MQ0=2;OQ=1180.60;QD=26.83;SB=-338.84	GT:AD:DP:GL:GQ	1/1:1,43:33:-121.66,-9.94,-0.01:99
+chr1	2040785	rs3107150	T	A	621.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.05;MQ0=0;OQ=2606.94;QD=34.76;SB=-964.53	GT:AD:DP:GL:GQ	1/1:0,75:72:-264.30,-21.69,-0.03:99
+chr1	2041373	rs3107151	T	G	405.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.29;MQ0=0;OQ=1384.90;QD=30.11;SB=-485.99	GT:AD:DP:GL:GQ	1/1:0,46:41:-142.10,-12.35,-0.02:99
+chr1	2042357	rs3107152	T	C	727.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2187.52;QD=34.72;SB=-1010.74	GT:AD:DP:GL:GQ	1/1:0,63:62:-222.36,-18.68,-0.02:99
+chr1	2042782	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.57;MQ=44.83;MQ0=0;OQ=64.06;QD=1.26;SB=2.03	GT:AD:DP:GL:GQ	0/1:44,7:48:-24.15,-14.46,-148.69:96.90
+chr1	2042814	.	C	G	7.67	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.26;MQ=39.19;MQ0=0;OQ=415.49;QD=7.69;SB=-85.80	GT:AD:DP:GL:GQ	0/1:38,16:51:-60.21,-15.38,-162.70:99
+chr1	2042818	.	A	G	548.88	SnpCluster	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=3.40;MQ=38.13;MQ0=0;QD=9.15;SB=-238.62	GT:AD:DP:GL:GQ	0/1:35,25:55:-74.74,-16.57,-136.02:99
+chr1	2042827	rs56946456	C	T	974.86	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.38;MQ=37.16;MQ0=0;QD=15.23;SB=-13.45	GT:AD:DP:GL:GQ	0/1:33,30:59:-118.54,-17.77,-108.89:99
+chr1	2042828	rs59510407	A	G	718.63	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=2.75;MQ=36.52;MQ0=0;QD=11.98;SB=-10.84	GT:AD:DP:GL:GQ	0/1:33,26:56:-92.01,-16.87,-122.40:99
+chr1	2042846	rs58866862	A	G	74.49	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=35.77;MQ0=0;QD=1.16;SB=32.14	GT:AD:DP:GL:GQ	0/1:43,21:44:-23.99,-13.25,-151.62:99
+chr1	2042857	rs61526019	C	T	19.11	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=37.11;MQ0=1;QD=0.30;SB=35.13	GT:AD:DP:GL:GQ	0/1:49,15:46:-19.05,-13.86,-151.53:51.90
+chr1	2042876	.	G	T	13.23	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=1;HaplotypeScore=9.69;MQ=38.17;MQ0=2;QD=0.18;SB=41.11	GT:AD:DP:GL:GQ	0/1:58,9:53:-20.55,-15.96,-167.03:45.86
+chr1	2042878	.	T	C	0.10	PASS	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=11.69;MQ=38.38;MQ0=2;OQ=1187.23;QD=16.96;SB=-479.73	GT:AD:DP:GL:GQ	0/1:15,55:50:-137.09,-15.08,-24.25:91.67
+chr1	2042931	.	A	G	53.02	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=15.54;MQ=37.98;MQ0=2;QD=0.69;SB=20.09	GT:AD:DP:GL:GQ	0/1:67,10:63:-27.57,-18.98,-213.37:85.85
+chr1	2042932	.	C	T	144.76	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=10.55;MQ=37.98;MQ0=2;QD=1.88;SB=20.04	GT:AD:DP:GL:GQ	0/1:64,13:62:-36.47,-18.71,-162.72:99
+chr1	2042933	rs61775451	A	G	2056.36	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=7.24;MQ=37.41;MQ0=2;QD=27.79;SB=-304.45	GT:AD:DP:GL:GQ	1/1:0,74:61:-209.25,-18.38,-0.03:99
+chr1	2042939	rs61775452	A	G	1556.23	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=44.30;MQ=35.88;MQ0=3;QD=19.21;SB=-241.65	GT:AD:DP:GL:GQ	0/1:26,55:67:-179.09,-20.18,-61.01:99
+chr1	2042967	.	G	A	494.62	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=42.03;MQ=31.07;MQ0=2;QD=5.75;SB=-10.00	GT:AD:DP:GL:GQ	0/1:65,21:57:-69.92,-17.17,-132.17:99
+chr1	2042968	.	T	C	324.84	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=41.51;MQ=30.57;MQ0=2;QD=3.82;SB=-7.00	GT:AD:DP:GL:GQ	0/1:68,17:56:-52.65,-16.88,-157.62:99
+chr1	2042975	.	G	A	918.15	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=43.08;MQ=30.97;MQ0=1;QD=11.92;SB=-7.00	GT:AD:DP:GL:GQ	0/1:43,34:50:-110.16,-15.06,-77.95:99
+chr1	2042993	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=37.83;MQ=26.92;MQ0=1;OQ=262.34;QD=4.60;SB=-10.00	GT:AD:DP:GL:GQ	0/1:38,19:39:-41.26,-11.74,-103.99:99
+chr1	2043003	.	A	G	593.68	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=39;Dels=0.03;HRun=0;HaplotypeScore=30.47;MQ=26.18;MQ0=1;QD=15.22;SB=-10.00	GT:AD:DP:GL:GQ	0/1:16,22:23:-69.27,-6.63,-8.02:13.91
+chr1	2043004	.	C	T	763.57	Indel;SnpCluster	AC=2;AF=1.00;AN=2;DP=36;Dels=0.06;HRun=0;HaplotypeScore=22.21;MQ=26.52;MQ0=1;QD=21.21;SB=-10.00	GT:AD:DP:GL:GQ	1/1:3,31:22:-82.94,-6.33,-3.00:33.26
+chr1	2043011	.	A	G	85.38	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=13.94;MQ=26.97;MQ0=0;QD=3.28;SB=-10.00	GT:AD:DP:GL:GQ	0/1:19,7:20:-17.84,-6.02,-61.94:99
+chr1	2043025	.	C	T	0.23	PASS	AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=7.88;MQ=23.26;MQ0=0;OQ=89.13;QD=11.14;SB=-10.00	GT:AD:DP:GL:GQ	1/1:3,5:3:-12.40,-0.90,-0.00:9.03
+chr1	2043058	.	C	T	0.16	PASS	AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=7.97;MQ=18.94;MQ0=5;OQ=124.33;QD=12.43;SB=-10.00	GT:AD:DP:GL:GQ	1/1:4,6:4:-15.97,-1.21,-0.00:12.04
+chr1	2043061	.	C	T	0.16	PASS	AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=9.08;MQ=17.30;MQ0=6;OQ=117.32;QD=9.78;SB=-10.00	GT:AD:DP:GL:GQ	1/1:4,8:4:-15.27,-1.21,-0.00:12.04
+chr1	2043097	.	C	T	1.40	PASS	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=4.78;MQ=17.14;MQ0=7;OQ=117.84;QD=7.86;SB=-10.00	GT:AD:DP:GL:GQ	0/1:11,4:5:-16.57,-1.51,-3.10:15.90
+chr1	2043134	rs62641630	A	G	85.81	Indel	AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=34.82;MQ=24.20;MQ0=2;QD=5.36;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,7:9:-14.57,-2.71,-19.58:99
+chr1	2043141	.	T	G	143.26	Indel	AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=21.33;MQ0=2;QD=11.94;SB=-10.00	GT:AD:DP:GL:GQ	1/1:3,9:5:-17.89,-1.51,-0.00:15.05
+chr1	2043178	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=18.82;MQ=19.76;MQ0=6;OQ=129.40;QD=2.70;SB=-10.00	GT:AD:DP:GL:GQ	0/1:34,14:15:-20.75,-4.53,-30.16:99
+chr1	2043181	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=18.51;MQ=19.26;MQ0=7;OQ=70.77;QD=1.31;SB=-10.00	GT:AD:DP:GL:GQ	0/1:41,12:15:-14.88,-4.52,-41.18:99
+chr1	2043199	.	T	C	326.46	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=71.39;MQ=18.51;MQ0=9;QD=3.23;SB=5.04	GT:AD:DP:GL:GQ	0/1:73,28:19:-41.66,-5.73,-27.12:99
+chr1	2043200	.	G	T	127.31	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=1;HaplotypeScore=109.06;MQ=18.45;MQ0=9;QD=1.24;SB=5.04	GT:AD:DP:GL:GQ	0/1:88,15:19:-21.74,-5.72,-47.36:99
+chr1	2043203	.	A	G	195.43	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=1;HaplotypeScore=58.32;MQ=18.15;MQ0=10;QD=1.74;SB=5.04	GT:AD:DP:GL:GQ	0/1:95,17:20:-28.85,-6.02,-47.43:99
+chr1	2043227	rs61775455	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=139;Dels=0.00;HRun=1;HaplotypeScore=26.18;MQ=17.76;MQ0=15;OQ=512.67;QD=3.69;SB=-282.20	GT:AD:DP:GL:GQ	0/1:22,117:18:-59.98,-5.43,-16.39:99
+chr1	2043250	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=40.25;MQ=18.52;MQ0=5;OQ=52.10;QD=0.80;SB=5.03	GT:AD:DP:GL:GQ	0/1:47,18:9:-11.21,-2.71,-18.54:84.93
+chr1	2043253	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=69.74;MQ=17.96;MQ0=6;OQ=126.28;QD=2.18;SB=-31.52	GT:AD:DP:GL:GQ	0/1:37,20:7:-18.02,-2.11,-6.74:46.31
+chr1	2043286	.	C	T	29.35	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=15.82;MQ=16.30;MQ0=5;QD=1.47;SB=-39.54	GT:AD:DP:GL:GQ	0/1:10,10:4:-7.42,-1.21,-6.19:49.87
+chr1	2043289	.	C	T	29.39	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=12.80;MQ=15.14;MQ0=5;QD=1.73;SB=-36.53	GT:AD:DP:GL:GQ	0/1:8,8:3:-7.13,-0.91,-2.70:17.92
+chr1	2043333	.	T	G	28.03	LowQual	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=18.60;MQ0=2;QD=4.00;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,7:2:-6.21,-0.60,-0.00:6.01
+chr1	2043370	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=30.96;MQ=17.94;MQ0=3;OQ=266.78;QD=3.51;SB=-158.18	GT:AD:DP:GL:GQ	0/1:20,55:9:-32.59,-2.71,-3.10:3.86
+chr1	2043387	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=305.93;MQ=17.79;MQ0=4;OQ=61.76;QD=0.60;SB=5.03	GT:AD:DP:GL:GQ	0/1:70,33:9:-12.17,-2.71,-18.55:94.59
+chr1	2043399	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=80.07;MQ=17.30;MQ0=8;OQ=50.40;QD=0.46;SB=-41.37	GT:AD:DP:GL:GQ	0/1:77,30:6:-10.13,-1.81,-8.76:69.51
+chr1	2043410	.	G	A	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=62.95;MQ=16.84;MQ0=8;OQ=120.99;QD=1.22;SB=-42.66	GT:AD:DP:GL:GQ	1/1:14,85:4:-15.63,-1.21,-0.00:12.04
+chr1	2043421	.	C	T	40.51	LowQual	AC=1;AF=0.50;AN=2;DP=97;Dels=0.01;HRun=0;HaplotypeScore=78.29;MQ=16.56;MQ0=9;QD=0.42;SB=-7.00	GT:AD:DP:GL:GQ	0/1:75,21:3:-8.24,-0.90,-2.77:18.65
+chr1	2043428	.	G	A	73.75	Indel	AC=2;AF=1.00;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=65.46;MQ=16.72;MQ0=6;QD=0.88;SB=-10.00	GT:AD:DP:GL:GQ	1/1:16,68:3:-10.87,-0.91,-0.00:9.02
+chr1	2043438	.	G	A	70.80	Indel	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=64.65;MQ=17.33;MQ0=2;QD=1.00;SB=-10.00	GT:AD:DP:GL:GQ	0/1:44,27:4:-11.57,-1.20,-3.47:22.64
+chr1	2043560	.	G	C	29.95	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=54.01;MQ=17.20;MQ0=4;QD=0.86;SB=-10.00	GT:AD:DP:GL:GQ	0/1:29,6:4:-7.49,-1.21,-7.00:57.86
+chr1	2043565	.	C	T	49.25	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=47.09;MQ=17.14;MQ0=4;QD=1.37;SB=-10.00	GT:AD:DP:GL:GQ	1/1:19,17:2:-8.33,-0.60,-0.00:6.02
+chr1	2043572	.	G	A	46.02	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=33.86;MQ=16.62;MQ0=6;QD=1.18;SB=-10.00	GT:AD:DP:GL:GQ	1/1:22,17:2:-8.01,-0.60,-0.00:6.02
+chr1	2043583	.	C	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=32.32;MQ=16.61;MQ0=6;OQ=173.76;QD=4.57;SB=-10.00	GT:AD:DP:GL:GQ	1/1:16,22:5:-20.94,-1.51,-0.00:15.05
+chr1	2043590	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=28.82;MQ=16.31;MQ0=5;OQ=78.84;QD=2.39;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,18:4:-12.37,-1.20,-2.87:16.64
+chr1	2043797	.	C	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=30.70;MQ=15.39;MQ0=12;OQ=90.55;QD=2.66;SB=-10.00	GT:AD:DP:GL:GQ	1/1:10,21:4:-15.80,-4.21,-3.24:9.74
+chr1	2043818	.	T	C	79	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=39.74;MQ=12.98;MQ0=29;QD=1.39;SB=-10.00	GT:AD:DP:GL:GQ	1/1:42,15:3:-11.39,-0.90,-0.00:9.03
+chr1	2043819	.	G	T	74.28	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=66.63;MQ=12.86;MQ0=30;QD=1.28;SB=-10.00	GT:AD:DP:GL:GQ	1/1:43,15:3:-10.92,-0.90,-0.00:9.03
+chr1	2043822	.	G	A	85.78	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=66.31;MQ=12.73;MQ0=32;QD=1.41;SB=-10.00	GT:AD:DP:GL:GQ	1/1:35,26:3:-12.07,-0.90,-0.00:9.03
+chr1	2043840	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=53.86;MQ=13.17;MQ0=31;OQ=75.78;QD=1.28;SB=-3.99	GT:AD:DP:GL:GQ	0/1:33,26:5:-12.37,-1.51,-6.39:48.86
+chr1	2043865	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=29.69;MQ=17.30;MQ0=6;OQ=56.87;QD=2.19;SB=-30.92	GT:AD:DP:GL:GQ	0/1:19,7:4:-10.17,-1.21,-3.00:17.97
+chr1	2043873	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=65.88;MQ=20.81;MQ0=0;OQ=78.81;QD=5.63;SB=-7.00	GT:AD:DP:GL:GQ	0/1:7,7:4:-12.37,-1.21,-3.20:19.92
+chr1	2044254	.	A	G	32.28	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;HRun=1;HaplotypeScore=4.00;MQ=14.52;MQ0=7;QD=1.90;SB=-10.00	GT:AD:DP:GL:GQ	1/1:8,9:2:-6.64,-0.60,-0.00:6.02
+chr1	2044261	.	G	T	34.69	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=14.97;MQ0=6;QD=2.17;SB=-10.00	GT:AD:DP:GL:GQ	1/1:8,8:2:-6.88,-0.60,-0.00:6.02
+chr1	2045053	.	A	G	0.05	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=1;HaplotypeScore=13.98;MQ=19.49;MQ0=2;OQ=141.20;QD=10.86;SB=-10.00	GT:AD:DP:GL:GQ	1/1:5,8:5:-17.68,-1.51,-0.00:15.04
+chr1	2045060	.	G	T	46.93	LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=16.54;MQ=19.21;MQ0=2;QD=3.35;SB=-10.00	GT:AD:DP:GL:GQ	0/1:9,5:5:-9.49,-1.51,-6.61:50.97
+chr1	2045064	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=17.54;MQ=18.55;MQ0=3;OQ=51.75;QD=3.45;SB=-10.00	GT:AD:DP:GL:GQ	0/1:6,9:5:-9.97,-1.51,-6.44:49.32
+chr1	2045454	.	C	T	0.01	FDRtranche2.00to10.00	AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=19.88;MQ=20.43;MQ0=9;OQ=198.28;QD=7.34;SB=-10.00	GT:AD:DP:GL:GQ	1/1:7,20:6:-23.40,-1.81,-0.00:18.06
+chr1	2045469	.	C	T	0.06	PASS	AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=12.29;MQ=20.17;MQ0=11;OQ=284.41;QD=8.89;SB=-48.56	GT:AD:DP:GL:GQ	1/1:9,23:8:-32.02,-2.41,-0.00:24.08
+chr1	2045505	.	C	T	28.68	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=18.97;MQ=24.13;MQ0=5;QD=0.54;SB=11.04	GT:AD:DP:GL:GQ	0/1:44,9:20:-12.18,-6.03,-54.06:61.51
+chr1	2045518	.	C	G	738.24	SnpCluster	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=15.01;MQ=25.23;MQ0=2;QD=13.67;SB=-291.20	GT:AD:DP:GL:GQ	0/1:10,44:25:-84.64,-7.53,-25.69:99
+chr1	2045519	.	G	A	107.30	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=14.97;MQ=25.69;MQ0=2;QD=1.95;SB=11.06	GT:AD:DP:GL:GQ	0/1:46,9:22:-20.64,-6.63,-60.44:99
+chr1	2045523	rs61775456	C	T	1156.65	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=31.40;MQ=26.13;MQ0=1;QD=21.03;SB=-340.35	GT:AD:DP:GL:GQ	1/1:5,50:30:-119.26,-9.04,-0.01:90.29
+chr1	2045530	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=38.81;MQ=25.91;MQ0=2;OQ=314.66;QD=4.56;SB=14.05	GT:AD:DP:GL:GQ	0/1:30,39:21:-41.08,-6.33,-36.84:99
+chr1	2045541	rs61775457	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=85.67;MQ=25.28;MQ0=4;OQ=1042.79;QD=14.28;SB=-111.96	GT:AD:DP:GL:GQ	0/1:30,43:36:-118.41,-10.85,-17.33:64.79
+chr1	2045548	rs61775458	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=80.30;MQ=24.94;MQ0=7;OQ=952.67;QD=11.48;SB=11.05	GT:AD:DP:GL:GQ	0/1:35,48:39:-110.31,-11.76,-31.30:99
+chr1	2045552	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=3;HaplotypeScore=82.09;MQ=25.54;MQ0=10;OQ=109.35;QD=1.09;SB=14.08	GT:AD:DP:GL:GQ	0/1:83,17:53:-30.20,-15.98,-173.43:99
+chr1	2045562	rs61775459	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=44.83;MQ=25.87;MQ0=15;OQ=1085.84;QD=10.54;SB=-112.96	GT:AD:DP:GL:GQ	0/1:18,82:44:-125.15,-13.28,-24.49:99
+chr1	2045577	rs61776561	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=71.26;MQ=25.93;MQ0=17;OQ=471.38;QD=4.36;SB=-66.29	GT:AD:DP:GL:GQ	0/1:83,25:48:-64.89,-14.47,-100.62:99
+chr1	2045590	rs61776562	C	G	1122.80	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=71.62;MQ=27.29;MQ0=12;QD=12.62;SB=-466.47	GT:AD:DP:GL:GQ	0/1:38,51:51:-130.94,-15.38,-82.60:99
+chr1	2045591	.	G	A	91.87	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=67.28;MQ=27.29;MQ0=12;QD=1.03;SB=20.08	GT:AD:DP:GL:GQ	0/1:68,21:39:-24.23,-11.76,-108.70:99
+chr1	2045595	rs61776563	C	T	1533.88	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=45.58;MQ=27.30;MQ0=11;QD=17.43;SB=-260.54	GT:AD:DP:GL:GQ	1/1:9,79:49:-170.95,-14.77,-14.14:6.27
+chr1	2045606	.	A	G	34.51	DPFilter;HARD_TO_VALIDATE;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=3;HaplotypeScore=43.22;MQ=27.00;MQ0=12;QD=0.42;SB=23.11	GT:AD:DP:GL:GQ	0/1:76,7:41:-19.11,-12.37,-129.33:67.35
+chr1	2045616	.	T	C	78.88	DPFilter;HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=250.84;MQ=27.16;MQ0=10;QD=1.21;SB=21.87	GT:AD:DP:GL:GQ	0/1:53,10:39:-22.94,-11.77,-110.81:99
+chr1	2045620	rs61776564	G	A	378.54	DPFilter;HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=91.32;MQ=25.99;MQ0=10;QD=7.14;SB=2.03	GT:AD:DP:GL:GQ	0/1:31,22:26:-48.98,-7.84,-44.75:99
+chr1	2045631	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=20.68;MQ=23.69;MQ0=10;OQ=345.67;QD=8.43;SB=-190.29	GT:AD:DP:GL:GQ	0/1:16,25:18:-43.28,-5.43,-21.54:99
+chr1	2045638	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=35.28;MQ=23.82;MQ0=10;OQ=167.44;QD=4.29;SB=-58.06	GT:AD:DP:GL:GQ	0/1:24,15:14:-24.25,-4.23,-24.00:99
+chr1	2045652	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=49.08;MQ=21.77;MQ0=9;OQ=173.85;QD=5.43;SB=-84.31	GT:AD:DP:GL:GQ	0/1:13,19:7:-22.76,-2.11,-3.10:9.89
+chr1	2045656	.	G	A	40.26	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=55.88;MQ=22.32;MQ0=8;QD=1.34;SB=-10.00	GT:AD:DP:GL:GQ	0/1:16,14:3:-8.21,-0.90,-3.07:21.65
+chr1	2045667	.	C	T	56.78	SnpCluster	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=27.04;MQ=25.03;MQ0=2;QD=2.18;SB=-3.99	GT:AD:DP:GL:GQ	0/1:9,17:7:-11.07,-2.11,-11.53:89.62
+chr1	2045670	.	C	T	22.25	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=24.25;MQ=25.19;MQ0=1;QD=0.93;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,19:3:-6.41,-0.91,-3.37:24.66
+chr1	2045674	.	G	A	38.46	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=35.09;MQ=29.74;MQ0=1;QD=1.54;SB=-10.00	GT:AD:DP:GL:GQ	0/1:10,15:4:-8.34,-1.21,-6.59:53.87
+chr1	2045688	rs61776565	C	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=37.51;MQ=32.86;MQ0=0;OQ=472.91;QD=12.78;SB=-219.35	GT:AD:DP:GL:GQ	1/1:8,29:13:-50.88,-3.92,-0.00:39.13
+chr1	2045716	rs11589827	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=37.92;MQ=32.79;MQ0=0;OQ=1051.52;QD=19.47;SB=-363.54	GT:AD:DP:GL:GQ	0/1:22,32:36:-119.28,-10.85,-21.22:99
+chr1	2045975	rs56260599	A	G	8.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=2.17;MQ=48.30;MQ0=0;OQ=1370.04;QD=29.78;SB=-550.86	GT:AD:DP:GL:GQ	1/1:0,45:39:-140.61,-11.75,-0.02:99
+chr1	2047610	rs3107154	A	C	149.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.43;MQ0=0;OQ=1416.93;QD=32.20;SB=-509.01	GT:AD:DP:GL:GQ	1/1:0,44:41:-145.30,-12.35,-0.02:99
+chr1	2047883	rs3128291	A	G	544.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1311.92;QD=28.52;SB=-584.18	GT:AD:DP:GL:GQ	1/1:0,46:44:-134.83,-13.28,-0.06:99
+chr1	2050384	rs3107155	T	C	5.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=1.93;MQ=59.45;MQ0=0;OQ=1167.72;QD=27.80;SB=-528.96	GT:AD:DP:GL:GQ	1/1:0,42:38:-120.40,-11.47,-0.04:99
+chr1	2050490	rs3107156	T	C	249.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=60.00;MQ0=0;OQ=2021.38;QD=30.17;SB=-957.45	GT:AD:DP:GL:GQ	1/1:0,67:63:-205.77,-19.00,-0.05:99
+chr1	2050592	rs10797427	C	T	209.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=2020.11;QD=36.73;SB=-999.03	GT:AD:DP:GL:GQ	1/1:0,54:53:-205.62,-15.97,-0.03:99
+chr1	2051236	rs6603815	T	C	200	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.85;MQ0=0;OQ=2560.21;QD=35.07;SB=-874.04	GT:AD:DP:GL:GQ	1/1:0,73:73:-259.63,-21.99,-0.03:99
+chr1	2051829	rs3107157	T	C	631.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.47;MQ0=0;OQ=1661.55;QD=30.21;SB=-807.71	GT:AD:DP:GL:GQ	1/1:0,55:52:-169.78,-15.68,-0.04:99
+chr1	2053024	rs2222217	G	A	330.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.94;MQ0=0;OQ=1814.00;QD=39.43;SB=-879.02	GT:AD:DP:GL:GQ	1/1:0,46:46:-185.00,-13.86,-0.01:99
+chr1	2055199	rs3128293	A	G	0.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=4;HaplotypeScore=2.50;MQ=57.87;MQ0=0;OQ=714.48;QD=32.48;SB=-354.81	GT:AD:DP:GL:GQ	1/1:0,22:21:-75.04,-6.33,-0.01:63.18
+chr1	2055203	rs3128294	G	C	31.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=2.50;MQ=59.11;MQ0=0;OQ=958.73;QD=36.87;SB=-480.55	GT:AD:DP:GL:GQ	1/1:0,26:24:-99.47,-7.24,-0.01:72.23
+chr1	2056850	rs55958603	C	T	1.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=3.45;MQ=57.77;MQ0=0;OQ=633.04;QD=15.07;SB=-129.09	GT:AD:DP:GL:GQ	0/1:21,21:38:-78.03,-11.45,-68.95:99
+chr1	2058340	rs3128295	C	T	135.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=57.98;MQ0=0;OQ=1478.85;QD=33.61;SB=-754.65	GT:AD:DP:GL:GQ	1/1:0,43:39:-151.49,-11.75,-0.02:99
+chr1	2058766	rs3128296	G	T	62.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=59.52;MQ0=0;OQ=1387.47;QD=35.58;SB=-366.86	GT:AD:DP:GL:GQ	1/1:0,39:38:-142.34,-11.45,-0.01:99
+chr1	2060181	rs411021	T	C	39.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.62;MQ0=0;OQ=1893.37;QD=29.58;SB=-877.01	GT:AD:DP:GL:GQ	1/1:0,64:60:-192.98,-18.10,-0.06:99
+chr1	2061200	rs424079	C	A	282.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.70;MQ0=0;OQ=2061.38;QD=33.25;SB=-816.15	GT:AD:DP:GL:GQ	1/1:2,60:59:-209.75,-17.78,-0.03:99
+chr1	2061416	rs436045	A	G	341.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1852.88;QD=31.95;SB=-463.52	GT:AD:DP:GL:GQ	1/1:0,58:55:-188.90,-16.57,-0.02:99
+chr1	2061625	rs364677	A	G	92.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.94;MQ=57.88;MQ0=0;OQ=1754.29;QD=33.10;SB=-829.10	GT:AD:DP:GL:GQ	1/1:0,53:50:-179.03,-15.06,-0.02:99
+chr1	2062860	rs2945573	A	G	10.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=3.09;MQ=53.50;MQ0=0;OQ=1269.78;QD=34.32;SB=-473.51	GT:AD:DP:GL:GQ	1/1:0,37:36:-130.57,-10.84,-0.01:99
+chr1	2063413	rs643076	A	G	32.55	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=23.27;MQ0=4;QD=3.26;SB=-41.68	GT:AD:DP:GL:GQ	1/1:0,9:2:-6.66,-0.60,-0.00:6.02
+chr1	2063477	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=1;HaplotypeScore=9.72;MQ=34.90;MQ0=16;OQ=82.45;QD=1.04;SB=5.04	GT:AD:DP:GL:GQ	0/1:72,7:47:-25.69,-14.16,-141.31:99
+chr1	2063706	rs56038539	T	C	3.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=41.37;MQ0=1;OQ=139.38;QD=19.91;SB=-78.92	GT:AD:DP:GL:GQ	1/1:0,7:5:-17.50,-1.51,-0.00:15.04
+chr1	2068664	.	C	T	1.14	PASS	AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=1;HaplotypeScore=4.59;MQ=58.77;MQ0=0;OQ=1604.59;QD=18.44;SB=-789.85	GT:AD:DP:GL:GQ	0/1:40,47:84:-189.05,-25.30,-139.35:99
+chr1	2076421	rs2459983	A	G	9.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=6.88;MQ=57.31;MQ0=0;OQ=556.13;QD=9.43;SB=-262.92	GT:AD:DP:GL:GQ	0/1:36,23:54:-75.17,-16.28,-123.64:99
+chr1	2080370	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=7.10;MQ=51.87;MQ0=1;OQ=83.25;QD=1.63;SB=68.25	GT:AD:DP:GL:GQ	0/1:34,17:35:-22.19,-10.58,-111.66:99
+chr1	2084392	rs12132341	G	A	174.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.02;MQ=59.31;MQ0=0;OQ=863.52;QD=15.99;SB=-268.13	GT:AD:DP:GL:GQ	0/1:26,28:52:-105.30,-15.67,-88.61:99
+chr1	2089742	rs12137653	G	A	181.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=58.90;MQ0=0;OQ=1123.18;QD=19.04;SB=-544.82	GT:AD:DP:GL:GQ	0/1:23,36:56:-132.48,-16.88,-70.24:99
+chr1	2096700	rs12135175	T	C	69.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=484.58;QD=34.61;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,14:14:-52.05,-4.22,-0.00:42.13
+chr1	2096756	rs12135178	T	C	1.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=63.69;QD=21.23;SB=-45.69	GT:AD:DP:GL:GQ	1/1:0,3:3:-9.86,-0.91,-0.00:9.02
+chr1	2097150	.	G	T	29.88	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=2;HaplotypeScore=4.60;MQ=59.01;MQ0=0;QD=1.57;SB=20.09	GT:AD:DP:GL:GQ	0/1:12,7:13:-10.19,-3.92,-36.97:62.71
+chr1	2103132	.	T	G	33.73	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=2;HaplotypeScore=13.23;MQ=58.26;MQ0=0;QD=0.50;SB=77.26	GT:AD:DP:GL:GQ	0/1:40,27:45:-20.22,-13.56,-132.60:66.56
+chr1	2103519	.	T	G	34.88	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=1;HaplotypeScore=24.16;MQ=56.69;MQ0=0;QD=0.66;SB=65.20	GT:AD:DP:GL:GQ	0/1:32,21:34:-17.01,-10.24,-99.26:67.71
+chr1	2110321	rs12145923	A	C	0.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=12.44;MQ=52.00;MQ0=0;OQ=558.55;QD=9.01;SB=-276.83	GT:AD:DP:GL:GQ	0/1:36,25:56:-76.01,-16.87,-110.27:99
+chr1	2119788	.	T	C	18.51	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=3;HaplotypeScore=2.86;MQ=58.76;MQ0=0;QD=0.33;SB=56.21	GT:AD:DP:GL:GQ	0/1:41,15:42:-17.79,-12.66,-139.27:51.28
+chr1	2129255	.	C	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=12.54;MQ=53.09;MQ0=0;OQ=134.48;QD=3.96;SB=-44.78	GT:AD:DP:GL:GQ	0/1:28,6:25:-24.27,-7.54,-83.09:99
+chr1	2130727	.	C	A	3.24	PASS	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=883.89;QD=21.05;SB=-232.51	GT:AD:DP:GL:GQ	0/1:13,29:42:-104.32,-12.65,-47.37:99
+chr1	2133967	rs2503715	A	G	158.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=60.00;MQ0=0;OQ=295.10;QD=12.30;SB=-168.37	GT:AD:DP:GL:GQ	0/1:13,11:24:-40.02,-7.23,-52.87:99
+chr1	2146787	.	G	T	26.55	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=20;HaplotypeScore=12.86;MQ=49.19;MQ0=1;QD=0.48;SB=62.22	GT:AD:DP:GL:GQ	0/1:43,12:38:-17.39,-11.45,-117.88:59.38
+chr1	2157661	.	T	G	18.80	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=2;HaplotypeScore=22.82;MQ=58.47;MQ0=0;QD=0.32;SB=110.33	GT:AD:DP:GL:GQ	0/1:45,13:50:-20.22,-15.06,-154.85:51.58
+chr1	2158219	.	G	A	102.84	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=58.11;MQ0=0;OQ=732.58;QD=15.59;SB=-362.51	GT:AD:DP:GL:GQ	0/1:23,24:45:-90.10,-13.56,-76.34:99
+chr1	2159397	.	G	A	168.87	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=557.34;QD=13.59;SB=-169.24	GT:AD:DP:GL:GQ	0/1:23,18:39:-70.77,-11.75,-72.68:99
+chr1	2162698	rs55996607	T	A	417.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=618.41;QD=12.13;SB=-230.72	GT:AD:DP:GL:GQ	0/1:28,23:50:-80.19,-15.06,-104.77:99
+chr1	2164572	rs263525	T	C	240.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=58.19;MQ0=0;OQ=1470.94;QD=30.02;SB=-709.84	GT:AD:DP:GL:GQ	1/1:0,49:48:-150.72,-14.48,-0.04:99
+chr1	2166877	rs4648817	C	T	227.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=42.45;MQ0=0;OQ=888.81;QD=15.06;SB=-258.26	GT:AD:DP:GL:GQ	0/1:29,28:53:-108.14,-15.97,-85.30:99
+chr1	2167087	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=78;Dels=0.03;HRun=20;HaplotypeScore=33.19;MQ=45.08;MQ0=3;OQ=60.74;QD=0.78;SB=86.28	GT:AD:DP:GL:GQ	0/1:57,18:48:-23.51,-14.16,-146.86:93.57
+chr1	2172859	rs55827021	G	A	215.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=60.00;MQ0=0;OQ=711.82;QD=15.47;SB=-343.87	GT:AD:DP:GL:GQ	0/1:21,25:42:-87.13,-12.66,-66.29:99
+chr1	2181828	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=5;HaplotypeScore=57.83;MQ=51.68;MQ0=2;OQ=160.28;QD=2.32;SB=74.25	GT:AD:DP:GL:GQ	0/1:46,21:51:-34.38,-15.07,-143.28:99
+chr1	2181834	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=20;HaplotypeScore=10.75;MQ=49.92;MQ0=3;OQ=651.07;QD=8.57;SB=86.24	GT:AD:DP:GL:GQ	0/1:47,28:67:-88.59,-20.20,-142.58:99
+chr1	2190201	rs4648625	G	T	81.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.89;MQ=59.03;MQ0=0;OQ=1500.00;QD=34.88;SB=-738.07	GT:AD:DP:GL:GQ	1/1:0,43:43:-153.60,-12.95,-0.02:99
+chr1	2194650	rs4648819	G	A	133.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=743.48;QD=16.52;SB=-314.80	GT:AD:DP:GL:GQ	0/1:22,23:44:-90.89,-13.26,-76.95:99
+chr1	2200056	rs55778641	A	C	21.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=4.74;MQ=60.00;MQ0=0;OQ=608.53;QD=12.95;SB=-87.63	GT:AD:DP:GL:GQ	0/1:21,26:44:-77.39,-13.25,-77.32:99
+chr1	2201955	.	C	T	11.73	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=16.61;MQ=30.48;MQ0=8;QD=0.49;SB=-3.98	GT:AD:DP:GL:GQ	0/1:18,6:8:-6.84,-2.41,-19.02:44.27
+chr1	2202003	.	A	G	11.74	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=1;HaplotypeScore=7.13;MQ=18.21;MQ0=12;QD=0.30;SB=-3.98	GT:AD:DP:GL:GQ	0/1:31,8:9:-7.14,-2.71,-26.71:44.28
+chr1	2202019	.	C	A	24.05	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=18.13;MQ0=6;QD=1.05;SB=-6.99	GT:AD:DP:GL:GQ	0/1:15,8:6:-7.50,-1.81,-11.06:56.87
+chr1	2202047	.	A	G	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=10.59;MQ=18.96;MQ0=8;OQ=148.17;QD=5.93;SB=-3.98	GT:AD:DP:GL:GQ	0/1:17,8:9:-20.81,-2.71,-12.59:98.81
+chr1	2202060	.	C	T	1.87	PASS	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=16.70;MQ0=15;OQ=178.09;QD=5.94;SB=-4.00	GT:AD:DP:GL:GQ	0/1:17,12:9:-23.81,-2.71,-8.44:57.22
+chr1	2202081	.	C	T	18.49	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=39;Dels=0.03;HRun=0;HaplotypeScore=43.99;MQ=16.84;MQ0=21;QD=0.47;SB=-6.99	GT:AD:DP:GL:GQ	0/1:31,7:8:-7.54,-2.41,-18.75:51.27
+chr1	2202085	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=40;Dels=0.03;HRun=0;HaplotypeScore=35.15;MQ=14.59;MQ0=24;OQ=74.01;QD=1.85;SB=-48.55	GT:AD:DP:GL:GQ	0/1:30,9:6:-12.50,-1.81,-8.79:69.79
+chr1	2202103	.	C	T	23.47	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=12.67;MQ=15.94;MQ0=20;QD=0.57;SB=-6.99	GT:AD:DP:GL:GQ	0/1:31,9:7:-7.74,-2.11,-15.15:56.28
+chr1	2202167	.	C	A	13.22	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=1;HaplotypeScore=11.12;MQ=8.91;MQ0=36;QD=0.22;SB=-10.00	GT:AD:DP:GL:GQ	0/1:51,9:4:-5.79,-1.21,-5.41:41.98
+chr1	2202296	.	C	A	18.94	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=1;HaplotypeScore=9.91;MQ=10.32;MQ0=37;QD=0.39;SB=-10.00	GT:AD:DP:GL:GQ	0/1:36,13:6:-6.98,-1.81,-13.53:51.72
+chr1	2202348	.	A	G	10.17	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=23.55;MQ=13.35;MQ0=40;QD=0.15;SB=-25.65	GT:AD:DP:GL:GQ	0/1:57,8:7:-6.37,-2.11,-18.82:42.57
+chr1	2202364	.	C	T	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=20.33;MQ0=13;OQ=62.56;QD=1.49;SB=-32.09	GT:AD:DP:GL:GQ	0/1:34,6:7:-15.23,-5.69,-14.13:84.42
+chr1	2202391	.	A	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=5.05;MQ=22.23;MQ0=9;OQ=175.98;QD=4.09;SB=-54.84	GT:AD:DP:GL:GQ	0/1:26,17:18:-26.30,-5.42,-41.13:99
+chr1	2202434	.	A	G	21.78	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=15.47;MQ=13.87;MQ0=17;QD=0.81;SB=-34.93	GT:AD:DP:GL:GQ	0/1:19,8:5:-6.97,-1.51,-11.89:54.59
+chr1	2202602	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=59.56;MQ=10.62;MQ0=43;OQ=145.43;QD=2.24;SB=-6.99	GT:AD:DP:GL:GQ	0/1:30,35:7:-19.94,-2.11,-6.77:46.57
+chr1	2202632	.	G	T	82.62	HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=11.21;MQ0=49;QD=1.18;SB=-10.00	GT:AD:DP:GL:GQ	0/1:61,9:9:-14.26,-2.71,-18.59:99
+chr1	2202667	.	A	C	16.33	DPFilter;HARD_TO_VALIDATE;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=25.34;MQ=10.07;MQ0=49;QD=0.22;SB=8.05	GT:AD:DP:GL:GQ	0/1:64,9:8:-7.32,-2.41,-22.67:49.06
+chr1	2202682	.	G	A	36.23	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=78.01;MQ=9.70;MQ0=44;QD=0.48;SB=-3.98	GT:AD:DP:GL:GQ	0/1:63,12:4:-8.11,-1.20,-7.39:61.88
+chr1	2202686	.	G	A	35.24	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=79.87;MQ=9.88;MQ0=42;QD=0.50;SB=-3.99	GT:AD:DP:GL:GQ	0/1:59,12:4:-8.01,-1.21,-5.99:47.86
+chr1	2202707	.	C	T	38.48	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=10.09;MQ=9.21;MQ0=26;QD=0.82;SB=-10.00	GT:AD:DP:GL:GQ	0/1:44,3:4:-8.34,-1.21,-5.59:43.85
+chr1	2202728	.	T	C	26.83	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=9.84;MQ=8.94;MQ0=16;QD=1.07;SB=-10.00	GT:AD:DP:GL:GQ	1/1:12,12:2:-6.09,-0.60,-0.00:6.01
+chr1	2202823	.	G	A	38.25	LowQual	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=1;HaplotypeScore=5.28;MQ=19.51;MQ0=2;QD=3.82;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,8:3:-8.01,-0.90,-3.57:26.65
+chr1	2203054	.	A	C	12.92	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=9.60;MQ0=26;QD=0.31;SB=-27.98	GT:AD:DP:GL:GQ	0/1:36,6:4:-5.76,-1.21,-6.84:45.53
+chr1	2203334	.	C	T	27.36	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=7.10;MQ=12.34;MQ0=21;QD=0.94;SB=-37.65	GT:AD:DP:GL:GQ	0/1:21,8:4:-7.23,-1.21,-5.77:45.59
+chr1	2203377	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=20.17;MQ=13.03;MQ0=22;OQ=140.31;QD=3.79;SB=-42.53	GT:AD:DP:GL:GQ	0/1:23,14:7:-19.42,-2.11,-7.14:50.30
+chr1	2203636	.	C	T	0.06	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=18.31;MQ0=12;OQ=75.25;QD=2.03;SB=-3.99	GT:AD:DP:GL:GQ	0/1:28,9:19:-16.53,-5.73,-47.88:99
+chr1	2203679	rs2643914	C	T	0.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=6.14;MQ=18.30;MQ0=12;OQ=93.96;QD=1.92;SB=-63.48	GT:AD:DP:GL:GQ	0/1:36,12:24:-19.91,-7.23,-64.90:99
+chr1	2203718	rs2645079	T	C	32.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.98;MQ0=8;OQ=123.75;QD=3.75;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,20:15:-20.18,-4.52,-29.86:99
+chr1	2203765	rs12117574	T	C	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=5.02;MQ=32.99;MQ0=11;OQ=133.28;QD=2.18;SB=-88.55	GT:AD:DP:GL:GQ	0/1:50,11:38:-28.07,-11.46,-111.19:99
+chr1	2204009	.	C	G	47.74	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=47.05;MQ0=0;OQ=366.61;QD=8.94;SB=-120.51	GT:AD:DP:GL:GQ	0/1:27,14:39:-51.71,-11.77,-108.96:99
+chr1	2206228	rs4648821	T	G	261.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.19;MQ0=0;OQ=657.01;QD=12.63;SB=-349.05	GT:AD:DP:GL:GQ	0/1:29,23:51:-84.34,-15.36,-102.93:99
+chr1	2206251	rs6689315	A	G	495.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.86;MQ0=0;OQ=794.59;QD=13.94;SB=-403.30	GT:AD:DP:GL:GQ	0/1:29,28:56:-99.61,-16.87,-113.15:99
+chr1	2206925	rs61759158	G	A	51.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=54.01;MQ0=0;OQ=371.96;QD=12.40;SB=-7.00	GT:AD:DP:GL:GQ	0/1:17,13:28:-48.92,-8.45,-48.51:99
+chr1	2207673	.	G	C	46.34	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=3;HaplotypeScore=11.90;MQ=55.68;MQ0=0;QD=1.03;SB=71.27	GT:AD:DP:GL:GQ	0/1:33,12:36:-18.77,-10.85,-141.59:79.18
+chr1	2207894	.	C	T	62.11	PASS	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=0;HaplotypeScore=3.51;MQ=60.00;MQ0=0;OQ=1408.04;QD=16.96;SB=-562.41	GT:AD:DP:GL:GQ	0/1:38,45:79:-167.91,-23.82,-117.96:99
+chr1	2208688	rs10910049	G	T	213.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=47.61;MQ0=2;OQ=399.96;QD=8.89;SB=-196.49	GT:AD:DP:GL:GQ	0/1:28,17:40:-55.33,-12.05,-79.33:99
+chr1	2208825	rs6691983	C	T	81.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.59;MQ=52.03;MQ0=1;OQ=657.40;QD=17.30;SB=-233.73	GT:AD:DP:GL:GQ	0/1:18,20:35:-79.57,-10.55,-49.20:99
+chr1	2208828	rs6682474	G	A	54.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.33;MQ=53.40;MQ0=1;OQ=696.36;QD=18.33;SB=-278.18	GT:AD:DP:GL:GQ	0/1:17,21:37:-84.07,-11.15,-57.35:99
+chr1	2209299	rs56051051	T	G	55.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=58.49;MQ0=0;OQ=442.31;QD=9.41;SB=-244.75	GT:AD:DP:GL:GQ	0/1:22,25:42:-60.17,-12.66,-79.16:99
+chr1	2209740	rs17372827	A	C	232.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=877.78;QD=13.10;SB=-279.93	GT:AD:DP:GL:GQ	0/1:36,31:66:-110.94,-19.88,-129.70:99
+chr1	2209930	rs4648823	T	A	295.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=59.11;MQ0=0;OQ=697.00;QD=13.40;SB=-278.32	GT:AD:DP:GL:GQ	0/1:27,24:50:-88.05,-15.06,-97.62:99
+chr1	2210285	rs2643884	T	C	4	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=5.32;MQ=58.60;MQ0=0;OQ=1465.33;QD=29.31;SB=-698.59	GT:AD:DP:GL:GQ	1/1:0,50:47:-150.17,-14.18,-0.05:99
+chr1	2210377	rs1039065	A	C	393.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.65;MQ0=0;OQ=1107.46;QD=29.14;SB=-383.86	GT:AD:DP:GL:GQ	1/1:0,38:36:-114.37,-10.85,-0.04:99
+chr1	2210509	rs2017143	C	T	306.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.15;MQ0=0;OQ=1280.02;QD=38.79;SB=-395.53	GT:AD:DP:GL:GQ	1/1:0,33:33:-131.60,-9.94,-0.01:99
+chr1	2211082	rs2643885	A	C	289.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.73;MQ0=0;OQ=1017.95;QD=35.10;SB=-113.02	GT:AD:DP:GL:GQ	1/1:0,29:29:-105.39,-8.74,-0.01:87.26
+chr1	2211133	rs2843166	C	A	247.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.20;MQ0=0;OQ=767.67;QD=31.99;SB=-111.83	GT:AD:DP:GL:GQ	1/1:0,24:23:-80.36,-6.93,-0.01:69.19
+chr1	2211394	rs903924	A	G	577.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=1710.61;QD=33.54;SB=-819.09	GT:AD:DP:GL:GQ	1/1:0,51:49:-174.66,-14.76,-0.02:99
+chr1	2211494	rs903923	G	C	2.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=5.22;MQ=56.20;MQ0=0;OQ=1828.69;QD=36.57;SB=-846.47	GT:AD:DP:GL:GQ	1/1:0,50:45:-186.48,-13.57,-0.02:99
+chr1	2211496	rs903922	A	T	57.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.95;MQ=56.42;MQ0=0;OQ=1691.54;QD=31.92;SB=-801.63	GT:AD:DP:GL:GQ	1/1:0,53:49:-172.77,-14.77,-0.03:99
+chr1	2211936	rs903921	G	A	86.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=57.20;MQ0=0;OQ=1373.97;QD=32.71;SB=-609.72	GT:AD:DP:GL:GQ	1/1:1,40:39:-143.60,-11.76,-2.62:91.42
+chr1	2212420	rs903920	A	G	98.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.39;MQ0=0;OQ=1274.47;QD=33.54;SB=-555.35	GT:AD:DP:GL:GQ	1/1:0,38:37:-131.05,-11.15,-0.02:99
+chr1	2212443	rs903919	T	C	439.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=897.63;QD=27.20;SB=-373.47	GT:AD:DP:GL:GQ	1/1:0,33:30:-93.38,-9.05,-0.03:90.19
+chr1	2212983	rs2172900	T	C	377	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1306.72;QD=32.67;SB=-161.75	GT:AD:DP:GL:GQ	1/1:0,40:40:-134.28,-12.05,-0.02:99
+chr1	2213118	rs2132303	T	C	18.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.55;MQ0=0;OQ=1347.55;QD=32.08;SB=-116.87	GT:AD:DP:GL:GQ	1/1:0,41:39:-138.35,-11.75,-0.01:99
+chr1	2214142	rs903617	A	G	32.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.29;MQ=58.97;MQ0=0;OQ=1261.61;QD=28.04;SB=-567.89	GT:AD:DP:GL:GQ	1/1:0,45:41:-129.80,-12.38,-0.05:99
+chr1	2214469	rs2643886	T	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=5;HaplotypeScore=4.66;MQ=57.70;MQ0=0;OQ=1258.31;QD=26.77;SB=-451.03	GT:AD:DP:GL:GQ	1/1:1,46:38:-129.44,-11.45,-0.02:99
+chr1	2214505	rs2645091	A	G	160.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=58.58;MQ0=0;OQ=1430.84;QD=31.11;SB=-424.25	GT:AD:DP:GL:GQ	1/1:0,46:44:-146.70,-13.26,-0.03:99
+chr1	2214736	rs10910050	A	C	929.01	Indel	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=9;HaplotypeScore=4.06;MQ=59.20;MQ0=0;QD=27.32;SB=-435.82	GT:AD:DP:GL:GQ	1/1:1,33:28:-96.50,-8.43,-0.01:84.23
+chr1	2215144	rs1532385	G	A	183.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=59.56;MQ0=0;OQ=1969.69;QD=37.88;SB=-987.83	GT:AD:DP:GL:GQ	1/1:1,51:50:-200.57,-15.06,-0.01:99
+chr1	2216193	rs903918	T	A	121.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=60.00;MQ0=0;OQ=1515.17;QD=34.44;SB=-696.39	GT:AD:DP:GL:GQ	1/1:0,44:41:-155.11,-12.35,-0.01:99
+chr1	2216414	.	T	G	45.79	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=2;HaplotypeScore=10.58;MQ=58.61;MQ0=0;QD=0.68;SB=86.26	GT:AD:DP:GL:GQ	0/1:37,30:42:-20.52,-12.66,-118.85:78.63
+chr1	2217282	rs2843163	C	T	190.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=4.18;MQ=57.17;MQ0=0;OQ=844.33;QD=16.89;SB=-357.35	GT:AD:DP:GL:GQ	0/1:22,28:45:-101.28,-13.56,-64.72:99
+chr1	2217535	rs56117572	A	C	228.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=59.71;MQ0=0;OQ=819.93;QD=12.61;SB=-293.99	GT:AD:DP:GL:GQ	0/1:33,32:61:-103.65,-18.38,-105.35:99
+chr1	2219307	rs2643888	A	G	69.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=2.64;MQ=59.39;MQ0=0;OQ=1301.49;QD=34.25;SB=-624.24	GT:AD:DP:GL:GQ	1/1:0,38:38:-133.76,-11.45,-0.02:99
+chr1	2219413	rs2843161	C	T	101.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=1668.32;QD=37.92;SB=-845.15	GT:AD:DP:GL:GQ	1/1:0,44:43:-170.43,-12.96,-0.01:99
+chr1	2219777	.	C	T	48.76	PASS	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=3.44;MQ=59.45;MQ0=0;OQ=599.56;QD=14.28;SB=-283.32	GT:AD:DP:GL:GQ	0/1:19,21:37:-74.40,-11.16,-63.66:99
+chr1	2220425	rs56341331	C	G	57.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.43;MQ=59.52;MQ0=0;OQ=468.59;QD=12.02;SB=-132.55	GT:AD:DP:GL:GQ	0/1:23,16:35:-60.70,-10.56,-79.04:99
+chr1	2221427	rs1809823	G	T	87.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=59.54;MQ0=0;OQ=673.61;QD=16.43;SB=-228.53	GT:AD:DP:GL:GQ	0/1:18,23:40:-82.70,-12.05,-57.34:99
+chr1	2221826	rs55710545	G	C	290.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.48;MQ0=0;OQ=503.65;QD=11.45;SB=-276.95	GT:AD:DP:GL:GQ	0/1:26,18:42:-66.31,-12.67,-107.95:99
+chr1	2223172	rs903618	A	G	139.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1447.93;QD=30.17;SB=-664.81	GT:AD:DP:GL:GQ	1/1:0,48:47:-148.43,-14.18,-0.05:99
+chr1	2224111	rs1496555	A	G	103.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=57.88;MQ0=0;OQ=1360.32;QD=32.39;SB=-504.48	GT:AD:DP:GL:GQ	1/1:0,42:39:-139.63,-11.75,-0.01:99
+chr1	2224763	rs2256178	C	T	433.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=665.60;QD=16.23;SB=-342.52	GT:AD:DP:GL:GQ	0/1:20,21:41:-82.21,-12.37,-61.19:99
+chr1	2225516	rs11577387	G	A	98.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=58.87;MQ0=0;OQ=626.11;QD=16.92;SB=-209.93	GT:AD:DP:GL:GQ	0/1:17,20:32:-75.54,-9.65,-40.72:99
+chr1	2226199	rs4648825	T	C	63.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=3.65;MQ=59.17;MQ0=0;OQ=999.95;QD=17.24;SB=-492.13	GT:AD:DP:GL:GQ	0/1:22,36:55:-119.85,-16.57,-85.50:99
+chr1	2226557	rs2643904	A	G	112.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.91;MQ=59.50;MQ0=0;OQ=1489.85;QD=32.39;SB=-771.11	GT:AD:DP:GL:GQ	1/1:0,46:44:-152.59,-13.26,-0.02:99
+chr1	2226618	rs2843158	G	C	77.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=1399.75;QD=34.99;SB=-297.26	GT:AD:DP:GL:GQ	1/1:0,40:37:-143.60,-11.18,-0.04:99
+chr1	2227108	rs11580302	A	G	15.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.17;MQ=58.99;MQ0=0;OQ=1313.96;QD=28.56;SB=-483.14	GT:AD:DP:GL:GQ	1/1:0,46:42:-135.02,-12.67,-0.04:99
+chr1	2228420	.	T	C	34.45	PASS	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.20;MQ0=0;OQ=345.13;QD=11.90;SB=-158.70	GT:AD:DP:GL:GQ	0/1:16,13:29:-46.53,-8.74,-63.45:99
+chr1	2229866	rs2173049	T	C	234.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.01;MQ0=0;OQ=1791.17;QD=29.36;SB=-845.65	GT:AD:DP:GL:GQ	1/1:0,60:57:-182.75,-17.19,-0.05:99
+chr1	2230243	rs2843157	C	T	3.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=5.43;MQ=58.16;MQ0=0;OQ=293.03;QD=7.71;SB=-52.03	GT:AD:DP:GL:GQ	0/1:21,15:25:-40.13,-7.54,-43.56:99
+chr1	2233378	rs2843156	C	T	2.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.97;MQ0=0;OQ=1676.83;QD=39.00;SB=-476.64	GT:AD:DP:GL:GQ	1/1:0,43:42:-171.28,-12.65,-0.01:99
+chr1	2234765	rs2843154	C	T	245.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.42;MQ0=0;OQ=364.59;QD=11.39;SB=-94.60	GT:AD:DP:GL:GQ	0/1:19,13:29:-48.48,-8.74,-59.24:99
+chr1	2235081	rs2843153	C	T	158.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.00;MQ0=0;OQ=1550.87;QD=36.93;SB=-657.38	GT:AD:DP:GL:GQ	1/1:0,42:40:-158.69,-12.05,-0.01:99
+chr1	2235299	rs2643902	T	C	83.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=58.80;MQ0=0;OQ=1694.87;QD=26.90;SB=-805.69	GT:AD:DP:GL:GQ	1/1:0,63:54:-173.12,-16.28,-0.05:99
+chr1	2235430	rs2843152	C	G	36.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=1353.71;QD=36.59;SB=-455.86	GT:AD:DP:GL:GQ	1/1:0,37:35:-138.99,-10.57,-0.03:99
+chr1	2235493	rs2843151	C	T	341.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=1519.57;QD=37.99;SB=-552.74	GT:AD:DP:GL:GQ	1/1:0,40:39:-155.55,-11.75,-0.01:99
+chr1	2237259	rs2643903	T	C	68.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.78;MQ0=0;OQ=1099.17;QD=28.93;SB=-371.38	GT:AD:DP:GL:GQ	1/1:0,38:35:-113.53,-10.55,-0.03:99
+chr1	2237347	rs2645076	A	G	8.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=892.74;QD=27.90;SB=-347.40	GT:AD:DP:GL:GQ	1/1:0,32:29:-92.89,-8.75,-0.03:87.17
+chr1	2237604	rs2843150	G	C	105.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.39;MQ0=0;OQ=929.83;QD=32.06;SB=-483.10	GT:AD:DP:GL:GQ	1/1:0,29:23:-96.58,-6.93,-0.01:69.23
+chr1	2237845	rs2643905	T	C	349.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=1229.58;QD=32.36;SB=-467.52	GT:AD:DP:GL:GQ	1/1:0,38:37:-126.56,-11.15,-0.02:99
+chr1	2238243	rs60565777	G	T	1452.57	Indel	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.48;MQ0=0;QD=34.58;SB=-671.66	GT:AD:DP:GL:GQ	1/1:0,42:42:-148.86,-12.66,-0.02:99
+chr1	2238484	rs12035836	A	C	189.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.53;MQ0=0;OQ=471.85;QD=11.80;SB=-205.81	GT:AD:DP:GL:GQ	0/1:20,20:36:-61.31,-10.85,-64.85:99
+chr1	2239096	rs2645077	G	A	27.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=2;HaplotypeScore=1.28;MQ=59.32;MQ0=0;OQ=1136.46;QD=33.43;SB=-382.99	GT:AD:DP:GL:GQ	1/1:0,33:31:-117.25,-9.35,-0.02:93.28
+chr1	2241682	.	G	A	17.89	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=4.02;MQ=57.94;MQ0=0;OQ=417.19;QD=12.27;SB=-164.16	GT:AD:DP:GL:GQ	0/1:17,17:31:-54.36,-9.35,-49.53:99
+chr1	2243754	rs56393204	G	A	58.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=58.84;MQ0=0;OQ=282.27;QD=14.11;SB=-81.31	GT:AD:DP:GL:GQ	0/1:7,11:14:-35.73,-4.22,-15.87:99
+chr1	2244770	rs2645075	T	C	149.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.02;MQ0=0;OQ=1276.49;QD=27.75;SB=-655.75	GT:AD:DP:GL:GQ	1/1:0,46:42:-131.28,-12.68,-0.05:99
+chr1	2245871	rs2645074	A	G	281.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.11;MQ0=0;OQ=516.48;QD=10.99;SB=-220.38	GT:AD:DP:GL:GQ	0/1:24,23:43:-67.90,-12.97,-87.14:99
+chr1	2246105	rs2843148	A	T	522.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.70;MQ0=0;OQ=1342.05;QD=33.55;SB=-593.22	GT:AD:DP:GL:GQ	1/1:0,40:36:-137.80,-10.84,-0.01:99
+chr1	2246150	.	C	T	22.21	PASS	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=51.90;MQ0=0;OQ=477.24;QD=15.39;SB=-219.23	GT:AD:DP:GL:GQ	0/1:15,16:26:-58.85,-7.84,-34.36:99
+chr1	2246331	.	T	A	1.20	PASS	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=56.18;MQ0=0;OQ=642.82;QD=20.09;SB=-121.93	GT:AD:DP:GL:GQ	0/1:11,21:32:-77.21,-9.64,-40.89:99
+chr1	2246422	.	C	T	17.03	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=2;HaplotypeScore=46.69;MQ=32.60;MQ0=2;QD=0.46;SB=17.08	GT:AD:DP:GL:GQ	0/1:33,4:25:-12.51,-7.53,-79.77:49.78
+chr1	2246424	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=2;HaplotypeScore=54.85;MQ=32.43;MQ0=2;OQ=173.30;QD=4.56;SB=-18.60	GT:AD:DP:GL:GQ	0/1:26,12:25:-28.15,-7.53,-68.25:99
+chr1	2246439	rs9725291	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=64.95;MQ=33.89;MQ0=1;OQ=86.92;QD=2.12;SB=-39.19	GT:AD:DP:GL:GQ	0/1:33,8:25:-19.51,-7.53,-71.60:99
+chr1	2246445	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=1;HaplotypeScore=48.09;MQ=35.48;MQ0=0;OQ=216.97;QD=4.82;SB=-10.56	GT:AD:DP:GL:GQ	0/1:34,11:29:-33.72,-8.74,-70.74:99
+chr1	2246456	.	C	T	34.43	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=27.71;MQ=37.83;MQ0=0;QD=0.69;SB=1.58	GT:AD:DP:GL:GQ	0/1:43,7:33:-16.67,-9.94,-103.65:67.27
+chr1	2246469	.	T	C	28.75	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=49;Dels=0.02;HRun=2;HaplotypeScore=77.34;MQ=40.72;MQ0=0;QD=0.59;SB=44.16	GT:AD:DP:GL:GQ	0/1:38,10:28:-14.30,-8.14,-89.44:61.58
+chr1	2246471	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=2;HaplotypeScore=72.35;MQ=42.43;MQ0=0;OQ=76.08;QD=1.58;SB=-6.17	GT:AD:DP:GL:GQ	0/1:36,12:29:-19.64,-8.74,-87.84:99
+chr1	2246484	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=2;HaplotypeScore=51.65;MQ=47.04;MQ0=0;OQ=81.71;QD=2.15;SB=50.19	GT:AD:DP:GL:GQ	0/1:29,8:26:-19.29,-7.83,-83.08:99
+chr1	2246793	.	G	A	5.64	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=3.91;MQ=55.18;MQ0=1;OQ=1074.55;QD=18.53;SB=-560.61	GT:AD:DP:GL:GQ	0/1:23,35:54:-127.01,-16.27,-81.39:99
+chr1	2247067	rs35006635	C	A	47.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.81;MQ0=0;OQ=1074.59;QD=21.07;SB=-429.40	GT:AD:DP:GL:GQ	1/1:0,28:51:-197.40,-96.91,-86.36:99
+chr1	2247213	rs12566205	C	T	241.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=57.90;MQ0=0;OQ=759.24;QD=13.09;SB=-368.12	GT:AD:DP:GL:GQ	0/1:33,25:57:-96.39,-17.18,-106.07:99
+chr1	2247351	rs2643892	C	T	241.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.94;MQ0=0;OQ=665.97;QD=19.59;SB=-340.91	GT:AD:DP:GL:GQ	0/1:14,20:33:-79.82,-9.94,-42.88:99
+chr1	2247555	rs10910051	G	A	197.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=4.80;MQ=58.86;MQ0=0;OQ=1049.52;QD=16.15;SB=-447.98	GT:AD:DP:GL:GQ	0/1:31,34:61:-126.63,-18.39,-90.57:99
+chr1	2247587	rs2643893	C	T	300.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=58.44;MQ0=0;OQ=2112.94;QD=35.22;SB=-1052.32	GT:AD:DP:GL:GQ	1/1:0,60:56:-214.91,-16.88,-0.03:99
+chr1	2247723	rs2645092	C	T	700.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=2085.22;QD=38.62;SB=-998.04	GT:AD:DP:GL:GQ	1/1:0,54:53:-212.12,-15.97,-0.01:99
+chr1	2247791	rs2645093	G	A	189.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=60.00;MQ0=0;OQ=700.42;QD=15.92;SB=-289.76	GT:AD:DP:GL:GQ	0/1:22,22:42:-85.99,-12.66,-67.45:99
+chr1	2248183	rs2643894	C	T	135.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=57.95;MQ0=0;OQ=1940.09;QD=35.27;SB=-797.32	GT:AD:DP:GL:GQ	1/1:0,55:52:-197.62,-15.67,-0.03:99
+chr1	2248333	rs2643895	G	A	408.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=2697.00;QD=39.09;SB=-1222.14	GT:AD:DP:GL:GQ	1/1:0,69:68:-273.30,-20.48,-0.02:99
+chr1	2248552	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.80;MQ=51.38;MQ0=0;OQ=50.72;QD=0.83;SB=23.47	GT:AD:DP:GL:GQ	0/1:53,7:56:-28.20,-19.84,-214.64:83.56
+chr1	2248554	.	G	A	35.21	LowQual	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=3;HaplotypeScore=5.80;MQ=51.10;MQ0=0;QD=0.57;SB=-8.06	GT:AD:DP:GL:GQ	0/1:56,6:58:-24.27,-17.47,-188.51:68.04
+chr1	2248658	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=56.92;MQ0=0;OQ=60.63;QD=0.88;SB=6.91	GT:AD:DP:GL:GQ	0/1:61,8:68:-29.84,-20.49,-240.21:93.47
+chr1	2249886	.	C	T	54.96	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=-0.12;MQ=60.00;MQ0=0;OQ=750.55;QD=14.72;SB=-348.88	GT:AD:DP:GL:GQ	0/1:25,26:44:-91.61,-13.27,-61.40:99
+chr1	2249910	rs2645063	G	A	24.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=5.82;MQ=59.50;MQ0=0;OQ=758.18;QD=16.48;SB=-336.52	GT:AD:DP:GL:GQ	0/1:22,24:45:-92.67,-13.57,-67.35:99
+chr1	2250405	rs2645064	G	A	151.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=58.71;MQ0=0;OQ=569.60;QD=15.82;SB=-242.53	GT:AD:DP:GL:GQ	0/1:16,20:34:-70.49,-10.25,-54.37:99
+chr1	2251037	rs35273536	C	T	60.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=4.05;MQ=58.82;MQ0=0;OQ=1072.47;QD=18.18;SB=-334.93	GT:AD:DP:GL:GQ	0/1:24,34:52:-128.89,-18.36,-63.36:99
+chr1	2253264	.	T	C	16.56	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=51.77;MQ0=0;QD=2.76;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,2:6:-6.74,-1.81,-16.62:49.30
+chr1	2253282	.	C	G	16.92	PASS	AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=51.16;MQ0=0;OQ=118.58;QD=9.88;SB=-10.00	GT:AD:DP:GL:GQ	0/1:6,6:11:-18.46,-3.32,-24.69:99
+chr1	2253362	rs12752072	T	C	172.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=253.44;QD=12.07;SB=-10.00	GT:AD:DP:GL:GQ	0/1:10,11:21:-34.96,-6.33,-38.76:99
+chr1	2254886	rs2645066	G	A	78.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=5.62;MQ=59.17;MQ0=0;OQ=893.72;QD=15.96;SB=-436.47	GT:AD:DP:GL:GQ	0/1:25,31:52:-108.33,-15.67,-85.72:99
+chr1	2255036	rs2645067	T	C	87.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.60;MQ0=0;OQ=995.78;QD=33.19;SB=-523.42	GT:AD:DP:GL:GQ	1/1:0,30:29:-103.17,-8.74,-0.01:87.25
+chr1	2255079	rs2643898	C	T	28.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=5.95;MQ=59.03;MQ0=0;OQ=590.58;QD=13.73;SB=-262.25	GT:AD:DP:GL:GQ	0/1:23,20:42:-75.01,-12.66,-72.41:99
+chr1	2255654	rs7546567	G	A	132.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.73;MQ0=0;OQ=454.68;QD=13.78;SB=-126.36	GT:AD:DP:GL:GQ	0/1:16,16:32:-61.47,-12.72,-52.76:99
+chr1	2255829	rs2843146	T	G	0.05	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=441.34;QD=27.58;SB=-113.02	GT:AD:DP:GL:GQ	1/1:0,16:14:-47.73,-4.22,-0.01:42.10
+chr1	2255938	rs2643899	T	C	18.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=58.69;MQ0=0;OQ=756.05;QD=23.63;SB=-323.76	GT:AD:DP:GL:GQ	1/1:0,32:26:-79.22,-7.85,-0.03:78.14
+chr1	2256793	rs903905	C	T	99.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=58.29;MQ0=0;OQ=354.28;QD=16.10;SB=-192.21	GT:AD:DP:GL:GQ	0/1:10,12:21:-45.05,-6.33,-27.84:99
+chr1	2258430	rs12091632	A	G	318.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=1030.69;QD=30.31;SB=-507.55	GT:AD:DP:GL:GQ	1/1:0,34:33:-106.69,-9.95,-0.03:99
+chr1	2258440	rs12085675	G	A	96.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.39;MQ0=0;OQ=1318.84;QD=34.71;SB=-520.68	GT:AD:DP:GL:GQ	1/1:0,37:35:-135.49,-10.55,-0.02:99
+chr1	2258510	rs28394874	C	G	5.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=4.06;MQ=57.77;MQ0=0;OQ=783.94;QD=18.67;SB=-330.90	GT:AD:DP:GL:GQ	0/1:17,25:36:-92.55,-10.88,-48.65:99
+chr1	2258528	rs35986070	A	G	102.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.27;MQ0=0;OQ=457.65;QD=16.95;SB=-106.83	GT:AD:DP:GL:GQ	0/1:11,16:27:-57.18,-8.13,-41.35:99
+chr1	2258538	rs2645069	T	C	177.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.13;MQ0=0;OQ=677.36;QD=27.09;SB=-198.05	GT:AD:DP:GL:GQ	1/1:0,25:23:-71.35,-6.94,-0.03:69.14
+chr1	2258598	rs2645070	A	G	16.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=60.00;MQ0=0;OQ=322.02;QD=18.94;SB=-156.34	GT:AD:DP:GL:GQ	0/1:4,13:17:-40.61,-5.13,-15.36:99
+chr1	2258651	rs2843145	A	G	4.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=3;HaplotypeScore=2.01;MQ=59.14;MQ0=0;OQ=426.64;QD=15.80;SB=-196.02	GT:AD:DP:GL:GQ	0/1:8,19:23:-52.88,-6.93,-31.12:99
+chr1	2258910	.	A	G	4.11	PASS	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=1;HaplotypeScore=4.17;MQ=58.13;MQ0=0;OQ=457.98;QD=13.09;SB=-246.31	GT:AD:DP:GL:GQ	0/1:17,18:33:-59.02,-9.94,-70.06:99
+chr1	2259759	rs2036085	T	C	103.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=626.01;QD=14.56;SB=-172.51	GT:AD:DP:GL:GQ	0/1:16,27:40:-77.94,-12.06,-63.91:99
+chr1	2259869	rs12734736	C	T	347.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=60.00;MQ0=0;OQ=965.34;QD=16.64;SB=-492.13	GT:AD:DP:GL:GQ	0/1:29,29:54:-116.09,-16.28,-80.58:99
+chr1	2259958	rs2843142	A	G	263.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=2.46;MQ=59.76;MQ0=0;OQ=1095.49;QD=13.87;SB=-502.48	GT:AD:DP:GL:GQ	0/1:40,39:78:-136.33,-23.50,-157.46:99
+chr1	2261724	rs2843141	C	T	591.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=1956.29;QD=36.91;SB=-863.62	GT:AD:DP:GL:GQ	1/1:0,53:52:-199.24,-15.68,-0.03:99
+chr1	2262086	rs1472318	C	T	44.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=57.36;MQ0=0;OQ=484.27;QD=19.37;SB=-215.23	GT:AD:DP:GL:GQ	0/1:8,16:22:-58.34,-6.63,-21.67:99
+chr1	2262763	rs2843139	A	G	28.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=0.87;MQ=58.77;MQ0=0;OQ=1612.91;QD=30.43;SB=-829.43	GT:AD:DP:GL:GQ	1/1:0,53:52:-164.94,-15.69,-0.06:99
+chr1	2262883	.	G	A	16	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=49.61;MQ0=5;QD=0.44;SB=-17.46	GT:AD:DP:GL:GQ	0/1:28,8:25:-12.42,-7.54,-69.64:48.73
+chr1	2263004	rs12730050	A	G	0.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=14.25;MQ=55.46;MQ0=1;OQ=1032.60;QD=11.35;SB=-477.87	GT:AD:DP:GL:GQ	0/1:51,40:84:-131.86,-25.32,-172.18:99
+chr1	2263146	rs2843138	T	C	3.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.02;HRun=0;HaplotypeScore=5.34;MQ=54.41;MQ0=0;OQ=1335.96;QD=29.04;SB=-625.83	GT:AD:DP:GL:GQ	1/1:0,44:44:-137.23,-12.97,-0.04:99
+chr1	2263291	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=4;HaplotypeScore=15.31;MQ=57.02;MQ0=0;OQ=65.39;QD=1.72;SB=65.25	GT:AD:DP:GL:GQ	0/1:31,7:33:-19.78,-9.96,-120.76:98.22
+chr1	2263292	.	A	G	14.86	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.96;MQ=57.52;MQ0=0;QD=0.41;SB=62.21	GT:AD:DP:GL:GQ	0/1:29,6:31:-14.10,-9.35,-99.44:47.55
+chr1	2263765	rs1472319	T	C	33.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=3.68;MQ=59.72;MQ0=0;OQ=1846.27;QD=27.56;SB=-842.46	GT:AD:DP:GL:GQ	1/1:0,67:60:-188.28,-18.10,-0.07:99
+chr1	2264170	rs12735747	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=4;HaplotypeScore=15.88;MQ=53.27;MQ0=1;OQ=600.98;QD=16.24;SB=-322.72	GT:AD:DP:GL:GQ	0/1:17,20:33:-73.32,-9.94,-46.93:99
+chr1	2264171	rs12740557	T	A	0.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=15.88;MQ=53.27;MQ0=1;OQ=596.15;QD=16.11;SB=-294.37	GT:AD:DP:GL:GQ	0/1:17,20:33:-72.84,-9.94,-48.77:99
+chr1	2264298	rs61288374	A	G	10.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=4.66;MQ=58.45;MQ0=0;OQ=219.39;QD=7.31;SB=-3.98	GT:AD:DP:GL:GQ	0/1:16,13:26:-33.06,-7.84,-58.70:99
+chr1	2264816	rs4648828	G	A	38.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.55;MQ=58.44;MQ0=0;OQ=661.80;QD=16.97;SB=-286.79	GT:AD:DP:GL:GQ	0/1:17,22:36:-80.32,-10.86,-47.76:99
+chr1	2264998	rs4648829	C	T	229.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.45;MQ0=0;OQ=171.83;QD=11.46;SB=-76.07	GT:AD:DP:GL:GQ	0/1:9,6:13:-24.38,-3.92,-22.89:99
+chr1	2265236	rs4648830	T	G	6.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.55;MQ0=0;OQ=452.22;QD=28.26;SB=-174.97	GT:AD:DP:GL:GQ	1/1:0,16:15:-48.82,-4.52,-0.01:45.09
+chr1	2265809	rs2643909	C	G	56	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=57.02;MQ0=0;OQ=1592.56;QD=34.62;SB=-562.49	GT:AD:DP:GL:GQ	1/1:0,46:39:-162.87,-11.76,-0.03:99
+chr1	2265882	.	G	A	8.69	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.87;MQ0=0;OQ=753.33;QD=18.37;SB=-247.76	GT:AD:DP:GL:GQ	0/1:17,24:37:-89.77,-11.15,-48.26:99
+chr1	2265933	.	T	C	0.10	PASS	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=3;HaplotypeScore=2.25;MQ=58.59;MQ0=0;OQ=218.96;QD=6.64;SB=-11.87	GT:AD:DP:GL:GQ	0/1:21,12:30:-34.22,-9.04,-78.51:99
+chr1	2266056	rs11589063	C	A	17.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=3.57;MQ=58.25;MQ0=0;OQ=453.86;QD=11.35;SB=-250.27	GT:AD:DP:GL:GQ	0/1:23,17:40:-60.72,-12.05,-77.71:99
+chr1	2266060	rs2843137	T	A	278.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=57.66;MQ0=0;OQ=421.83;QD=10.55;SB=-226.71	GT:AD:DP:GL:GQ	0/1:23,17:37:-56.61,-11.15,-79.80:99
+chr1	2266231	rs11589451	C	A	57.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=5.26;MQ=58.41;MQ0=0;OQ=597.75;QD=10.67;SB=-255.49	GT:AD:DP:GL:GQ	0/1:32,24:50:-78.13,-15.07,-90.69:99
+chr1	2266279	rs11590175	A	G	185.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.15;MQ0=0;OQ=537.72;QD=10.97;SB=-262.22	GT:AD:DP:GL:GQ	0/1:22,25:41:-69.42,-12.37,-72.12:99
+chr1	2266621	.	G	A	34.89	PASS	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=3.35;MQ=59.21;MQ0=0;OQ=474.72;QD=13.56;SB=-211.70	GT:AD:DP:GL:GQ	0/1:17,18:29:-59.50,-8.75,-41.35:99
+chr1	2267026	.	G	A	47.30	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.99;MQ0=0;OQ=613.73;QD=16.59;SB=-254.78	GT:AD:DP:GL:GQ	0/1:17,20:34:-74.91,-10.25,-50.44:99
+chr1	2267073	.	T	C	188.99	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.75;MQ0=0;OQ=394.61;QD=9.87;SB=-211.55	GT:AD:DP:GL:GQ	0/1:22,18:38:-54.20,-11.45,-84.44:99
+chr1	2267410	rs61762093	G	C	176.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.35;MQ=56.22;MQ0=0;OQ=747.58;QD=15.26;SB=-308.18	GT:AD:DP:GL:GQ	0/1:27,22:44:-91.30,-13.26,-97.18:99
+chr1	2267687	rs2843134	G	A	624.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=2217.24;QD=36.95;SB=-1015.91	GT:AD:DP:GL:GQ	1/1:0,60:58:-225.33,-17.48,-0.02:99
+chr1	2267975	rs12409523	G	C	1.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=5.47;MQ=59.03;MQ0=0;OQ=822.23;QD=17.13;SB=-209.63	GT:AD:DP:GL:GQ	0/1:24,24:46:-99.39,-13.88,-93.78:99
+chr1	2268100	rs2132595	C	T	240.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.35;MQ0=0;OQ=844.37;QD=16.56;SB=-387.19	GT:AD:DP:GL:GQ	0/1:23,28:47:-101.89,-14.17,-71.24:99
+chr1	2268508	rs2843133	A	G	0.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=4;HaplotypeScore=2.38;MQ=57.65;MQ0=0;OQ=995.04;QD=26.19;SB=-340.62	GT:AD:DP:GL:GQ	1/1:0,38:30:-103.10,-9.04,-0.01:90.24
+chr1	2268841	rs2643910	C	T	6.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=3.07;MQ=58.25;MQ0=0;OQ=784.65;QD=19.62;SB=-334.39	GT:AD:DP:GL:GQ	0/1:16,24:39:-93.50,-11.75,-52.91:99
+chr1	2269677	rs56030548	C	T	80.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=57.12;MQ0=0;OQ=443.83;QD=15.85;SB=-131.12	GT:AD:DP:GL:GQ	0/1:13,15:27:-55.80,-8.14,-42.23:99
+chr1	2269999	rs35941092	C	T	0.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=8.68;MQ=48.71;MQ0=0;OQ=64.58;QD=4.61;SB=-21.48	GT:AD:DP:GL:GQ	0/1:10,4:14:-13.97,-4.23,-30.76:97.42
+chr1	2270100	.	T	A	5.69	PASS	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=56.04;MQ0=0;OQ=92.13;QD=5.12;SB=-47.85	GT:AD:DP:GL:GQ	0/1:13,5:18:-17.92,-5.42,-46.07:99
+chr1	2270283	rs2645072	A	C	0.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=4;HaplotypeScore=0.16;MQ=56.22;MQ0=0;OQ=963.23;QD=33.21;SB=-173.01	GT:AD:DP:GL:GQ	1/1:0,29:28:-99.92,-8.44,-0.01:84.24
+chr1	2270521	rs2055204	G	A	60.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=3.82;MQ=59.66;MQ0=0;OQ=983.74;QD=17.89;SB=-468.43	GT:AD:DP:GL:GQ	0/1:22,33:52:-117.32,-15.67,-79.90:99
+chr1	2271586	rs7527871	A	C	436.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=784.91;QD=12.08;SB=-319.01	GT:AD:DP:GL:GQ	0/1:36,29:64:-101.05,-19.28,-130.62:99
+chr1	2271838	rs1039063	T	G	2.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=5;HaplotypeScore=1.22;MQ=60.00;MQ0=0;OQ=495.93;QD=11.27;SB=-259.90	GT:AD:DP:GL:GQ	0/1:22,22:41:-65.23,-12.35,-74.62:99
+chr1	2271995	rs10910053	G	A	269.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=60.00;MQ0=0;OQ=928.57;QD=18.95;SB=-437.81	GT:AD:DP:GL:GQ	0/1:20,29:47:-110.30,-14.16,-67.66:99
+chr1	2272064	.	G	A	22.07	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.67;MQ=59.48;MQ0=0;OQ=676.05;QD=15.36;SB=-356.51	GT:AD:DP:GL:GQ	0/1:22,22:42:-83.55,-12.66,-69.45:99
+chr1	2272233	.	C	T	4.84	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=3.42;MQ=59.14;MQ0=0;OQ=912.77;QD=16.90;SB=-354.47	GT:AD:DP:GL:GQ	0/1:26,28:53:-110.53,-15.96,-92.85:99
+chr1	2272335	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=2.06;MQ=56.98;MQ0=0;OQ=124.90;QD=3.20;SB=56.19	GT:AD:DP:GL:GQ	0/1:24,15:32:-25.41,-9.64,-85.35:99
+chr1	2272540	rs2279704	C	T	249.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=59.55;MQ0=0;OQ=742.26;QD=14.55;SB=-245.76	GT:AD:DP:GL:GQ	0/1:25,25:47:-91.67,-14.16,-87.05:99
+chr1	2272636	rs2254874	G	C	9.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=3.74;MQ=56.62;MQ0=0;OQ=1562.16;QD=37.19;SB=-628.86	GT:AD:DP:GL:GQ	1/1:0,42:38:-159.82,-11.46,-0.02:99
+chr1	2272850	rs2036082	C	T	429.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=669.32;QD=14.55;SB=-278.20	GT:AD:DP:GL:GQ	0/1:25,21:46:-84.08,-13.87,-81.55:99
+chr1	2273702	rs2643912	G	T	414.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=338.96;QD=15.41;SB=-195.57	GT:AD:DP:GL:GQ	0/1:9,13:21:-43.50,-6.33,-31.88:99
+chr1	2273756	rs2840528	A	G	171.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.44;MQ0=0;OQ=666.96;QD=16.27;SB=-294.48	GT:AD:DP:GL:GQ	0/1:18,23:41:-82.33,-12.35,-70.40:99
+chr1	2273863	rs2645082	T	C	3.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=2.08;MQ=58.41;MQ0=0;OQ=1044.33;QD=23.73;SB=-369.45	GT:AD:DP:GL:GQ	1/1:0,44:35:-108.06,-10.56,-0.04:99
+chr1	2274055	rs3795272	T	C	1.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=3;HaplotypeScore=4.58;MQ=58.20;MQ0=0;OQ=382.95;QD=8.15;SB=-128.51	GT:AD:DP:GL:GQ	0/1:28,19:44:-54.84,-13.26,-106.89:99
+chr1	2274346	rs12049067	C	T	357.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=57.77;MQ0=0;OQ=508.21;QD=12.71;SB=-252.25	GT:AD:DP:GL:GQ	0/1:22,18:38:-65.56,-11.45,-75.12:99
+chr1	2274758	rs2840529	T	G	24.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=0.63;MQ=59.39;MQ0=0;OQ=311.73;QD=8.20;SB=-145.73	GT:AD:DP:GL:GQ	0/1:25,13:34:-44.70,-10.25,-72.81:99
+chr1	2275042	rs2036083	A	T	221.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.71;MQ=59.63;MQ0=0;OQ=509.88;QD=10.20;SB=-241.63	GT:AD:DP:GL:GQ	0/1:29,21:43:-67.22,-12.95,-90.87:99
+chr1	2275274	rs2843129	G	A	298.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.43;MQ0=0;OQ=2821.79;QD=38.65;SB=-1326.28	GT:AD:DP:GL:GQ	1/1:0,73:71:-285.78,-21.39,-0.02:99
+chr1	2276807	rs1039100	A	G	434.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1195.19;QD=31.45;SB=-467.43	GT:AD:DP:GL:GQ	1/1:0,38:36:-123.12,-10.85,-0.02:99
+chr1	2277377	rs2645083	T	C	625.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=1448.36;QD=34.48;SB=-607.22	GT:AD:DP:GL:GQ	1/1:0,42:42:-148.44,-12.65,-0.02:99
+chr1	2277394	rs11577374	C	T	128.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=58.95;MQ0=0;OQ=767.18;QD=17.44;SB=-322.88	GT:AD:DP:GL:GQ	0/1:20,24:40:-92.06,-12.06,-52.10:99
+chr1	2277476	rs2645085	T	C	300.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.58;MQ0=0;OQ=627.13;QD=11.40;SB=-216.37	GT:AD:DP:GL:GQ	0/1:27,28:51:-81.37,-15.38,-100.48:99
+chr1	2277708	rs16825067	G	C	15.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=3.52;MQ=58.92;MQ0=0;OQ=727.07;QD=18.64;SB=-379.89	GT:AD:DP:GL:GQ	0/1:17,22:37:-87.14,-11.15,-70.33:99
+chr1	2278607	rs2645086	T	C	275.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.11;MQ0=0;OQ=269.17;QD=10.35;SB=-101.72	GT:AD:DP:GL:GQ	0/1:13,13:25:-37.74,-7.54,-47.79:99
+chr1	2279110	rs903912	C	G	0.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=12.20;MQ=57.42;MQ0=0;OQ=679.10;QD=12.81;SB=-356.81	GT:AD:DP:GL:GQ	0/1:28,25:46:-85.06,-13.87,-109.25:99
+chr1	2279111	rs903913	T	C	0.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.02;HRun=1;HaplotypeScore=12.09;MQ=57.42;MQ0=0;OQ=643.89;QD=12.15;SB=-297.64	GT:AD:DP:GL:GQ	0/1:27,25:52:-83.04,-15.37,-108.03:99
+chr1	2279181	rs903914	G	A	327.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=59.27;MQ0=0;OQ=1113.86;QD=17.68;SB=-571.62	GT:AD:DP:GL:GQ	0/1:30,33:61:-133.06,-18.39,-88.20:99
+chr1	2280148	rs2840544	T	C	12.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=59.49;MQ0=0;OQ=176.15;QD=3.91;SB=-95.61	GT:AD:DP:GL:GQ	0/1:34,11:43:-33.87,-12.97,-121.04:99
+chr1	2280520	rs2645088	T	C	494.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=961.96;QD=28.29;SB=-437.29	GT:AD:DP:GL:GQ	1/1:0,34:31:-99.81,-9.35,-0.03:93.20
+chr1	2280750	rs2840543	C	T	201	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.69;MQ0=0;OQ=2174.81;QD=36.25;SB=-926.73	GT:AD:DP:GL:GQ	1/1:0,60:56:-221.09,-16.88,-0.02:99
+chr1	2280771	rs2645089	G	A	262.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=676.44;QD=13.53;SB=-331.88	GT:AD:DP:GL:GQ	0/1:29,21:47:-85.09,-14.16,-84.51:99
+chr1	2281127	rs6424093	A	G	144.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.16;MQ0=0;OQ=492.45;QD=11.73;SB=-156.68	GT:AD:DP:GL:GQ	0/1:23,19:40:-64.58,-12.05,-85.73:99
+chr1	2281540	rs2840542	T	C	309.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=56.56;MQ0=0;OQ=2607.54;QD=33.86;SB=-1074.11	GT:AD:DP:GL:GQ	1/1:0,77:73:-264.36,-21.99,-0.02:99
+chr1	2282015	rs2840541	T	C	311.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=585.20;QD=9.75;SB=-280.12	GT:AD:DP:GL:GQ	0/1:36,24:60:-79.89,-18.08,-145.26:99
+chr1	2282269	rs2645090	T	C	432.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=613.50;QD=9.16;SB=-290.16	GT:AD:DP:GL:GQ	0/1:38,29:64:-83.92,-19.29,-153.60:99
+chr1	2283026	rs2250799	G	A	138.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.62;MQ0=0;OQ=1864.73;QD=38.06;SB=-791.54	GT:AD:DP:GL:GQ	1/1:0,49:48:-190.08,-14.47,-0.02:99
+chr1	2284017	rs10797420	G	A	1.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=10.89;MQ=55.69;MQ0=1;OQ=1110.47;QD=17.63;SB=-493.05	GT:AD:DP:GL:GQ	0/1:28,34:55:-130.90,-16.57,-82.96:99
+chr1	2284704	rs55873848	C	T	485.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.27;MQ0=0;OQ=939.68;QD=16.78;SB=-471.48	GT:AD:DP:GL:GQ	0/1:26,30:53:-113.22,-15.97,-82.15:99
+chr1	2284890	rs7530501	T	G	19.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=5.02;MQ=57.51;MQ0=0;OQ=731.65;QD=13.80;SB=-124.84	GT:AD:DP:GL:GQ	0/1:25,28:51:-91.81,-15.36,-86.72:99
+chr1	2285068	rs57840322	G	A	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=6;HaplotypeScore=29.71;MQ=39.31;MQ0=0;OQ=1533.11;QD=35.65;SB=-660.69	GT:AD:DP:GL:GQ	1/1:0,43:40:-156.91,-12.05,-0.01:99
+chr1	2285112	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=42;Dels=0.05;HRun=7;HaplotypeScore=20.40;MQ=45.44;MQ0=0;OQ=661.72;QD=15.76;SB=-259.95	GT:AD:DP:GL:GQ	0/1:19,21:41:-81.21,-11.75,-63.70:99
+chr1	2285126	rs6682345	A	T	200.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=50.08;MQ0=0;OQ=1898.67;QD=35.16;SB=-880.24	GT:AD:DP:GL:GQ	1/1:1,53:53:-197.20,-15.96,-3.75:99
+chr1	2285128	rs6682346	A	T	359.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=50.28;MQ0=0;OQ=737.49;QD=13.41;SB=-376.75	GT:AD:DP:GL:GQ	0/1:30,25:55:-93.60,-16.56,-117.95:99
+chr1	2285638	rs10910055	A	C	76.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=3.44;MQ=49.97;MQ0=2;OQ=838.51;QD=11.65;SB=-398.65	GT:AD:DP:GL:GQ	0/1:39,33:60:-105.20,-18.07,-117.50:99
+chr1	2285783	rs12026746	C	T	166.61	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=27.98;MQ=27.61;MQ0=1;QD=3.54;SB=-10.00	GT:AD:DP:GL:GQ	0/1:32,15:30:-28.99,-9.05,-73.71:99
+chr1	2285784	.	A	G	712.90	SnpCluster	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=27.98;MQ=27.61;MQ0=1;QD=15.17;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,34:30:-83.61,-9.04,-20.49:99
+chr1	2285789	.	T	C	107.62	SnpCluster	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=51.95;MQ=27.67;MQ0=1;QD=2.20;SB=-10.00	GT:AD:DP:GL:GQ	0/1:37,12:31:-23.38,-9.34,-102.78:99
+chr1	2285797	.	C	T	99.87	SnpCluster	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=37.97;MQ=27.29;MQ0=3;QD=1.72;SB=-6.99	GT:AD:DP:GL:GQ	0/1:46,12:38:-24.73,-11.46,-107.35:99
+chr1	2285798	rs6685453	A	G	587.05	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=37.13;MQ=27.02;MQ0=4;QD=10.12;SB=-34.94	GT:AD:DP:GL:GQ	0/1:35,23:38:-73.44,-11.45,-64.40:99
+chr1	2285805	rs2840539	G	A	1277.62	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=29.98;MQ=27.32;MQ0=3;QD=21.65;SB=-159.63	GT:AD:DP:GL:GQ	0/1:13,46:41:-143.39,-12.35,-21.42:90.69
+chr1	2285956	rs7539098	A	T	36.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=32.84;MQ0=4;OQ=256.31;QD=4.93;SB=-97.36	GT:AD:DP:GL:GQ	0/1:30,22:31:-38.25,-9.34,-84.38:99
+chr1	2285957	rs7539099	A	T	39.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=32.84;MQ0=4;OQ=262.32;QD=5.04;SB=-99.37	GT:AD:DP:GL:GQ	0/1:29,23:31:-38.85,-9.34,-83.38:99
+chr1	2286519	rs12029098	A	G	0.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=10.29;MQ=20.58;MQ0=25;OQ=214.67;QD=3.41;SB=-10.00	GT:AD:DP:GL:GQ	0/1:52,10:32:-34.39,-9.64,-87.93:99
+chr1	2286535	rs10910056	C	T	41.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=18.11;MQ0=29;OQ=264.94;QD=4.49;SB=-10.00	GT:AD:DP:GL:GQ	0/1:49,10:24:-37.01,-7.23,-58.35:99
+chr1	2286632	rs12062221	G	A	163.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.73;MQ0=23;OQ=318.86;QD=6.13;SB=-122.97	GT:AD:DP:GL:GQ	0/1:37,15:21:-41.50,-6.33,-38.58:99
+chr1	2286682	rs10910057	T	C	259.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=21.36;MQ0=18;OQ=880.98;QD=17.98;SB=-392.60	GT:AD:DP:GL:GQ	1/1:18,31:25:-91.69,-7.53,-0.01:75.23
+chr1	2287320	rs7366927	T	C	67.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=20.66;MQ0=24;OQ=467.32;QD=6.97;SB=-192.02	GT:AD:DP:GL:GQ	0/1:40,27:33:-59.96,-9.95,-57.33:99
+chr1	2287795	rs10910058	A	T	108.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.68;MQ0=0;OQ=672.40;QD=13.18;SB=-131.84	GT:AD:DP:GL:GQ	0/1:26,25:50:-85.58,-15.06,-97.61:99
+chr1	2287854	rs10910059	G	C	295.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.70;MQ0=0;OQ=1098.70;QD=16.90;SB=-242.39	GT:AD:DP:GL:GQ	0/1:34,31:65:-132.74,-19.58,-150.89:99
+chr1	2288115	rs4648834	A	G	229.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=58.69;MQ0=0;OQ=974.25;QD=11.88;SB=-367.23	GT:AD:DP:GL:GQ	0/1:45,37:80:-124.81,-24.10,-176.65:99
+chr1	2288354	rs55960350	C	A	363.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=56.19;MQ0=0;OQ=926.53;QD=15.44;SB=-445.49	GT:AD:DP:GL:GQ	0/1:29,31:60:-114.01,-18.07,-107.19:99
+chr1	2288496	rs10453826	G	A	57.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=3;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=1349.11;QD=17.75;SB=-668.70	GT:AD:DP:GL:GQ	0/1:36,39:75:-160.78,-22.59,-131.92:99
+chr1	2288624	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=61;Dels=0.02;HRun=18;HaplotypeScore=24.48;MQ=54.73;MQ0=1;OQ=401.02;QD=6.57;SB=-41.45	GT:AD:DP:GL:GQ	0/1:43,17:55:-59.67,-16.28,-122.97:99
+chr1	2288630	rs28792725	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.02;HRun=6;HaplotypeScore=25.44;MQ=54.48;MQ0=1;OQ=211.43;QD=3.92;SB=68.22	GT:AD:DP:GL:GQ	0/1:42,11:47:-38.29,-13.87,-121.95:99
+chr1	2288943	rs6704200	G	A	186.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.03;MQ0=0;OQ=2659.42;QD=39.69;SB=-1189.57	GT:AD:DP:GL:GQ	1/1:0,67:67:-269.55,-20.19,-0.02:99
+chr1	2289098	rs12069579	C	T	14.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=4;HaplotypeScore=1.46;MQ=57.20;MQ0=1;OQ=865.75;QD=14.43;SB=-343.49	GT:AD:DP:GL:GQ	0/1:32,28:57:-107.04,-17.18,-97.55:99
+chr1	2289170	rs12069588	C	T	455.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=1016.01;QD=15.88;SB=-357.83	GT:AD:DP:GL:GQ	0/1:33,31:64:-124.17,-19.28,-114.93:99
+chr1	2289171	rs12071572	A	G	466.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=819.05;QD=12.80;SB=-318.26	GT:AD:DP:GL:GQ	0/1:33,31:63:-104.18,-18.99,-126.28:99
+chr1	2289487	rs7545940	T	C	276.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=59.67;MQ0=0;OQ=618.09;QD=11.04;SB=-316.36	GT:AD:DP:GL:GQ	0/1:32,24:55:-81.66,-16.57,-127.86:99
+chr1	2289511	rs2840538	T	C	82.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=3.41;MQ=59.24;MQ0=0;OQ=1874.35;QD=34.08;SB=-939.34	GT:AD:DP:GL:GQ	1/1:0,55:54:-191.04,-16.27,-0.02:99
+chr1	2289772	rs7546224	T	C	223.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.97;MQ0=0;OQ=650.32;QD=11.02;SB=-248.17	GT:AD:DP:GL:GQ	0/1:33,26:58:-85.80,-17.48,-124.44:99
+chr1	2290017	rs12070927	C	A	51.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=59.12;MQ0=0;OQ=1316.41;QD=19.08;SB=-657.73	GT:AD:DP:GL:GQ	0/1:26,43:67:-155.11,-20.18,-89.64:99
+chr1	2290238	rs7514750	G	C	5.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=1.63;MQ=56.12;MQ0=0;OQ=999.16;QD=16.93;SB=-161.14	GT:AD:DP:GL:GQ	0/1:29,30:55:-119.78,-16.58,-120.03:99
+chr1	2290509	rs7542190	C	T	358.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.38;MQ0=0;OQ=592.85;QD=11.62;SB=-156.20	GT:AD:DP:GL:GQ	0/1:31,20:49:-77.34,-14.77,-99.87:99
+chr1	2290635	rs7554609	A	G	100.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.39;MQ=57.81;MQ0=0;OQ=439.50;QD=11.27;SB=-190.14	GT:AD:DP:GL:GQ	0/1:19,19:37:-60.47,-13.23,-75.89:99
+chr1	2290654	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=20;HaplotypeScore=28.09;MQ=53.25;MQ0=0;OQ=241.28;QD=4.02;SB=92.32	GT:AD:DP:GL:GQ	0/1:44,16:53:-43.38,-15.97,-152.46:99
+chr1	2290675	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=20;HaplotypeScore=29.22;MQ=49.62;MQ0=0;OQ=64.81;QD=0.94;SB=71.20	GT:AD:DP:GL:GQ	0/1:52,14:46:-23.33,-13.56,-132.10:97.65
+chr1	2291469	rs2840535	G	T	504.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=896.75;QD=14.95;SB=-459.55	GT:AD:DP:GL:GQ	0/1:30,30:59:-110.74,-17.78,-88.69:99
+chr1	2291551	rs6665546	G	A	392.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=1434.00;QD=17.70;SB=-726.06	GT:AD:DP:GL:GQ	0/1:39,42:81:-171.09,-24.41,-128.82:99
+chr1	2292331	rs2453567	C	T	202.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=54.48;MQ0=0;OQ=1114.28;QD=17.14;SB=-425.43	GT:AD:DP:GL:GQ	0/1:31,34:60:-132.80,-18.08,-88.05:99
+chr1	2292376	rs2453566	T	C	254.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=52.46;MQ0=0;OQ=498.58;QD=10.18;SB=-208.48	GT:AD:DP:GL:GQ	0/1:22,27:40:-65.21,-12.06,-74.69:99
+chr1	2293426	rs2840534	A	G	74.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=4.04;MQ=59.63;MQ0=0;OQ=998.53;QD=16.11;SB=-332.38	GT:AD:DP:GL:GQ	0/1:27,35:61:-121.51,-18.38,-106.86:99
+chr1	2297776	rs2843165	A	C	120.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=714.07;QD=14.28;SB=-105.81	GT:AD:DP:GL:GQ	0/1:23,27:49:-89.45,-14.76,-84.29:99
+chr1	2298377	rs2843162	C	G	368.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=490.57;QD=15.82;SB=-257.11	GT:AD:DP:GL:GQ	0/1:17,14:31:-61.68,-9.34,-73.31:99
+chr1	2298942	rs2843160	T	G	117.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=5.47;MQ=59.17;MQ0=0;OQ=634.08;QD=11.32;SB=-278.70	GT:AD:DP:GL:GQ	0/1:27,29:53:-82.67,-15.98,-90.35:99
+chr1	2302255	rs2643908	C	T	314.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.55;MQ0=0;OQ=684.01;QD=13.41;SB=-309.40	GT:AD:DP:GL:GQ	0/1:26,25:46:-85.54,-13.86,-88.50:99
+chr1	2303400	rs2843132	A	G	8.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=3.40;MQ=59.58;MQ0=0;OQ=438.03;QD=9.96;SB=-158.56	GT:AD:DP:GL:GQ	0/1:24,20:38:-58.54,-11.45,-84.41:99
+chr1	2304179	rs2643901	T	C	196.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.98;MQ=59.45;MQ0=0;OQ=721.33;QD=17.17;SB=-281.01	GT:AD:DP:GL:GQ	0/1:15,26:39:-87.17,-11.75,-56.36:99
+chr1	2305298	rs2645060	G	A	178.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=3.33;MQ=60.00;MQ0=0;OQ=1082.92;QD=18.05;SB=-486.00	GT:AD:DP:GL:GQ	0/1:25,35:57:-128.76,-17.18,-76.49:99
+chr1	2305540	rs2843128	A	G	194.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=59.59;MQ0=0;OQ=482.38;QD=10.49;SB=-248.93	GT:AD:DP:GL:GQ	0/1:24,22:42:-64.18,-12.66,-86.34:99
+chr1	2305577	rs2843127	A	G	547.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.15;MQ0=0;OQ=527.20;QD=11.98;SB=-284.59	GT:AD:DP:GL:GQ	0/1:25,19:44:-69.26,-13.26,-98.42:99
+chr1	2306175	rs2843126	A	G	188.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=58.39;MQ0=0;OQ=344.67;QD=9.07;SB=-143.56	GT:AD:DP:GL:GQ	0/1:18,19:33:-47.70,-9.95,-71.62:99
+chr1	2306848	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=13;HaplotypeScore=4.17;MQ=55.00;MQ0=0;OQ=100.30;QD=4.18;SB=17.09	GT:AD:DP:GL:GQ	0/1:17,7:16:-18.14,-4.82,-46.21:99
+chr1	2309288	rs903903	A	G	560.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1265.25;QD=17.33;SB=-657.78	GT:AD:DP:GL:GQ	0/1:28,45:70:-150.90,-21.10,-100.41:99
+chr1	2309390	rs2645061	G	T	558.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=773.84;QD=12.28;SB=-380.71	GT:AD:DP:GL:GQ	0/1:36,27:63:-99.64,-18.97,-129.32:99
+chr1	2310428	.	G	A	99.95	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=70;Dels=0.04;HRun=15;HaplotypeScore=39.00;MQ=46.05;MQ0=0;QD=1.43;SB=52.68	GT:AD:DP:GL:GQ	0/1:53,14:55:-29.56,-16.28,-149.90:99
+chr1	2313868	rs2840533	C	T	252.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.46;MQ=59.24;MQ0=0;OQ=794.28;QD=14.44;SB=-234.49	GT:AD:DP:GL:GQ	0/1:29,26:54:-98.98,-16.27,-105.03:99
+chr1	2314319	.	A	G	42.45	LowQual	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=50.37;MQ0=0;QD=0.63;SB=-7.70	GT:AD:DP:GL:GQ	0/1:58,9:63:-26.51,-18.98,-220.77:75.28
+chr1	2314326	.	A	G	0.25	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=50.58;MQ0=0;OQ=173.32;QD=2.44;SB=-79.68	GT:AD:DP:GL:GQ	0/1:59,12:69:-41.40,-20.79,-226.63:99
+chr1	2314333	rs41315342	C	T	21.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=49.96;MQ0=0;OQ=309.71;QD=4.62;SB=-180.11	GT:AD:DP:GL:GQ	0/1:53,14:62:-52.95,-18.70,-157.19:99
+chr1	2315408	.	G	A	4.80	PASS	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=3.55;MQ=59.13;MQ0=0;OQ=1258.74;QD=16.78;SB=-356.05	GT:AD:DP:GL:GQ	0/1:37,38:74:-151.46,-22.30,-126.73:99
+chr1	2315869	rs1123571	G	A	390.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.65;MQ0=0;OQ=976.67;QD=13.95;SB=-457.41	GT:AD:DP:GL:GQ	0/1:38,32:64:-120.23,-19.28,-120.05:99
+chr1	2316672	rs903911	A	G	4.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=4.83;MQ=58.81;MQ0=0;OQ=646.68;QD=16.58;SB=-230.30	GT:AD:DP:GL:GQ	0/1:16,22:38:-79.40,-11.45,-61.89:99
+chr1	2317675	rs2840532	C	T	230.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=59.63;MQ0=0;OQ=2453.68;QD=38.95;SB=-993.83	GT:AD:DP:GL:GQ	1/1:0,63:62:-248.97,-18.68,-0.02:99
+chr1	2318574	rs2645081	A	G	8.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=6.83;MQ=58.95;MQ0=0;OQ=2467.67;QD=30.85;SB=-995.94	GT:AD:DP:GL:GQ	1/1:0,79:71:-250.38,-21.39,-0.03:99
+chr1	2319521	rs6698680	A	G	273.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.27;MQ0=0;OQ=618.22;QD=12.12;SB=-195.44	GT:AD:DP:GL:GQ	0/1:27,24:49:-79.88,-14.77,-98.83:99
+chr1	2319668	rs3001344	A	G	117.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=59.27;MQ0=0;OQ=3223.06;QD=35.42;SB=-1436.46	GT:AD:DP:GL:GQ	1/1:0,91:90:-325.91,-27.11,-0.03:99
+chr1	2319862	rs6698978	A	G	270.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=53.38;MQ0=0;OQ=935.78;QD=15.60;SB=-478.67	GT:AD:DP:GL:GQ	0/1:27,33:58:-114.34,-17.47,-100.10:99
+chr1	2319876	rs6685829	C	T	18.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=6.10;MQ=50.59;MQ0=0;OQ=722.12;QD=12.24;SB=-192.86	GT:AD:DP:GL:GQ	0/1:35,24:57:-92.67,-17.18,-109.45:99
+chr1	2320050	rs6693447	T	G	274.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=59.41;MQ0=0;OQ=1099.08;QD=15.48;SB=-483.82	GT:AD:DP:GL:GQ	0/1:33,38:70:-134.27,-21.08,-119.27:99
+chr1	2321898	rs55912310	A	G	16.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=6.30;MQ=59.22;MQ0=0;OQ=1063.46;QD=13.63;SB=-443.56	GT:AD:DP:GL:GQ	0/1:40,38:76:-132.53,-22.90,-155.79:99
+chr1	2322251	rs12037485	C	T	255.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=54.76;MQ0=0;OQ=603.45;QD=12.57;SB=-317.81	GT:AD:DP:GL:GQ	0/1:27,21:45:-77.19,-13.56,-84.03:99
+chr1	2322525	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=3;HaplotypeScore=18.90;MQ=37.53;MQ0=0;OQ=105.39;QD=3.90;SB=-31.65	GT:AD:DP:GL:GQ	0/1:20,7:25:-21.36,-7.54,-75.64:99
+chr1	2322526	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=17.62;MQ=38.02;MQ0=0;OQ=76.24;QD=2.63;SB=-0.98	GT:AD:DP:GL:GQ	0/1:23,6:24:-18.14,-7.23,-69.35:99
+chr1	2322566	.	C	T	184.67	Indel	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=7.93;MQ=44.33;MQ0=0;QD=9.72;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,7:16:-26.58,-4.82,-31.47:99
+chr1	2322586	.	T	C	43.94	LowQual	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=2;HaplotypeScore=6.02;MQ=50.39;MQ0=0;QD=3.38;SB=-10.00	GT:AD:DP:GL:GQ	0/1:9,4:11:-10.99,-3.32,-30.04:76.77
+chr1	2322650	.	T	C	18.09	LowQual	AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=2;HaplotypeScore=5.99;MQ=43.00;MQ0=0;QD=3.01;SB=-3.98	GT:AD:DP:GL:GQ	0/1:4,2:6:-6.89,-1.81,-15.35:50.86
+chr1	2322668	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=1;HaplotypeScore=16.47;MQ=36.20;MQ0=0;OQ=99.28;QD=6.62;SB=-3.98	GT:AD:DP:GL:GQ	0/1:11,4:11:-16.52,-3.31,-24.94:99
+chr1	2322705	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=18.95;MQ=39.10;MQ0=0;OQ=127.82;QD=7.99;SB=-6.99	GT:AD:DP:GL:GQ	0/1:11,5:12:-19.68,-3.62,-24.01:99
+chr1	2322711	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=2;HaplotypeScore=13.96;MQ=44.08;MQ0=0;OQ=161.06;QD=8.05;SB=-38.94	GT:AD:DP:GL:GQ	0/1:13,7:16:-24.21,-4.82,-34.51:99
+chr1	2322848	rs3001337	T	C	21.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.78;MQ0=0;OQ=436.82;QD=19.86;SB=-71.91	GT:AD:DP:GL:GQ	1/1:0,22:15:-47.28,-4.52,-0.02:45.08
+chr1	2322891	rs3001336	G	A	52.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.61;MQ=57.77;MQ0=0;OQ=1380.55;QD=34.51;SB=-210.77	GT:AD:DP:GL:GQ	1/1:0,39:36:-141.66,-10.85,-0.02:99
+chr1	2324121	.	G	T	2.67	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=60.00;MQ0=0;OQ=1012.17;QD=19.85;SB=-217.60	GT:AD:DP:GL:GQ	0/1:19,32:51:-119.87,-15.37,-54.76:99
+chr1	2324716	rs41315648	C	T	55.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=58.50;MQ0=0;OQ=419.39;QD=13.53;SB=-59.02	GT:AD:DP:GL:GQ	0/1:17,14:29:-53.97,-8.74,-50.19:99
+chr1	2325536	rs1129333	A	G	283.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.63;MQ0=0;OQ=1733.67;QD=33.99;SB=-802.65	GT:AD:DP:GL:GQ	1/1:0,51:50:-176.97,-15.06,-0.02:99
+chr1	2327137	rs11586985	C	T	102.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=429.81;QD=12.28;SB=-139.15	GT:AD:DP:GL:GQ	0/1:21,14:35:-56.82,-10.56,-64.66:99
+chr1	2327397	rs2494426	C	G	233.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=927.58;QD=37.10;SB=-342.73	GT:AD:DP:GL:GQ	1/1:0,25:23:-96.36,-6.94,-0.02:69.23
+chr1	2327420	rs55746053	G	A	222.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.19;MQ0=0;OQ=251.55;QD=10.94;SB=-144.16	GT:AD:DP:GL:GQ	0/1:13,10:21:-34.77,-6.33,-37.00:99
+chr1	2327986	rs3795269	C	A	81.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=3.48;MQ=59.11;MQ0=0;OQ=721.54;QD=13.88;SB=-337.19	GT:AD:DP:GL:GQ	0/1:25,27:47:-89.60,-14.16,-76.64:99
+chr1	2328429	rs2494427	T	C	699.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=1614.58;QD=34.35;SB=-832.33	GT:AD:DP:GL:GQ	1/1:0,47:46:-165.06,-13.86,-0.02:99
+chr1	2328739	rs6671420	G	A	245.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.24;MQ=58.64;MQ0=0;OQ=433.47;QD=13.98;SB=-240.76	GT:AD:DP:GL:GQ	0/1:16,15:30:-55.68,-9.05,-50.08:99
+chr1	2328934	rs2494428	C	T	252.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=60.00;MQ0=0;OQ=2537.82;QD=38.45;SB=-908.73	GT:AD:DP:GL:GQ	1/1:0,66:65:-257.39,-19.59,-0.03:99
+chr1	2328975	rs2494599	T	C	150.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=60.00;MQ0=0;OQ=1601.93;QD=34.08;SB=-647.90	GT:AD:DP:GL:GQ	1/1:0,47:46:-163.80,-13.86,-0.02:99
+chr1	2328999	rs6671730	G	A	141.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=617.02;QD=15.43;SB=-196.85	GT:AD:DP:GL:GQ	0/1:20,20:39:-76.74,-11.75,-69.55:99
+chr1	2329255	rs2494429	A	G	318.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.40;MQ0=0;OQ=347.51;QD=11.21;SB=-114.76	GT:AD:DP:GL:GQ	0/1:16,15:29:-46.78,-8.74,-56.84:99
+chr1	2329287	rs4648634	C	T	185.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.86;MQ=59.06;MQ0=0;OQ=270.55;QD=13.53;SB=-158.18	GT:AD:DP:GL:GQ	0/1:11,9:17:-35.47,-5.13,-24.67:99
+chr1	2329933	.	C	G	22.59	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=4.69;MQ=58.67;MQ0=0;OQ=614.01;QD=12.53;SB=-287.97	GT:AD:DP:GL:GQ	0/1:22,27:40:-76.76,-12.08,-83.82:99
+chr1	2330060	rs2494598	T	C	290.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=58.95;MQ0=0;OQ=481.10;QD=12.03;SB=-246.32	GT:AD:DP:GL:GQ	0/1:19,21:39:-63.16,-11.76,-72.17:99
+chr1	2332427	.	C	T	0.21	PASS	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=10.66;MQ=58.03;MQ0=0;OQ=1034.47;QD=16.96;SB=-503.70	GT:AD:DP:GL:GQ	0/1:28,33:58:-124.21,-17.48,-97.70:99
+chr1	2333054	rs2494597	T	C	55.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.48;MQ0=0;OQ=1376.62;QD=31.29;SB=-454.42	GT:AD:DP:GL:GQ	1/1:0,44:41:-141.27,-12.35,-0.02:99
+chr1	2334551	rs2494595	A	G	104.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=58.99;MQ0=0;OQ=304.12;QD=13.22;SB=-164.34	GT:AD:DP:GL:GQ	0/1:12,11:22:-40.32,-6.63,-44.91:99
+chr1	2334785	rs9424320	T	C	95.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.20;MQ0=0;OQ=385.94;QD=13.31;SB=-75.78	GT:AD:DP:GL:GQ	0/1:11,17:25:-49.42,-7.54,-38.41:99
+chr1	2335959	rs7556447	C	G	349.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=56.82;MQ0=0;OQ=713.10;QD=13.71;SB=-329.23	GT:AD:DP:GL:GQ	0/1:30,22:47:-88.76,-14.16,-115.39:99
+chr1	2336342	rs4648839	T	C	24.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=49.60;MQ0=0;OQ=479.90;QD=20.87;SB=-161.36	GT:AD:DP:GL:GQ	1/1:1,22:17:-51.60,-5.13,-0.02:51.09
+chr1	2336383	rs10910065	G	C	120.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=52.63;MQ0=0;OQ=649.76;QD=18.05;SB=-286.56	GT:AD:DP:GL:GQ	0/1:17,19:34:-78.51,-10.25,-66.28:99
+chr1	2336384	rs10910066	T	C	189.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=52.63;MQ0=0;OQ=539.82;QD=14.99;SB=-236.31	GT:AD:DP:GL:GQ	0/1:17,19:36:-68.12,-10.85,-65.37:99
+chr1	2336612	.	G	A	111.33	PASS	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=53.01;MQ0=0;OQ=620.89;QD=13.80;SB=-302.81	GT:AD:DP:GL:GQ	0/1:24,21:40:-77.43,-12.05,-71.03:99
+chr1	2337326	rs12746918	C	T	6.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=7.69;MQ=54.86;MQ0=0;OQ=484.18;QD=9.68;SB=-259.25	GT:AD:DP:GL:GQ	0/1:29,21:42:-64.36,-12.66,-87.95:99
+chr1	2337359	.	C	T	7.61	PASS	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=4.85;MQ=55.32;MQ0=0;OQ=435.73;QD=9.68;SB=-169.11	GT:AD:DP:GL:GQ	0/1:27,17:41:-59.22,-12.37,-82.09:99
+chr1	2337436	.	G	T	34.30	PASS	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=57.73;MQ0=0;OQ=368.11;QD=11.87;SB=-146.62	GT:AD:DP:GL:GQ	0/1:16,15:30:-49.13,-9.04,-55.91:99
+chr1	2337592	rs12184328	G	A	0.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=8.46;MQ=57.94;MQ0=0;OQ=510.09;QD=15.00;SB=-111.95	GT:AD:DP:GL:GQ	0/1:17,16:33:-64.24,-9.94,-57.68:99
+chr1	2337900	rs10910068	T	C	14.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=3;HaplotypeScore=1.32;MQ=56.47;MQ0=0;OQ=310.27;QD=9.13;SB=-165.49	GT:AD:DP:GL:GQ	0/1:15,19:29:-43.06,-8.75,-59.62:99
+chr1	2339629	rs2494432	G	A	402.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.15;MQ0=0;OQ=824.63;QD=16.83;SB=-334.87	GT:AD:DP:GL:GQ	0/1:23,26:44:-99.01,-13.26,-63.50:99
+chr1	2339896	.	C	T	167.28	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=715.32;QD=13.50;SB=-333.31	GT:AD:DP:GL:GQ	0/1:31,22:52:-90.49,-15.68,-97.09:99
+chr1	2340772	rs10910070	G	A	197.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=60.00;MQ0=0;OQ=631.24;QD=14.35;SB=-260.25	GT:AD:DP:GL:GQ	0/1:23,21:43:-79.37,-12.96,-74.56:99
+chr1	2340956	rs11577147	A	G	10.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=289.51;QD=8.77;SB=-78.79	GT:AD:DP:GL:GQ	0/1:19,14:32:-41.88,-9.65,-72.03:99
+chr1	2341435	rs11590507	G	A	0.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=5.72;MQ=57.66;MQ0=0;OQ=472.75;QD=15.76;SB=-44.54	GT:AD:DP:GL:GQ	0/1:14,15:29:-59.30,-8.74,-51.63:99
+chr1	2341559	rs3935659	T	C	7.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=3.23;MQ=59.25;MQ0=0;OQ=287.36;QD=11.49;SB=-29.91	GT:AD:DP:GL:GQ	0/1:13,12:25:-39.55,-7.53,-50.79:99
+chr1	2341739	rs3935660	C	T	165.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=58.09;MQ0=0;OQ=670.17;QD=13.68;SB=-195.21	GT:AD:DP:GL:GQ	0/1:27,21:42:-82.97,-12.67,-64.00:99
+chr1	2342006	rs12731309	C	T	203.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=58.88;MQ0=0;OQ=846.80;QD=15.68;SB=-399.13	GT:AD:DP:GL:GQ	0/1:28,26:51:-103.32,-15.36,-93.02:99
+chr1	2342252	.	A	T	13.40	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=20.03;MQ=56.40;MQ0=0;QD=0.29;SB=20.83	GT:AD:DP:GL:GQ	0/1:37,6:32:-14.24,-9.64,-106.31:46.04
+chr1	2342253	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=16;HaplotypeScore=7.92;MQ=56.40;MQ0=0;OQ=132.41;QD=2.82;SB=14.63	GT:AD:DP:GL:GQ	0/1:39,8:37:-27.67,-11.15,-101.20:99
+chr1	2342945	rs10910071	A	G	300.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=58.83;MQ0=0;OQ=1016.43;QD=13.20;SB=-494.01	GT:AD:DP:GL:GQ	0/1:41,36:76:-127.82,-22.90,-155.86:99
+chr1	2343155	rs12143389	C	T	127	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=58.70;MQ0=1;OQ=925.95;QD=15.69;SB=-402.44	GT:AD:DP:GL:GQ	0/1:31,28:58:-113.35,-17.47,-107.32:99
+chr1	2343729	rs35799953	G	T	69.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.02;MQ0=0;OQ=852.19;QD=13.75;SB=-419.16	GT:AD:DP:GL:GQ	0/1:33,29:62:-107.18,-18.68,-104.15:99
+chr1	2343876	rs34574702	C	T	503.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1119.07;QD=15.54;SB=-507.56	GT:AD:DP:GL:GQ	0/1:37,35:71:-136.60,-21.41,-114.39:99
+chr1	2344230	rs12022832	T	C	209.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=1.97;MQ=58.42;MQ0=0;OQ=1122.84;QD=12.62;SB=-438.76	GT:AD:DP:GL:GQ	0/1:44,45:86:-141.48,-25.92,-179.52:99
+chr1	2344260	rs12096965	C	T	229.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.88;MQ0=0;OQ=1606.93;QD=18.26;SB=-801.37	GT:AD:DP:GL:GQ	0/1:41,47:83:-188.99,-25.01,-117.57:99
+chr1	2344423	rs12097032	C	T	484.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=986.20;QD=13.33;SB=-465.97	GT:AD:DP:GL:GQ	0/1:43,31:74:-124.19,-22.29,-159.47:99
+chr1	2344746	rs10797421	G	A	65.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.32;MQ0=1;OQ=3166.01;QD=39.09;SB=-1482.03	GT:AD:DP:GL:GQ	1/1:0,81:79:-320.20,-23.80,-0.02:99
+chr1	2345260	.	A	G	75.95	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=59.23;MQ0=0;OQ=680.86;QD=11.35;SB=-282.57	GT:AD:DP:GL:GQ	0/1:36,24:58:-88.84,-17.47,-139.70:99
+chr1	2346437	rs4648840	A	G	47.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.94;MQ0=0;OQ=537.49;QD=18.53;SB=-194.00	GT:AD:DP:GL:GQ	0/1:11,18:29:-65.77,-8.74,-43.90:99
+chr1	2346772	rs2494433	G	A	58.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=3.58;MQ=56.91;MQ0=0;OQ=1163.67;QD=17.63;SB=-493.51	GT:AD:DP:GL:GQ	0/1:29,36:61:-138.03,-18.37,-99.55:99
+chr1	2347335	rs2494434	T	C	559.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.75;MQ0=0;OQ=1472.38;QD=29.45;SB=-544.87	GT:AD:DP:GL:GQ	1/1:0,50:48:-150.87,-14.48,-0.05:99
+chr1	2347933	rs2494588	C	T	188.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=57.48;MQ0=0;OQ=702.34;QD=16.33;SB=-327.35	GT:AD:DP:GL:GQ	0/1:19,24:41:-85.88,-12.36,-61.93:99
+chr1	2348381	rs55852252	G	A	9.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=6.28;MQ=58.74;MQ0=0;OQ=406.10;QD=10.98;SB=-128.60	GT:AD:DP:GL:GQ	0/1:20,16:33:-53.85,-9.96,-60.26:99
+chr1	2348618	rs2494587	C	T	128.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=58.45;MQ0=0;OQ=376.88;QD=12.56;SB=-173.14	GT:AD:DP:GL:GQ	0/1:17,13:28:-49.41,-8.44,-50.72:99
+chr1	2348708	rs12116913	G	C	294.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=640.63;QD=17.31;SB=-259.09	GT:AD:DP:GL:GQ	0/1:14,23:34:-77.61,-10.26,-60.10:99
+chr1	2349777	rs2494436	T	C	163.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=59.34;MQ0=0;OQ=309.46;QD=8.84;SB=-92.69	GT:AD:DP:GL:GQ	0/1:19,16:32:-43.87,-9.64,-70.50:99
+chr1	2349800	rs7515934	C	T	251.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=58.83;MQ0=0;OQ=424.25;QD=11.78;SB=-175.26	GT:AD:DP:GL:GQ	0/1:19,17:28:-54.15,-8.45,-42.69:99
+chr1	2350992	rs10910075	C	T	473.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=647.50;QD=14.08;SB=-334.47	GT:AD:DP:GL:GQ	0/1:24,22:45:-81.60,-13.57,-79.99:99
+chr1	2351241	.	T	G	21.83	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=2;HaplotypeScore=2.69;MQ=59.58;MQ0=0;QD=0.40;SB=68.21	GT:AD:DP:GL:GQ	0/1:36,19:40:-17.52,-12.05,-117.29:54.64
+chr1	2351880	rs4531246	G	T	25.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=6.77;MQ=57.66;MQ0=0;OQ=504.52;QD=12.61;SB=-172.18	GT:AD:DP:GL:GQ	0/1:16,23:33:-63.68,-9.95,-50.73:99
+chr1	2352624	rs10797424	A	T	924.88	Indel	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=6.64;MQ=59.45;MQ0=0;QD=16.52;SB=-353.59	GT:AD:DP:GL:GQ	0/1:25,31:52:-111.44,-15.67,-81.17:99
+chr1	2352687	rs2494641	C	T	290.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=59.48;MQ0=0;OQ=558.90;QD=11.89;SB=-269.24	GT:AD:DP:GL:GQ	0/1:28,19:43:-72.14,-12.96,-80.82:99
+chr1	2353187	rs2494640	G	C	26.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=4.41;MQ=59.56;MQ0=0;OQ=532.94;QD=10.25;SB=-240.06	GT:AD:DP:GL:GQ	0/1:33,18:51:-71.97,-15.39,-132.20:99
+chr1	2361858	rs12756220	T	C	1.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=140;Dels=0.00;HRun=2;HaplotypeScore=7.14;MQ=34.26;MQ0=3;OQ=1721.38;QD=12.30;SB=-137.87	GT:AD:DP:GL:GQ	0/1:41,97:98:-204.99,-29.57,-118.98:99
+chr1	2361893	rs34648463	T	G	24.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=3.90;MQ=42.90;MQ0=5;OQ=1167.25;QD=12.83;SB=-195.79	GT:AD:DP:GL:GQ	0/1:32,58:69:-140.80,-20.79,-99.18:99
+chr1	2361936	rs28669301	A	C	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=18.37;MQ=47.88;MQ0=0;OQ=797.11;QD=9.96;SB=-212.34	GT:AD:DP:GL:GQ	0/1:30,48:65:-102.59,-19.60,-99.90:99
+chr1	2361993	rs2494638	G	C	0.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=3.02;MQ=48.10;MQ0=3;OQ=294.71;QD=3.68;SB=53.21	GT:AD:DP:GL:GQ	0/1:57,23:60:-50.84,-18.09,-206.36:99
+chr1	2363043	.	G	A	28.79	PASS	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.42;MQ=59.14;MQ0=0;OQ=346.36;QD=12.83;SB=-157.68	GT:AD:DP:GL:GQ	0/1:14,13:24:-45.16,-7.24,-42.35:99
+chr1	2380627	.	C	G	34.70	LowQual	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=57.50;MQ0=0;QD=0.48;SB=-30.39	GT:AD:DP:GL:GQ	0/1:66,6:63:-25.74,-18.99,-243.93:67.54
+chr1	2380700	rs28508164	T	C	2.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.08;MQ0=1;OQ=73.76;QD=1.76;SB=-56.90	GT:AD:DP:GL:GQ	0/1:36,6:33:-20.60,-9.94,-107.88:99
+chr1	2380723	.	G	C	46.32	LowQual	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=2;HaplotypeScore=2.29;MQ=49.69;MQ0=1;QD=2.72;SB=-23.39	GT:AD:DP:GL:GQ	0/1:12,5:11:-11.23,-3.32,-34.81:79.16
+chr1	2380725	.	C	T	43.06	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=4.03;MQ=49.69;MQ0=1;QD=2.53;SB=5.04	GT:AD:DP:GL:GQ	0/1:12,5:11:-10.90,-3.32,-27.83:75.90
+chr1	2380739	.	G	C	31.92	LowQual	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=2;HaplotypeScore=1.16;MQ=44.53;MQ0=1;QD=1.88;SB=-3.98	GT:AD:DP:GL:GQ	0/1:10,7:9:-9.19,-2.71,-29.02:64.75
+chr1	2380741	.	C	T	23.47	LowQual	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=43.38;MQ0=1;QD=1.47;SB=-3.99	GT:AD:DP:GL:GQ	0/1:10,6:8:-8.04,-2.42,-18.12:56.29
+chr1	2380787	.	C	G	11.87	PASS	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=3.66;MQ=41.08;MQ0=2;OQ=228.10;QD=9.12;SB=-107.32	GT:AD:DP:GL:GQ	0/1:13,12:14:-30.31,-4.22,-31.36:99
+chr1	2380789	.	T	C	0.06	PASS	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=2;HaplotypeScore=3.66;MQ=41.08;MQ0=2;OQ=146.59;QD=5.86;SB=-69.76	GT:AD:DP:GL:GQ	0/1:13,12:14:-22.16,-4.22,-27.36:99
+chr1	2380812	.	C	T	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=1;HaplotypeScore=13.92;MQ=46.38;MQ0=1;OQ=329.40;QD=9.98;SB=-91.91	GT:AD:DP:GL:GQ	0/1:15,18:19:-41.95,-5.73,-28.82:99
+chr1	2380819	.	C	G	37.83	LowQual	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=9.81;MQ=46.57;MQ0=1;QD=1.08;SB=-27.83	GT:AD:DP:GL:GQ	0/1:27,8:18:-12.49,-5.42,-65.92:70.67
+chr1	2382567	.	A	G	10.80	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.42;MQ0=0;OQ=573.70;QD=14.34;SB=-186.56	GT:AD:DP:GL:GQ	0/1:16,24:36:-71.50,-10.85,-55.65:99
+chr1	2390539	rs56368227	C	T	147.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.76;MQ=58.63;MQ0=0;OQ=772.55;QD=15.15;SB=-231.31	GT:AD:DP:GL:GQ	0/1:25,25:47:-96.89,-16.35,-71.90:99
+chr1	2391510	rs942818	T	C	169.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=1503.43;QD=30.07;SB=-692.23	GT:AD:DP:GL:GQ	1/1:0,50:44:-153.95,-13.26,-0.02:99
+chr1	2393714	rs10910080	G	A	120.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=2.52;MQ=58.38;MQ0=0;OQ=343.05;QD=13.19;SB=-140.60	GT:AD:DP:GL:GQ	0/1:13,13:24:-44.83,-7.24,-36.59:99
+chr1	2394116	rs2494626	C	T	263.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=58.95;MQ0=0;OQ=492.85;QD=12.32;SB=-207.19	GT:AD:DP:GL:GQ	0/1:23,17:37:-63.72,-11.16,-67.50:99
+chr1	2398521	rs1536155	A	G	7.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=3;HaplotypeScore=2.26;MQ=58.44;MQ0=0;OQ=280.60;QD=10.39;SB=-38.80	GT:AD:DP:GL:GQ	0/1:14,13:25:-38.88,-7.54,-51.71:99
+chr1	2399136	rs12049628	A	G	275.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=58.16;MQ0=0;OQ=457.42;QD=9.94;SB=-243.30	GT:AD:DP:GL:GQ	0/1:24,22:43:-61.98,-12.96,-96.02:99
+chr1	2399220	rs59417818	G	A	58.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=60.00;MQ0=0;OQ=406.26;QD=15.63;SB=-103.61	GT:AD:DP:GL:GQ	0/1:12,13:24:-51.14,-7.23,-38.48:99
+chr1	2399752	rs12727342	A	G	0.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=4.77;MQ=57.40;MQ0=0;OQ=225.70;QD=6.10;SB=-108.60	GT:AD:DP:GL:GQ	0/1:20,17:31:-35.20,-9.35,-75.95:99
+chr1	2399993	.	G	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=1;HaplotypeScore=4.11;MQ=57.31;MQ0=0;OQ=125.38;QD=3.58;SB=53.21	GT:AD:DP:GL:GQ	0/1:25,10:27:-23.96,-8.14,-94.75:99
+chr1	2400649	rs11799501	C	T	116.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=4.89;MQ=60.00;MQ0=0;OQ=748.36;QD=14.39;SB=-393.78	GT:AD:DP:GL:GQ	0/1:28,24:51:-93.50,-15.38,-86.98:99
+chr1	2401311	rs10797428	A	G	76.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=3;HaplotypeScore=1.05;MQ=59.53;MQ0=0;OQ=638.41;QD=15.96;SB=-314.23	GT:AD:DP:GL:GQ	0/1:15,25:38:-78.58,-11.46,-54.60:99
+chr1	2402139	rs4648638	A	T	283.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.43;MQ0=0;OQ=382.69;QD=11.60;SB=-121.80	GT:AD:DP:GL:GQ	0/1:19,14:31:-50.89,-9.34,-63.99:99
+chr1	2403494	rs942817	G	C	329.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=58.68;MQ0=0;OQ=865.92;QD=18.82;SB=-441.92	GT:AD:DP:GL:GQ	0/1:21,25:43:-102.83,-12.96,-79.86:99
+chr1	2404788	rs4995304	G	A	54.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=55.45;MQ0=0;OQ=801.00;QD=19.54;SB=-282.18	GT:AD:DP:GL:GQ	0/1:16,24:39:-95.13,-11.75,-53.28:99
+chr1	2405062	.	T	G	6.04	PASS	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=55.86;MQ0=0;OQ=164.49;QD=7.15;SB=2.04	GT:AD:DP:GL:GQ	0/1:15,8:23:-26.66,-6.93,-55.71:99
+chr1	2405078	.	C	T	5.98	PASS	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=52.76;MQ0=0;OQ=151.99;QD=6.61;SB=-0.99	GT:AD:DP:GL:GQ	0/1:16,7:20:-24.51,-6.03,-50.27:99
+chr1	2405106	.	G	T	34.21	LowQual	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=4.38;MQ=49.04;MQ0=0;QD=1.63;SB=-10.00	GT:AD:DP:GL:GQ	0/1:16,5:14:-10.92,-4.22,-37.23:67.05
+chr1	2405179	.	T	G	0.09	PASS	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=3;HaplotypeScore=3.52;MQ=52.14;MQ0=0;OQ=147.78;QD=8.21;SB=-98.66	GT:AD:DP:GL:GQ	0/1:11,7:13:-21.98,-3.92,-24.09:99
+chr1	2405189	.	T	C	0.04	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;HRun=3;HaplotypeScore=5.56;MQ=47.05;MQ0=0;OQ=344.28;QD=18.12;SB=-173.40	GT:AD:DP:GL:GQ	1/1:0,19:11:-38.02,-3.32,-0.01:33.08
+chr1	2405210	.	C	A	0.76	PASS	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=2.86;MQ=39.01;MQ0=0;OQ=86.77;QD=6.20;SB=-60.75	GT:AD:DP:GL:GQ	0/1:10,4:8:-14.37,-2.41,-11.67:92.61
+chr1	2405220	.	G	C	0.99	PASS	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=39.01;MQ0=0;OQ=62.38;QD=4.46;SB=-40.43	GT:AD:DP:GL:GQ	0/1:10,4:7:-11.64,-2.12,-15.93:95.21
+chr1	2405254	.	T	C	25.50	LowQual	AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=3;HaplotypeScore=1.85;MQ=37.93;MQ0=1;QD=3.64;SB=-6.99	GT:AD:DP:GL:GQ	0/1:3,4:4:-7.04,-1.21,-6.92:57.17
+chr1	2405275	.	C	A	10.07	PASS	AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=1;HaplotypeScore=2.14;MQ=32.15;MQ0=1;OQ=98.76;QD=10.97;SB=-39.94	GT:AD:DP:GL:GQ	1/1:5,4:4:-13.41,-1.21,-0.00:12.03
+chr1	2405285	.	G	C	5.32	PASS	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=37.51;MQ0=1;OQ=185.89;QD=12.39;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,7:7:-23.98,-2.11,-4.50:23.85
+chr1	2405307	.	G	C	0.94	PASS	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=44.11;MQ0=0;OQ=225.33;QD=17.33;SB=-6.99	GT:AD:DP:GL:GQ	0/1:5,8:9:-28.53,-2.71,-8.94:62.30
+chr1	2405357	rs61763948	T	C	6.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=58.63;MQ0=0;OQ=296.15;QD=17.42;SB=-3.98	GT:AD:DP:GL:GQ	0/1:4,13:16:-37.72,-4.82,-15.46:99
+chr1	2406217	rs4648639	G	A	225.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=51.38;MQ0=0;OQ=834.51;QD=18.14;SB=-265.24	GT:AD:DP:GL:GQ	0/1:20,26:45:-100.29,-13.55,-72.00:99
+chr1	2407818	rs4648640	G	A	162.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.42;MQ=59.09;MQ0=0;OQ=709.86;QD=15.43;SB=-272.15	GT:AD:DP:GL:GQ	0/1:23,23:44:-87.53,-13.26,-76.87:99
+chr1	2408795	rs10910082	C	T	122.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.49;MQ0=0;OQ=319.86;QD=7.11;SB=-107.45	GT:AD:DP:GL:GQ	0/1:33,12:44:-48.52,-13.25,-117.65:99
+chr1	2410450	rs10752744	T	C	140.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=60.00;MQ0=0;OQ=499.26;QD=10.62;SB=-158.91	GT:AD:DP:GL:GQ	0/1:28,19:47:-67.37,-14.16,-113.54:99
+chr1	2410773	rs6668720	A	G	120.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=58.84;MQ0=0;OQ=320.90;QD=8.02;SB=-52.83	GT:AD:DP:GL:GQ	0/1:24,16:36:-46.22,-10.85,-86.61:99
+chr1	2412474	rs2477699	G	A	360.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=58.60;MQ0=0;OQ=676.25;QD=13.52;SB=-318.34	GT:AD:DP:GL:GQ	0/1:25,25:46:-84.77,-13.86,-87.14:99
+chr1	2413426	rs3001349	C	G	122.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=4.47;MQ=59.07;MQ0=0;OQ=984.04;QD=19.68;SB=-507.27	GT:AD:DP:GL:GQ	0/1:22,28:50:-116.76,-15.07,-93.45:99
+chr1	2414277	rs2477701	T	C	471.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=1313.31;QD=32.03;SB=-482.12	GT:AD:DP:GL:GQ	1/1:0,41:41:-134.95,-12.36,-0.03:99
+chr1	2414754	rs2477702	T	C	257.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=58.58;MQ0=0;OQ=407.32;QD=11.31;SB=-181.54	GT:AD:DP:GL:GQ	0/1:18,17:33:-53.96,-9.95,-62.99:99
+chr1	2415234	.	G	A	52.54	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.50;MQ=58.25;MQ0=0;OQ=558.86;QD=13.97;SB=-294.85	GT:AD:DP:GL:GQ	0/1:20,20:36:-70.03,-10.86,-54.36:99
+chr1	2415852	rs2477703	C	T	47.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=7.69;MQ=58.80;MQ0=0;OQ=763.15;QD=13.16;SB=-352.50	GT:AD:DP:GL:GQ	0/1:34,24:57:-96.78,-17.18,-104.35:99
+chr1	2416626	rs3001347	A	G	166.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=58.74;MQ0=0;OQ=303.26;QD=8.20;SB=-170.50	GT:AD:DP:GL:GQ	0/1:20,17:33:-43.56,-9.95,-71.18:99
+chr1	2417572	rs3762444	C	T	276.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=447.88;QD=14.93;SB=-199.90	GT:AD:DP:GL:GQ	0/1:15,15:29:-56.82,-8.74,-44.39:99
+chr1	2418734	rs2477706	T	C	40.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=58.67;MQ0=0;OQ=224.99;QD=6.43;SB=-131.52	GT:AD:DP:GL:GQ	0/1:20,15:30:-34.83,-9.05,-71.11:99
+chr1	2422191	rs4648641	C	A	142.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.65;MQ0=0;OQ=139.36;QD=6.33;SB=-88.78	GT:AD:DP:GL:GQ	0/1:13,9:20:-23.25,-6.03,-44.88:99
+chr1	2422622	rs4648642	G	A	142.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=59.39;MQ0=0;OQ=411.20;QD=10.82;SB=-172.27	GT:AD:DP:GL:GQ	0/1:23,15:36:-55.26,-10.86,-70.83:99
+chr1	2422899	.	G	A	37.84	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=59.45;MQ0=0;OQ=458.87;QD=13.50;SB=-199.87	GT:AD:DP:GL:GQ	0/1:18,16:31:-58.52,-9.34,-51.58:99
+chr1	2423328	.	G	A	53.96	PASS	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=296.62;QD=12.90;SB=-35.64	GT:AD:DP:GL:GQ	0/1:13,10:22:-39.58,-6.63,-40.93:99
+chr1	2423754	rs55874156	G	A	35.47	LowQual	AC=1;AF=0.50;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;QD=5.91;SB=-7.00	GT:AD:DP:GL:GQ	0/1:3,3:5:-8.34,-1.51,-8.96:68.30
+chr1	2423760	rs12736998	C	T	230.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=70.89;QD=11.81;SB=-46.66	GT:AD:DP:GL:GQ	0/1:3,3:6:-12.18,-1.81,-9.71:78.98
+chr1	2424604	rs3814298	C	T	190.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=60.00;MQ0=0;OQ=798.59;QD=18.57;SB=-384.92	GT:AD:DP:GL:GQ	0/1:19,24:41:-95.50,-12.36,-53.02:99
+chr1	2428628	rs12725663	C	T	86.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=59.46;MQ0=0;OQ=892.70;QD=20.76;SB=-466.01	GT:AD:DP:GL:GQ	0/1:16,27:41:-104.92,-12.36,-47.45:99
+chr1	2429459	rs2494621	C	A	2.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=3;HaplotypeScore=1.26;MQ=59.48;MQ0=0;OQ=889.11;QD=20.21;SB=-361.22	GT:AD:DP:GL:GQ	0/1:15,29:43:-105.15,-12.95,-49.46:99
+chr1	2429541	rs4648559	C	T	370.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=862.47;QD=17.60;SB=-340.86	GT:AD:DP:GL:GQ	0/1:22,27:49:-104.31,-14.78,-68.65:99
+chr1	2429545	rs3791180	G	C	362.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=669.25;QD=13.12;SB=-329.42	GT:AD:DP:GL:GQ	0/1:24,27:45:-83.79,-13.58,-96.76:99
+chr1	2434274	rs7535528	G	A	398.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=57.41;MQ0=0;OQ=974.09;QD=16.23;SB=-447.47	GT:AD:DP:GL:GQ	0/1:29,31:55:-117.28,-16.58,-80.59:99
+chr1	2440170	rs56168662	G	C	440.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=641.06;QD=13.94;SB=-291.00	GT:AD:DP:GL:GQ	0/1:24,22:44:-80.67,-13.28,-95.39:99
+chr1	2442429	rs2985862	T	C	118.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=58.11;MQ0=0;OQ=446.59;QD=12.07;SB=-57.29	GT:AD:DP:GL:GQ	0/1:20,17:36:-58.79,-10.85,-82.58:99
+chr1	2442985	.	C	G	26.50	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=2.73;MQ=57.66;MQ0=0;QD=0.66;SB=53.21	GT:AD:DP:GL:GQ	0/1:27,13:28:-14.38,-8.45,-107.19:59.33
+chr1	2443996	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=42.41;MQ=51.42;MQ0=0;OQ=532.54;QD=4.29;SB=-103.57	GT:AD:DP:GL:GQ	0/1:93,31:115:-91.18,-34.64,-325.86:99
+chr1	2444008	rs12757829	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=141;Dels=0.00;HRun=1;HaplotypeScore=24.89;MQ=51.04;MQ0=0;OQ=890.38;QD=6.31;SB=-413.05	GT:AD:DP:GL:GQ	0/1:89,52:127:-130.59,-38.27,-352.78:99
+chr1	2444025	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=0;HaplotypeScore=101.62;MQ=51.11;MQ0=0;OQ=575.04;QD=3.76;SB=-161.02	GT:AD:DP:GL:GQ	0/1:119,34:145:-104.47,-43.68,-467.68:99
+chr1	2444046	rs11582708	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.00;HRun=3;HaplotypeScore=36.45;MQ=48.57;MQ0=0;OQ=119.48;QD=0.71;SB=230.81	GT:AD:DP:GL:GQ	0/1:152,17:154:-61.64,-46.41,-606.32:99
+chr1	2444064	rs11583446	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=165;Dels=0.00;HRun=0;HaplotypeScore=21.72;MQ=47.52;MQ0=0;OQ=2894.91;QD=17.54;SB=-1278.77	GT:AD:DP:GL:GQ	0/1:56,109:148:-337.38,-44.60,-196.45:99
+chr1	2444078	rs2494629	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=179;Dels=0.00;HRun=0;HaplotypeScore=85.91;MQ=46.23;MQ0=1;OQ=3166.59;QD=17.69;SB=-903.91	GT:AD:DP:GL:GQ	0/1:79,100:143:-363.06,-43.11,-245.67:99
+chr1	2444084	rs11583448	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=183;Dels=0.00;HRun=0;HaplotypeScore=146.19;MQ=45.66;MQ0=1;OQ=1337.56;QD=7.31;SB=32.08	GT:AD:DP:GL:GQ	0/1:128,54:167:-187.36,-50.32,-447.47:99
+chr1	2444090	rs11582711	C	T	0.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=184;Dels=0.00;HRun=1;HaplotypeScore=9.96;MQ=45.23;MQ0=1;OQ=1767.35;QD=9.61;SB=-110.22	GT:AD:DP:GL:GQ	0/1:119,64:165:-229.73,-49.72,-378.76:99
+chr1	2444114	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=167;Dels=0.00;HRun=1;HaplotypeScore=224.24;MQ=44.82;MQ0=1;OQ=1189.56;QD=7.12;SB=-484.53	GT:AD:DP:GL:GQ	0/1:105,62:153:-168.35,-46.11,-399.99:99
+chr1	2444123	rs60947977	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=164;Dels=0.00;HRun=1;HaplotypeScore=187.19;MQ=44.56;MQ0=1;OQ=222.03;QD=1.35;SB=140.46	GT:AD:DP:GL:GQ	0/1:146,18:145:-69.17,-43.68,-451.95:99
+chr1	2444144	rs12735280	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=159;Dels=0.00;HRun=0;HaplotypeScore=41.21;MQ=45.78;MQ0=2;OQ=126.97;QD=0.80;SB=158.55	GT:AD:DP:GL:GQ	0/1:146,13:126:-53.98,-38.00,-474.20:99
+chr1	2444156	rs61763952	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=143;Dels=0.00;HRun=1;HaplotypeScore=50.63;MQ=44.65;MQ0=2;OQ=841.78;QD=5.89;SB=-177.38	GT:AD:DP:GL:GQ	0/1:107,36:119:-123.33,-35.87,-307.59:99
+chr1	2444175	.	A	G	1992.57	SnpCluster	AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=1;HaplotypeScore=57.72;MQ=43.73;MQ0=1;QD=16.74;SB=-969.28	GT:AD:DP:GL:GQ	0/1:46,73:107:-234.78,-32.23,-167.74:99
+chr1	2444179	.	C	T	733.69	SnpCluster	AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=1;HaplotypeScore=94.68;MQ=43.15;MQ0=1;QD=6.79;SB=-249.70	GT:AD:DP:GL:GQ	0/1:79,29:94:-104.98,-28.32,-236.84:99
+chr1	2444180	.	T	C	74.50	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=102.88;MQ=43.30;MQ0=1;QD=0.72;SB=40.74	GT:AD:DP:GL:GQ	0/1:89,15:92:-38.46,-27.73,-318.94:99
+chr1	2444188	.	C	T	230.63	SnpCluster	AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=1;HaplotypeScore=69.58;MQ=42.94;MQ0=1;QD=2.33;SB=-68.96	GT:AD:DP:GL:GQ	0/1:80,18:83:-51.35,-25.01,-254.74:99
+chr1	2444203	rs12723596	A	G	0.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=13.04;MQ=41.89;MQ0=1;OQ=932.46;QD=10.25;SB=-166.34	GT:AD:DP:GL:GQ	0/1:48,43:72:-118.23,-21.70,-146.57:99
+chr1	2444214	.	T	G	33.51	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=1;HaplotypeScore=90.11;MQ=41.94;MQ0=0;QD=0.39;SB=20.19	GT:AD:DP:GL:GQ	0/1:75,10:71:-28.02,-21.39,-222.83:66.35
+chr1	2444236	rs3001351	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.00;HRun=1;HaplotypeScore=44.56;MQ=42.21;MQ0=1;OQ=1478.32;QD=13.82;SB=-341.03	GT:AD:DP:GL:GQ	0/1:32,75:79:-174.93,-23.81,-103.79:99
+chr1	2444239	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=57.18;MQ=42.22;MQ0=1;OQ=253.01;QD=2.32;SB=-45.72	GT:AD:DP:GL:GQ	0/1:94,15:81:-52.98,-24.40,-242.61:99
+chr1	2444569	rs2494625	T	C	30.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.30;MQ0=0;OQ=234.27;QD=7.10;SB=-122.64	GT:AD:DP:GL:GQ	0/1:20,13:30:-35.75,-9.04,-76.61:99
+chr1	2445722	rs12131236	C	T	283.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=971.15;QD=13.87;SB=-406.34	GT:AD:DP:GL:GQ	0/1:39,31:69:-121.19,-20.79,-133.37:99
+chr1	2446063	rs3122922	A	G	422.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.95;MQ0=0;OQ=840.10;QD=14.48;SB=-338.93	GT:AD:DP:GL:GQ	0/1:28,30:57:-104.46,-17.17,-113.53:99
+chr1	2452678	rs2494603	T	C	117.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.28;MQ0=0;OQ=471.49;QD=14.73;SB=-130.66	GT:AD:DP:GL:GQ	0/1:12,20:28:-58.88,-8.44,-38.02:99
+chr1	2452695	rs10910087	A	G	48.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=58.97;MQ0=0;OQ=650.54;QD=14.46;SB=-235.28	GT:AD:DP:GL:GQ	0/1:22,23:45:-81.90,-13.56,-89.06:99
+chr1	2453274	rs11583602	G	A	37.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.57;MQ0=0;OQ=1048.89;QD=19.42;SB=-532.12	GT:AD:DP:GL:GQ	0/1:23,31:52:-123.83,-15.66,-80.52:99
+chr1	2453609	rs4648645	G	T	421.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=634.41;QD=13.22;SB=-255.25	GT:AD:DP:GL:GQ	0/1:25,23:48:-81.19,-14.46,-89.13:99
+chr1	2453905	rs6694195	G	A	6.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=641.00;QD=22.10;SB=-187.27	GT:AD:DP:GL:GQ	0/1:9,20:26:-75.22,-7.83,-25.34:99
+chr1	2454427	rs12406506	G	T	168.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.39;MQ0=0;OQ=384.63;QD=10.12;SB=-161.15	GT:AD:DP:GL:GQ	0/1:22,16:36:-52.59,-10.85,-75.30:99
+chr1	2454955	rs11585747	C	T	158.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=58.68;MQ0=0;OQ=442.85;QD=9.63;SB=-209.92	GT:AD:DP:GL:GQ	0/1:30,16:43:-60.53,-12.97,-87.57:99
+chr1	2455004	rs9803764	C	T	21.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=718.09;QD=21.76;SB=-255.79	GT:AD:DP:GL:GQ	0/1:12,21:31:-84.43,-9.34,-35.39:99
+chr1	2455189	rs11584295	G	A	326.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=59.30;MQ0=0;OQ=897.10;QD=14.95;SB=-369.89	GT:AD:DP:GL:GQ	0/1:30,30:57:-110.18,-17.19,-92.60:99
+chr1	2455531	rs4648561	T	C	59.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=4.71;MQ=60.00;MQ0=0;OQ=506.09;QD=9.04;SB=-221.92	GT:AD:DP:GL:GQ	0/1:28,28:51:-69.27,-15.38,-110.78:99
+chr1	2455652	rs3001339	C	T	0.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=4;HaplotypeScore=3.44;MQ=59.16;MQ0=0;OQ=1028.71;QD=18.70;SB=-294.19	GT:AD:DP:GL:GQ	0/1:22,32:53:-122.12,-15.97,-77.91:99
+chr1	2455772	rs6661956	C	T	143.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=537.50;QD=14.93;SB=-189.16	GT:AD:DP:GL:GQ	0/1:19,17:35:-67.58,-10.55,-58.49:99
+chr1	2455810	rs2494605	A	G	6.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=3.59;MQ=59.41;MQ0=0;OQ=1343.57;QD=34.45;SB=-641.25	GT:AD:DP:GL:GQ	1/1:0,39:38:-137.96,-11.45,-0.01:99
+chr1	2456285	rs2985860	T	G	0.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=9.84;MQ=58.13;MQ0=0;OQ=394.22;QD=7.88;SB=-79.96	GT:AD:DP:GL:GQ	0/1:20,30:34:-52.96,-10.25,-63.38:99
+chr1	2456493	rs2494606	A	G	522.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=1382.51;QD=30.72;SB=-394.30	GT:AD:DP:GL:GQ	1/1:0,45:44:-141.87,-13.27,-0.04:99
+chr1	2460535	.	T	C	626.63	Indel	AC=1;AF=0.50;AN=2;DP=47;Dels=0.04;HRun=0;HaplotypeScore=9.81;MQ=45.54;MQ0=0;QD=13.33;SB=-234.30	GT:AD:DP:GL:GQ	0/1:22,23:45:-78.90,-12.95,-84.01:99
+chr1	2460708	rs12042279	G	A	153.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=58.99;MQ0=0;OQ=696.74;QD=15.15;SB=-237.53	GT:AD:DP:GL:GQ	0/1:24,22:46:-86.83,-13.87,-76.84:99
+chr1	2461941	rs1886731	T	C	87.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=203.62;QD=14.54;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,9:14:-27.87,-4.22,-19.55:99
+chr1	2462004	rs4487972	G	C	44.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=1.24;MQ=56.62;MQ0=0;OQ=71.85;QD=10.26;SB=-10.00	GT:AD:DP:GL:GQ	0/1:3,4:6:-12.28,-1.81,-12.84:99
+chr1	2464065	rs942824	T	C	72.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.60;MQ=59.36;MQ0=0;OQ=370.87;QD=10.30;SB=-61.73	GT:AD:DP:GL:GQ	0/1:20,16:34:-50.61,-10.24,-77.88:99
+chr1	2465072	rs10797429	G	C	201.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=57.71;MQ0=0;OQ=487.96;QD=13.19;SB=-257.25	GT:AD:DP:GL:GQ	0/1:21,16:34:-62.33,-10.25,-80.32:99
+chr1	2465334	rs55929178	C	T	11.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=4.63;MQ=56.91;MQ0=0;OQ=721.66;QD=14.73;SB=-233.74	GT:AD:DP:GL:GQ	0/1:26,23:43:-88.40,-12.95,-74.05:99
+chr1	2467218	rs12097268	T	A	23.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=190.70;QD=11.22;SB=-35.94	GT:AD:DP:GL:GQ	0/1:9,8:17:-27.48,-5.13,-30.96:99
+chr1	2468371	rs2477678	T	A	119.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=60.00;MQ0=0;OQ=463.47;QD=13.24;SB=-147.88	GT:AD:DP:GL:GQ	0/1:17,17:32:-59.27,-9.64,-59.80:99
+chr1	2469843	rs1974044	A	G	45.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=3.40;MQ=59.34;MQ0=0;OQ=371.34;QD=10.61;SB=-193.60	GT:AD:DP:GL:GQ	0/1:21,14:32:-50.06,-9.64,-71.49:99
+chr1	2471303	.	C	T	62.24	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=41.42;MQ0=6;OQ=776.47;QD=14.38;SB=-282.22	GT:AD:DP:GL:GQ	0/1:29,25:42:-93.59,-12.66,-60.88:99
+chr1	2472781	rs2147905	T	C	210.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=57.08;MQ0=0;OQ=779.17;QD=15.90;SB=-258.93	GT:AD:DP:GL:GQ	0/1:21,26:47:-95.36,-14.16,-80.25:99
+chr1	2473130	rs3748825	T	C	24.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=50.53;MQ0=0;OQ=489.49;QD=14.40;SB=-174.97	GT:AD:DP:GL:GQ	0/1:17,17:34:-62.48,-10.24,-67.15:99
+chr1	2473158	rs2985858	C	G	170.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.64;MQ=52.63;MQ0=0;OQ=759.64;QD=17.67;SB=-375.14	GT:AD:DP:GL:GQ	0/1:22,21:42:-91.90,-12.65,-91.93:99
+chr1	2474608	rs4449972	T	C	1.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=17.16;MQ0=14;OQ=59.70;QD=2.60;SB=-42.68	GT:AD:DP:GL:GQ	0/1:13,10:7:-11.36,-2.11,-16.47:92.53
+chr1	2474629	rs2764846	G	T	13.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=13.44;MQ0=12;OQ=72.28;QD=4.25;SB=-10.00	GT:AD:DP:GL:GQ	1/1:7,10:3:-10.72,-0.90,-0.00:9.03
+chr1	2474959	rs10910088	A	G	3.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=22.58;MQ0=15;OQ=106.75;QD=3.44;SB=-10.00	GT:AD:DP:GL:GQ	0/1:16,14:12:-17.58,-3.63,-21.51:99
+chr1	2475164	rs2182176	C	T	397.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=48.51;MQ0=0;OQ=552.02;QD=13.14;SB=-223.69	GT:AD:DP:GL:GQ	0/1:24,18:39:-70.24,-11.76,-69.97:99
+chr1	2475556	rs1555791	C	G	11.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=2.88;MQ=58.58;MQ0=0;OQ=550.02;QD=11.96;SB=-241.08	GT:AD:DP:GL:GQ	0/1:27,19:40:-70.37,-12.08,-87.80:99
+chr1	2475800	rs10910089	C	A	3.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=9.04;MQ=58.28;MQ0=0;OQ=671.47;QD=13.70;SB=-238.39	GT:AD:DP:GL:GQ	0/1:23,26:46:-84.29,-13.86,-77.00:99
+chr1	2476366	rs61054170	G	A	7.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=6.03;MQ=57.64;MQ0=0;OQ=224.60;QD=8.64;SB=-97.61	GT:AD:DP:GL:GQ	0/1:16,10:23:-32.68,-6.93,-48.70:99
+chr1	2476391	rs2495365	T	C	262.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=56.62;MQ0=0;OQ=373.37;QD=12.04;SB=-190.59	GT:AD:DP:GL:GQ	0/1:16,15:29:-49.36,-8.74,-57.56:99
+chr1	2476740	rs11577783	T	C	207.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=58.69;MQ0=0;OQ=459.72;QD=9.19;SB=-194.29	GT:AD:DP:GL:GQ	0/1:30,20:49:-64.03,-14.78,-111.22:99
+chr1	2476777	rs7550231	C	T	162.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.21;MQ0=0;OQ=483.70;QD=13.44;SB=-69.05	GT:AD:DP:GL:GQ	0/1:20,15:32:-61.30,-9.65,-52.93:99
+chr1	2477765	rs7515633	T	C	23.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=58.71;MQ0=0;OQ=253.35;QD=14.07;SB=-51.83	GT:AD:DP:GL:GQ	0/1:8,10:18:-34.04,-5.43,-30.81:99
+chr1	2477769	rs7544646	G	C	297.66	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=2;HaplotypeScore=6.07;MQ=56.04;MQ0=0;QD=16.54;SB=-32.86	GT:AD:DP:GL:GQ	0/1:9,9:14:-37.27,-4.22,-20.23:99
+chr1	2477776	.	G	C	10.29	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=1;HaplotypeScore=18.19;MQ=56.92;MQ0=0;QD=0.45;SB=20.10	GT:AD:DP:GL:GQ	0/1:13,10:13:-8.19,-3.92,-49.87:42.70
+chr1	2477778	.	A	C	172	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=2;HaplotypeScore=22.60;MQ=57.66;MQ0=0;QD=5.73;SB=23.08	GT:AD:DP:GL:GQ	0/1:12,18:21:-26.81,-6.33,-40.53:99
+chr1	2477836	rs2843396	C	G	11.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=3.04;MQ=59.36;MQ0=0;OQ=1290.53;QD=35.85;SB=-556.54	GT:AD:DP:GL:GQ	1/1:0,36:34:-132.68,-10.27,-0.04:99
+chr1	2478204	rs10910090	G	A	182.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=59.53;MQ0=0;OQ=449.68;QD=11.24;SB=-202.69	GT:AD:DP:GL:GQ	0/1:23,17:38:-59.71,-11.46,-71.62:99
+chr1	2479633	rs8725	C	T	49.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.46;MQ=59.51;MQ0=0;OQ=577.64;QD=12.29;SB=-219.70	GT:AD:DP:GL:GQ	0/1:27,20:42:-73.71,-12.66,-80.51:99
+chr1	2480088	rs2234167	C	T	215.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=60.00;MQ0=0;OQ=519.75;QD=13.33;SB=-131.13	GT:AD:DP:GL:GQ	0/1:22,17:38:-66.72,-11.46,-63.96:99
+chr1	2481753	rs11573988	C	A	159.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.54;MQ0=0;OQ=542.33;QD=13.23;SB=-158.65	GT:AD:DP:GL:GQ	0/1:20,21:37:-68.66,-11.14,-62.61:99
+chr1	2483213	rs2234161	G	A	326.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.71;MQ0=0;OQ=435.68;QD=12.10;SB=-173.67	GT:AD:DP:GL:GQ	0/1:20,16:32:-56.50,-9.65,-56.89:99
+chr1	2483476	rs2281852	G	T	352.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=59.50;MQ0=0;OQ=604.05;QD=13.13;SB=-299.46	GT:AD:DP:GL:GQ	0/1:23,23:43:-76.65,-12.96,-66.34:99
+chr1	2483520	rs2257763	G	T	186.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.87;MQ=58.41;MQ0=0;OQ=599.64;QD=13.63;SB=-190.60	GT:AD:DP:GL:GQ	0/1:21,23:41:-75.60,-12.36,-64.98:99
+chr1	2485488	rs2495366	C	T	214.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=59.54;MQ0=0;OQ=410.34;QD=10.01;SB=-177.87	GT:AD:DP:GL:GQ	0/1:24,17:33:-54.27,-9.95,-57.69:99
+chr1	2485810	rs1886730	A	G	395.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=201.47;QD=10.07;SB=-95.61	GT:AD:DP:GL:GQ	0/1:11,9:20:-29.46,-6.03,-42.35:99
+chr1	2486265	rs4870	T	C	17.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=53.94;MQ0=0;OQ=133.00;QD=5.54;SB=-10.85	GT:AD:DP:GL:GQ	0/1:16,8:22:-23.21,-6.63,-59.96:99
+chr1	2486652	rs2227313	A	G	323.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=361.41;QD=9.04;SB=-171.95	GT:AD:DP:GL:GQ	0/1:24,16:39:-51.18,-11.76,-90.45:99
+chr1	2486755	rs2227312	G	T	192.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.51;MQ0=0;OQ=435.37;QD=11.46;SB=-199.58	GT:AD:DP:GL:GQ	0/1:21,17:35:-57.36,-10.54,-70.01:99
+chr1	2489670	rs4449972	A	G	6.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=14.84;MQ0=21;OQ=104.96;QD=3.09;SB=-10.00	GT:AD:DP:GL:GQ	0/1:18,15:5:-15.28,-1.51,-4.27:27.62
+chr1	2489758	rs4385650	G	C	16.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=2.00;MQ=35.98;MQ0=1;OQ=450.14;QD=15.00;SB=-208.64	GT:AD:DP:GL:GQ	0/1:17,13:27:-56.44,-8.15,-54.66:99
+chr1	2490753	rs4648647	G	A	26.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=1.33;MQ=50.09;MQ0=0;OQ=371.65;QD=10.04;SB=-147.20	GT:AD:DP:GL:GQ	0/1:24,13:35:-51.00,-10.56,-68.63:99
+chr1	2490924	.	G	A	58.67	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=40.19;MQ0=3;OQ=773.22;QD=14.59;SB=-281.28	GT:AD:DP:GL:GQ	0/1:27,26:42:-93.26,-12.65,-67.56:99
+chr1	2491198	rs10797432	C	T	12.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=7.73;MQ=51.44;MQ0=1;OQ=449.43;QD=8.48;SB=-221.51	GT:AD:DP:GL:GQ	0/1:35,17:47:-62.39,-14.17,-101.99:99
+chr1	2491376	rs10910092	A	G	353.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.86;MQ0=0;OQ=953.50;QD=15.89;SB=-479.29	GT:AD:DP:GL:GQ	0/1:27,33:59:-116.41,-17.77,-105.03:99
+chr1	2491870	rs10797433	T	C	399.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.09;MQ0=0;OQ=643.74;QD=13.99;SB=-281.26	GT:AD:DP:GL:GQ	0/1:20,26:45:-81.22,-13.56,-79.26:99
+chr1	2492640	rs6667605	C	T	284.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=60.00;MQ0=0;OQ=1076.76;QD=20.32;SB=-511.53	GT:AD:DP:GL:GQ	0/1:22,31:53:-126.92,-15.96,-81.92:99
+chr1	2492694	rs6672381	A	G	59.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=2.96;MQ=59.67;MQ0=0;OQ=836.72;QD=14.68;SB=-261.21	GT:AD:DP:GL:GQ	0/1:25,31:56:-103.83,-16.88,-100.88:99
+chr1	2493042	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=3;HaplotypeScore=24.29;MQ=58.55;MQ0=0;OQ=229.07;QD=5.45;SB=41.17	GT:AD:DP:GL:GQ	0/1:24,18:31:-35.54,-9.35,-97.62:99
+chr1	2494094	rs6671426	C	A	112.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=782.65;QD=13.98;SB=-297.63	GT:AD:DP:GL:GQ	0/1:30,26:56:-98.41,-16.86,-108.17:99
+chr1	2494223	rs28734787	T	C	285.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.94;MQ=59.74;MQ0=0;OQ=1016.84;QD=14.32;SB=-488.08	GT:AD:DP:GL:GQ	0/1:37,34:71:-126.35,-21.38,-153.97:99
+chr1	2495573	rs10910093	C	T	602.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1162.34;QD=15.92;SB=-466.49	GT:AD:DP:GL:GQ	0/1:38,35:73:-141.53,-22.01,-121.32:99
+chr1	2496089	rs55658746	T	C	89.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.87;MQ=57.64;MQ0=0;OQ=790.54;QD=12.35;SB=-411.26	GT:AD:DP:GL:GQ	0/1:36,28:63:-101.32,-18.98,-139.07:99
+chr1	2496219	rs2477685	G	T	165.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=55.91;MQ0=0;OQ=1646.89;QD=32.29;SB=-779.73	GT:AD:DP:GL:GQ	1/1:1,50:48:-168.30,-14.46,-0.02:99
+chr1	2496348	rs10910094	C	T	138.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=47.91;MQ0=1;OQ=444.30;QD=9.66;SB=-141.63	GT:AD:DP:GL:GQ	0/1:26,19:40:-59.77,-12.06,-79.45:99
+chr1	2497303	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=4;HaplotypeScore=6.77;MQ=59.20;MQ0=0;OQ=63.06;QD=2.17;SB=17.06	GT:AD:DP:GL:GQ	0/1:13,16:15:-14.11,-4.52,-33.25:95.89
+chr1	2497798	rs10752745	A	G	23.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=2.74;MQ=53.22;MQ0=0;OQ=566.34;QD=12.59;SB=-208.51	GT:AD:DP:GL:GQ	0/1:24,21:42:-72.57,-12.65,-89.49:99
+chr1	2498203	rs6675676	G	C	138.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=30.17;MQ0=2;OQ=540.65;QD=15.02;SB=-227.70	GT:AD:DP:GL:GQ	0/1:18,18:32:-67.01,-9.66,-62.30:99
+chr1	2500615	rs10910095	G	A	293.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=53.83;MQ0=0;OQ=619.40;QD=15.49;SB=-326.87	GT:AD:DP:GL:GQ	0/1:18,21:35:-75.77,-10.55,-51.15:99
+chr1	2501140	rs10797434	C	T	359.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=59.72;MQ0=0;OQ=1006.21;QD=15.25;SB=-442.36	GT:AD:DP:GL:GQ	0/1:35,31:65:-123.49,-19.58,-121.16:99
+chr1	2501248	rs12129508	G	A	509.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1099.72;QD=18.33;SB=-426.78	GT:AD:DP:GL:GQ	0/1:28,32:59:-131.03,-17.77,-95.59:99
+chr1	2502312	rs4648648	G	A	10.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=5.67;MQ=56.86;MQ0=0;OQ=538.80;QD=17.96;SB=-254.77	GT:AD:DP:GL:GQ	0/1:13,17:27:-65.30,-8.13,-39.62:99
+chr1	2502510	rs4648649	T	C	255.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=58.39;MQ0=0;OQ=590.46;QD=13.42;SB=-228.32	GT:AD:DP:GL:GQ	0/1:17,27:40:-74.40,-12.07,-60.31:99
+chr1	2502570	rs10910096	T	C	112.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.22;MQ0=0;OQ=671.99;QD=19.20;SB=-218.66	GT:AD:DP:GL:GQ	0/1:13,22:35:-81.03,-10.54,-52.21:99
+chr1	2502755	.	G	A	190.59	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=20;HaplotypeScore=16.86;MQ=48.05;MQ0=1;QD=2.32;SB=89.22	GT:AD:DP:GL:GQ	0/1:62,20:60:-40.44,-18.10,-157.12:99
+chr1	2502759	.	G	A	95.63	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=4;HaplotypeScore=8.02;MQ=49.03;MQ0=1;QD=1.15;SB=92.21	GT:AD:DP:GL:GQ	0/1:62,21:60:-30.94,-18.09,-170.87:99
+chr1	2502764	.	G	A	61.94	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=4;HaplotypeScore=11.73;MQ=52.06;MQ0=1;QD=0.77;SB=101.27	GT:AD:DP:GL:GQ	0/1:64,16:66:-29.37,-19.89,-196.86:94.78
+chr1	2502769	.	G	A	36.83	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=4;HaplotypeScore=29.21;MQ=54.00;MQ0=1;QD=0.49;SB=101.32	GT:AD:DP:GL:GQ	0/1:66,9:67:-27.16,-20.19,-206.36:69.66
+chr1	2502915	rs4486391	A	T	575.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=706.11;QD=12.61;SB=-348.36	GT:AD:DP:GL:GQ	0/1:31,25:55:-90.46,-16.56,-121.47:99
+chr1	2502965	rs735000	C	T	134.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=59.41;MQ0=0;OQ=774.05;QD=19.85;SB=-347.38	GT:AD:DP:GL:GQ	0/1:16,23:37:-91.84,-11.15,-44.36:99
+chr1	2503076	rs734999	C	T	284.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=51.96;MQ0=0;OQ=837.38;QD=13.51;SB=-164.65	GT:AD:DP:GL:GQ	0/1:35,27:61:-105.40,-18.37,-127.82:99
+chr1	2503492	rs2016175	C	G	123.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=50.82;MQ0=0;OQ=1084.11;QD=19.71;SB=-398.00	GT:AD:DP:GL:GQ	0/1:24,31:54:-127.97,-16.28,-102.13:99
+chr1	2503538	rs2016366	A	T	76.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=3.79;MQ=51.20;MQ0=0;OQ=1061.50;QD=16.33;SB=-509.95	GT:AD:DP:GL:GQ	0/1:31,34:63:-128.41,-18.98,-104.88:99
+chr1	2504435	rs2094074	C	T	20.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=6.13;MQ=59.30;MQ0=0;OQ=1039.69;QD=17.04;SB=-426.84	GT:AD:DP:GL:GQ	0/1:29,32:61:-125.64,-18.39,-96.67:99
+chr1	2506299	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=15.52;MQ=57.83;MQ0=0;OQ=93.19;QD=2.39;SB=56.19	GT:AD:DP:GL:GQ	0/1:27,12:31:-21.95,-9.34,-90.63:99
+chr1	2511290	rs10910097	C	T	251.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=59.70;MQ0=0;OQ=1148.10;QD=18.52;SB=-511.69	GT:AD:DP:GL:GQ	0/1:27,35:61:-136.47,-18.38,-99.00:99
+chr1	2512252	rs2296443	G	A	195.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.53;MQ0=0;OQ=544.43;QD=13.61;SB=-235.74	GT:AD:DP:GL:GQ	0/1:18,22:33:-67.68,-9.95,-51.18:99
+chr1	2515036	.	A	C	42.97	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=58.51;MQ0=0;OQ=337.76;QD=7.68;SB=-183.81	GT:AD:DP:GL:GQ	0/1:27,17:42:-49.72,-12.66,-93.24:99
+chr1	2517538	rs2260976	A	G	4.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=2.14;MQ=56.76;MQ0=0;OQ=1272.91;QD=31.05;SB=-372.36	GT:AD:DP:GL:GQ	1/1:0,41:39:-130.90,-11.76,-0.03:99
+chr1	2517993	rs2843401	T	C	105.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=57.77;MQ0=0;OQ=962.33;QD=26.73;SB=-342.23	GT:AD:DP:GL:GQ	1/1:0,36:31:-99.85,-9.36,-0.04:93.19
+chr1	2518542	rs2843402	T	C	221.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=60.00;MQ0=0;OQ=1968.59;QD=35.79;SB=-942.98	GT:AD:DP:GL:GQ	1/1:0,55:55:-200.46,-16.56,-0.01:99
+chr1	2518859	rs2764845	G	T	123.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=60.00;MQ0=0;OQ=1822.58;QD=33.75;SB=-893.66	GT:AD:DP:GL:GQ	1/1:0,54:52:-185.86,-15.67,-0.02:99
+chr1	2518957	rs2843403	T	C	21.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=1.02;MQ=56.17;MQ0=0;OQ=926.62;QD=29.89;SB=-317.56	GT:AD:DP:GL:GQ	1/1:0,31:28:-96.27,-8.44,-0.02:84.21
+chr1	2519052	rs2764842	A	G	76.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=1201.00;QD=30.79;SB=-460.21	GT:AD:DP:GL:GQ	1/1:0,39:38:-123.72,-11.46,-0.03:99
+chr1	2519220	rs2764841	G	A	268.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=59.01;MQ0=0;OQ=1602.47;QD=34.10;SB=-756.02	GT:AD:DP:GL:GQ	1/1:0,46:43:-163.85,-12.96,-0.02:99
+chr1	2519297	rs2764840	C	T	22.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=57.55;MQ0=0;OQ=1701.90;QD=37.00;SB=-691.34	GT:AD:DP:GL:GQ	1/1:0,46:43:-173.78,-12.95,-0.01:99
+chr1	2520418	rs2843404	T	C	200.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.75;MQ0=0;OQ=2535.27;QD=33.80;SB=-857.06	GT:AD:DP:GL:GQ	1/1:0,75:73:-257.13,-21.99,-0.02:99
+chr1	2520554	rs2764848	G	A	508.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2620.71;QD=40.32;SB=-1288.71	GT:AD:DP:GL:GQ	1/1:0,65:65:-265.67,-19.58,-0.01:99
+chr1	2521232	rs2985855	A	C	625.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.53;MQ0=0;OQ=2344.13;QD=34.47;SB=-1125.14	GT:AD:DP:GL:GQ	1/1:0,68:67:-238.02,-20.18,-0.02:99
+chr1	2521327	rs6689711	T	C	152.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.71;MQ0=0;OQ=2140.18;QD=32.93;SB=-405.31	GT:AD:DP:GL:GQ	1/1:0,65:64:-217.64,-19.29,-0.04:99
+chr1	2521365	rs6681973	C	T	205.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=1951.81;QD=38.27;SB=-716.95	GT:AD:DP:GL:GQ	1/1:0,51:50:-198.79,-15.07,-0.02:99
+chr1	2521374	rs6682043	C	A	555.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=1757.71;QD=35.87;SB=-715.96	GT:AD:DP:GL:GQ	1/1:0,49:49:-179.37,-14.76,-0.01:99
+chr1	2521839	.	A	G	1244.02	Indel	AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.74;MQ0=0;QD=31.90;SB=-233.75	GT:AD:DP:GL:GQ	1/1:1,38:37:-132.07,-11.15,-4.08:70.65
+chr1	2522276	rs2985859	T	C	630.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.35;MQ0=0;OQ=2205.91;QD=35.58;SB=-1051.93	GT:AD:DP:GL:GQ	1/1:0,62:62:-224.19,-18.67,-0.02:99
+chr1	2522366	rs3001837	G	A	528.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.76;MQ0=0;OQ=2660.16;QD=39.12;SB=-1251.03	GT:AD:DP:GL:GQ	1/1:0,68:68:-269.62,-20.49,-0.02:99
+chr1	2522484	rs2985857	C	T	472.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=3579.52;QD=41.62;SB=-1476.96	GT:AD:DP:GL:GQ	1/1:0,86:86:-356.95,-25.90,-0.02:99
+chr1	2522759	rs6424092	C	A	529.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2798.98;QD=36.83;SB=-1322.91	GT:AD:DP:GL:GQ	1/1:0,76:75:-283.50,-22.58,-0.01:99
+chr1	2523213	.	A	C	18.95	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=2;HaplotypeScore=7.65;MQ=59.48;MQ0=0;QD=0.43;SB=47.15	GT:AD:DP:GL:GQ	0/1:27,17:32:-14.82,-9.65,-87.52:51.73
+chr1	2530333	.	T	C	29.61	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=7.38;MQ=54.61;MQ0=1;QD=0.64;SB=33.57	GT:AD:DP:GL:GQ	0/1:37,5:39:-21.30,-15.06,-133.42:62.44
+chr1	2530381	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=20.91;MQ=54.33;MQ0=2;OQ=131.02;QD=2.85;SB=56.21	GT:AD:DP:GL:GQ	0/1:39,7:40:-28.44,-12.05,-138.25:99
+chr1	2537888	rs4379628	A	G	6.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=4.46;MQ=59.75;MQ0=0;OQ=2299.26;QD=31.07;SB=-964.39	GT:AD:DP:GL:GQ	1/1:0,74:72:-233.58,-21.72,-0.07:99
+chr1	2541362	.	T	C	301.82	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=1099.72;QD=15.94;SB=-567.63	GT:AD:DP:GL:GQ	0/1:31,38:67:-133.44,-20.18,-122.76:99
+chr1	2541645	rs12117343	C	T	412.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=59.64;MQ0=0;OQ=1073.30;QD=16.77;SB=-513.05	GT:AD:DP:GL:GQ	0/1:32,32:63:-129.60,-18.99,-99.14:99
+chr1	2543980	rs61765771	T	G	318.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=60.00;MQ0=0;OQ=635.63;QD=14.45;SB=-332.88	GT:AD:DP:GL:GQ	0/1:20,24:43:-79.80,-12.95,-72.63:99
+chr1	2546847	.	G	A	17.21	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.27;MQ0=0;OQ=1072.92;QD=19.87;SB=-329.89	GT:AD:DP:GL:GQ	0/1:19,35:49:-125.34,-14.77,-58.33:99
+chr1	2547051	rs7523364	C	T	194.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=55.15;MQ0=0;OQ=3310.62;QD=39.41;SB=-1353.31	GT:AD:DP:GL:GQ	1/1:0,84:83:-330.06,-25.01,-0.03:99
+chr1	2547391	rs6422657	C	T	186.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=2783.42;QD=38.13;SB=-1334.38	GT:AD:DP:GL:GQ	1/1:1,71:72:-284.61,-21.69,-2.69:99
+chr1	2548168	rs6668149	A	C	205.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.44;MQ0=0;OQ=2627.68;QD=35.04;SB=-1288.37	GT:AD:DP:GL:GQ	1/1:0,75:74:-266.37,-22.29,-0.02:99
+chr1	2548600	rs12748729	C	T	627.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2890.24;QD=37.05;SB=-1331.37	GT:AD:DP:GL:GQ	1/1:0,78:77:-292.65,-23.21,-0.04:99
+chr1	2549449	rs12730932	T	G	82.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.16;MQ0=0;OQ=1601.53;QD=32.03;SB=-737.35	GT:AD:DP:GL:GQ	1/1:0,50:47:-163.76,-14.16,-0.02:99
+chr1	2550595	rs4648657	A	G	5.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.33;MQ0=0;OQ=350.17;QD=25.01;SB=-43.68	GT:AD:DP:GL:GQ	1/1:0,14:13:-38.62,-3.93,-0.02:39.06
+chr1	2550742	rs4648658	G	A	10.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.23;MQ0=0;OQ=551.80;QD=32.46;SB=-125.66	GT:AD:DP:GL:GQ	1/1:0,17:15:-58.77,-4.52,-0.01:45.14
+chr1	2550763	rs4648659	T	G	0.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=55.52;MQ0=0;OQ=309.18;QD=19.32;SB=-86.14	GT:AD:DP:GL:GQ	1/1:0,16:12:-34.52,-3.62,-0.02:36.01
+chr1	2551146	rs28532547	T	G	110.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=53.21;MQ0=0;OQ=1059.23;QD=30.26;SB=-548.02	GT:AD:DP:GL:GQ	1/1:0,35:32:-109.53,-9.64,-0.02:96.26
+chr1	2552029	rs4648564	C	T	0.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=7.47;MQ=58.85;MQ0=1;OQ=2625.23;QD=39.18;SB=-1028.39	GT:AD:DP:GL:GQ	1/1:1,66:66:-266.13,-19.88,-0.02:99
+chr1	2553110	rs12749591	G	T	349.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=723.50;QD=32.89;SB=-266.61	GT:AD:DP:GL:GQ	1/1:0,22:22:-75.95,-6.63,-0.01:66.17
+chr1	2553270	.	G	T	45.57	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=10.71;MQ=58.27;MQ0=0;QD=1.69;SB=20.06	GT:AD:DP:GL:GQ	0/1:17,10:20:-13.87,-6.03,-50.95:78.40
+chr1	2554043	rs6698817	T	C	9.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=887.43;QD=26.89;SB=-424.17	GT:AD:DP:GL:GQ	1/1:0,33:29:-92.36,-8.75,-0.03:87.20
+chr1	2554325	rs12752515	T	C	17.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.11;MQ0=0;OQ=775.65;QD=29.83;SB=-403.34	GT:AD:DP:GL:GQ	1/1:0,26:25:-81.17,-7.54,-0.02:75.18
+chr1	2554665	rs12723864	A	G	160.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=60.00;MQ0=0;OQ=414.17;QD=9.86;SB=-197.61	GT:AD:DP:GL:GQ	0/1:26,16:42:-57.35,-12.65,-104.43:99
+chr1	2555187	rs55649610	G	T	258.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=951.34;QD=20.68;SB=-431.11	GT:AD:DP:GL:GQ	0/1:14,32:46:-112.28,-13.86,-47.81:99
+chr1	2555885	.	C	T	1.81	PASS	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=57.89;MQ0=0;OQ=690.84;QD=23.82;SB=-291.84	GT:AD:DP:GL:GQ	0/1:8,21:28:-80.81,-8.44,-25.16:99
+chr1	2556197	.	T	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=11.22;MQ=54.79;MQ0=0;OQ=66.20;QD=3.31;SB=-59.09	GT:AD:DP:GL:GQ	0/1:16,4:14:-14.12,-4.22,-33.87:99
+chr1	2556342	rs6657378	T	G	21.29	LowQual	AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=3.31;MQ=37.32;MQ0=0;QD=3.04;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,2:5:-6.92,-1.51,-9.22:54.10
+chr1	2556350	rs6671623	G	A	0.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=1;HaplotypeScore=6.12;MQ=40.03;MQ0=1;OQ=207.84;QD=25.98;SB=-95.34	GT:AD:DP:GL:GQ	1/1:1,7:6:-24.36,-1.81,-0.00:18.06
+chr1	2556357	rs6671625	G	A	182.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.68;MQ0=1;OQ=89.01;QD=14.84;SB=-50.56	GT:AD:DP:GL:GQ	1/1:1,5:3:-12.39,-0.90,-0.00:9.03
+chr1	2556483	rs61765773	C	T	0.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=11.29;MQ=45.87;MQ0=1;OQ=153.35;QD=5.11;SB=26.06	GT:AD:DP:GL:GQ	0/1:23,7:20:-24.65,-6.03,-43.69:99
+chr1	2556797	rs61765774	G	C	178.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.58;MQ0=0;OQ=587.02;QD=17.79;SB=-197.49	GT:AD:DP:GL:GQ	0/1:16,17:32:-71.63,-9.64,-64.58:99
+chr1	2557281	rs12756665	C	T	187.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.25;MQ=59.28;MQ0=0;OQ=722.29;QD=11.29;SB=-327.75	GT:AD:DP:GL:GQ	0/1:40,24:64:-94.79,-19.28,-146.15:99
+chr1	2557351	rs12739597	A	G	96.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=59.10;MQ0=0;OQ=470.82;QD=7.03;SB=-215.20	GT:AD:DP:GL:GQ	0/1:44,23:67:-70.56,-20.20,-177.79:99
+chr1	2557360	rs6666788	A	G	33.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=2.28;MQ=59.11;MQ0=0;OQ=2385.56;QD=35.08;SB=-1067.87	GT:AD:DP:GL:GQ	1/1:0,68:67:-242.16,-20.18,-0.02:99
+chr1	2558285	rs4648661	T	C	264.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=58.76;MQ0=0;OQ=708.13;QD=11.80;SB=-352.07	GT:AD:DP:GL:GQ	0/1:29,30:58:-91.59,-17.49,-110.76:99
+chr1	2559883	rs4648565	A	G	68.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=1657.37;QD=34.53;SB=-734.30	GT:AD:DP:GL:GQ	1/1:0,48:47:-169.34,-14.16,-0.02:99
+chr1	2561683	rs28690427	A	G	44.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.48;MQ0=0;OQ=1625.27;QD=33.17;SB=-564.36	GT:AD:DP:GL:GQ	1/1:0,49:47:-166.13,-14.16,-0.02:99
+chr1	2563059	rs4648662	A	G	36.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=57.88;MQ0=0;OQ=986.78;QD=31.83;SB=-278.44	GT:AD:DP:GL:GQ	1/1:0,30:28:-102.27,-8.43,-0.01:84.25
+chr1	2563587	rs4648663	A	C	432.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=1398.67;QD=33.30;SB=-656.05	GT:AD:DP:GL:GQ	1/1:0,42:41:-143.47,-12.35,-0.02:99
+chr1	2563763	rs12726651	C	T	270.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.90;MQ0=0;OQ=164.81;QD=9.69;SB=-74.06	GT:AD:DP:GL:GQ	0/1:11,6:16:-24.59,-4.82,-34.68:99
+chr1	2563938	rs9970196	T	C	22.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.81;MQ=59.28;MQ0=0;OQ=1014.31;QD=31.70;SB=-295.06	GT:AD:DP:GL:GQ	1/1:0,32:30:-105.04,-9.04,-0.02:90.22
+chr1	2566315	rs6604989	T	C	18.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.60;MQ0=0;OQ=1647.45;QD=28.40;SB=-794.64	GT:AD:DP:GL:GQ	1/1:0,58:52:-168.38,-15.68,-0.05:99
+chr1	2568080	rs12744876	G	T	183.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=58.84;MQ0=0;OQ=1106.09;QD=17.02;SB=-318.70	GT:AD:DP:GL:GQ	0/1:29,35:64:-133.17,-19.27,-104.78:99
+chr1	2571402	rs28611770	A	G	632.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.32;MQ0=1;OQ=2534.42;QD=35.20;SB=-1124.79	GT:AD:DP:GL:GQ	1/1:0,72:70:-257.05,-21.08,-0.02:99
+chr1	2571473	.	C	T	26.42	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=54.51;MQ0=1;OQ=420.48;QD=8.58;SB=-192.15	GT:AD:DP:GL:GQ	0/1:33,16:41:-57.68,-12.35,-93.81:99
+chr1	2571476	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=3;HaplotypeScore=3.65;MQ=54.65;MQ0=1;OQ=290.92;QD=5.94;SB=-124.22	GT:AD:DP:GL:GQ	0/1:34,15:41:-44.73,-12.36,-110.26:99
+chr1	2571505	.	C	T	0.62	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=52.42;MQ0=0;OQ=231.01;QD=4.20;SB=-18.13	GT:AD:DP:GL:GQ	0/1:42,13:52:-42.05,-15.67,-144.47:99
+chr1	2571527	.	A	T	14.96	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.42;MQ=51.64;MQ0=0;OQ=434.87;QD=7.91;SB=-142.65	GT:AD:DP:GL:GQ	0/1:35,20:51:-62.14,-15.37,-122.01:99
+chr1	2572200	rs12732266	C	G	51.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=5.49;MQ=58.04;MQ0=0;OQ=559.70;QD=11.91;SB=-261.11	GT:AD:DP:GL:GQ	0/1:26,21:41:-71.62,-12.36,-99.19:99
+chr1	2573315	rs12738064	C	T	887.13	DPFilter;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=133;Dels=0.00;HRun=0;HaplotypeScore=171.89;MQ=24.26;MQ0=9;QD=6.67;SB=-137.01	GT:AD:DP:GL:GQ	1/1:10,119:25:-96.41,-11.12,-4.11:70.06
+chr1	2573322	.	T	G	343.20	DPFilter;SnpCluster	AC=2;AF=1.00;AN=2;DP=144;Dels=0.01;HRun=0;HaplotypeScore=333.45;MQ=22.10;MQ0=11;QD=2.38;SB=-10.00	GT:AD:DP:GL:GQ	1/1:29,104:11:-37.91,-3.31,-0.00:33.09
+chr1	2573323	.	C	G	95.88	DPFilter;SnpCluster	AC=2;AF=1.00;AN=2;DP=144;Dels=0.01;HRun=1;HaplotypeScore=342.46;MQ=22.10;MQ0=11;QD=0.67;SB=-10.00	GT:AD:DP:GL:GQ	1/1:103,36:3:-13.08,-0.90,-0.00:9.03
+chr1	2573324	.	G	C	506.46	DPFilter;Indel;SnpCluster	AC=2;AF=1.00;AN=2;DP=147;Dels=0.01;HRun=1;HaplotypeScore=339.64;MQ=22.28;MQ0=11;QD=3.45;SB=-10.00	GT:AD:DP:GL:GQ	1/1:15,116:14:-57.88,-7.75,-3.65:41.01
+chr1	2573329	rs12734173	G	A	146.94	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=218;Dels=0.00;HRun=1;HaplotypeScore=513.41;MQ=21.01;MQ0=20;QD=0.67;SB=-10.00	GT:AD:DP:GL:GQ	0/1:132,84:24:-25.21,-7.23,-67.73:99
+chr1	2573338	.	C	G	83.26	DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=0;HaplotypeScore=710.09;MQ=20.03;MQ0=40;QD=0.29;SB=-0.97	GT:AD:DP:GL:GQ	0/1:254,26:38:-23.06,-11.45,-135.55:99
+chr1	2573342	.	C	A	213.70	DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=322;Dels=0.00;HRun=1;HaplotypeScore=673.88;MQ=20.07;MQ0=46;QD=0.66;SB=1.99	GT:AD:DP:GL:GQ	0/1:277,45:41:-37.01,-12.35,-108.15:99
+chr1	2573345	.	A	C	1425.86	DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=338;Dels=0.02;HRun=3;HaplotypeScore=632.90;MQ=20.26;MQ0=48;QD=4.22;SB=-172.79	GT:AD:DP:GL:GQ	0/1:132,186:90:-176.25,-30.38,-146.77:99
+chr1	2573350	.	T	C	293.04	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=399;Dels=0.00;HRun=0;HaplotypeScore=691.94;MQ=19.84;MQ0=54;QD=0.73;SB=44.71	GT:AD:DP:GL:GQ	0/1:277,71:78:-104.74,-72.15,-238.43:99
+chr1	2573354	.	C	A	62.42	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=432;Dels=0.00;HRun=1;HaplotypeScore=848.73;MQ=19.94;MQ0=56;QD=0.14;SB=50.16	GT:AD:DP:GL:GQ	0/1:379,40:51:-24.89,-15.36,-155.69:95.25
+chr1	2573358	.	T	C	129.61	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=457;Dels=0.00;HRun=1;HaplotypeScore=683.78;MQ=19.93;MQ0=58;QD=0.28;SB=-34.65	GT:AD:DP:GL:GQ	0/1:367,56:52:-42.68,-26.43,-169.09:99
+chr1	2573364	rs55738582	C	G	575.47	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=473;Dels=0.00;HRun=1;HaplotypeScore=961.37;MQ=19.71;MQ0=62;QD=1.22;SB=-67.52	GT:AD:DP:GL:GQ	0/1:411,23:43:-73.79,-12.96,-105.12:99
+chr1	2573370	rs55790383	G	A	775.08	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=470;Dels=0.00;HRun=1;HaplotypeScore=917.62;MQ=19.72;MQ0=61;QD=1.65;SB=-367.90	GT:AD:DP:GL:GQ	0/1:265,173:48:-98.76,-17.97,-89.48:99
+chr1	2573371	rs55657722	G	C	3489.08	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=470;Dels=0.00;HRun=0;HaplotypeScore=944.58;MQ=19.72;MQ0=61;QD=7.42;SB=-1002.13	GT:AD:DP:GL:GQ	1/1:47,398:84:-347.91,-28.85,-3.68:99
+chr1	2573372	.	A	G	46.25	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=482;Dels=0.00;HRun=2;HaplotypeScore=999.26;MQ=19.79;MQ0=62;QD=0.10;SB=26.11	GT:AD:DP:GL:GQ	0/1:425,48:54:-24.18,-16.27,-184.96:79.08
+chr1	2573374	.	C	A	193.31	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=490;Dels=0.00;HRun=1;HaplotypeScore=979.59;MQ=19.99;MQ0=60;QD=0.39;SB=-75.64	GT:AD:DP:GL:GQ	0/1:438,45:65:-48.93,-26.32,-189.47:99
+chr1	2573382	.	C	A	261.06	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=502;Dels=0.01;HRun=1;HaplotypeScore=946.29;MQ=19.95;MQ0=64;QD=0.52;SB=17.04	GT:AD:DP:GL:GQ	0/1:391,72:71:-67.99,-38.60,-197.52:99
+chr1	2573383	.	C	G	55.13	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=502;Dels=0.00;HRun=0;HaplotypeScore=899.21;MQ=20.04;MQ0=63;QD=0.11;SB=37.79	GT:AD:DP:GL:GQ	0/1:438,33:65:-35.38,-26.59,-240.37:87.97
+chr1	2573385	.	C	A	145.75	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=503;Dels=0.00;HRun=0;HaplotypeScore=828.45;MQ=20.02;MQ0=64;QD=0.29;SB=-23.06	GT:AD:DP:GL:GQ	0/1:432,48:49:-35.99,-18.13,-141.74:99
+chr1	2573390	.	T	C	166.49	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=483;Dels=0.01;HRun=0;HaplotypeScore=660.44;MQ=20.15;MQ0=61;QD=0.34;SB=-43.82	GT:AD:DP:GL:GQ	0/1:342,96:43:-35.67,-15.74,-120.66:99
+chr1	2573404	rs56352113	A	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=412;Dels=0.00;HRun=1;HaplotypeScore=785.14;MQ=20.24;MQ0=50;OQ=1746.05;QD=4.24;SB=-272.76	GT:AD:DP:GL:GQ	1/1:48,316:72:-242.08,-66.55,-63.89:26.61
+chr1	2573410	rs12759490	A	G	148.65	DPFilter;HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DB;DP=383;Dels=0.00;HRun=0;HaplotypeScore=682.21;MQ=20.35;MQ0=44;QD=0.39;SB=-43.26	GT:AD:DP:GL:GQ	0/1:276,96:57:-35.34,-17.19,-178.84:99
+chr1	2573423	.	C	A	163.64	DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=284;Dels=0.00;HRun=1;HaplotypeScore=927.03;MQ=21.34;MQ0=33;QD=0.58;SB=26.07	GT:AD:DP:GL:GQ	0/1:224,38:48:-34.11,-14.46,-128.40:99
+chr1	2573426	.	C	A	487.43	DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=275;Dels=0.00;HRun=0;HaplotypeScore=598.86;MQ=21.74;MQ0=31;QD=1.77;SB=-144.61	GT:AD:DP:GL:GQ	0/1:229,39:67:-72.21,-20.18,-167.89:99
+chr1	2573431	.	T	A	55.01	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=244;Dels=0.00;HRun=0;HaplotypeScore=414.88;MQ=22.20;MQ0=23;QD=0.23;SB=-37.64	GT:AD:DP:GL:GQ	0/1:198,17:62:-42.64,-33.85,-190.83:87.85
+chr1	2573439	rs12738268	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=199;Dels=0.00;HRun=0;HaplotypeScore=197.41;MQ=23.56;MQ0=17;OQ=1379.28;QD=6.93;SB=-473.52	GT:AD:DP:GL:GQ	0/1:75,107:51:-156.58,-15.37,-36.65:99
+chr1	2573442	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=0;HaplotypeScore=181.20;MQ=23.67;MQ0=14;OQ=103.36;QD=0.53;SB=32.13	GT:AD:DP:GL:GQ	0/1:179,11:55:-39.39,-25.77,-162.27:99
+chr1	2573451	.	A	G	329.45	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=156;Dels=0.00;HRun=0;HaplotypeScore=168.85;MQ=25.71;MQ0=9;QD=2.11;SB=-36.23	GT:AD:DP:GL:GQ	0/1:80,76:54:-52.50,-16.27,-154.97:99
+chr1	2573454	rs55760918	C	G	556.39	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=140;Dels=0.00;HRun=0;HaplotypeScore=206.74;MQ=26.90;MQ0=8;QD=3.97;SB=-52.80	GT:AD:DP:GL:GQ	0/1:46,88:51:-74.30,-15.38,-138.45:99
+chr1	2573455	rs56258540	A	C	134.39	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=145;Dels=0.00;HRun=1;HaplotypeScore=218.70;MQ=26.73;MQ0=9;QD=0.93;SB=-34.89	GT:AD:DP:GL:GQ	0/1:91,52:51:-34.62,-17.90,-142.52:99
+chr1	2573485	rs55714819	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=241;Dels=0.00;HRun=1;HaplotypeScore=172.11;MQ=27.92;MQ0=9;OQ=766.38;QD=3.18;SB=-61.60	GT:AD:DP:GL:GQ	0/1:152,84:106:-115.24,-35.32,-271.38:99
+chr1	2573510	rs61765777	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=332;Dels=0.00;HRun=1;HaplotypeScore=336.11;MQ=27.14;MQ0=14;OQ=2271.13;QD=6.84;SB=-383.23	GT:AD:DP:GL:GQ	0/1:103,229:130:-269.56,-39.16,-232.28:99
+chr1	2573523	.	C	T	271.88	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=476;Dels=0.00;HRun=0;HaplotypeScore=388.59;MQ=26.03;MQ0=25;QD=0.57;SB=-54.44	GT:AD:DP:GL:GQ	0/1:421,51:171:-82.00,-51.53,-495.80:99
+chr1	2573524	.	G	A	673.59	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=489;Dels=0.00;HRun=0;HaplotypeScore=381.72;MQ=26.07;MQ0=26;QD=1.38;SB=-235.66	GT:AD:DP:GL:GQ	0/1:348,136:174:-123.14,-52.50,-452.42:99
+chr1	2573532	.	A	G	266.78	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=584;Dels=0.00;HRun=0;HaplotypeScore=454.81;MQ=26.29;MQ0=38;QD=0.46;SB=-50.09	GT:AD:DP:GL:GQ	0/1:462,118:225:-100.76,-70.80,-803.69:99
+chr1	2573533	.	C	T	518.62	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=590;Dels=0.00;HRun=0;HaplotypeScore=454.86;MQ=26.25;MQ0=38;QD=0.88;SB=-177.22	GT:AD:DP:GL:GQ	0/1:555,34:221:-123.94,-68.80,-639.87:99
+chr1	2573545	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=760;Dels=0.00;HRun=0;HaplotypeScore=554.01;MQ=25.28;MQ0=58;OQ=2752.41;QD=3.62;SB=-334.08	GT:AD:DP:GL:GQ	0/1:504,247:275:-368.19,-89.67,-758.94:99
+chr1	2573551	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=816;Dels=0.00;HRun=0;HaplotypeScore=706.82;MQ=24.77;MQ0=61;OQ=92.57;QD=0.11;SB=99.33	GT:AD:DP:GL:GQ	0/1:767,48:306:-104.74,-92.20,-1021.89:99
+chr1	2573560	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=935;Dels=0.00;HRun=0;HaplotypeScore=771.90;MQ=24.19;MQ0=82;OQ=1354.07;QD=1.45;SB=-436.68	GT:AD:DP:GL:GQ	0/1:723,199:339:-248.95,-110.26,-942.99:99
+chr1	2573563	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=967;Dels=0.00;HRun=0;HaplotypeScore=867.36;MQ=23.97;MQ0=86;OQ=1389.93;QD=1.44;SB=161.22	GT:AD:DP:GL:GQ	0/1:819,137:345:-262.46,-120.18,-962.42:99
+chr1	2573572	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1012;Dels=0.00;HRun=0;HaplotypeScore=731.51;MQ=23.62;MQ0=98;OQ=634.63;QD=0.63;SB=-79.47	GT:AD:DP:GL:GQ	0/1:773,210:334:-172.80,-106.05,-1139.69:99
+chr1	2573600	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=878;Dels=0.00;HRun=0;HaplotypeScore=653.71;MQ=23.12;MQ0=120;OQ=1122.68;QD=1.28;SB=-567.08	GT:AD:DP:GL:GQ	0/1:678,154:296:-246.10,-130.55,-807.07:99
+chr1	2573603	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=862;Dels=0.00;HRun=0;HaplotypeScore=618.67;MQ=23.10;MQ0=123;OQ=316.50;QD=0.37;SB=-169.71	GT:AD:DP:GL:GQ	0/1:783,67:305:-136.37,-101.44,-918.41:99
+chr1	2573643	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=406;Dels=0.00;HRun=0;HaplotypeScore=240.70;MQ=22.59;MQ0=105;OQ=101.01;QD=0.25;SB=40.47	GT:AD:DP:GL:GQ	0/1:341,64:133:-53.47,-40.09,-445.02:99
+chr1	2573645	.	T	G	27.32	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=393;Dels=0.00;HRun=0;HaplotypeScore=214.15;MQ=22.61;MQ0=102;QD=0.07;SB=22.12	GT:AD:DP:GL:GQ	0/1:333,60:125:-43.68,-37.67,-396.83:60.15
+chr1	2573659	rs28581291	G	C	4615.63	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=333;Dels=0.00;HRun=1;HaplotypeScore=205.79;MQ=24.13;MQ0=78;QD=13.86;SB=-1212.00	GT:AD:DP:GL:GQ	0/1:35,294:132:-460.56,-39.52,-82.06:99
+chr1	2573662	.	C	T	559.05	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=354;Dels=0.00;HRun=0;HaplotypeScore=280.21;MQ=24.11;MQ0=79;QD=1.58;SB=-274.91	GT:AD:DP:GL:GQ	0/1:309,45:145:-102.89,-43.70,-398.94:99
+chr1	2573665	.	C	G	1510.34	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=408;Dels=0.00;HRun=0;HaplotypeScore=325.78;MQ=24.58;MQ0=76;QD=3.70;SB=-297.94	GT:AD:DP:GL:GQ	0/1:264,141:179:-211.73,-57.41,-536.45:99
+chr1	2573688	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=651;Dels=0.00;HRun=2;HaplotypeScore=395.85;MQ=24.99;MQ0=65;OQ=362.26;QD=0.56;SB=-155.57	GT:AD:DP:GL:GQ	0/1:581,65:307:-140.30,-100.79,-1081.14:99
+chr1	2573689	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=665;Dels=0.00;HRun=0;HaplotypeScore=525.06;MQ=24.91;MQ0=65;OQ=1827.67;QD=2.75;SB=-517.28	GT:AD:DP:GL:GQ	0/1:550,112:319:-282.15,-96.10,-903.12:99
+chr1	2573699	rs28514305	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=700;Dels=0.00;HRun=1;HaplotypeScore=627.89;MQ=25.13;MQ0=51;OQ=504.00;QD=0.72;SB=-50.28	GT:AD:DP:GL:GQ	0/1:553,135:325:-164.84,-111.15,-1100.31:99
+chr1	2573722	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=939;Dels=0.00;HRun=0;HaplotypeScore=511.14;MQ=24.55;MQ0=41;OQ=652.05;QD=0.69;SB=-156.78	GT:AD:DP:GL:GQ	0/1:833,100:448:-203.46,-134.97,-1376.56:99
+chr1	2573743	.	C	A	1376.46	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=920;Dels=0.01;HRun=1;HaplotypeScore=1049.31;MQ=24.03;MQ0=45;QD=1.50;SB=-654.94	GT:AD:DP:GL:GQ	0/1:771,125:393:-273.72,-132.79,-1119.66:99
+chr1	2573744	.	C	A	2246.36	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=920;Dels=0.00;HRun=0;HaplotypeScore=1100.48;MQ=24.05;MQ0=45;QD=2.44;SB=-774.39	GT:AD:DP:GL:GQ	0/1:696,198:389:-363.03,-135.11,-1033.83:99
+chr1	2573747	.	C	T	2541.21	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=900;Dels=0.00;HRun=0;HaplotypeScore=1014.50;MQ=23.93;MQ0=43;QD=2.82;SB=-593.64	GT:AD:DP:GL:GQ	0/1:671,157:361:-422.27,-164.86,-953.11:99
+chr1	2573753	.	A	T	936.20	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=863;Dels=0.00;HRun=0;HaplotypeScore=1289.29;MQ=23.50;MQ0=46;QD=1.08;SB=-444.50	GT:AD:DP:GL:GQ	0/1:735,98:311:-195.18,-98.28,-961.18:99
+chr1	2573759	.	C	T	306.11	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=786;Dels=0.00;HRun=0;HaplotypeScore=944.88;MQ=23.40;MQ0=46;QD=0.39;SB=80.59	GT:AD:DP:GL:GQ	0/1:568,186:262:-146.29,-112.39,-779.46:99
+chr1	2573762	.	C	T	1224.46	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=751;Dels=0.00;HRun=0;HaplotypeScore=1008.25;MQ=23.38;MQ0=43;QD=1.63;SB=32.31	GT:AD:DP:GL:GQ	0/1:549,181:260:-207.81,-82.08,-705.47:99
+chr1	2573768	.	G	A	69.35	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=690;Dels=0.00;HRun=0;HaplotypeScore=1128.47;MQ=23.25;MQ0=39;QD=0.10;SB=181.10	GT:AD:DP:GL:GQ	0/1:645,45:222:-77.09,-66.88,-732.33:99
+chr1	2573775	rs61765778	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=598;Dels=0.00;HRun=0;HaplotypeScore=829.09;MQ=23.11;MQ0=35;OQ=51.56;QD=0.09;SB=-51.39	GT:AD:DP:GL:GQ	0/1:411,178:176:-78.89,-70.45,-552.62:84.40
+chr1	2573784	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=482;Dels=0.00;HRun=0;HaplotypeScore=533.05;MQ=23.86;MQ0=35;OQ=97.06;QD=0.20;SB=-41.06	GT:AD:DP:GL:GQ	0/1:428,39:135:-57.53,-44.54,-428.93:99
+chr1	2573791	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=376;Dels=0.00;HRun=0;HaplotypeScore=279.62;MQ=25.08;MQ0=23;OQ=809.10;QD=2.15;SB=-122.99	GT:AD:DP:GL:GQ	0/1:249,119:103:-122.37,-38.18,-240.78:99
+chr1	2573803	rs61765779	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=238;Dels=0.00;HRun=0;HaplotypeScore=273.29;MQ=27.85;MQ0=11;OQ=738.52;QD=3.10;SB=-305.23	GT:AD:DP:GL:GQ	0/1:82,152:68:-97.64,-20.50,-141.62:99
+chr1	2573809	rs61765805	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.00;HRun=1;HaplotypeScore=207.51;MQ=30.86;MQ0=7;OQ=486.71;QD=2.85;SB=-123.47	GT:AD:DP:GL:GQ	0/1:47,107:55:-75.59,-23.64,-159.88:99
+chr1	2573825	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=103;Dels=0.04;HRun=2;HaplotypeScore=133.51;MQ=37.12;MQ0=1;OQ=152.18;QD=1.48;SB=68.24	GT:AD:DP:GL:GQ	0/1:42,51:50:-47.81,-29.31,-160.18:99
+chr1	2573831	rs55855140	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=126.91;MQ=39.65;MQ0=1;OQ=158.89;QD=1.62;SB=62.19	GT:AD:DP:GL:GQ	0/1:53,43:46:-39.96,-20.79,-124.08:99
+chr1	2573842	.	A	C	115.63	SnpCluster	AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=142.04;MQ=40.93;MQ0=1;QD=1.17;SB=-71.86	GT:AD:DP:GL:GQ	0/1:45,45:51:-30.22,-15.37,-141.99:99
+chr1	2573846	rs61765806	C	G	427.99	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=158.02;MQ=39.65;MQ0=2;QD=3.34;SB=50.19	GT:AD:DP:GL:GQ	0/1:94,33:65:-65.70,-19.61,-201.59:99
+chr1	2573851	.	G	A	820.83	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=140;Dels=0.00;HRun=1;HaplotypeScore=122.19;MQ=40.52;MQ0=2;QD=5.86;SB=-152.15	GT:AD:DP:GL:GQ	0/1:66,72:74:-107.66,-22.30,-166.53:99
+chr1	2573859	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=126.84;MQ=40.41;MQ0=2;OQ=121.72;QD=0.77;SB=152.53	GT:AD:DP:GL:GQ	0/1:122,36:93:-43.49,-28.03,-346.24:99
+chr1	2573901	rs35515286	G	C	550.86	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=206;Dels=0.00;HRun=0;HaplotypeScore=105.96;MQ=43.03;MQ0=1;QD=2.67;SB=237.50	GT:AD:DP:GL:GQ	0/1:135,63:142:-119.31,-60.94,-520.06:99
+chr1	2573904	.	G	C	824.37	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=3;HaplotypeScore=109.03;MQ=42.87;MQ0=2;QD=4.04;SB=193.35	GT:AD:DP:GL:GQ	0/1:129,71:137:-131.62,-45.90,-468.47:99
+chr1	2573907	.	C	T	232.33	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=234;Dels=0.00;HRun=0;HaplotypeScore=169.38;MQ=41.15;MQ0=2;QD=0.99;SB=246.29	GT:AD:DP:GL:GQ	0/1:198,35:151:-72.01,-45.49,-466.42:99
+chr1	2573937	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=313;Dels=0.00;HRun=2;HaplotypeScore=156.05;MQ=41.48;MQ0=6;OQ=610.21;QD=1.95;SB=184.28	GT:AD:DP:GL:GQ	0/1:179,131:178:-121.09,-56.78,-561.52:99
+chr1	2573955	rs4648664	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=309;Dels=0.01;HRun=0;HaplotypeScore=189.00;MQ=39.75;MQ0=9;OQ=5144.30;QD=16.65;SB=-1373.56	GT:AD:DP:GL:GQ	0/1:99,207:204:-513.43,-64.42,-219.84:99
+chr1	2573957	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=309;Dels=0.00;HRun=0;HaplotypeScore=210.03;MQ=39.51;MQ0=9;OQ=1411.76;QD=4.57;SB=186.52	GT:AD:DP:GL:GQ	0/1:164,144:192:-204.89,-60.43,-482.07:99
+chr1	2573977	rs36074084	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=329;Dels=0.14;HRun=3;HaplotypeScore=420.13;MQ=34.94;MQ0=9;OQ=1855.95;QD=5.64;SB=145.19	GT:AD:DP:GL:GQ	0/1:152,125:193:-244.66,-55.78,-561.08:99
+chr1	2573987	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=436;Dels=0.02;HRun=3;HaplotypeScore=523.62;MQ=29.87;MQ0=18;OQ=97.02;QD=0.22;SB=235.20	GT:AD:DP:GL:GQ	0/1:315,109:216:-76.87,-63.88,-657.84:99
+chr1	2574006	rs56001931	C	A	193.50	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=578;Dels=0.00;HRun=0;HaplotypeScore=796.32;MQ=26.82;MQ0=27;QD=0.33;SB=-95.26	GT:AD:DP:GL:GQ	0/1:506,46:197:-84.56,-61.92,-620.37:99
+chr1	2574010	.	G	A	47.43	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=576;Dels=0.00;HRun=1;HaplotypeScore=936.31;MQ=26.86;MQ0=27;QD=0.08;SB=305.98	GT:AD:DP:GL:GQ	0/1:514,37:196:-70.15,-62.12,-641.00:80.27
+chr1	2574012	.	G	A	1112.09	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=567;Dels=0.00;HRun=1;HaplotypeScore=881.66;MQ=26.70;MQ0=27;QD=1.96;SB=173.94	GT:AD:DP:GL:GQ	0/1:337,218:205:-176.25,-61.76,-573.77:99
+chr1	2574013	rs35375421	G	C	2739.83	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=556;Dels=0.00;HRun=0;HaplotypeScore=907.42;MQ=26.74;MQ0=27;QD=4.93;SB=-98.82	GT:AD:DP:GL:GQ	0/1:185,358:186:-340.69,-63.42,-477.87:99
+chr1	2574046	rs61765808	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=633;Dels=0.00;HRun=1;HaplotypeScore=769.62;MQ=25.77;MQ0=33;OQ=2369.47;QD=3.74;SB=-14.31	GT:AD:DP:GL:GQ	0/1:214,394:219:-332.81,-92.58,-459.77:99
+chr1	2574062	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=571;Dels=0.02;HRun=0;HaplotypeScore=1395.05;MQ=27.31;MQ0=25;OQ=270.74;QD=0.47;SB=9.21	GT:AD:DP:GL:GQ	0/1:393,159:156:-79.45,-49.09,-466.84:99
+chr1	2574081	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=574;Dels=0.00;HRun=0;HaplotypeScore=636.02;MQ=28.62;MQ0=23;OQ=102.79;QD=0.18;SB=258.30	GT:AD:DP:GL:GQ	0/1:339,178:156:-99.87,-86.31,-482.50:99
+chr1	2574099	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=481;Dels=0.01;HRun=2;HaplotypeScore=469.12;MQ=32.08;MQ0=15;OQ=332.15;QD=0.69;SB=-15.43	GT:AD:DP:GL:GQ	0/1:184,278:155:-88.85,-52.35,-456.19:99
+chr1	2574112	rs4648665	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=407;Dels=0.00;HRun=1;HaplotypeScore=376.40;MQ=32.86;MQ0=13;OQ=5520.38;QD=13.56;SB=-1708.96	GT:AD:DP:GL:GQ	1/1:7,385:151:-551.04,-45.49,-0.05:99
+chr1	2574233	rs6678571	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=482;Dels=0.00;HRun=0;HaplotypeScore=317.44;MQ=37.14;MQ0=103;OQ=51.18;QD=0.11;SB=33.13	GT:AD:DP:GL:GQ	0/1:400,76:222:-75.35,-66.94,-654.61:84.02
+chr1	2574280	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=411;Dels=0.00;HRun=0;HaplotypeScore=206.24;MQ=40.63;MQ0=25;OQ=702.83;QD=1.71;SB=165.25	GT:AD:DP:GL:GQ	0/1:262,145:248:-148.35,-74.78,-882.77:99
+chr1	2574370	rs56005609	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=224;Dels=0.00;HRun=0;HaplotypeScore=51.47;MQ=47.47;MQ0=12;OQ=160.10;QD=0.71;SB=-105.06	GT:AD:DP:GL:GQ	0/1:203,21:172:-71.19,-51.89,-483.26:99
+chr1	2574383	rs4648666	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=215;Dels=0.00;HRun=0;HaplotypeScore=154.22;MQ=48.52;MQ0=8;OQ=4531.65;QD=21.08;SB=-1293.59	GT:AD:DP:GL:GQ	0/1:45,169:169:-452.16,-50.92,-131.50:99
+chr1	2574398	rs4648667	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=297;Dels=0.00;HRun=0;HaplotypeScore=177.69;MQ=43.72;MQ0=17;OQ=1775.91;QD=5.98;SB=-869.96	GT:AD:DP:GL:GQ	0/1:211,86:190:-238.16,-57.29,-446.26:99
+chr1	2574435	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=784;Dels=0.00;HRun=0;HaplotypeScore=476.42;MQ=30.94;MQ0=61;OQ=552.66;QD=0.70;SB=-126.39	GT:AD:DP:GL:GQ	0/1:497,287:235:-129.39,-70.84,-631.70:99
+chr1	2574468	.	A	C	45.91	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=925;Dels=0.00;HRun=3;HaplotypeScore=499.34;MQ=30.78;MQ0=79;QD=0.05;SB=344.95	GT:AD:DP:GL:GQ	0/1:799,98:301:-105.40,-97.53,-960.73:78.74
+chr1	2574499	.	C	A	22.95	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=665;Dels=0.00;HRun=2;HaplotypeScore=681.86;MQ=36.15;MQ0=63;QD=0.03;SB=89.36	GT:AD:DP:GL:GQ	0/1:533,92:270:-145.98,-140.40,-853.73:55.76
+chr1	2574516	rs61765812	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=416;Dels=0.00;HRun=0;HaplotypeScore=217.32;MQ=43.57;MQ0=35;OQ=129.59;QD=0.31;SB=68.68	GT:AD:DP:GL:GQ	0/1:278,133:243:-89.48,-73.24,-851.13:99
+chr1	2574566	rs28558799	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=282;Dels=0.00;HRun=0;HaplotypeScore=119.44;MQ=43.46;MQ0=13;OQ=5625.16;QD=19.95;SB=-2459.11	GT:AD:DP:GL:GQ	0/1:49,230:200:-561.52,-60.25,-174.15:99
+chr1	2574594	rs56062029	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=452;Dels=0.00;HRun=2;HaplotypeScore=294.75;MQ=33.13;MQ0=30;OQ=1117.30;QD=2.47;SB=-453.09	GT:AD:DP:GL:GQ	0/1:369,56:211:-181.97,-66.96,-565.43:99
+chr1	2574621	rs57267388	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=571;Dels=0.00;HRun=0;HaplotypeScore=771.91;MQ=31.23;MQ0=33;OQ=342.14;QD=0.60;SB=-185.77	GT:AD:DP:GL:GQ	0/1:283,102:222:-153.52,-116.02,-729.22:99
+chr1	2574649	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=993;Dels=0.00;HRun=0;HaplotypeScore=693.61;MQ=28.27;MQ0=75;OQ=1079.32;QD=1.09;SB=-556.01	GT:AD:DP:GL:GQ	0/1:844,137:401:-235.64,-124.42,-1471.20:99
+chr1	2574659	.	A	C	29.66	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=980;Dels=0.00;HRun=3;HaplotypeScore=948.25;MQ=27.73;MQ0=79;QD=0.03;SB=242.38	GT:AD:DP:GL:GQ	0/1:842,123:385:-128.64,-122.39,-1217.71:62.50
+chr1	2574737	rs61765814	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=400;Dels=0.00;HRun=0;HaplotypeScore=203.09;MQ=41.26;MQ0=24;OQ=736.68;QD=1.84;SB=-0.60	GT:AD:DP:GL:GQ	0/1:202,185:205:-145.42,-68.47,-717.91:99
+chr1	2574757	rs61765815	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=370;Dels=0.00;HRun=0;HaplotypeScore=249.27;MQ=42.55;MQ0=25;OQ=384.28;QD=1.04;SB=73.46	GT:AD:DP:GL:GQ	0/1:205,136:201:-108.67,-66.96,-637.57:99
+chr1	2574806	rs61765816	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=433;Dels=0.00;HRun=0;HaplotypeScore=271.20;MQ=41.78;MQ0=23;OQ=447.69;QD=1.03;SB=-108.45	GT:AD:DP:GL:GQ	0/1:271,156:236:-119.20,-71.14,-762.60:99
+chr1	2574851	rs6691639	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=333;Dels=0.00;HRun=0;HaplotypeScore=216.92;MQ=45.13;MQ0=5;OQ=7151.39;QD=21.48;SB=-2958.67	GT:AD:DP:GL:GQ	0/1:25,306:212:-714.14,-63.86,-81.27:99
+chr1	2574904	rs6604990	T	C	6413.62	DPFilter;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=427;Dels=0.06;HRun=3;HaplotypeScore=563.84;MQ=34.54;MQ0=9;QD=15.02;SB=-2045.14	GT:AD:DP:GL:GQ	1/1:119,272:189:-640.36,-56.34,-15.02:99
+chr1	2574911	.	A	C	149.58	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=456;Dels=0.00;HRun=3;HaplotypeScore=557.08;MQ=32.46;MQ0=11;QD=0.33;SB=-79.57	GT:AD:DP:GL:GQ	0/1:298,141:171:-69.76,-51.52,-530.42:99
+chr1	2574914	.	A	G	786.99	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=464;Dels=0.02;HRun=1;HaplotypeScore=590.68;MQ=31.99;MQ0=11;QD=1.70;SB=-166.87	GT:AD:DP:GL:GQ	0/1:189,264:184:-140.25,-58.27,-581.91:99
+chr1	2574924	rs61765818	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=562;Dels=0.00;HRun=1;HaplotypeScore=584.85;MQ=29.44;MQ0=16;OQ=664.13;QD=1.18;SB=-72.04	GT:AD:DP:GL:GQ	0/1:412,132:178:-126.09,-56.39,-566.98:99
+chr1	2574942	rs60506177	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=681;Dels=0.00;HRun=2;HaplotypeScore=1240.22;MQ=29.22;MQ0=28;OQ=4364.77;QD=6.41;SB=-1487.53	GT:AD:DP:GL:GQ	0/1:160,495:256:-435.48,-89.03,-503.32:99
+chr1	2574956	rs59191334	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=906;Dels=0.00;HRun=0;HaplotypeScore=851.71;MQ=29.72;MQ0=44;OQ=1149.69;QD=1.27;SB=-284.23	GT:AD:DP:GL:GQ	0/1:632,252:274:-200.91,-82.66,-713.01:99
+chr1	2574986	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=944;Dels=0.00;HRun=1;HaplotypeScore=1818.61;MQ=31.01;MQ0=59;OQ=1122.41;QD=1.19;SB=-398.32	GT:AD:DP:GL:GQ	0/1:745,146:351:-246.18,-130.65,-980.48:99
+chr1	2575019	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=719;Dels=0.00;HRun=0;HaplotypeScore=472.84;MQ=36.86;MQ0=62;OQ=2013.75;QD=2.80;SB=-548.67	GT:AD:DP:GL:GQ	0/1:509,205:351:-310.40,-105.75,-919.85:99
+chr1	2575034	rs61763547	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=646;Dels=0.00;HRun=1;HaplotypeScore=246.19;MQ=38.01;MQ0=57;OQ=1218.08;QD=1.89;SB=297.56	GT:AD:DP:GL:GQ	0/1:304,285:351:-300.74,-175.64,-1150.43:99
+chr1	2575068	.	C	G	824.18	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=841;Dels=0.00;HRun=0;HaplotypeScore=834.43;MQ=32.24;MQ0=93;QD=0.98;SB=69.34	GT:AD:DP:GL:GQ	0/1:592,151:395:-352.89,-267.19,-1451.52:99
+chr1	2575069	rs11510858	C	A	2054.73	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=851;Dels=0.00;HRun=0;HaplotypeScore=833.69;MQ=32.03;MQ0=94;QD=2.41;SB=-732.04	GT:AD:DP:GL:GQ	0/1:701,130:386:-337.44,-128.68,-1037.66:99
+chr1	2575076	.	C	G	56.74	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=869;Dels=0.00;HRun=2;HaplotypeScore=716.58;MQ=31.37;MQ0=95;QD=0.07;SB=276.82	GT:AD:DP:GL:GQ	0/1:773,41:392:-146.00,-137.04,-1458.73:89.57
+chr1	2575191	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=619;Dels=0.01;HRun=3;HaplotypeScore=666.18;MQ=32.68;MQ0=22;OQ=1037.47;QD=1.68;SB=-98.59	GT:AD:DP:GL:GQ	0/1:385,224:265:-186.87,-79.84,-734.84:99
+chr1	2575196	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=669;Dels=0.00;HRun=0;HaplotypeScore=585.81;MQ=31.95;MQ0=25;OQ=410.40;QD=0.61;SB=138.71	GT:AD:DP:GL:GQ	0/1:518,139:278:-128.14,-83.81,-902.17:99
+chr1	2575224	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=936;Dels=0.00;HRun=0;HaplotypeScore=711.05;MQ=30.70;MQ0=52;OQ=206.48;QD=0.22;SB=16.18	GT:AD:DP:GL:GQ	0/1:817,101:399:-165.30,-141.37,-1545.34:99
+chr1	2575246	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=981;Dels=0.00;HRun=1;HaplotypeScore=733.47;MQ=31.11;MQ0=67;OQ=1892.73;QD=1.93;SB=-760.65	GT:AD:DP:GL:GQ	0/1:771,204:430:-322.12,-129.56,-1274.76:99
+chr1	2575261	rs6692051	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=945;Dels=0.00;HRun=3;HaplotypeScore=358.84;MQ=32.03;MQ0=68;OQ=2338.43;QD=2.47;SB=-661.83	GT:AD:DP:GL:GQ	0/1:802,142:427:-365.78,-128.65,-1131.84:99
+chr1	2575299	.	G	T	161.49	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=614;Dels=0.00;HRun=1;HaplotypeScore=591.39;MQ=37.63;MQ0=50;QD=0.26;SB=20.79	GT:AD:DP:GL:GQ	0/1:494,69:362:-227.05,-207.62,-1136.93:99
+chr1	2575300	rs61765821	T	C	1192.57	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=603;Dels=0.00;HRun=0;HaplotypeScore=567.88;MQ=38.04;MQ0=47;QD=1.98;SB=-535.85	GT:AD:DP:GL:GQ	0/1:348,222:348:-246.80,-124.26,-1045.28:99
+chr1	2575308	.	C	A	283.33	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=591;Dels=0.00;HRun=1;HaplotypeScore=502.16;MQ=39.21;MQ0=53;QD=0.48;SB=90.50	GT:AD:DP:GL:GQ	0/1:465,102:356:-142.06,-110.45,-1099.38:99
+chr1	2575350	rs28411086	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=541;Dels=0.00;HRun=2;HaplotypeScore=281.76;MQ=38.20;MQ0=48;OQ=2021.31;QD=3.74;SB=-545.18	GT:AD:DP:GL:GQ	0/1:247,291:277:-288.88,-83.46,-673.01:99
+chr1	2575391	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=992;Dels=0.00;HRun=2;HaplotypeScore=510.05;MQ=30.36;MQ0=68;OQ=227.39;QD=0.23;SB=145.08	GT:AD:DP:GL:GQ	0/1:854,132:434:-160.44,-134.42,-1359.22:99
+chr1	2575398	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1075;Dels=0.00;HRun=0;HaplotypeScore=310.34;MQ=30.19;MQ0=65;OQ=528.27;QD=0.49;SB=20.12	GT:AD:DP:GL:GQ	0/1:895,162:479:-203.83,-147.72,-1593.06:99
+chr1	2575422	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1315;Dels=0.00;HRun=1;HaplotypeScore=628.02;MQ=29.05;MQ0=70;OQ=417.47;QD=0.32;SB=307.23	GT:AD:DP:GL:GQ	0/1:1146,168:592:-223.40,-178.37,-1814.12:99
+chr1	2575443	rs6678990	C	G	1968.81	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=1397;Dels=0.00;HRun=0;HaplotypeScore=834.10;MQ=29.41;MQ0=63;QD=1.41;SB=-880.90	GT:AD:DP:GL:GQ	0/1:1263,104:657:-428.32,-228.16,-2407.74:99
+chr1	2575448	.	C	T	306.07	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=1347;Dels=0.00;HRun=0;HaplotypeScore=969.72;MQ=29.55;MQ0=58;QD=0.23;SB=98.85	GT:AD:DP:GL:GQ	0/1:1166,127:596:-237.42,-203.53,-1765.67:99
+chr1	2575453	.	G	A	633.22	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=1324;Dels=0.01;HRun=0;HaplotypeScore=1094.28;MQ=29.55;MQ0=52;QD=0.48;SB=22.83	GT:AD:DP:GL:GQ	0/1:1098,210:631:-255.45,-188.85,-1774.06:99
+chr1	2575459	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1275;Dels=0.00;HRun=1;HaplotypeScore=976.35;MQ=29.72;MQ0=48;OQ=260.30;QD=0.20;SB=456.22	GT:AD:DP:GL:GQ	0/1:1186,88:626:-217.90,-188.59,-2068.65:99
+chr1	2575467	.	A	T	1827.05	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=1257;Dels=0.00;HRun=0;HaplotypeScore=1002.71;MQ=30.06;MQ0=39;QD=1.45;SB=-471.84	GT:AD:DP:GL:GQ	0/1:1025,208:608:-372.29,-186.30,-1881.69:99
+chr1	2575472	.	C	A	9687.38	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=1255;Dels=0.00;HRun=1;HaplotypeScore=858.65;MQ=30.07;MQ0=41;QD=7.72;SB=-1503.87	GT:AD:DP:GL:GQ	0/1:729,316:639:-967.74,-542.07,-1662.70:99
+chr1	2575476	rs28479903	C	T	328.26	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=1232;Dels=0.00;HRun=0;HaplotypeScore=989.29;MQ=30.12;MQ0=43;QD=0.27;SB=122.56	GT:AD:DP:GL:GQ	0/1:1040,174:572:-219.19,-183.08,-1716.97:99
+chr1	2575484	rs61765822	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=1214;Dels=0.00;HRun=0;HaplotypeScore=468.08;MQ=30.51;MQ0=43;OQ=1888.53;QD=1.56;SB=-874.96	GT:AD:DP:GL:GQ	0/1:984,212:602:-396.91,-204.77,-1679.64:99
+chr1	2575509	rs7367485	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=1003;Dels=0.00;HRun=3;HaplotypeScore=708.39;MQ=31.59;MQ0=44;OQ=1317.31;QD=1.31;SB=-683.17	GT:AD:DP:GL:GQ	0/1:599,311:447:-397.20,-262.18,-1298.11:99
+chr1	2575527	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=899;Dels=0.00;HRun=1;HaplotypeScore=616.46;MQ=32.40;MQ0=36;OQ=2129.63;QD=2.37;SB=-658.87	GT:AD:DP:GL:GQ	0/1:666,188:432:-362.76,-146.52,-1154.94:99
+chr1	2575536	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=816;Dels=0.00;HRun=1;HaplotypeScore=629.02;MQ=33.06;MQ0=36;OQ=245.82;QD=0.30;SB=187.48	GT:AD:DP:GL:GQ	0/1:660,150:389:-147.61,-119.74,-1232.57:99
+chr1	2575553	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=672;Dels=0.00;HRun=0;HaplotypeScore=869.01;MQ=35.62;MQ0=23;OQ=1048.35;QD=1.56;SB=44.73	GT:AD:DP:GL:GQ	0/1:542,123:340:-220.20,-112.08,-1057.17:99
+chr1	2575577	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=529;Dels=0.00;HRun=0;HaplotypeScore=616.14;MQ=41.10;MQ0=11;OQ=295.55;QD=0.56;SB=93.12	GT:AD:DP:GL:GQ	0/1:363,155:340:-135.27,-102.43,-1079.29:99
+chr1	2575583	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=497;Dels=0.00;HRun=0;HaplotypeScore=739.15;MQ=41.67;MQ0=9;OQ=177.97;QD=0.36;SB=340.79	GT:AD:DP:GL:GQ	0/1:426,63:314:-122.58,-101.50,-1218.09:99
+chr1	2575632	rs6686754	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=363;Dels=0.00;HRun=1;HaplotypeScore=439.13;MQ=46.08;MQ0=4;OQ=7215.73;QD=19.88;SB=-2967.87	GT:AD:DP:GL:GQ	0/1:59,294:248:-720.57,-74.71,-189.55:99
+chr1	2575661	rs28498367	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=482;Dels=0.00;HRun=0;HaplotypeScore=598.03;MQ=41.57;MQ0=4;OQ=4453.10;QD=9.24;SB=-977.05	GT:AD:DP:GL:GQ	0/1:194,269:275:-444.31,-82.91,-730.02:99
+chr1	2575692	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=647;Dels=0.00;HRun=1;HaplotypeScore=594.08;MQ=36.97;MQ0=17;OQ=2155.18;QD=3.33;SB=272.10	GT:AD:DP:GL:GQ	0/1:259,365:295:-329.81,-111.01,-802.38:99
+chr1	2575711	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=667;Dels=0.00;HRun=3;HaplotypeScore=1191.59;MQ=36.49;MQ0=18;OQ=1467.43;QD=2.20;SB=-170.23	GT:AD:DP:GL:GQ	0/1:245,407:245:-231.00,-80.98,-619.30:99
+chr1	2575718	.	C	T	91.63	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=668;Dels=0.07;HRun=0;HaplotypeScore=726.36;MQ=36.74;MQ0=18;QD=0.14;SB=390.06	GT:AD:DP:GL:GQ	0/1:453,157:278:-93.88,-81.43,-798.07:99
+chr1	2575725	.	C	T	321.62	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=662;Dels=0.00;HRun=1;HaplotypeScore=724.85;MQ=36.17;MQ0=17;QD=0.49;SB=411.17	GT:AD:DP:GL:GQ	0/1:600,56:323:-132.74,-97.29,-1057.81:99
+chr1	2575728	.	A	T	148.72	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=660;Dels=0.00;HRun=0;HaplotypeScore=737.53;MQ=36.50;MQ0=17;QD=0.23;SB=417.37	GT:AD:DP:GL:GQ	0/1:600,48:321:-114.85,-96.69,-1096.48:99
+chr1	2575731	.	G	A	128.25	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=638;Dels=0.00;HRun=1;HaplotypeScore=523.34;MQ=37.45;MQ0=16;QD=0.20;SB=259.66	GT:AD:DP:GL:GQ	0/1:525,83:335:-143.82,-127.71,-1107.68:99
+chr1	2575750	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=473;Dels=0.00;HRun=1;HaplotypeScore=339.24;MQ=40.86;MQ0=6;OQ=314.90;QD=0.67;SB=-156.95	GT:AD:DP:GL:GQ	0/1:417,42:281:-123.25,-88.47,-781.88:99
+chr1	2575766	rs6694964	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=418;Dels=0.00;HRun=0;HaplotypeScore=190.54;MQ=43.00;MQ0=6;OQ=9217.59;QD=22.05;SB=-3555.11	GT:AD:DP:GL:GQ	0/1:33,383:267:-920.76,-80.43,-83.85:34.20
+chr1	2575784	rs28583924	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=426;Dels=0.00;HRun=0;HaplotypeScore=272.61;MQ=42.95;MQ0=8;OQ=181.28;QD=0.43;SB=6.29	GT:AD:DP:GL:GQ	0/1:359,64:257:-98.92,-77.51,-960.45:99
+chr1	2575825	rs6689281	T	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=557;Dels=0.01;HRun=2;HaplotypeScore=469.61;MQ=35.81;MQ0=25;OQ=9475.08;QD=17.01;SB=-3650.18	GT:AD:DP:GL:GQ	1/1:3,541:282:-946.51,-86.27,-2.51:99
+chr1	2575851	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=634;Dels=0.00;HRun=0;HaplotypeScore=686.59;MQ=33.18;MQ0=30;OQ=77.00;QD=0.12;SB=-18.66	GT:AD:DP:GL:GQ	0/1:437,151:251:-86.73,-75.75,-723.32:99
+chr1	2575861	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=670;Dels=0.00;HRun=0;HaplotypeScore=1084.95;MQ=32.16;MQ0=34;OQ=174.30;QD=0.26;SB=144.01	GT:AD:DP:GL:GQ	0/1:448,201:255:-97.68,-76.97,-707.97:99
+chr1	2575918	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=659;Dels=0.00;HRun=0;HaplotypeScore=602.10;MQ=33.55;MQ0=33;OQ=1205.47;QD=1.83;SB=-331.68	GT:AD:DP:GL:GQ	0/1:520,139:294:-212.43,-88.60,-836.61:99
+chr1	2575963	rs61765824	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=414;Dels=0.00;HRun=0;HaplotypeScore=225.65;MQ=45.71;MQ0=16;OQ=175.37;QD=0.42;SB=-3.54	GT:AD:DP:GL:GQ	0/1:256,154:262:-99.81,-78.99,-882.64:99
+chr1	2576027	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=375;Dels=0.00;HRun=0;HaplotypeScore=441.20;MQ=41.08;MQ0=22;OQ=359.44;QD=0.96;SB=-25.38	GT:AD:DP:GL:GQ	0/1:347,27:212:-103.15,-63.92,-790.76:99
+chr1	2576035	rs55917765	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=384;Dels=0.02;HRun=4;HaplotypeScore=406.51;MQ=41.42;MQ0=19;OQ=289.17;QD=0.75;SB=-132.89	GT:AD:DP:GL:GQ	0/1:212,141:214:-106.50,-74.30,-717.21:99
+chr1	2576075	rs57994724	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=300;Dels=0.03;HRun=4;HaplotypeScore=363.80;MQ=42.84;MQ0=2;OQ=76.42;QD=0.25;SB=-28.60	GT:AD:DP:GL:GQ	0/1:192,90:162:-61.96,-51.03,-580.93:99
+chr1	2576111	rs58221160	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=281;Dels=0.00;HRun=1;HaplotypeScore=182.21;MQ=43.93;MQ0=7;OQ=597.72;QD=2.13;SB=-221.46	GT:AD:DP:GL:GQ	0/1:232,45:207:-125.42,-62.37,-596.71:99
+chr1	2576240	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1159;Dels=0.00;HRun=0;HaplotypeScore=623.69;MQ=25.02;MQ0=69;OQ=409.78;QD=0.35;SB=-223.95	GT:AD:DP:GL:GQ	0/1:968,178:369:-162.51,-118.25,-1426.92:99
+chr1	2576263	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1066;Dels=0.00;HRun=1;HaplotypeScore=622.37;MQ=26.52;MQ0=59;OQ=159.54;QD=0.15;SB=19.45	GT:AD:DP:GL:GQ	0/1:984,81:387:-135.82,-116.58,-1209.01:99
+chr1	2576333	.	C	G	40.07	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=1;HaplotypeScore=154.83;MQ=40.65;MQ0=29;QD=0.18;SB=-8.93	GT:AD:DP:GL:GQ	0/1:181,32:158:-64.21,-56.92,-644.64:72.91
+chr1	2576335	.	C	T	1221.15	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=0;HaplotypeScore=167.65;MQ=40.55;MQ0=30;QD=5.65;SB=-581.17	GT:AD:DP:GL:GQ	0/1:122,94:144:-168.83,-43.43,-331.79:99
+chr1	2576336	rs28676518	G	A	1105.16	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=214;Dels=0.00;HRun=0;HaplotypeScore=205.71;MQ=40.45;MQ0=30;QD=5.16;SB=-168.80	GT:AD:DP:GL:GQ	0/1:170,44:143:-156.87,-43.08,-364.02:99
+chr1	2576346	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=74.98;MQ=40.01;MQ0=31;OQ=210.24;QD=1.17;SB=-126.34	GT:AD:DP:GL:GQ	0/1:138,41:111:-57.78,-33.47,-394.51:99
+chr1	2576366	rs61765835	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=158;Dels=0.00;HRun=0;HaplotypeScore=35.61;MQ=33.02;MQ0=57;OQ=96.35;QD=0.61;SB=-36.52	GT:AD:DP:GL:GQ	0/1:92,66:79:-36.73,-23.81,-255.03:99
+chr1	2576428	rs61765837	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=303;Dels=0.00;HRun=2;HaplotypeScore=260.74;MQ=16.89;MQ0=145;OQ=101.18;QD=0.33;SB=-66.11	GT:AD:DP:GL:GQ	0/1:155,144:52:-29.09,-15.69,-174.52:99
+chr1	2576448	rs61765838	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=595;Dels=0.00;HRun=0;HaplotypeScore=426.54;MQ=17.45;MQ0=199;OQ=372.66;QD=0.63;SB=-42.53	GT:AD:DP:GL:GQ	0/1:377,206:114:-74.98,-34.43,-280.80:99
+chr1	2576460	rs61765839	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=687;Dels=0.00;HRun=1;HaplotypeScore=471.75;MQ=17.40;MQ0=212;OQ=453.85;QD=0.66;SB=-3.98	GT:AD:DP:GL:GQ	0/1:511,164:138:-90.25,-41.59,-375.50:99
+chr1	2576472	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=774;Dels=0.03;HRun=1;HaplotypeScore=800.59;MQ=17.54;MQ0=228;OQ=234.98;QD=0.30;SB=-38.37	GT:AD:DP:GL:GQ	0/1:618,98:166:-76.78,-50.00,-493.07:99
+chr1	2576534	rs57105227	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=374;Dels=0.00;HRun=1;HaplotypeScore=347.91;MQ=18.87;MQ0=112;OQ=329.07;QD=0.88;SB=-154.80	GT:AD:DP:GL:GQ	0/1:156,198:111:-73.27,-37.08,-391.39:99
+chr1	2576577	rs4648668	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=122;Dels=0.00;HRun=1;HaplotypeScore=59.62;MQ=22.81;MQ0=26;OQ=851.22;QD=6.98;SB=10.08	GT:AD:DP:GL:GQ	0/1:55,66:69:-109.20,-20.79,-201.97:99
+chr1	2576600	rs4648566	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=1;HaplotypeScore=109.15;MQ=20.95;MQ0=39;OQ=455.68;QD=3.38;SB=83.24	GT:AD:DP:GL:GQ	0/1:105,30:52:-64.51,-15.66,-117.10:99
+chr1	2576616	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=178.18;MQ=20.10;MQ0=38;OQ=374.43;QD=2.62;SB=-39.54	GT:AD:DP:GL:GQ	0/1:116,27:44:-54.00,-13.27,-93.80:99
+chr1	2576848	rs61765840	G	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=141;Dels=0.00;HRun=1;HaplotypeScore=22.44;MQ=39.05;MQ0=35;OQ=52.46;QD=0.37;SB=-15.32	GT:AD:DP:GL:GQ	0/1:129,12:77:-31.72,-23.19,-231.93:85.30
+chr1	2577010	rs4648671	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=239;Dels=0.00;HRun=0;HaplotypeScore=65.16;MQ=37.14;MQ0=12;OQ=5199.52;QD=21.76;SB=-2266.90	GT:AD:DP:GL:GQ	1/1:7,232:163:-518.95,-49.17,-3.73:99
+chr1	2577062	rs28507281	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=295;Dels=0.00;HRun=0;HaplotypeScore=78.67;MQ=40.58;MQ0=11;OQ=1143.65;QD=3.88;SB=-492.64	GT:AD:DP:GL:GQ	0/1:238,57:237:-189.11,-71.46,-605.04:99
+chr1	2577084	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=307;Dels=0.00;HRun=0;HaplotypeScore=72.39;MQ=39.59;MQ0=17;OQ=519.07;QD=1.69;SB=-15.56	GT:AD:DP:GL:GQ	0/1:259,48:248:-129.89,-74.70,-751.71:99
+chr1	2577123	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=291;Dels=0.00;HRun=1;HaplotypeScore=84.53;MQ=39.37;MQ0=26;OQ=265.40;QD=0.91;SB=-39.23	GT:AD:DP:GL:GQ	0/1:250,41:219:-95.80,-65.98,-773.71:99
+chr1	2577397	rs58719822	G	C	0.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=190;Dels=0.00;HRun=0;HaplotypeScore=14.16;MQ=39.42;MQ0=19;OQ=6097.98;QD=32.09;SB=-764.81	GT:AD:DP:GL:GQ	1/1:1,189:137:-608.80,-41.28,-0.05:99
+chr1	2577433	rs60264562	G	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=207;Dels=0.05;HRun=4;HaplotypeScore=105.46;MQ=35.87;MQ0=25;OQ=5113.11;QD=24.70;SB=-614.98	GT:AD:DP:GL:GQ	1/1:9,184:123:-510.31,-38.53,-16.18:99
+chr1	2577515	.	A	C	17.95	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=331;Dels=0.00;HRun=3;HaplotypeScore=311.11;MQ=35.94;MQ0=23;QD=0.05;SB=173.50	GT:AD:DP:GL:GQ	0/1:258,71:167:-55.40,-50.33,-521.31:50.72
+chr1	2577549	rs4648567	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=289;Dels=0.00;HRun=0;HaplotypeScore=107.18;MQ=38.40;MQ0=7;OQ=5448.91;QD=18.85;SB=-2125.98	GT:AD:DP:GL:GQ	1/1:24,231:174:-543.89,-82.79,-51.97:99
+chr1	2577655	.	G	C	44.44	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=2;HaplotypeScore=58.73;MQ=26.75;MQ0=23;QD=0.33;SB=26.12	GT:AD:DP:GL:GQ	0/1:116,10:43:-24.31,-16.59,-159.35:77.27
+chr1	2577671	rs58842912	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=128.81;MQ=16.71;MQ0=28;OQ=137.08;QD=1.46;SB=-35.94	GT:AD:DP:GL:GQ	0/1:63,25:12:-20.61,-3.62,-16.30:99
+chr1	2577677	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=3;HaplotypeScore=117.98;MQ=17.54;MQ0=28;OQ=281.66;QD=3.03;SB=-45.56	GT:AD:DP:GL:GQ	0/1:33,58:12:-35.06,-3.61,-7.69:40.79
+chr1	2577682	.	T	C	14.20	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=57.79;MQ=17.58;MQ0=34;QD=0.14;SB=-10.00	GT:AD:DP:GL:GQ	0/1:68,26:4:-5.89,-1.21,-7.84:46.86
+chr1	2577700	.	T	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=167.08;MQ=18.58;MQ0=41;OQ=266.89;QD=2.36;SB=-10.00	GT:AD:DP:GL:GQ	1/1:35,36:10:-34.52,-6.65,-4.25:23.97
+chr1	2577709	.	C	T	15.40	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=131;Dels=0.00;HRun=0;HaplotypeScore=233.03;MQ=18.07;MQ0=48;QD=0.12;SB=-10.00	GT:AD:DP:GL:GQ	0/1:96,13:7:-9.83,-5.02,-17.83:48.10
+chr1	2577721	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=74.87;MQ=18.10;MQ0=63;OQ=399.60;QD=2.20;SB=-10.00	GT:AD:DP:GL:GQ	0/1:147,35:41:-55.60,-12.35,-87.25:99
+chr1	2577722	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=54.78;MQ=18.15;MQ0=62;OQ=179.28;QD=0.99;SB=-10.00	GT:AD:DP:GL:GQ	0/1:160,20:38:-32.69,-11.48,-98.33:99
+chr1	2577735	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=1;HaplotypeScore=37.61;MQ=17.86;MQ0=65;OQ=262.32;QD=1.37;SB=-10.00	GT:AD:DP:GL:GQ	0/1:173,18:55:-46.08,-16.57,-148.55:99
+chr1	2577740	rs61763463	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.00;HRun=1;HaplotypeScore=34.83;MQ=17.84;MQ0=63;OQ=1671.60;QD=8.99;SB=-10.00	GT:AD:DP:GL:GQ	0/1:52,133:54:-186.71,-16.27,-40.75:99
+chr1	2577765	.	C	A	125.78	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=41.35;MQ=16.77;MQ0=52;QD=0.87;SB=-10.00	GT:AD:DP:GL:GQ	0/1:91,53:26:-23.70,-7.84,-54.51:99
+chr1	2577769	.	C	T	71.72	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=43.82;MQ=16.10;MQ0=52;QD=0.54;SB=-10.00	GT:AD:DP:GL:GQ	0/1:87,47:21:-16.80,-6.34,-49.74:99
+chr1	2577770	.	G	C	89.65	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=1;HaplotypeScore=42.82;MQ=16.09;MQ0=52;QD=0.67;SB=-10.00	GT:AD:DP:GL:GQ	0/1:85,48:21:-18.58,-6.33,-66.40:99
+chr1	2577784	rs61761450	G	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=93.26;MQ=15.12;MQ0=44;OQ=499.20;QD=4.62;SB=-10.00	GT:AD:DP:GL:GQ	1/1:36,72:12:-53.51,-3.62,-0.00:36.12
+chr1	2577796	rs28368363	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=154.23;MQ=14.20;MQ0=39;OQ=53.95;QD=0.56;SB=-10.00	GT:AD:DP:GL:GQ	0/1:68,23:5:-10.19,-1.51,-6.10:45.96
+chr1	2577799	rs61765844	A	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=4;HaplotypeScore=106.56;MQ=13.50;MQ0=38;OQ=136.44;QD=1.53;SB=-10.00	GT:AD:DP:GL:GQ	1/1:37,52:5:-17.20,-1.51,-0.00:15.04
+chr1	2577815	rs61761446	G	A	0.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=16.91;MQ=12.99;MQ0=33;OQ=113.87;QD=2.19;SB=-10.00	GT:AD:DP:GL:GQ	1/1:30,21:4:-14.92,-1.21,-0.00:12.04
+chr1	2577825	.	G	A	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=32.84;MQ=14.16;MQ0=28;OQ=149.17;QD=3.17;SB=-10.00	GT:AD:DP:GL:GQ	1/1:28,19:5:-18.48,-1.51,-0.00:15.04
+chr1	2577833	.	C	T	42.25	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=22.86;MQ=13.04;MQ0=28;QD=0.98;SB=-10.00	GT:AD:DP:GL:GQ	1/1:33,10:2:-7.63,-0.60,-0.00:6.02
+chr1	2577851	.	G	T	0.04	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=11.27;MQ=14.57;MQ0=20;OQ=148.54;QD=4.24;SB=-10.00	GT:AD:DP:GL:GQ	1/1:17,14:6:-18.43,-1.81,-0.01:18.02
+chr1	2577883	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=114.78;MQ=19.71;MQ0=31;OQ=87.78;QD=0.84;SB=-10.00	GT:AD:DP:GL:GQ	0/1:82,22:16:-16.89,-4.83,-35.06:99
+chr1	2577892	rs61761448	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=139.63;MQ=19.08;MQ0=41;OQ=358.39;QD=3.04;SB=-10.00	GT:AD:DP:GL:GQ	0/1:46,69:13:-43.04,-3.92,-5.80:18.77
+chr1	2577904	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=1;HaplotypeScore=169.18;MQ=18.99;MQ0=45;OQ=432.72;QD=3.38;SB=-10.00	GT:AD:DP:GL:GQ	0/1:56,72:16:-51.38,-4.83,-6.85:20.23
+chr1	2577913	.	A	G	43.14	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=228.63;MQ=18.89;MQ0=43;QD=0.37;SB=-10.00	GT:AD:DP:GL:GQ	0/1:102,14:7:-9.71,-2.11,-14.52:75.98
+chr1	2577923	.	G	A	12.44	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=0;HaplotypeScore=139.34;MQ=19.75;MQ0=38;QD=0.10;SB=-10.00	GT:AD:DP:GL:GQ	0/1:84,37:10:-7.51,-3.01,-26.55:45.02
+chr1	2577924	.	T	C	61.88	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=137.09;MQ=19.68;MQ0=38;QD=0.52;SB=-10.00	GT:AD:DP:GL:GQ	0/1:94,23:11:-12.79,-3.32,-26.27:94.71
+chr1	2577931	rs61763465	G	C	371.46	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=106.32;MQ=19.54;MQ0=35;QD=3.50;SB=-10.00	GT:AD:DP:GL:GQ	1/1:30,75:9:-40.73,-2.71,-0.00:27.09
+chr1	2577945	rs61765845	G	C	1059.87	HARD_TO_VALIDATE;Indel	AC=2;AF=1.00;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=141.04;MQ=19.73;MQ0=38;QD=10.00;SB=-10.00	GT:AD:DP:GL:GQ	1/1:31,70:26:-113.65,-11.26,-4.08:71.85
+chr1	2577953	.	A	G	356.53	HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=136.50;MQ=18.50;MQ0=43;QD=3.64;SB=-10.00	GT:AD:DP:GL:GQ	0/1:78,20:16:-43.76,-4.82,-8.02:32
+chr1	2577977	.	G	A	20.69	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=1;HaplotypeScore=16.21;MQ=15.79;MQ0=48;QD=0.27;SB=-10.00	GT:AD:DP:GL:GQ	0/1:72,5:20:-11.37,-6.02,-58.36:53.49
+chr1	2579397	rs61761374	C	G	193.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=22.35;MQ0=6;OQ=1341.59;QD=14.91;SB=-551.47	GT:AD:DP:GL:GQ	0/1:44,46:77:-160.66,-23.22,-161.20:99
+chr1	2580726	.	T	G	35.92	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.11;MQ=5.25;MQ0=59;QD=0.59;SB=-10.00	GT:AD:DP:GL:GQ	1/1:58,2:2:-7.00,-0.60,-0.00:6.02
+chr1	2580768	.	T	C	36.28	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=5.74;MQ0=49;QD=0.71;SB=-10.00	GT:AD:DP:GL:GQ	1/1:46,5:2:-7.04,-0.60,-0.00:6.02
+chr1	2580784	rs11488598	T	A	45.88	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=6.33;MQ0=40;QD=1.09;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,41:2:-8.00,-0.60,-0.00:6.02
+chr1	2581065	rs61761440	A	C	33.92	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=9.03;MQ=10.33;MQ0=29;QD=0.71;SB=-10.00	GT:AD:DP:GL:GQ	1/1:28,20:2:-6.80,-0.60,-0.00:6.02
+chr1	2581076	.	T	A	42.69	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=11.35;MQ0=18;QD=1.33;SB=-10.00	GT:AD:DP:GL:GQ	1/1:16,15:2:-7.68,-0.60,-0.00:6.02
+chr1	2581088	.	A	C	35.92	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=15.32;MQ0=5;QD=3.27;SB=-10.00	GT:AD:DP:GL:GQ	1/1:3,8:2:-7.00,-0.60,-0.00:6.02
+chr1	2581203	.	C	G	46.77	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=12.99;MQ=10.81;MQ0=53;QD=0.69;SB=5.05	GT:AD:DP:GL:GQ	0/1:57,11:14:-12.18,-4.22,-47.55:79.61
+chr1	2581221	rs4648702	C	A	0.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=1;HaplotypeScore=12.38;MQ=17.15;MQ0=42;OQ=109.22;QD=1.11;SB=-5.56	GT:AD:DP:GL:GQ	0/1:80,16:46:-28.07,-13.86,-128.22:99
+chr1	2581257	rs4648701	T	A	0.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=134;Dels=0.00;HRun=0;HaplotypeScore=5.16;MQ=20.38;MQ0=25;OQ=3859.45;QD=28.80;SB=-1801.06	GT:AD:DP:GL:GQ	1/1:0,134:101:-384.94,-30.42,-0.03:99
+chr1	2587428	.	A	C	37.49	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=14.36;MQ0=8;QD=1.10;SB=-45.01	GT:AD:DP:GL:GQ	1/1:0,34:2:-7.16,-0.60,-0.00:6.02
+chr1	2593169	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=425;Dels=0.00;HRun=1;HaplotypeScore=105.62;MQ=17.46;MQ0=82;OQ=848.96;QD=2.00;SB=-332.82	GT:AD:DP:GL:GQ	0/1:365,60:163:-137.29,-49.11,-428.79:99
+chr1	2596443	.	C	T	41.24	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=12.40;MQ0=7;QD=3.75;SB=-10.00	GT:AD:DP:GL:GQ	1/1:7,4:2:-7.53,-0.60,-0.00:6.02
+chr1	2596445	.	T	G	36.05	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=2.31;MQ=11.87;MQ0=8;QD=3.00;SB=-10.00	GT:AD:DP:GL:GQ	1/1:5,7:2:-7.01,-0.60,-0.00:6.02
+chr1	2596476	.	G	A	46.02	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;HRun=1;HaplotypeScore=26.89;MQ=5.53;MQ0=56;QD=0.77;SB=-10.00	GT:AD:DP:GL:GQ	1/1:58,2:2:-8.01,-0.60,-0.00:6.02
+chr1	2596850	.	G	C	35.05	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=11.43;MQ0=28;QD=0.82;SB=-10.00	GT:AD:DP:GL:GQ	0/1:29,14:5:-8.30,-1.51,-13.08:67.88
+chr1	2596943	.	C	A	49.59	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=50.99;MQ=11.35;MQ0=54;QD=0.70;SB=-6.99	GT:AD:DP:GL:GQ	0/1:65,5:13:-12.16,-3.92,-30.66:82.43
+chr1	2597318	.	T	C	31.81	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=14.62;MQ=5.54;MQ0=70;QD=0.42;SB=-10.00	GT:AD:DP:GL:GQ	1/1:73,2:2:-6.59,-0.60,-0.00:6.01
+chr1	2598250	.	T	A	27.90	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=1;HaplotypeScore=2.24;MQ=16.56;MQ0=5;QD=1.27;SB=-0.98	GT:AD:DP:GL:GQ	0/1:19,3:5:-7.58,-1.51,-10.62:60.73
+chr1	2598257	.	G	T	12.16	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=10.71;MQ=15.61;MQ0=8;QD=0.55;SB=-0.98	GT:AD:DP:GL:GQ	0/1:19,3:5:-5.98,-1.51,-10.70:44.72
+chr1	2598656	.	G	A	10.26	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=1;HaplotypeScore=114.17;MQ=5.78;MQ0=152;QD=0.06;SB=-10.00	GT:AD:DP:GL:GQ	0/1:161,14:1:-4.27,-0.30,-0.00:1.76
+chr1	2598795	.	G	A	10.26	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=47.85;MQ=7.17;MQ0=69;QD=0.12;SB=-10.00	GT:AD:DP:GL:GQ	0/1:84,2:1:-4.27,-0.30,-0.00:1.76
+chr1	2598944	.	A	C	17.83	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=1;HaplotypeScore=67.67;MQ=10.48;MQ0=39;QD=0.27;SB=-25.99	GT:AD:DP:GL:GQ	0/1:48,17:3:-5.96,-0.91,-2.50:15.92
+chr1	2598946	.	A	G	34.06	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=82.40;MQ=11.36;MQ0=42;QD=0.46;SB=-10.00	GT:AD:DP:GL:GQ	0/1:70,4:3:-7.59,-0.90,-4.17:32.64
+chr1	2598950	.	C	A	54.26	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=105.52;MQ=12.29;MQ0=47;QD=0.53;SB=-3.99	GT:AD:DP:GL:GQ	0/1:94,7:7:-10.82,-2.11,-14.32:87.10
+chr1	2599001	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=0;HaplotypeScore=31.75;MQ=12.68;MQ0=54;OQ=83.85;QD=0.63;SB=-3.99	GT:AD:DP:GL:GQ	0/1:91,33:10:-18.26,-6.59,-21.60:99
+chr1	2599015	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=2;HaplotypeScore=24.68;MQ=11.50;MQ0=72;OQ=64.97;QD=0.46;SB=-43.54	GT:AD:DP:GL:GQ	0/1:128,12:9:-12.49,-2.71,-23.15:97.80
+chr1	2599040	rs61761456	A	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=133;Dels=0.00;HRun=0;HaplotypeScore=87.15;MQ=9.23;MQ0=88;OQ=72.77;QD=0.55;SB=-10.00	GT:AD:DP:GL:GQ	1/1:81,14:5:-17.43,-7.71,-6.64:10.71
+chr1	2599044	rs61761457	T	A	33.25	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=131;Dels=0.00;HRun=1;HaplotypeScore=64.29;MQ=9.30;MQ0=86;QD=0.25;SB=-10.00	GT:AD:DP:GL:GQ	0/1:104,11:6:-11.67,-5.06,-13.57:66.08
+chr1	2599198	.	C	T	23.45	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=16.24;MQ=14.99;MQ0=19;QD=0.50;SB=-3.99	GT:AD:DP:GL:GQ	0/1:29,18:5:-7.14,-1.51,-10.24:56.27
+chr1	2599218	.	G	A	105.55	HARD_TO_VALIDATE;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=106.10;MQ=16.73;MQ0=11;QD=2.29;SB=-69.07	GT:AD:DP:GL:GQ	0/1:28,17:6:-15.65,-1.81,-6.14:43.30
+chr1	2599225	.	C	G	35.32	HARD_TO_VALIDATE;Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=82.64;MQ=16.87;MQ0=11;QD=0.78;SB=-10.88	GT:AD:DP:GL:GQ	0/1:36,6:7:-14.02,-7.20,-19.31:68.16
+chr1	2599228	.	G	A	323.86	HARD_TO_VALIDATE;Indel;SnpCluster	AC=2;AF=1.00;AN=2;DP=46;Dels=0.04;HRun=0;HaplotypeScore=68.32;MQ=16.68;MQ0=12;QD=7.04;SB=-89.34	GT:AD:DP:GL:GQ	1/1:16,28:10:-35.98,-3.02,-0.01:30.08
+chr1	2599239	.	T	A	19.57	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=43.45;MQ=14.62;MQ0=19;QD=0.36;SB=-4.42	GT:AD:DP:GL:GQ	0/1:49,2:7:-12.49,-7.25,-17.00:52.36
+chr1	2599247	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=40.77;MQ=14.18;MQ0=20;OQ=70.13;QD=1.35;SB=-7.01	GT:AD:DP:GL:GQ	0/1:29,21:6:-12.11,-1.81,-8.56:67.52
+chr1	2599654	.	G	C	12.35	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=1;HaplotypeScore=26.39;MQ=2.65;MQ0=119;QD=0.10;SB=-10.00	GT:AD:DP:GL:GQ	0/1:119,1:1:-4.49,-0.30,-0.00:1.76
+chr1	2601422	.	A	G	25.82	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=114;Dels=0.00;HRun=0;HaplotypeScore=10.71;MQ=4.09;MQ0=110;QD=0.23;SB=-10.00	GT:AD:DP:GL:GQ	1/1:99,14:2:-5.99,-0.60,-0.00:6.01
+chr1	2601437	.	T	C	35.28	DPFilter;HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=133;Dels=0.00;HRun=0;HaplotypeScore=12.99;MQ=3.79;MQ0=129;QD=0.27;SB=-10.00	GT:AD:DP:GL:GQ	1/1:103,30:2:-6.94,-0.60,-0.00:6.02
+chr1	2601504	.	G	A	41.24	DPFilter;HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=19.74;MQ=3.30;MQ0=165;QD=0.25;SB=-10.00	GT:AD:DP:GL:GQ	1/1:158,9:2:-7.53,-0.60,-0.00:6.02
+chr1	2601515	.	A	C	43.05	DPFilter;HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=155;Dels=0.00;HRun=2;HaplotypeScore=7.29;MQ=3.29;MQ0=153;QD=0.28;SB=-10.00	GT:AD:DP:GL:GQ	1/1:91,64:2:-7.71,-0.60,-0.00:6.02
+chr1	2601516	.	G	A	0.02	FDRtranche1.00to2.00	AC=2;AF=1.00;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=6.38;MQ=3.29;MQ0=153;OQ=51.25;QD=0.33;SB=-10.00	GT:AD:DP:GL:GQ	1/1:89,66:2:-8.53,-0.60,-0.00:6.02
+chr1	2601859	.	G	A	39.02	DPFilter;HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=20.82;MQ=4.64;MQ0=146;QD=0.24;SB=-10.00	GT:AD:DP:GL:GQ	1/1:150,13:2:-7.31,-0.60,-0.00:6.02
+chr1	2603248	rs11486046	A	C	0.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=4;HaplotypeScore=1.14;MQ=19.37;MQ0=3;OQ=283.27;QD=11.33;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,23:9:-31.91,-2.71,-0.00:27.08
+chr1	2603587	.	A	G	31.28	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=24.46;MQ=5.10;MQ0=81;QD=0.34;SB=-10.00	GT:AD:DP:GL:GQ	1/1:74,19:2:-6.54,-0.60,-0.00:6.01
+chr1	2603630	.	C	T	0.04	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=4.88;MQ=7.26;MQ0=55;OQ=82.12;QD=1.35;SB=-10.00	GT:AD:DP:GL:GQ	1/1:51,10:3:-11.70,-0.90,-0.00:9.03
+chr1	2603684	.	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=23.79;MQ=8.35;MQ0=58;OQ=160.35;QD=2.36;SB=-10.00	GT:AD:DP:GL:GQ	1/1:55,13:6:-19.61,-1.81,-0.00:18.04
+chr1	2603850	.	C	G	10.08	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=0;HaplotypeScore=68.31;MQ=3.10;MQ0=215;QD=0.04;SB=-10.00	GT:AD:DP:GL:GQ	0/1:213,10:1:-4.25,-0.30,-0.00:1.76
+chr1	2604182	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=169;Dels=0.00;HRun=1;HaplotypeScore=49.21;MQ=7.86;MQ0=143;OQ=70.78;QD=0.42;SB=-10.00	GT:AD:DP:GL:GQ	0/1:162,7:11:-13.68,-3.31,-27.79:99
+chr1	2604202	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=174;Dels=0.00;HRun=0;HaplotypeScore=66.53;MQ=7.81;MQ0=146;OQ=55.73;QD=0.32;SB=-10.00	GT:AD:DP:GL:GQ	0/1:164,10:11:-12.17,-3.31,-27.45:88.56
+chr1	2604211	.	C	A	34.20	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=202;Dels=0.00;HRun=0;HaplotypeScore=110.16;MQ=8.09;MQ0=168;QD=0.17;SB=-10.00	GT:AD:DP:GL:GQ	0/1:190,11:14:-10.92,-4.22,-40.03:67.04
+chr1	2604257	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=82.11;MQ=12.16;MQ0=114;OQ=80.38;QD=0.46;SB=32.96	GT:AD:DP:GL:GQ	0/1:146,20:31:-22.91,-11.59,-89.29:99
+chr1	2604263	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=1;HaplotypeScore=133.02;MQ=12.71;MQ0=105;OQ=191.66;QD=1.14;SB=50.18	GT:AD:DP:GL:GQ	0/1:122,46:33:-32.40,-9.95,-88.01:99
+chr1	2604269	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=77.37;MQ=13.05;MQ0=90;OQ=192.77;QD=1.32;SB=17.43	GT:AD:DP:GL:GQ	0/1:70,69:33:-34.89,-12.33,-71.96:99
+chr1	2604305	.	T	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=7.47;MQ=17.34;MQ0=29;OQ=55.74;QD=0.69;SB=74.25	GT:AD:DP:GL:GQ	0/1:58,22:37:-20.01,-11.15,-121.92:88.58
+chr1	2604310	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=4.63;MQ=18.11;MQ0=23;OQ=69.18;QD=0.93;SB=74.24	GT:AD:DP:GL:GQ	0/1:55,19:37:-21.34,-11.14,-111.00:99
+chr1	2604358	.	C	T	71.23	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=0;HaplotypeScore=145.78;MQ=14.15;MQ0=44;QD=0.82;SB=11.06	GT:AD:DP:GL:GQ	0/1:71,13:12:-14.02,-3.62,-30.75:99
+chr1	2604359	.	C	A	74.64	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=131.89;MQ=14.13;MQ0=41;QD=0.91;SB=5.02	GT:AD:DP:GL:GQ	0/1:26,56:10:-13.76,-3.01,-18.66:99
+chr1	2604363	.	G	C	180.85	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=2;HaplotypeScore=137.79;MQ=13.57;MQ0=46;QD=2.10;SB=2.04	GT:AD:DP:GL:GQ	0/1:29,40:11:-24.68,-3.31,-21.48:99
+chr1	2604377	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=82.82;MQ=13.39;MQ0=50;OQ=54.76;QD=0.61;SB=-10.00	GT:AD:DP:GL:GQ	0/1:65,25:4:-9.97,-1.21,-3.57:23.65
+chr1	2604397	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=1;HaplotypeScore=150.87;MQ=13.17;MQ0=49;OQ=71.12;QD=0.83;SB=-10.00	GT:AD:DP:GL:GQ	0/1:47,38:4:-11.60,-1.21,-3.90:26.92
+chr1	2604403	.	T	C	38.45	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=82;Dels=0.00;HRun=2;HaplotypeScore=145.51;MQ=12.80;MQ0=46;QD=0.47;SB=-10.00	GT:AD:DP:GL:GQ	1/1:13,58:3:-10.84,-4.28,-3.54:7.45
+chr1	2604424	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=48.30;MQ=13.20;MQ0=33;OQ=76.83;QD=1.35;SB=-6.99	GT:AD:DP:GL:GQ	0/1:21,30:6:-12.78,-1.81,-6.73:49.16
+chr1	2604431	.	C	T	25.24	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=33.49;MQ=13.71;MQ0=25;QD=0.55;SB=-7.01	GT:AD:DP:GL:GQ	0/1:40,3:5:-7.32,-1.51,-9.43:58.07
+chr1	2604444	.	G	C	43.47	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=38.64;MQ=15.55;MQ0=13;QD=1.67;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,16:4:-12.26,-4.63,-7.13:24.99
+chr1	2604449	.	G	C	30.45	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=21;Dels=0.10;HRun=4;HaplotypeScore=30.98;MQ=14.63;MQ0=12;QD=1.45;SB=-10.00	GT:AD:DP:GL:GQ	0/1:6,6:4:-11.16,-4.83,-7.63:28
+chr1	2604508	.	G	C	0.07	PASS	AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=11.01;MQ=14.95;MQ0=13;OQ=265.66;QD=7.81;SB=-10.00	GT:AD:DP:GL:GQ	1/1:9,25:7:-30.15,-2.11,-0.00:21.07
+chr1	2604516	.	G	T	0.07	PASS	AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;HRun=1;HaplotypeScore=5.00;MQ=14.42;MQ0=18;OQ=191.90;QD=4.68;SB=-10.00	GT:AD:DP:GL:GQ	1/1:15,26:7:-22.77,-2.11,-0.00:21.05
+chr1	2604535	rs61763522	A	G	0.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=9.63;MQ=11.76;MQ0=38;OQ=251.64;QD=3.87;SB=-10.00	GT:AD:DP:GL:GQ	1/1:12,53:8:-28.75,-2.41,-0.00:24.07
+chr1	2604555	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=35.24;MQ=12.18;MQ0=57;OQ=115.73;QD=1.24;SB=14.08	GT:AD:DP:GL:GQ	0/1:66,27:12:-18.47,-3.62,-35.84:99
+chr1	2604572	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=3;HaplotypeScore=50.74;MQ=13.39;MQ0=78;OQ=55.27;QD=0.40;SB=20.07	GT:AD:DP:GL:GQ	0/1:127,10:20:-14.84,-6.03,-56.38:88.11
+chr1	2604579	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=1;HaplotypeScore=62.98;MQ=13.28;MQ0=75;OQ=144.76;QD=1.05;SB=20.08	GT:AD:DP:GL:GQ	0/1:125,13:18:-23.19,-5.43,-45.19:99
+chr1	2604585	rs61763523	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=140;Dels=0.00;HRun=1;HaplotypeScore=70.32;MQ=13.11;MQ0=76;OQ=158.49;QD=1.13;SB=-6.99	GT:AD:DP:GL:GQ	0/1:102,37:9:-21.84,-2.71,-10.97:82.64
+chr1	2604597	.	A	G	110.83	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=107.90;MQ=13.27;MQ0=78;QD=0.74;SB=8.05	GT:AD:DP:GL:GQ	0/1:135,14:14:-18.58,-4.22,-35.74:99
+chr1	2604601	.	A	C	218.40	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=111.25;MQ=13.41;MQ0=75;QD=1.51;SB=4.22	GT:AD:DP:GL:GQ	0/1:108,36:15:-33.23,-8.10,-26.51:99
+chr1	2604603	.	T	C	273.40	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=2;HaplotypeScore=107.87;MQ=13.23;MQ0=76;QD=1.89;SB=-75.88	GT:AD:DP:GL:GQ	0/1:65,76:14:-34.84,-4.22,-16.55:99
+chr1	2604631	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=169;Dels=0.00;HRun=1;HaplotypeScore=78.83;MQ=15.93;MQ0=66;OQ=130.30;QD=0.77;SB=-43.00	GT:AD:DP:GL:GQ	0/1:129,40:31:-25.65,-9.34,-87.13:99
+chr1	2604640	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=154;Dels=0.00;HRun=0;HaplotypeScore=101.27;MQ=16.99;MQ0=53;OQ=84.42;QD=0.55;SB=-10.00	GT:AD:DP:GL:GQ	0/1:93,61:34:-21.98,-10.25,-116.76:99
+chr1	2604659	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=1;HaplotypeScore=114.19;MQ=17.85;MQ0=39;OQ=180.46;QD=1.31;SB=-10.00	GT:AD:DP:GL:GQ	0/1:106,32:34:-31.57,-10.24,-88.52:99
+chr1	2604673	rs7415296	T	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=120;Dels=0.00;HRun=1;HaplotypeScore=73.29;MQ=18.57;MQ0=29;OQ=1125.63;QD=9.38;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,107:33:-116.16,-9.94,-0.01:99
+chr1	2604706	rs6673862	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=39.35;MQ=23.53;MQ0=16;OQ=454.13;QD=4.83;SB=-3.99	GT:AD:DP:GL:GQ	0/1:51,43:41:-61.05,-12.35,-88.54:99
+chr1	2604709	rs6604993	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=41.02;MQ=25.10;MQ0=15;OQ=512.66;QD=5.40;SB=-34.93	GT:AD:DP:GL:GQ	0/1:48,47:45:-68.11,-13.56,-92.92:99
+chr1	2604721	rs61763524	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=115.04;MQ=25.76;MQ0=12;OQ=386.36;QD=4.15;SB=-44.44	GT:AD:DP:GL:GQ	0/1:49,44:40:-53.97,-12.05,-114.41:99
+chr1	2604728	rs61763525	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=150.75;MQ=27.24;MQ0=8;OQ=52.75;QD=0.62;SB=-10.00	GT:AD:DP:GL:GQ	0/1:49,22:37:-19.70,-11.14,-117.15:85.59
+chr1	2604813	rs6687492	A	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.04;HRun=2;HaplotypeScore=47.11;MQ=23.79;MQ0=20;OQ=1537.32;QD=16.53;SB=-154.02	GT:AD:DP:GL:GQ	1/1:2,87:44:-157.33,-12.95,-0.02:99
+chr1	2604848	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=9.77;MQ=17.69;MQ0=30;OQ=71.77;QD=1.30;SB=-10.00	GT:AD:DP:GL:GQ	0/1:37,18:14:-14.68,-4.22,-36.61:99
+chr1	2604864	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=28.67;MQ=16.02;MQ0=35;OQ=77.33;QD=1.17;SB=-10.00	GT:AD:DP:GL:GQ	0/1:62,4:12:-14.63,-3.61,-28.91:99
+chr1	2604867	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=23.02;MQ=16.18;MQ0=37;OQ=170.35;QD=2.43;SB=-10.00	GT:AD:DP:GL:GQ	0/1:59,11:15:-24.84,-4.52,-31.52:99
+chr1	2604879	.	A	G	48.78	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=25.49;MQ=18.59;MQ0=41;QD=0.57;SB=-6.99	GT:AD:DP:GL:GQ	0/1:79,7:20:-14.19,-6.03,-66.66:81.62
+chr1	2604892	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=1;HaplotypeScore=62.88;MQ=20.71;MQ0=36;OQ=145.34;QD=1.60;SB=-40.00	GT:AD:DP:GL:GQ	0/1:67,21:27:-25.95,-8.13,-71.88:99
+chr1	2604894	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=93;Dels=0.01;HRun=1;HaplotypeScore=55.68;MQ=20.44;MQ0=36;OQ=138.96;QD=1.49;SB=-41.95	GT:AD:DP:GL:GQ	0/1:67,21:26:-25.01,-7.83,-77.06:99
+chr1	2604912	rs61763528	T	G	20.95	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=50.36;MQ=22.66;MQ0=25;QD=0.19;SB=-10.00	GT:AD:DP:GL:GQ	0/1:76,35:29:-14.11,-8.74,-95.07:53.75
+chr1	2604916	rs61763529	T	G	194.85	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=113;Dels=0.00;HRun=0;HaplotypeScore=46.31;MQ=24.02;MQ0=23;QD=1.72;SB=-10.00	GT:AD:DP:GL:GQ	0/1:75,37:38:-34.21,-11.44,-107.06:99
+chr1	2604917	rs61763530	C	G	1480.34	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=47.31;MQ=24.13;MQ0=22;QD=13.22;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,96:38:-168.50,-25.75,-16.88:88.75
+chr1	2604946	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=236;Dels=0.00;HRun=1;HaplotypeScore=63.84;MQ=27.71;MQ0=21;OQ=79.42;QD=0.34;SB=27.56	GT:AD:DP:GL:GQ	0/1:204,31:106:-43.16,-31.93,-335.49:99
+chr1	2604947	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=236;Dels=0.00;HRun=1;HaplotypeScore=57.70;MQ=27.78;MQ0=20;OQ=56.57;QD=0.24;SB=26.25	GT:AD:DP:GL:GQ	0/1:201,34:107:-41.17,-32.23,-378.22:89.40
+chr1	2604959	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=241;Dels=0.00;HRun=1;HaplotypeScore=113.45;MQ=29.01;MQ0=17;OQ=854.86;QD=3.55;SB=-18.43	GT:AD:DP:GL:GQ	0/1:165,75:109:-121.61,-32.84,-284.29:99
+chr1	2604960	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=1;HaplotypeScore=123.76;MQ=29.06;MQ0=17;OQ=593.64;QD=2.47;SB=71.18	GT:AD:DP:GL:GQ	0/1:190,50:108:-95.18,-32.53,-286.72:99
+chr1	2604983	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=1;HaplotypeScore=495.52;MQ=29.66;MQ0=13;OQ=71.64;QD=0.32;SB=60.44	GT:AD:DP:GL:GQ	0/1:161,61:71:-31.89,-21.44,-242.50:99
+chr1	2604984	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=1;HaplotypeScore=666.90;MQ=29.67;MQ0=14;OQ=53.59;QD=0.24;SB=51.85	GT:AD:DP:GL:GQ	0/1:162,59:73:-33.13,-24.49,-250.82:86.43
+chr1	2604994	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=301;Dels=0.00;HRun=1;HaplotypeScore=445.50;MQ=27.33;MQ0=32;OQ=911.93;QD=3.03;SB=-289.52	GT:AD:DP:GL:GQ	0/1:244,47:103:-139.58,-45.10,-310.97:99
+chr1	2605000	.	A	G	39.90	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=313;Dels=0.00;HRun=0;HaplotypeScore=296.02;MQ=26.42;MQ0=37;QD=0.13;SB=95.30	GT:AD:DP:GL:GQ	0/1:236,73:110:-42.96,-35.69,-387.52:72.73
+chr1	2605008	.	C	A	80.14	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=308;Dels=0.00;HRun=1;HaplotypeScore=230.13;MQ=26.37;MQ0=45;QD=0.26;SB=104.26	GT:AD:DP:GL:GQ	0/1:278,18:127:-64.22,-52.92,-396.67:99
+chr1	2605010	.	C	A	77.92	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=309;Dels=0.00;HRun=1;HaplotypeScore=334.39;MQ=26.26;MQ0=46;QD=0.25;SB=101.18	GT:AD:DP:GL:GQ	0/1:276,18:125:-51.79,-40.71,-371.85:99
+chr1	2605026	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=292;Dels=0.00;HRun=0;HaplotypeScore=503.51;MQ=24.87;MQ0=63;OQ=127.24;QD=0.44;SB=-33.91	GT:AD:DP:GL:GQ	0/1:107,181:82:-40.71,-24.70,-242.51:99
+chr1	2605040	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=333;Dels=0.00;HRun=0;HaplotypeScore=585.35;MQ=23.26;MQ0=69;OQ=164.03;QD=0.49;SB=60.04	GT:AD:DP:GL:GQ	0/1:234,98:87:-48.89,-29.20,-293.13:99
+chr1	2605055	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=394;Dels=0.00;HRun=0;HaplotypeScore=493.35;MQ=22.62;MQ0=80;OQ=367.10;QD=0.93;SB=90.44	GT:AD:DP:GL:GQ	0/1:300,89:126:-77.94,-37.95,-375.51:99
+chr1	2605064	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=394;Dels=0.00;HRun=1;HaplotypeScore=562.83;MQ=22.35;MQ0=77;OQ=111.09;QD=0.28;SB=241.07	GT:AD:DP:GL:GQ	0/1:342,17:127:-65.55,-51.15,-483.41:99
+chr1	2605074	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=367;Dels=0.02;HRun=1;HaplotypeScore=550.64;MQ=22.20;MQ0=72;OQ=1826.16;QD=4.98;SB=11.30	GT:AD:DP:GL:GQ	0/1:140,136:125:-251.01,-65.11,-307.30:99
+chr1	2605078	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=360;Dels=0.00;HRun=1;HaplotypeScore=645.39;MQ=22.69;MQ0=67;OQ=145.82;QD=0.41;SB=80.26	GT:AD:DP:GL:GQ	0/1:281,25:108:-50.40,-32.54,-347.91:99
+chr1	2605087	rs9442451	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=302;Dels=0.00;HRun=1;HaplotypeScore=515.01;MQ=23.21;MQ0=61;OQ=1550.28;QD=5.13;SB=0.26	GT:AD:DP:GL:GQ	0/1:127,172:83:-183.36,-25.04,-152.30:99
+chr1	2605095	rs7411254	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=295;Dels=0.00;HRun=0;HaplotypeScore=864.08;MQ=22.89;MQ0=61;OQ=861.12;QD=2.92;SB=-439.01	GT:AD:DP:GL:GQ	0/1:231,62:100:-119.53,-30.13,-233.73:99
+chr1	2605099	rs61763531	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=268;Dels=0.03;HRun=1;HaplotypeScore=671.07;MQ=23.34;MQ0=56;OQ=331.54;QD=1.24;SB=62.18	GT:AD:DP:GL:GQ	0/1:101,158:88:-62.36,-25.93,-228.22:99
+chr1	2605116	rs61763532	G	T	727.77	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=280;Dels=0.00;HRun=0;HaplotypeScore=340.71;MQ=26.06;MQ0=38;QD=2.60;SB=80.25	GT:AD:DP:GL:GQ	0/1:98,160:86:-122.32,-46.26,-192.83:99
+chr1	2605118	.	G	A	130.78	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=2;HaplotypeScore=353.34;MQ=26.07;MQ0=39;QD=0.45;SB=68.17	GT:AD:DP:GL:GQ	0/1:266,20:82:-41.07,-24.71,-249.92:99
+chr1	2605120	.	A	G	143.56	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=286;Dels=0.00;HRun=0;HaplotypeScore=391.53;MQ=26.07;MQ0=38;QD=0.50;SB=44.57	GT:AD:DP:GL:GQ	0/1:230,56:92:-45.37,-27.73,-305.63:99
+chr1	2605121	.	C	A	843.63	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=283;Dels=0.00;HRun=2;HaplotypeScore=384.52;MQ=26.08;MQ0=38;QD=2.98;SB=80.20	GT:AD:DP:GL:GQ	0/1:195,69:112:-123.96,-36.31,-258.00:99
+chr1	2605143	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=261;Dels=0.00;HRun=0;HaplotypeScore=165.80;MQ=26.36;MQ0=57;OQ=2061.60;QD=7.90;SB=82.92	GT:AD:DP:GL:GQ	0/1:135,121:131:-251.29,-41.84,-249.16:99
+chr1	2605152	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=276;Dels=0.00;HRun=0;HaplotypeScore=166.41;MQ=25.95;MQ0=68;OQ=1747.63;QD=6.33;SB=68.24	GT:AD:DP:GL:GQ	0/1:180,94:128:-216.61,-38.56,-254.69:99
+chr1	2605164	rs56278231	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=99.67;MQ=26.36;MQ0=65;OQ=2109.83;QD=7.59;SB=62.23	GT:AD:DP:GL:GQ	0/1:140,134:129:-253.13,-38.87,-210.06:99
+chr1	2605176	rs61763533	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=283;Dels=0.00;HRun=4;HaplotypeScore=192.72;MQ=26.37;MQ0=64;OQ=2285.97;QD=8.08;SB=50.20	GT:AD:DP:GL:GQ	0/1:155,126:135:-272.62,-40.74,-266.81:99
+chr1	2605179	rs7415101	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=293;Dels=0.00;HRun=0;HaplotypeScore=210.05;MQ=26.19;MQ0=65;OQ=1158.68;QD=3.95;SB=-384.91	GT:AD:DP:GL:GQ	0/1:236,57:97:-148.38,-29.23,-220.79:99
+chr1	2605208	.	C	A	465.30	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=269;Dels=0.00;HRun=1;HaplotypeScore=227.21;MQ=26.15;MQ0=63;QD=1.73;SB=32.07	GT:AD:DP:GL:GQ	0/1:153,116:69:-70.60,-20.78,-175.32:99
+chr1	2605210	.	C	A	482.33	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=1;HaplotypeScore=189.40;MQ=26.42;MQ0=62;QD=1.81;SB=32.08	GT:AD:DP:GL:GQ	0/1:149,115:67:-71.70,-20.18,-161.20:99
+chr1	2605214	rs61082664	T	C	967.30	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=276;Dels=0.00;HRun=2;HaplotypeScore=127.28;MQ=27.64;MQ0=60;QD=3.50;SB=23.10	GT:AD:DP:GL:GQ	0/1:97,178:76:-122.91,-22.90,-161.42:99
+chr1	2605243	.	G	T	751.64	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=305;Dels=0.00;HRun=1;HaplotypeScore=253.27;MQ=31.30;MQ0=36;QD=2.46;SB=71.20	GT:AD:DP:GL:GQ	0/1:173,132:102:-109.18,-30.73,-247.59:99
+chr1	2605244	rs28455054	T	C	853.34	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=304;Dels=0.00;HRun=0;HaplotypeScore=224.13;MQ=31.61;MQ0=34;QD=2.81;SB=-69.58	GT:AD:DP:GL:GQ	0/1:99,183:104:-137.17,-48.55,-265.91:99
+chr1	2605247	.	C	T	78.33	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=307;Dels=0.00;HRun=0;HaplotypeScore=241.73;MQ=32.15;MQ0=30;QD=0.26;SB=92.28	GT:AD:DP:GL:GQ	0/1:261,44:108:-43.66,-32.54,-342.18:99
+chr1	2605252	.	C	A	302.63	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=316;Dels=0.00;HRun=1;HaplotypeScore=325.23;MQ=32.85;MQ0=33;QD=0.96;SB=113.24	GT:AD:DP:GL:GQ	0/1:197,119:109:-66.39,-32.84,-311.74:99
+chr1	2605255	rs55876897	A	C	449.77	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=317;Dels=0.00;HRun=3;HaplotypeScore=260.93;MQ=33.01;MQ0=35;QD=1.42;SB=-150.70	GT:AD:DP:GL:GQ	0/1:239,77:117:-83.21,-34.95,-326.08:99
+chr1	2605259	rs56999649	T	G	716.83	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=300;Dels=0.00;HRun=1;HaplotypeScore=227.19;MQ=34.47;MQ0=29;QD=2.39;SB=-184.23	GT:AD:DP:GL:GQ	0/1:116,182:121:-111.42,-36.45,-316.52:99
+chr1	2605264	rs4648676	C	T	210.17	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=316;Dels=0.00;HRun=0;HaplotypeScore=557.56;MQ=35.06;MQ0=25;QD=0.67;SB=-21.82	GT:AD:DP:GL:GQ	0/1:289,24:136:-67.74,-43.44,-416.85:99
+chr1	2605334	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=408;Dels=0.00;HRun=4;HaplotypeScore=186.79;MQ=36.75;MQ0=7;OQ=1485.59;QD=3.64;SB=-538.59	GT:AD:DP:GL:GQ	0/1:275,118:294:-243.85,-92.01,-1014.23:99
+chr1	2605341	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=415;Dels=0.00;HRun=0;HaplotypeScore=229.92;MQ=36.33;MQ0=7;OQ=215.75;QD=0.52;SB=102.02	GT:AD:DP:GL:GQ	0/1:365,48:297:-114.34,-89.49,-957.91:99
+chr1	2605353	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=430;Dels=0.00;HRun=0;HaplotypeScore=200.04;MQ=35.29;MQ0=7;OQ=112.93;QD=0.26;SB=60.60	GT:AD:DP:GL:GQ	0/1:389,39:313:-108.94,-94.36,-1191.77:99
+chr1	2605354	rs4648678	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=435;Dels=0.00;HRun=0;HaplotypeScore=203.33;MQ=35.33;MQ0=8;OQ=1038.03;QD=2.39;SB=-273.03	GT:AD:DP:GL:GQ	0/1:373,60:307:-199.57,-92.49,-955.77:99
+chr1	2605374	rs61763535	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=451;Dels=0.00;HRun=4;HaplotypeScore=174.52;MQ=33.98;MQ0=15;OQ=1772.73;QD=3.93;SB=-155.11	GT:AD:DP:GL:GQ	0/1:257,185:286:-266.74,-86.18,-803.52:99
+chr1	2605416	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=641;Dels=0.00;HRun=0;HaplotypeScore=116.73;MQ=29.52;MQ0=38;OQ=101.05;QD=0.16;SB=-26.09	GT:AD:DP:GL:GQ	0/1:592,49:383:-128.76,-115.37,-1229.08:99
+chr1	2605473	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=505;Dels=0.00;HRun=1;HaplotypeScore=72.40;MQ=31.01;MQ0=19;OQ=529.76;QD=1.05;SB=-238.32	GT:AD:DP:GL:GQ	0/1:450,54:383:-171.63,-115.37,-1165.16:99
+chr1	2605495	rs56293461	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=486;Dels=0.00;HRun=0;HaplotypeScore=95.08;MQ=32.56;MQ0=15;OQ=821.52;QD=1.69;SB=-409.31	GT:AD:DP:GL:GQ	0/1:403,80:369:-196.58,-111.15,-1127.43:99
+chr1	2605529	rs28651038	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=428;Dels=0.00;HRun=0;HaplotypeScore=82.79;MQ=34.53;MQ0=16;OQ=2602.34;QD=6.08;SB=-653.43	GT:AD:DP:GL:GQ	0/1:288,123:298:-353.40,-89.88,-659.17:99
+chr1	2605657	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=389;Dels=0.01;HRun=3;HaplotypeScore=175.38;MQ=30.03;MQ0=70;OQ=99.64;QD=0.26;SB=74.25	GT:AD:DP:GL:GQ	0/1:326,61:215:-77.75,-64.51,-660.65:99
+chr1	2605686	.	A	C	325.50	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=398;Dels=0.00;HRun=0;HaplotypeScore=501.75;MQ=28.89;MQ0=57;QD=0.82;SB=95.28	GT:AD:DP:GL:GQ	0/1:281,115:207:-98.21,-62.38,-634.44:99
+chr1	2605688	.	T	C	330.54	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=397;Dels=0.00;HRun=2;HaplotypeScore=497.47;MQ=28.92;MQ0=57;QD=0.83;SB=65.64	GT:AD:DP:GL:GQ	0/1:226,152:200:-122.31,-85.97,-661.75:99
+chr1	2605695	rs55827558	C	T	892.89	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=401;Dels=0.00;HRun=0;HaplotypeScore=534.98;MQ=29.24;MQ0=57;QD=2.23;SB=9.18	GT:AD:DP:GL:GQ	0/1:315,49:193:-153.53,-60.96,-575.72:99
+chr1	2605725	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=284;Dels=0.00;HRun=0;HaplotypeScore=360.95;MQ=32.85;MQ0=34;OQ=61.42;QD=0.22;SB=89.31	GT:AD:DP:GL:GQ	0/1:168,111:137:-50.75,-41.32,-529.65:94.25
+chr1	2605754	.	C	T	591.89	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=467.58;MQ=37.63;MQ0=15;QD=2.12;SB=140.37	GT:AD:DP:GL:GQ	0/1:235,40:127:-100.77,-38.29,-327.93:99
+chr1	2605755	.	G	A	525.10	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=436.48;MQ=37.79;MQ0=15;QD=1.94;SB=80.56	GT:AD:DP:GL:GQ	0/1:156,112:135:-96.50,-40.71,-357.83:99
+chr1	2605761	rs61763538	C	G	1339.29	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=259;Dels=0.00;HRun=1;HaplotypeScore=254.24;MQ=38.34;MQ0=17;QD=5.17;SB=4.72	GT:AD:DP:GL:GQ	0/1:84,169:121:-173.69,-36.48,-327.29:99
+chr1	2605783	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=297;Dels=0.00;HRun=0;HaplotypeScore=293.73;MQ=35.79;MQ0=20;OQ=562.93;QD=1.90;SB=121.81	GT:AD:DP:GL:GQ	0/1:195,74:123:-135.97,-76.40,-335.89:99
+chr1	2605795	.	G	A	252.45	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=324;Dels=0.00;HRun=0;HaplotypeScore=499.11;MQ=34.45;MQ0=20;QD=0.78;SB=203.66	GT:AD:DP:GL:GQ	0/1:201,116:126:-66.49,-37.96,-390.94:99
+chr1	2605804	.	C	T	66.11	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=356;Dels=0.00;HRun=0;HaplotypeScore=268.83;MQ=34.41;MQ0=22;QD=0.19;SB=-31.15	GT:AD:DP:GL:GQ	0/1:312,39:152:-58.55,-48.66,-460.06:98.95
+chr1	2605805	.	G	A	2340.79	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=356;Dels=0.00;HRun=0;HaplotypeScore=224.04;MQ=34.36;MQ0=23;QD=6.58;SB=164.74	GT:AD:DP:GL:GQ	0/1:199,157:186:-293.46,-56.10,-343.74:99
+chr1	2605831	.	C	T	1118.55	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=295;Dels=0.00;HRun=0;HaplotypeScore=238.92;MQ=35.23;MQ0=23;QD=3.79;SB=174.98	GT:AD:DP:GL:GQ	0/1:220,69:156:-162.17,-47.03,-376.03:99
+chr1	2605834	.	C	T	954.45	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=236.05;MQ=35.80;MQ0=20;QD=3.42;SB=200.51	GT:AD:DP:GL:GQ	0/1:218,59:162:-147.54,-48.81,-432.29:99
+chr1	2605836	.	T	G	306.78	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=263;Dels=0.00;HRun=0;HaplotypeScore=206.04;MQ=36.89;MQ0=20;QD=1.17;SB=188.58	GT:AD:DP:GL:GQ	0/1:205,52:142:-88.13,-54.17,-440.06:99
+chr1	2605841	.	A	G	545.99	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=232;Dels=0.00;HRun=1;HaplotypeScore=155.67;MQ=38.58;MQ0=20;QD=2.35;SB=182.62	GT:AD:DP:GL:GQ	0/1:160,70:131:-97.35,-39.47,-411.37:99
+chr1	2605874	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=232;Dels=0.00;HRun=0;HaplotypeScore=124.99;MQ=42.37;MQ0=11;OQ=512.21;QD=2.21;SB=-14.46	GT:AD:DP:GL:GQ	0/1:155,74:147:-102.43,-47.93,-470.53:99
+chr1	2605886	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=0;HaplotypeScore=108.30;MQ=44.38;MQ0=8;OQ=363.46;QD=1.81;SB=149.68	GT:AD:DP:GL:GQ	0/1:128,71:139:-81.51,-41.88,-451.45:99
+chr1	2605893	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=197;Dels=0.00;HRun=0;HaplotypeScore=120.52;MQ=42.83;MQ0=17;OQ=327.45;QD=1.66;SB=185.60	GT:AD:DP:GL:GQ	0/1:128,68:129:-77.12,-41.09,-417.50:99
+chr1	2605899	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=1;HaplotypeScore=109.97;MQ=40.67;MQ0=24;OQ=225.12;QD=1.10;SB=176.57	GT:AD:DP:GL:GQ	0/1:183,21:132:-65.55,-39.76,-408.38:99
+chr1	2605937	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=2;HaplotypeScore=54.75;MQ=35.12;MQ0=33;OQ=125.52;QD=0.63;SB=203.69	GT:AD:DP:GL:GQ	0/1:151,48:110:-48.99,-33.15,-378.43:99
+chr1	2605949	rs55869659	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=295;Dels=0.00;HRun=1;HaplotypeScore=266.34;MQ=30.03;MQ0=43;OQ=1589.71;QD=5.39;SB=-453.79	GT:AD:DP:GL:GQ	0/1:231,64:135:-202.93,-40.67,-294.60:99
+chr1	2605976	rs6683769	G	C	6974.39	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=343;Dels=0.02;HRun=3;HaplotypeScore=423.51;MQ=29.44;MQ0=37;QD=20.33;SB=-2874.56	GT:AD:DP:GL:GQ	1/1:19,284:159:-696.44,-51.43,-8.07:99
+chr1	2605977	rs6661848	C	T	1027.05	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=358;Dels=0.00;HRun=0;HaplotypeScore=456.32;MQ=29.31;MQ0=37;QD=2.87;SB=-210.09	GT:AD:DP:GL:GQ	0/1:307,50:125:-143.65,-37.67,-316.41:99
+chr1	2605979	.	C	A	1028.24	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=357;Dels=0.00;HRun=1;HaplotypeScore=354.37;MQ=29.31;MQ0=37;QD=2.88;SB=152.21	GT:AD:DP:GL:GQ	0/1:297,56:154:-152.50,-46.39,-400.06:99
+chr1	2605985	.	A	G	302.88	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=344;Dels=0.00;HRun=1;HaplotypeScore=327.75;MQ=29.96;MQ0=33;QD=0.88;SB=170.59	GT:AD:DP:GL:GQ	0/1:269,70:128:-72.14,-38.56,-425.79:99
+chr1	2606004	.	C	T	951.09	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=0;HaplotypeScore=672.95;MQ=32.63;MQ0=23;QD=3.28;SB=87.89	GT:AD:DP:GL:GQ	0/1:220,66:128:-136.98,-38.59,-302.88:99
+chr1	2606005	rs6683777	G	A	1342.36	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=287;Dels=0.00;HRun=0;HaplotypeScore=631.13;MQ=33.21;MQ0=21;QD=4.68;SB=-76.00	GT:AD:DP:GL:GQ	0/1:85,177:126:-230.50,-92.98,-257.82:99
+chr1	2606006	rs57008511	G	T	1549.99	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=289;Dels=0.00;HRun=0;HaplotypeScore=644.99;MQ=33.16;MQ0=21;QD=5.36;SB=-385.70	GT:AD:DP:GL:GQ	0/1:228,60:127:-196.55,-38.27,-243.78:99
+chr1	2606009	.	A	T	459	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=281;Dels=0.00;HRun=0;HaplotypeScore=430.52;MQ=33.69;MQ0=19;QD=1.63;SB=105.62	GT:AD:DP:GL:GQ	0/1:113,66:123:-152.84,-103.65,-371.87:99
+chr1	2606031	.	C	G	597.38	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=1;HaplotypeScore=164.77;MQ=37.58;MQ0=8;QD=2.69;SB=139.07	GT:AD:DP:GL:GQ	0/1:114,51:127:-143.77,-80.75,-412.83:99
+chr1	2606038	.	C	A	277.03	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=0;HaplotypeScore=107.00;MQ=38.94;MQ0=8;QD=1.28;SB=120.78	GT:AD:DP:GL:GQ	0/1:160,54:121:-67.44,-36.45,-363.09:99
+chr1	2606041	.	G	T	124.23	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=206;Dels=0.00;HRun=0;HaplotypeScore=125.82;MQ=39.98;MQ0=7;QD=0.60;SB=144.54	GT:AD:DP:GL:GQ	0/1:161,44:113:-49.75,-34.04,-340.70:99
+chr1	2606206	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=315;Dels=0.00;HRun=1;HaplotypeScore=256.44;MQ=28.06;MQ0=39;OQ=155.48;QD=0.49;SB=-29.90	GT:AD:DP:GL:GQ	0/1:209,63:107:-66.50,-47.67,-397.67:99
+chr1	2606217	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=250;Dels=0.00;HRun=3;HaplotypeScore=224.65;MQ=29.86;MQ0=28;OQ=458.20;QD=1.83;SB=-95.78	GT:AD:DP:GL:GQ	0/1:87,160:81:-76.54,-27.44,-208.99:99
+chr1	2606220	rs36162961	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=249;Dels=0.00;HRun=0;HaplotypeScore=180.31;MQ=29.93;MQ0=27;OQ=201.47;QD=0.81;SB=-7.21	GT:AD:DP:GL:GQ	0/1:213,32:103:-54.47,-31.04,-311.81:99
+chr1	2606247	rs6662065	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=156;Dels=0.00;HRun=0;HaplotypeScore=58.65;MQ=36.60;MQ0=15;OQ=2337.23;QD=14.98;SB=-1097.47	GT:AD:DP:GL:GQ	0/1:41,86:97:-280.18,-43.17,-102.47:99
+chr1	2606279	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=1;HaplotypeScore=25.92;MQ=42.76;MQ0=2;OQ=312.76;QD=2.56;SB=-74.63	GT:AD:DP:GL:GQ	0/1:94,28:104:-65.90,-31.34,-343.27:99
+chr1	2606294	rs28562476	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=129;Dels=0.00;HRun=0;HaplotypeScore=45.48;MQ=41.64;MQ0=3;OQ=158.71;QD=1.23;SB=-91.27	GT:AD:DP:GL:GQ	0/1:99,30:98:-48.69,-29.54,-326.61:99
+chr1	2606300	rs6662172	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=148;Dels=0.00;HRun=1;HaplotypeScore=45.57;MQ=40.35;MQ0=4;OQ=2445.81;QD=16.53;SB=-1064.82	GT:AD:DP:GL:GQ	0/1:63,84:112:-281.60,-33.73,-119.13:99
+chr1	2606379	rs28410393	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=27.63;MQ=39.78;MQ0=6;OQ=368.46;QD=3.02;SB=6.71	GT:AD:DP:GL:GQ	0/1:95,26:92:-67.86,-27.73,-327.77:99
+chr1	2606380	rs28520729	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=27.50;MQ=39.82;MQ0=6;OQ=559.99;QD=4.71;SB=-194.85	GT:AD:DP:GL:GQ	0/1:94,25:96:-88.22,-28.94,-322.33:99
+chr1	2606465	rs28436923	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=147;Dels=0.00;HRun=0;HaplotypeScore=131.13;MQ=40.98;MQ0=13;OQ=2035.71;QD=13.85;SB=-905.49	GT:AD:DP:GL:GQ	0/1:80,64:81:-231.26,-24.41,-73.56:99
+chr1	2606518	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=0;HaplotypeScore=218.01;MQ=25.24;MQ0=20;OQ=216.97;QD=1.17;SB=68.19	GT:AD:DP:GL:GQ	0/1:119,56:69:-45.78,-20.79,-195.94:99
+chr1	2606520	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=182;Dels=0.01;HRun=1;HaplotypeScore=197.55;MQ=24.90;MQ0=18;OQ=425.87;QD=2.34;SB=7.72	GT:AD:DP:GL:GQ	0/1:98,71:68:-66.40,-20.53,-203.96:99
+chr1	2606555	rs55641610	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=142;Dels=0.00;HRun=0;HaplotypeScore=86.83;MQ=22.44;MQ0=15;OQ=611.31;QD=4.31;SB=-217.67	GT:AD:DP:GL:GQ	0/1:66,72:64:-83.70,-19.29,-186.04:99
+chr1	2606567	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=132;Dels=0.00;HRun=1;HaplotypeScore=115.34;MQ=22.30;MQ0=19;OQ=114.64;QD=0.87;SB=-3.31	GT:AD:DP:GL:GQ	0/1:113,14:59:-32.52,-17.77,-180.72:99
+chr1	2606594	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=41.70;MQ=23.56;MQ0=16;OQ=75.03;QD=0.63;SB=28.48	GT:AD:DP:GL:GQ	0/1:83,36:66:-30.68,-19.89,-255.45:99
+chr1	2606643	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=21.80;MQ=30.64;MQ0=12;OQ=1721.23;QD=15.37;SB=-793.00	GT:AD:DP:GL:GQ	0/1:46,66:82:-200.11,-24.70,-94.60:99
+chr1	2606798	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=16.08;MQ=18.33;MQ0=33;OQ=155.22;QD=2.13;SB=-92.26	GT:AD:DP:GL:GQ	0/1:36,34:23:-29.36,-10.56,-75.52:99
+chr1	2607095	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=174;Dels=0.00;HRun=0;HaplotypeScore=115.98;MQ=20.76;MQ0=93;OQ=63.80;QD=0.37;SB=-35.41	GT:AD:DP:GL:GQ	0/1:164,10:54:-25.95,-16.29,-195.04:96.63
+chr1	2607127	rs28555663	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=71.01;MQ=31.05;MQ0=18;OQ=1628.35;QD=13.57;SB=-397.76	GT:AD:DP:GL:GQ	0/1:27,60:78:-215.41,-49.30,-93.76:99
+chr1	2607162	rs61763542	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=215;Dels=0.00;HRun=1;HaplotypeScore=85.56;MQ=29.70;MQ0=30;OQ=368.13;QD=1.71;SB=-56.56	GT:AD:DP:GL:GQ	0/1:178,35:124:-77.45,-37.35,-360.47:99
+chr1	2607163	.	G	A	13.12	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=2;HaplotypeScore=87.56;MQ=29.61;MQ0=31;QD=0.06;SB=-11.83	GT:AD:DP:GL:GQ	0/1:187,28:129:-43.44,-38.86,-425.52:45.74
+chr1	2607204	.	G	C	43.54	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=196;Dels=0.00;HRun=0;HaplotypeScore=43.04;MQ=31.64;MQ0=30;QD=0.22;SB=-29.18	GT:AD:DP:GL:GQ	0/1:170,26:109:-40.50,-32.86,-424.67:76.37
+chr1	2607231	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=1;HaplotypeScore=72.77;MQ=31.17;MQ0=24;OQ=125.47;QD=0.87;SB=-42.71	GT:AD:DP:GL:GQ	0/1:125,19:75:-38.43,-22.60,-228.94:99
+chr1	2607242	rs61763545	G	T	46.85	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=36.90;MQ=31.04;MQ0=29;QD=0.40;SB=43.89	GT:AD:DP:GL:GQ	0/1:84,30:54:-24.25,-16.28,-154.98:79.69
+chr1	2607298	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=68.12;MQ=14.41;MQ0=82;OQ=66.90;QD=0.45;SB=20.86	GT:AD:DP:GL:GQ	0/1:129,10:21:-19.87,-9.89,-58.18:99
+chr1	2607355	rs61765818	C	T	12.91	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=56.37;MQ=16.61;MQ0=62;QD=0.11;SB=29.06	GT:AD:DP:GL:GQ	0/1:90,27:23:-11.49,-6.94,-61.93:45.51
+chr1	2607366	.	A	G	13.05	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=2;HaplotypeScore=34.50;MQ=17.10;MQ0=55;QD=0.12;SB=29.12	GT:AD:DP:GL:GQ	0/1:102,6:22:-11.19,-6.63,-75.23:45.67
+chr1	2607368	rs61763546	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=35.70;MQ=17.26;MQ0=53;OQ=303.93;QD=2.87;SB=-146.92	GT:AD:DP:GL:GQ	0/1:46,59:26:-41.51,-7.84,-47.60:99
+chr1	2607409	.	G	A	15.60	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=56.89;MQ=28.46;MQ0=6;QD=0.24;SB=38.64	GT:AD:DP:GL:GQ	0/1:41,24:37:-15.99,-11.15,-106.07:48.31
+chr1	2607422	rs56133135	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=3;HaplotypeScore=19.37;MQ=32.69;MQ0=0;OQ=693.38;QD=12.61;SB=2.03	GT:AD:DP:GL:GQ	0/1:26,28:39:-84.38,-11.76,-83.37:99
+chr1	2607465	rs61763547	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=40.98;MQ=25.86;MQ0=35;OQ=388.51;QD=4.63;SB=-36.91	GT:AD:DP:GL:GQ	0/1:60,23:42:-54.79,-12.65,-94.92:99
+chr1	2607520	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=176;Dels=0.00;HRun=1;HaplotypeScore=43.55;MQ=22.90;MQ0=79;OQ=121.23;QD=0.69;SB=8.68	GT:AD:DP:GL:GQ	0/1:158,14:67:-35.59,-20.18,-205.83:99
+chr1	2607562	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=147;Dels=0.00;HRun=0;HaplotypeScore=58.31;MQ=31.97;MQ0=28;OQ=222.37;QD=1.51;SB=-108.77	GT:AD:DP:GL:GQ	0/1:118,16:74:-51.32,-25.80,-191.60:99
+chr1	2607568	rs61763549	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=0;HaplotypeScore=80.59;MQ=33.84;MQ0=16;OQ=1066.74;QD=7.90;SB=-480.14	GT:AD:DP:GL:GQ	0/1:64,70:72:-131.67,-21.72,-176.26:99
+chr1	2607579	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=1;HaplotypeScore=59.49;MQ=32.83;MQ0=15;OQ=376.87;QD=2.37;SB=-134.64	GT:AD:DP:GL:GQ	0/1:129,30:89:-67.78,-26.81,-244.98:99
+chr1	2607622	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=166;Dels=0.00;HRun=1;HaplotypeScore=74.61;MQ=28.79;MQ0=41;OQ=121.71;QD=0.73;SB=1.49	GT:AD:DP:GL:GQ	0/1:144,22:68:-35.94,-20.49,-206.61:99
+chr1	2607635	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=177;Dels=0.00;HRun=1;HaplotypeScore=30.67;MQ=24.43;MQ0=69;OQ=168.44;QD=0.95;SB=-26.38	GT:AD:DP:GL:GQ	0/1:144,24:48:-34.61,-14.49,-156.01:99
+chr1	2607650	.	G	A	36.08	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=1;HaplotypeScore=75.42;MQ=22.15;MQ0=92;QD=0.19;SB=17.06	GT:AD:DP:GL:GQ	0/1:183,11:48:-21.35,-14.46,-155.19:68.92
+chr1	2607670	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=229;Dels=0.00;HRun=0;HaplotypeScore=160.50;MQ=16.74;MQ0=141;OQ=99.29;QD=0.43;SB=62.11	GT:AD:DP:GL:GQ	0/1:219,9:33:-23.18,-9.97,-80.62:99
+chr1	2607674	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=226;Dels=0.00;HRun=0;HaplotypeScore=115.26;MQ=15.31;MQ0=147;OQ=144.37;QD=0.64;SB=59.23	GT:AD:DP:GL:GQ	0/1:144,82:32:-27.37,-9.65,-111.07:99
+chr1	2607705	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=307;Dels=0.00;HRun=0;HaplotypeScore=135.41;MQ=9.50;MQ0=238;OQ=88.23;QD=0.29;SB=44.16	GT:AD:DP:GL:GQ	0/1:293,13:26:-19.94,-7.83,-70.73:99
+chr1	2607732	.	A	G	46.69	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=264;Dels=0.00;HRun=0;HaplotypeScore=160.28;MQ=9.40;MQ0=205;QD=0.18;SB=38.16	GT:AD:DP:GL:GQ	0/1:246,15:21:-14.28,-6.33,-70.03:79.52
+chr1	2607768	.	C	G	49.76	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=95.94;MQ=10.01;MQ0=124;QD=0.30;SB=-3.98	GT:AD:DP:GL:GQ	0/1:136,25:16:-13.08,-4.82,-52.20:82.60
+chr1	2607891	rs7416366	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=58.84;MQ=34.41;MQ0=14;OQ=1644.48;QD=13.48;SB=-506.65	GT:AD:DP:GL:GQ	0/1:59,63:73:-189.73,-22.00,-69.36:99
+chr1	2607919	.	C	G	24.55	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=221;Dels=0.00;HRun=0;HaplotypeScore=83.78;MQ=30.54;MQ0=25;QD=0.11;SB=109.84	GT:AD:DP:GL:GQ	0/1:205,16:120:-41.91,-36.17,-462.22:57.38
+chr1	2607925	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=1;HaplotypeScore=102.41;MQ=29.59;MQ0=28;OQ=208.07;QD=0.92;SB=12.89	GT:AD:DP:GL:GQ	0/1:171,51:116:-59.04,-34.95,-344.67:99
+chr1	2607990	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=0;HaplotypeScore=62.53;MQ=19.75;MQ0=60;OQ=143.02;QD=0.67;SB=-11.93	GT:AD:DP:GL:GQ	0/1:169,45:70:-38.68,-21.10,-211.21:99
+chr1	2608016	rs61763552	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=154;Dels=0.00;HRun=1;HaplotypeScore=33.08;MQ=18.38;MQ0=35;OQ=157.73;QD=1.02;SB=-56.91	GT:AD:DP:GL:GQ	0/1:74,80:55:-35.63,-16.57,-153.82:99
+chr1	2608035	rs60386739	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=141;Dels=0.00;HRun=1;HaplotypeScore=68.10;MQ=20.23;MQ0=19;OQ=139.83;QD=0.99;SB=-34.61	GT:AD:DP:GL:GQ	0/1:123,11:68:-37.75,-20.49,-226.75:99
+chr1	2608187	.	T	A	19.78	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=100.91;MQ=20.82;MQ0=35;QD=0.14;SB=68.21	GT:AD:DP:GL:GQ	0/1:73,68:45:-18.82,-13.56,-139.70:52.57
+chr1	2608269	rs28464857	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.00;HRun=0;HaplotypeScore=134.04;MQ=20.25;MQ0=84;OQ=169.32;QD=0.91;SB=-92.57	GT:AD:DP:GL:GQ	0/1:170,15:57:-37.38,-17.17,-176.94:99
+chr1	2608484	rs28436796	C	G	0.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=9.24;MQ=47.84;MQ0=1;OQ=487.04;QD=5.47;SB=-196.59	GT:AD:DP:GL:GQ	0/1:66,21:74:-74.31,-22.32,-232.63:99
+chr1	2608664	rs4074927	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=182;Dels=0.01;HRun=1;HaplotypeScore=99.89;MQ=34.06;MQ0=19;OQ=2375.90;QD=13.05;SB=-939.83	GT:AD:DP:GL:GQ	0/1:91,85:111:-274.32,-33.45,-107.97:99
+chr1	2608867	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=118;Dels=0.01;HRun=2;HaplotypeScore=20.49;MQ=45.47;MQ0=7;OQ=974.46;QD=8.26;SB=-210.08	GT:AD:DP:GL:GQ	0/1:62,55:87:-126.99,-26.26,-221.81:99
+chr1	2609068	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=221;Dels=0.00;HRun=3;HaplotypeScore=118.35;MQ=34.13;MQ0=24;OQ=526.94;QD=2.38;SB=137.47	GT:AD:DP:GL:GQ	0/1:93,112:118:-95.11,-39.14,-362.67:99
+chr1	2609088	rs6604995	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=244;Dels=0.00;HRun=1;HaplotypeScore=80.61;MQ=35.58;MQ0=31;OQ=2415.96;QD=9.90;SB=-1183.52	GT:AD:DP:GL:GQ	0/1:168,75:136:-285.85,-40.97,-232.15:99
+chr1	2609117	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=242;Dels=0.00;HRun=0;HaplotypeScore=86.85;MQ=40.05;MQ0=22;OQ=564.86;QD=2.33;SB=136.90	GT:AD:DP:GL:GQ	0/1:188,54:147:-104.06,-44.29,-429.75:99
+chr1	2609119	.	T	A	10.35	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=1;HaplotypeScore=66.02;MQ=40.40;MQ0=19;QD=0.04;SB=-13.71	GT:AD:DP:GL:GQ	0/1:216,24:153:-50.36,-46.09,-521.00:42.77
+chr1	2609136	rs6680012	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=252;Dels=0.00;HRun=0;HaplotypeScore=138.11;MQ=41.19;MQ0=14;OQ=1288.83;QD=5.11;SB=-20.42	GT:AD:DP:GL:GQ	0/1:111,140:159:-180.06,-47.89,-385.06:99
+chr1	2609225	rs61765683	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=279;Dels=0.00;HRun=0;HaplotypeScore=196.30;MQ=28.44;MQ0=55;OQ=715.74;QD=2.57;SB=-196.88	GT:AD:DP:GL:GQ	0/1:215,53:119:-124.19,-49.34,-290.35:99
+chr1	2609273	rs4648680	A	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=189;Dels=0.00;HRun=0;HaplotypeScore=41.61;MQ=19.84;MQ0=34;OQ=2444.19;QD=12.93;SB=-891.61	GT:AD:DP:GL:GQ	1/1:0,186:71:-248.05,-21.40,-0.04:99
+chr1	2609305	rs6672446	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=196;Dels=0.00;HRun=1;HaplotypeScore=44.27;MQ=21.28;MQ0=40;OQ=1443.42;QD=7.36;SB=-313.15	GT:AD:DP:GL:GQ	0/1:121,75:90:-174.74,-27.11,-141.16:99
+chr1	2609332	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=1;HaplotypeScore=25.23;MQ=24.42;MQ0=31;OQ=1010.88;QD=5.29;SB=-411.33	GT:AD:DP:GL:GQ	0/1:130,60:101:-134.82,-30.45,-224.41:99
+chr1	2609354	rs61765685	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=264;Dels=0.00;HRun=0;HaplotypeScore=43.36;MQ=26.38;MQ0=47;OQ=877.95;QD=3.33;SB=-290.40	GT:AD:DP:GL:GQ	0/1:123,140:122:-127.86,-36.78,-326.56:99
+chr1	2609381	.	C	A	220.25	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=378;Dels=0.00;HRun=0;HaplotypeScore=205.42;MQ=26.54;MQ0=63;QD=0.58;SB=-92.16	GT:AD:DP:GL:GQ	0/1:327,50:132:-65.07,-39.76,-400.14:99
+chr1	2609387	.	C	A	185.57	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=439;Dels=0.00;HRun=0;HaplotypeScore=250.48;MQ=26.77;MQ0=67;QD=0.42;SB=5.95	GT:AD:DP:GL:GQ	0/1:387,52:145:-65.52,-43.68,-445.14:99
+chr1	2609389	.	C	T	92.18	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=450;Dels=0.00;HRun=0;HaplotypeScore=251.37;MQ=26.71;MQ0=67;QD=0.20;SB=175.01	GT:AD:DP:GL:GQ	0/1:391,58:155:-59.19,-46.69,-504.94:99
+chr1	2609452	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=378;Dels=0.00;HRun=2;HaplotypeScore=241.26;MQ=31.94;MQ0=54;OQ=971.37;QD=2.57;SB=-357.67	GT:AD:DP:GL:GQ	0/1:305,73:146:-144.40,-43.98,-395.70:99
+chr1	2609455	rs58318704	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=356;Dels=0.00;HRun=0;HaplotypeScore=220.51;MQ=31.91;MQ0=49;OQ=2158.97;QD=6.06;SB=-1017.43	GT:AD:DP:GL:GQ	0/1:79,219:141:-270.22,-51.04,-310.17:99
+chr1	2609547	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=1;HaplotypeScore=66.94;MQ=35.31;MQ0=17;OQ=674.03;QD=3.60;SB=-244.40	GT:AD:DP:GL:GQ	0/1:135,50:133:-110.75,-40.07,-356.06:99
+chr1	2609555	rs28575476	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.00;HRun=0;HaplotypeScore=68.51;MQ=35.35;MQ0=12;OQ=1288.35;QD=7.53;SB=-481.51	GT:AD:DP:GL:GQ	0/1:88,78:120:-168.27,-36.15,-252.36:99
+chr1	2609591	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=0;HaplotypeScore=34.97;MQ=33.84;MQ0=11;OQ=2484.13;QD=14.44;SB=-938.03	GT:AD:DP:GL:GQ	0/1:84,88:135:-292.43,-40.73,-257.29:99
+chr1	2609644	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=353;Dels=0.00;HRun=1;HaplotypeScore=213.12;MQ=29.19;MQ0=26;OQ=1530.86;QD=4.34;SB=-311.00	GT:AD:DP:GL:GQ	0/1:205,118:177:-209.80,-53.43,-491.62:99
+chr1	2609668	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=375;Dels=0.01;HRun=0;HaplotypeScore=299.53;MQ=28.31;MQ0=38;OQ=119.51;QD=0.32;SB=-39.52	GT:AD:DP:GL:GQ	0/1:330,33:168:-65.89,-50.66,-484.68:99
+chr1	2609669	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=370;Dels=0.01;HRun=3;HaplotypeScore=295.29;MQ=28.20;MQ0=38;OQ=509.10;QD=1.38;SB=-148.65	GT:AD:DP:GL:GQ	0/1:202,146:144:-97.68,-43.48,-474.43:99
+chr1	2609682	.	T	C	10.13	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=358;Dels=0.00;HRun=1;HaplotypeScore=318.76;MQ=28.20;MQ0=43;QD=0.03;SB=29.61	GT:AD:DP:GL:GQ	0/1:328,21:141:-56.49,-52.23,-495.36:42.52
+chr1	2609688	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=357;Dels=0.00;HRun=0;HaplotypeScore=304.49;MQ=28.68;MQ0=43;OQ=540.31;QD=1.51;SB=-146.86	GT:AD:DP:GL:GQ	0/1:288,44:135:-97.99,-40.67,-405.76:99
+chr1	2609713	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=325;Dels=0.00;HRun=2;HaplotypeScore=235.46;MQ=29.07;MQ0=50;OQ=183.31;QD=0.56;SB=-70.06	GT:AD:DP:GL:GQ	0/1:293,30:98:-51.18,-29.56,-309.43:99
+chr1	2609764	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=67.69;MQ=41.15;MQ0=28;OQ=547.70;QD=3.06;SB=-220.32	GT:AD:DP:GL:GQ	0/1:154,22:97:-87.34,-29.29,-296.73:99
+chr1	2609770	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=51.04;MQ=41.72;MQ0=28;OQ=50.39;QD=0.29;SB=107.80	GT:AD:DP:GL:GQ	0/1:92,83:96:-37.25,-28.93,-332.67:83.23
+chr1	2609843	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=18.24;MQ=41.49;MQ0=22;OQ=514.69;QD=3.78;SB=-103.96	GT:AD:DP:GL:GQ	0/1:89,47:97:-83.99,-29.23,-261.15:99
+chr1	2609879	rs60995822	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=53.77;MQ=31.75;MQ0=20;OQ=1688.97;QD=13.62;SB=-590.07	GT:AD:DP:GL:GQ	0/1:21,102:69:-192.97,-20.79,-48.84:99
+chr1	2609938	rs61765691	T	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=210;Dels=0.00;HRun=0;HaplotypeScore=78.06;MQ=23.32;MQ0=40;OQ=3717.12;QD=17.70;SB=-1751.06	GT:AD:DP:GL:GQ	1/1:3,206:105:-370.71,-31.64,-0.05:99
+chr1	2610024	rs60041779	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.00;HRun=0;HaplotypeScore=93.88;MQ=40.95;MQ0=10;OQ=112.09;QD=0.90;SB=83.51	GT:AD:DP:GL:GQ	0/1:77,47:69:-35.30,-20.81,-248.60:99
+chr1	2610174	rs61765693	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=331;Dels=0.00;HRun=1;HaplotypeScore=45.52;MQ=28.55;MQ0=47;OQ=762.69;QD=2.30;SB=-121.02	GT:AD:DP:GL:GQ	0/1:162,168:127:-117.91,-38.35,-381.81:99
+chr1	2610186	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=354;Dels=0.00;HRun=0;HaplotypeScore=102.42;MQ=26.42;MQ0=47;OQ=1467.29;QD=4.14;SB=-129.66	GT:AD:DP:GL:GQ	0/1:303,49:127:-191.55,-41.54,-284.06:99
+chr1	2610220	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=358;Dels=0.00;HRun=0;HaplotypeScore=158.15;MQ=26.10;MQ0=33;OQ=52.73;QD=0.15;SB=-33.83	GT:AD:DP:GL:GQ	0/1:323,33:128:-47.12,-38.57,-405.99:85.57
+chr1	2610228	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=347;Dels=0.00;HRun=0;HaplotypeScore=258.31;MQ=25.86;MQ0=32;OQ=417.23;QD=1.20;SB=-217.33	GT:AD:DP:GL:GQ	0/1:235,103:129:-86.15,-41.14,-407.87:99
+chr1	2610288	rs61765694	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=240;Dels=0.00;HRun=0;HaplotypeScore=161.76;MQ=34.28;MQ0=24;OQ=460.60;QD=1.92;SB=-235.27	GT:AD:DP:GL:GQ	0/1:119,106:122:-91.58,-42.24,-307.51:99
+chr1	2610304	rs57887432	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=214;Dels=0.00;HRun=1;HaplotypeScore=126.12;MQ=34.24;MQ0=19;OQ=2078.47;QD=9.71;SB=-912.59	GT:AD:DP:GL:GQ	0/1:141,72:106:-243.09,-31.96,-204.85:99
+chr1	2610325	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=0;HaplotypeScore=58.60;MQ=38.14;MQ0=8;OQ=610.61;QD=3.94;SB=-307.83	GT:AD:DP:GL:GQ	0/1:117,38:94:-92.67,-28.33,-261.00:99
+chr1	2610342	rs58318302	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=64.33;MQ=41.99;MQ0=6;OQ=1628.60;QD=14.67;SB=-308.68	GT:AD:DP:GL:GQ	0/1:43,66:83:-191.15,-25.00,-121.94:99
+chr1	2610414	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=331;Dels=0.00;HRun=0;HaplotypeScore=235.51;MQ=30.47;MQ0=22;OQ=935.47;QD=2.83;SB=-429.72	GT:AD:DP:GL:GQ	0/1:275,53:139:-142.25,-45.42,-348.13:99
+chr1	2610415	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=337;Dels=0.00;HRun=1;HaplotypeScore=237.48;MQ=30.55;MQ0=22;OQ=1122.12;QD=3.33;SB=-419.64	GT:AD:DP:GL:GQ	0/1:156,170:150:-188.30,-72.80,-443.59:99
+chr1	2610441	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=398;Dels=0.00;HRun=0;HaplotypeScore=305.07;MQ=30.41;MQ0=29;OQ=523.24;QD=1.31;SB=-254.15	GT:AD:DP:GL:GQ	0/1:145,184:159:-118.96,-63.35,-451.63:99
+chr1	2610473	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=351;Dels=0.00;HRun=1;HaplotypeScore=331.68;MQ=29.41;MQ0=37;OQ=1376.69;QD=3.92;SB=-162.02	GT:AD:DP:GL:GQ	0/1:286,64:127:-179.22,-38.27,-253.78:99
+chr1	2610474	rs28418735	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=350;Dels=0.03;HRun=3;HaplotypeScore=309.89;MQ=29.49;MQ0=38;OQ=65.43;QD=0.19;SB=221.76	GT:AD:DP:GL:GQ	0/1:271,68:132:-49.66,-39.83,-486.19:98.27
+chr1	2610506	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=0;HaplotypeScore=143.13;MQ=32.96;MQ0=24;OQ=241.48;QD=1.21;SB=-28.90	GT:AD:DP:GL:GQ	0/1:85,107:74:-49.73,-22.29,-227.60:99
+chr1	2610517	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=3;HaplotypeScore=142.26;MQ=34.55;MQ0=20;OQ=220.80;QD=1.35;SB=75.68	GT:AD:DP:GL:GQ	0/1:65,82:63:-52.24,-26.88,-202.10:99
+chr1	2610573	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=104.72;MQ=37.56;MQ0=8;OQ=553.10;QD=3.29;SB=-39.90	GT:AD:DP:GL:GQ	0/1:88,80:80:-82.71,-24.12,-188.70:99
+chr1	2610594	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=122;Dels=0.02;HRun=0;HaplotypeScore=84.91;MQ=43.41;MQ0=3;OQ=1001.55;QD=8.21;SB=-522.00	GT:AD:DP:GL:GQ	0/1:52,66:81:-127.86,-24.42,-216.74:99
+chr1	2610598	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=2;HaplotypeScore=59.26;MQ=42.74;MQ0=3;OQ=1239.36;QD=9.61;SB=-593.34	GT:AD:DP:GL:GQ	0/1:51,77:86:-153.17,-25.95,-194.38:99
+chr1	2610632	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=184;Dels=0.00;HRun=0;HaplotypeScore=151.91;MQ=39.51;MQ0=6;OQ=369.19;QD=2.01;SB=-62.83	GT:AD:DP:GL:GQ	0/1:154,30:112:-73.95,-33.75,-316.70:99
+chr1	2610635	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=139.15;MQ=38.51;MQ0=6;OQ=274.48;QD=1.35;SB=-41.80	GT:AD:DP:GL:GQ	0/1:164,37:123:-67.82,-37.08,-455.22:99
+chr1	2610665	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=1;HaplotypeScore=315.73;MQ=36.51;MQ0=11;OQ=1591.77;QD=7.40;SB=-670.77	GT:AD:DP:GL:GQ	0/1:149,65:109:-195.35,-32.89,-252.45:99
+chr1	2610712	rs55957791	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=331.10;MQ=30.73;MQ0=38;OQ=351.17;QD=1.26;SB=50.69	GT:AD:DP:GL:GQ	0/1:157,116:120:-81.22,-42.82,-389.65:99
+chr1	2610714	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=276;Dels=0.03;HRun=1;HaplotypeScore=276.80;MQ=30.44;MQ0=40;OQ=799.29;QD=2.90;SB=-215.74	GT:AD:DP:GL:GQ	0/1:208,58:112:-116.35,-33.14,-272.42:99
+chr1	2610938	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=61.08;MQ=40.33;MQ0=9;OQ=2312.34;QD=13.21;SB=-496.11	GT:AD:DP:GL:GQ	0/1:80,95:114:-268.87,-34.35,-152.15:99
+chr1	2610982	rs61765696	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=168;Dels=0.00;HRun=1;HaplotypeScore=77.40;MQ=36.09;MQ0=4;OQ=730.22;QD=4.35;SB=-250.72	GT:AD:DP:GL:GQ	0/1:133,34:93:-104.33,-28.02,-240.35:99
+chr1	2610988	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=177;Dels=0.00;HRun=2;HaplotypeScore=104.66;MQ=37.43;MQ0=4;OQ=180.91;QD=1.02;SB=-14.66	GT:AD:DP:GL:GQ	0/1:124,53:103:-52.42,-31.04,-397.79:99
+chr1	2611005	rs28657620	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=175;Dels=0.00;HRun=0;HaplotypeScore=240.92;MQ=35.09;MQ0=11;OQ=589.04;QD=3.37;SB=-319.71	GT:AD:DP:GL:GQ	0/1:148,26:83:-87.21,-25.02,-177.35:99
+chr1	2611008	rs61765697	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=177;Dels=0.00;HRun=0;HaplotypeScore=268.58;MQ=34.75;MQ0=11;OQ=814.23;QD=4.60;SB=-203.16	GT:AD:DP:GL:GQ	0/1:94,75:81:-109.12,-24.42,-183.44:99
+chr1	2611037	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=212;Dels=0.00;HRun=3;HaplotypeScore=47.75;MQ=33.75;MQ0=25;OQ=310.37;QD=1.46;SB=128.35	GT:AD:DP:GL:GQ	0/1:180,32:105:-65.95,-31.63,-301.79:99
+chr1	2611075	.	C	A	675.15	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=198;Dels=0.00;HRun=0;HaplotypeScore=289.45;MQ=35.67;MQ0=15;QD=3.41;SB=-245.12	GT:AD:DP:GL:GQ	0/1:138,49:92:-105.75,-34.95,-225.78:99
+chr1	2611076	.	C	A	59.41	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=0;HaplotypeScore=288.77;MQ=35.79;MQ0=15;QD=0.30;SB=-43.36	GT:AD:DP:GL:GQ	0/1:179,20:91:-36.64,-27.42,-281.03:92.25
+chr1	2611077	.	T	C	1287	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=3;HaplotypeScore=272.49;MQ=35.97;MQ0=16;QD=6.47;SB=-518.91	GT:AD:DP:GL:GQ	0/1:56,142:93:-160.01,-28.02,-190.32:99
+chr1	2611149	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=0;HaplotypeScore=128.93;MQ=29.89;MQ0=30;OQ=118.35;QD=0.49;SB=-20.53	GT:AD:DP:GL:GQ	0/1:190,53:92:-42.83,-27.72,-276.95:99
+chr1	2611155	rs61765698	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=245;Dels=0.00;HRun=0;HaplotypeScore=130.50;MQ=30.96;MQ0=25;OQ=203.44;QD=0.83;SB=-29.37	GT:AD:DP:GL:GQ	0/1:191,50:97:-52.56,-28.94,-359.64:99
+chr1	2611193	rs61029569	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=154;Dels=0.01;HRun=0;HaplotypeScore=78.67;MQ=38.69;MQ0=8;OQ=1417.86;QD=9.21;SB=-633.08	GT:AD:DP:GL:GQ	0/1:43,100:84:-170.37,-25.30,-121.64:99
+chr1	2611212	rs28774982	C	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=125;Dels=0.00;HRun=0;HaplotypeScore=29.20;MQ=42.14;MQ0=3;OQ=3660.18;QD=29.28;SB=-1724.01	GT:AD:DP:GL:GQ	1/1:0,124:85:-365.02,-25.61,-0.03:99
+chr1	2611218	rs28581654	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=132;Dels=0.00;HRun=1;HaplotypeScore=33.13;MQ=42.84;MQ0=2;OQ=1779.64;QD=13.48;SB=-735.33	GT:AD:DP:GL:GQ	0/1:39,85:92:-211.73,-30.48,-139.53:99
+chr1	2611236	rs61765699	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=181;Dels=0.00;HRun=1;HaplotypeScore=137.95;MQ=39.80;MQ0=14;OQ=1598.49;QD=8.83;SB=-821.38	GT:AD:DP:GL:GQ	0/1:99,78:96:-192.06,-28.93,-137.58:99
+chr1	2611310	.	G	C	25	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=214;Dels=0.00;HRun=2;HaplotypeScore=68.15;MQ=29.71;MQ0=28;QD=0.12;SB=77.64	GT:AD:DP:GL:GQ	0/1:182,25:80:-33.47,-27.69,-302.15:57.82
+chr1	2611331	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=0;HaplotypeScore=171.01;MQ=28.57;MQ0=19;OQ=169.19;QD=1.00;SB=32.13	GT:AD:DP:GL:GQ	0/1:101,40:47:-34.37,-14.17,-141.57:99
+chr1	2611336	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=160;Dels=0.00;HRun=0;HaplotypeScore=142.89;MQ=27.04;MQ0=20;OQ=617.89;QD=3.86;SB=-201.64	GT:AD:DP:GL:GQ	0/1:32,126:45:-78.63,-13.56,-88.17:99
+chr1	2611359	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=160;Dels=0.00;HRun=2;HaplotypeScore=100.78;MQ=27.44;MQ0=19;OQ=605.72;QD=3.79;SB=-223.68	GT:AD:DP:GL:GQ	0/1:36,124:39:-75.62,-11.76,-86.35:99
+chr1	2611360	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=172;Dels=0.01;HRun=0;HaplotypeScore=100.05;MQ=27.08;MQ0=24;OQ=169.30;QD=0.98;SB=23.10	GT:AD:DP:GL:GQ	0/1:135,36:41:-32.56,-12.35,-112.95:99
+chr1	2611385	.	A	G	25.43	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=202;Dels=0.00;HRun=0;HaplotypeScore=141.90;MQ=28.13;MQ0=36;QD=0.13;SB=77.25	GT:AD:DP:GL:GQ	0/1:184,18:55:-22.41,-16.58,-186.56:58.25
+chr1	2611395	.	C	A	10.87	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=190;Dels=0.00;HRun=1;HaplotypeScore=214.46;MQ=28.47;MQ0=34;QD=0.06;SB=44.16	GT:AD:DP:GL:GQ	0/1:160,27:48:-18.79,-14.46,-145.75:43.33
+chr1	2611409	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=176;Dels=0.00;HRun=0;HaplotypeScore=170.63;MQ=30.96;MQ0=28;OQ=246.71;QD=1.40;SB=-63.23	GT:AD:DP:GL:GQ	0/1:66,90:51:-46.30,-18.34,-146.08:99
+chr1	2611417	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=201.92;MQ=31.46;MQ0=25;OQ=276.60;QD=1.55;SB=-61.04	GT:AD:DP:GL:GQ	0/1:50,88:59:-67.59,-36.64,-159.73:99
+chr1	2611440	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=180;Dels=0.00;HRun=0;HaplotypeScore=297.52;MQ=31.70;MQ0=24;OQ=229.57;QD=1.28;SB=65.18	GT:AD:DP:GL:GQ	0/1:152,22:68:-46.74,-20.49,-196.70:99
+chr1	2611441	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=4;HaplotypeScore=281.36;MQ=31.83;MQ0=24;OQ=677.61;QD=3.87;SB=-187.78	GT:AD:DP:GL:GQ	0/1:57,116:70:-92.13,-21.09,-155.28:99
+chr1	2611460	.	G	C	143.72	DPFilter;HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=209;Dels=0.02;HRun=1;HaplotypeScore=206.53;MQ=28.72;MQ0=29;QD=0.69;SB=95.33	GT:AD:DP:GL:GQ	0/1:169,33:67:-37.89,-20.23,-223.47:99
+chr1	2611462	.	G	C	346.96	DPFilter;HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=206;Dels=0.00;HRun=0;HaplotypeScore=159.36;MQ=28.99;MQ0=26;QD=1.68;SB=95.35	GT:AD:DP:GL:GQ	0/1:176,30:73:-60.00,-22.02,-249.89:99
+chr1	2611473	.	C	A	226.87	DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=197;Dels=0.00;HRun=0;HaplotypeScore=716.79;MQ=27.80;MQ0=23;QD=1.15;SB=98.33	GT:AD:DP:GL:GQ	0/1:167,28:68:-46.46,-20.49,-193.68:99
+chr1	2611481	.	A	C	47.15	DPFilter;HARD_TO_VALIDATE;Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=3;HaplotypeScore=376.14;MQ=26.76;MQ0=25;QD=0.22;SB=4.29	GT:AD:DP:GL:GQ	0/1:158,51:68:-32.16,-24.16,-211.95:79.99
+chr1	2611482	rs28657015	C	T	493.48	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=216;Dels=0.03;HRun=0;HaplotypeScore=277.76;MQ=26.81;MQ0=24;QD=2.28;SB=-58.33	GT:AD:DP:GL:GQ	0/1:180,23:71:-73.42,-20.79,-178.37:99
+chr1	2611484	.	G	A	123.65	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=1;HaplotypeScore=257.24;MQ=26.43;MQ0=26;QD=0.57;SB=52.66	GT:AD:DP:GL:GQ	0/1:181,35:66:-35.53,-19.88,-208.25:99
+chr1	2611506	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=1;HaplotypeScore=227.39;MQ=23.92;MQ0=38;OQ=83.72;QD=0.34;SB=1.08	GT:AD:DP:GL:GQ	0/1:205,36:67:-31.84,-20.19,-209.30:99
+chr1	2611529	.	G	C	1369.67	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=0;HaplotypeScore=198.19;MQ=24.21;MQ0=25;QD=7.40;SB=-595.38	GT:AD:DP:GL:GQ	0/1:36,136:57:-168.20,-27.95,-90.83:99
+chr1	2611531	.	T	A	49.73	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=1;HaplotypeScore=167.31;MQ=24.09;MQ0=26;QD=0.27;SB=30.12	GT:AD:DP:GL:GQ	0/1:175,9:48:-26.14,-17.88,-160.86:82.57
+chr1	2611537	.	A	C	10.75	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=1;HaplotypeScore=150.76;MQ=24.75;MQ0=25;QD=0.06;SB=49.53	GT:AD:DP:GL:GQ	0/1:160,17:47:-21.51,-17.19,-149.44:43.20
+chr1	2611551	.	C	A	34.16	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=166;Dels=0.02;HRun=1;HaplotypeScore=423.66;MQ=25.51;MQ0=20;QD=0.21;SB=47.16	GT:AD:DP:GL:GQ	0/1:139,17:37:-21.33,-14.63,-112.07:67
+chr1	2611559	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=150;Dels=0.01;HRun=3;HaplotypeScore=531.42;MQ=25.48;MQ0=17;OQ=388.67;QD=2.59;SB=-7.62	GT:AD:DP:GL:GQ	0/1:47,82:45:-90.78,-48.63,-105.70:99
+chr1	2611586	.	G	A	21.13	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=158;Dels=0.00;HRun=1;HaplotypeScore=127.50;MQ=28.93;MQ0=18;QD=0.13;SB=47.15	GT:AD:DP:GL:GQ	0/1:123,29:42:-18.05,-12.65,-132.34:53.94
+chr1	2611593	.	C	A	39.57	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=0;HaplotypeScore=189.22;MQ=30.35;MQ0=16;QD=0.29;SB=47.17	GT:AD:DP:GL:GQ	0/1:123,13:39:-18.99,-11.75,-120.10:72.41
+chr1	2611600	.	T	C	291.60	SnpCluster	AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=2;HaplotypeScore=197.17;MQ=32.27;MQ0=10;QD=2.58;SB=-146.84	GT:AD:DP:GL:GQ	0/1:38,66:38:-47.43,-14.99,-100.79:99
+chr1	2611602	.	C	G	76.87	SnpCluster	AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=173.17;MQ=32.76;MQ0=9;QD=0.68;SB=-63.17	GT:AD:DP:GL:GQ	0/1:81,31:39:-22.73,-11.76,-142.68:99
+chr1	2611613	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=122.16;MQ=34.85;MQ0=5;OQ=326.72;QD=4.08;SB=-171.57	GT:AD:DP:GL:GQ	0/1:20,59:33:-49.07,-13.11,-79.40:99
+chr1	2611623	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=114.07;MQ=31.99;MQ0=3;OQ=59.10;QD=0.57;SB=53.18	GT:AD:DP:GL:GQ	0/1:44,51:42:-30.56,-21.37,-135.55:91.94
+chr1	2611678	.	C	A	64.73	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=1;HaplotypeScore=80.70;MQ=27.19;MQ0=13;QD=0.45;SB=-53.00	GT:AD:DP:GL:GQ	0/1:121,21:50:-24.83,-15.07,-143.50:97.56
+chr1	2611679	.	C	T	18.94	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=0;HaplotypeScore=77.77;MQ=26.46;MQ0=13;QD=0.14;SB=-28.00	GT:AD:DP:GL:GQ	0/1:130,7:48:-19.64,-14.46,-152.87:51.72
+chr1	2611680	.	C	A	348.12	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=72.18;MQ=26.57;MQ0=13;QD=2.58;SB=-130.78	GT:AD:DP:GL:GQ	0/1:71,64:46:-51.95,-13.86,-109.26:99
+chr1	2611697	rs28420770	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.01;HRun=1;HaplotypeScore=63.25;MQ=30.55;MQ0=12;OQ=549.37;QD=5.97;SB=-271.47	GT:AD:DP:GL:GQ	0/1:70,21:28:-66.35,-8.13,-30.04:99
+chr1	2611699	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=39.05;MQ=32.12;MQ0=10;OQ=169.31;QD=2.23;SB=14.08	GT:AD:DP:GL:GQ	0/1:20,50:24:-27.45,-7.24,-73.47:99
+chr1	2611710	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=70.70;MQ=31.94;MQ0=10;OQ=120.36;QD=1.56;SB=14.06	GT:AD:DP:GL:GQ	0/1:29,48:25:-22.85,-7.53,-69.69:99
+chr1	2611716	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=60.36;MQ=32.04;MQ0=11;OQ=222.09;QD=2.71;SB=-31.85	GT:AD:DP:GL:GQ	0/1:24,55:26:-33.33,-7.83,-79.05:99
+chr1	2611761	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=2;HaplotypeScore=77.17;MQ=34.64;MQ0=9;OQ=73.97;QD=1.01;SB=-32.72	GT:AD:DP:GL:GQ	0/1:30,33:31:-23.41,-12.73,-88.75:99
+chr1	2611777	.	A	C	23.19	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=20.98;MQ=38.72;MQ0=5;QD=0.42;SB=23.10	GT:AD:DP:GL:GQ	0/1:24,30:28:-14.03,-8.43,-89.75:56.01
+chr1	2611805	.	A	G	44.82	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=14.04;MQ=39.70;MQ0=6;QD=0.79;SB=-36.77	GT:AD:DP:GL:GQ	0/1:29,28:32:-17.41,-9.64,-104.85:77.66
+chr1	2611822	.	C	T	55.46	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=121;Dels=0.00;HRun=0;HaplotypeScore=122.77;MQ=30.12;MQ0=10;QD=0.46;SB=-42.84	GT:AD:DP:GL:GQ	0/1:92,29:48:-23.31,-14.48,-136.72:88.30
+chr1	2611823	.	G	A	42.96	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=122.08;MQ=30.26;MQ0=10;QD=0.35;SB=5.54	GT:AD:DP:GL:GQ	0/1:91,15:51:-29.64,-22.06,-149.48:75.79
+chr1	2611827	.	C	G	117.16	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=1;HaplotypeScore=109.01;MQ=29.94;MQ0=10;QD=0.92;SB=-46.17	GT:AD:DP:GL:GQ	0/1:97,15:52:-50.99,-35.99,-189.94:99
+chr1	2611857	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=244;Dels=0.00;HRun=1;HaplotypeScore=130.70;MQ=25.34;MQ0=25;OQ=261.41;QD=1.07;SB=-55.24	GT:AD:DP:GL:GQ	0/1:221,22:85:-55.03,-25.61,-242.15:99
+chr1	2611880	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=0;HaplotypeScore=242.50;MQ=25.49;MQ0=23;OQ=371.36;QD=1.47;SB=-110.03	GT:AD:DP:GL:GQ	0/1:223,22:91:-74.78,-34.36,-326.09:99
+chr1	2611909	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=117.77;MQ=27.67;MQ0=16;OQ=1593.34;QD=8.80;SB=-695.72	GT:AD:DP:GL:GQ	0/1:25,155:74:-184.91,-22.29,-95.32:99
+chr1	2611913	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=162;Dels=0.01;HRun=0;HaplotypeScore=121.10;MQ=28.43;MQ0=16;OQ=688.73;QD=4.25;SB=-310.55	GT:AD:DP:GL:GQ	0/1:24,47:69:-160.80,-88.65,-165.59:99
+chr1	2611940	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=1;HaplotypeScore=46.12;MQ=30.62;MQ0=15;OQ=640.18;QD=4.61;SB=-181.43	GT:AD:DP:GL:GQ	0/1:50,89:56:-84.19,-16.88,-155.00:99
+chr1	2611948	.	A	C	23.15	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=1;HaplotypeScore=36.39;MQ=28.65;MQ0=12;QD=0.17;SB=47.17	GT:AD:DP:GL:GQ	0/1:116,20:55:-22.17,-16.57,-171.47:55.97
+chr1	2612014	rs28499205	G	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=56.64;MQ=32.76;MQ0=15;OQ=1145.21;QD=14.50;SB=-563.07	GT:AD:DP:GL:GQ	1/1:1,78:27:-118.11,-8.13,-0.01:81.27
+chr1	2612058	rs61765702	C	T	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=180;Dels=0.00;HRun=0;HaplotypeScore=18.96;MQ=27.13;MQ0=31;OQ=323.91;QD=1.80;SB=-155.18	GT:AD:DP:GL:GQ	0/1:143,37:66:-55.56,-19.88,-179.35:99
+chr1	2612062	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=184;Dels=0.00;HRun=0;HaplotypeScore=39.83;MQ=27.44;MQ0=33;OQ=304.96;QD=1.66;SB=-159.14	GT:AD:DP:GL:GQ	0/1:147,37:67:-53.98,-20.20,-229.14:99
+chr1	2612081	rs61765703	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=136;Dels=0.01;HRun=2;HaplotypeScore=85.10;MQ=27.93;MQ0=25;OQ=1205.35;QD=8.86;SB=-216.92	GT:AD:DP:GL:GQ	0/1:19,114:53:-139.78,-15.97,-53.09:99
+chr1	2612085	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=1;HaplotypeScore=63.07;MQ=28.64;MQ0=22;OQ=1108.83;QD=8.66;SB=-225.89	GT:AD:DP:GL:GQ	0/1:16,110:51:-129.53,-15.36,-50.00:99
+chr1	2612107	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=161;Dels=0.00;HRun=1;HaplotypeScore=61.85;MQ=27.81;MQ0=21;OQ=276.90;QD=1.72;SB=-68.50	GT:AD:DP:GL:GQ	0/1:116,39:58:-48.45,-17.48,-165.18:99
+chr1	2612151	rs61765704	A	C	24.50	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=129;Dels=0.02;HRun=0;HaplotypeScore=220.24;MQ=28.08;MQ0=15;QD=0.19;SB=6.59	GT:AD:DP:GL:GQ	0/1:44,80:28:-14.16,-8.43,-88.22:57.33
+chr1	2612161	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=149;Dels=0.05;HRun=2;HaplotypeScore=289.32;MQ=26.74;MQ0=14;OQ=154.71;QD=1.04;SB=-60.88	GT:AD:DP:GL:GQ	0/1:35,100:29:-27.20,-8.44,-77.78:99
+chr1	2612175	rs61765705	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=189;Dels=0.00;HRun=1;HaplotypeScore=208.27;MQ=26.09;MQ0=18;OQ=54.71;QD=0.29;SB=-8.07	GT:AD:DP:GL:GQ	0/1:131,51:39:-26.91,-18.15,-132.87:87.54
+chr1	2612187	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=1;HaplotypeScore=211.77;MQ=24.98;MQ0=26;OQ=72.89;QD=0.35;SB=45.47	GT:AD:DP:GL:GQ	0/1:143,55:44:-28.75,-18.18,-125.97:99
+chr1	2612211	.	C	A	45.89	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=208;Dels=0.00;HRun=1;HaplotypeScore=262.96;MQ=25.29;MQ0=30;QD=0.22;SB=-5.55	GT:AD:DP:GL:GQ	0/1:190,13:50:-25.52,-17.65,-153.60:78.73
+chr1	2612261	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=1;HaplotypeScore=73.22;MQ=36.24;MQ0=2;OQ=156.42;QD=1.55;SB=-48.52	GT:AD:DP:GL:GQ	0/1:66,32:53:-34.90,-15.97,-147.29:99
+chr1	2612283	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=4;HaplotypeScore=43.06;MQ=38.47;MQ0=2;OQ=327.02;QD=4.74;SB=-23.62	GT:AD:DP:GL:GQ	0/1:32,34:36:-46.54,-10.55,-82.71:99
+chr1	2612309	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=19.73;MQ=36.93;MQ0=0;OQ=479.11;QD=9.39;SB=-112.96	GT:AD:DP:GL:GQ	0/1:16,33:31:-63.92,-12.72,-54.61:99
+chr1	2612321	rs58055515	A	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.06;HRun=2;HaplotypeScore=36.08;MQ=38.02;MQ0=0;OQ=654.82;QD=13.64;SB=-115.75	GT:AD:DP:GL:GQ	1/1:1,35:27:-89.55,-24.40,-20.49:39.17
+chr1	2612344	.	C	G	24.81	LowQual	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=2;HaplotypeScore=34.46;MQ=40.80;MQ0=2;QD=0.48;SB=-19.81	GT:AD:DP:GL:GQ	0/1:23,28:23:-12.71,-6.94,-79.49:57.63
+chr1	2612349	rs56814247	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=26.66;MQ=40.32;MQ0=2;OQ=741.43;QD=14.54;SB=-345.45	GT:AD:DP:GL:GQ	1/1:6,45:24:-77.75,-7.24,-0.02:72.17
+chr1	2612359	.	A	C	18.09	LowQual	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=26.16;MQ=43.64;MQ0=3;QD=0.33;SB=-28.97	GT:AD:DP:GL:GQ	0/1:34,20:31:-14.42,-9.34,-99.97:50.86
+chr1	2612360	.	A	C	30.50	LowQual	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=3;HaplotypeScore=20.17;MQ=44.05;MQ0=2;QD=0.58;SB=-0.42	GT:AD:DP:GL:GQ	0/1:26,25:28:-14.77,-8.43,-87.24:63.33
+chr1	2612401	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=2;HaplotypeScore=42.26;MQ=44.22;MQ0=1;OQ=144.16;QD=2.72;SB=-18.17	GT:AD:DP:GL:GQ	0/1:29,20:34:-31.58,-13.88,-103.42:99
+chr1	2612402	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=41.27;MQ=43.87;MQ0=1;OQ=96.43;QD=1.85;SB=-29.80	GT:AD:DP:GL:GQ	0/1:26,21:30:-21.97,-9.04,-85.20:99
+chr1	2612447	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=39.94;MQ=46.94;MQ0=0;OQ=81.12;QD=1.66;SB=23.03	GT:AD:DP:GL:GQ	0/1:31,17:32:-23.40,-12.01,-88.55:99
+chr1	2612451	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=20.86;MQ=47.66;MQ0=0;OQ=53.68;QD=1.14;SB=26.08	GT:AD:DP:GL:GQ	0/1:30,14:32:-18.30,-9.65,-100.77:86.52
+chr1	2612461	.	A	C	44.60	LowQual	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=34.01;MQ=47.11;MQ0=0;QD=0.86;SB=-23.85	GT:AD:DP:GL:GQ	0/1:42,10:33:-17.68,-9.94,-101.23:77.43
+chr1	2612468	.	C	G	44.05	LowQual	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=46.41;MQ=45.54;MQ0=0;QD=0.76;SB=-1.30	GT:AD:DP:GL:GQ	0/1:51,7:35:-18.24,-10.55,-129.78:76.89
+chr1	2612500	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=0;HaplotypeScore=111.55;MQ=36.58;MQ0=2;OQ=75.18;QD=0.91;SB=-6.47	GT:AD:DP:GL:GQ	0/1:42,40:29:-19.55,-8.75,-75.63:99
+chr1	2612520	.	C	T	19.28	LowQual	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=133.17;MQ=33.82;MQ0=3;QD=0.19;SB=-16.60	GT:AD:DP:GL:GQ	0/1:87,13:36:-16.06,-10.85,-103.87:52.07
+chr1	2612521	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=3;HaplotypeScore=133.17;MQ=33.95;MQ0=3;OQ=122.65;QD=1.20;SB=-13.90	GT:AD:DP:GL:GQ	0/1:59,34:32:-39.02,-23.47,-101.66:99
+chr1	2612546	rs56822453	C	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=1;HaplotypeScore=145.71;MQ=34.54;MQ0=2;OQ=1448.77;QD=15.58;SB=-452.10	GT:AD:DP:GL:GQ	1/1:7,78:40:-172.07,-31.81,-23.61:81.95
+chr1	2612548	.	A	G	23.46	LowQual	AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=0;HaplotypeScore=130.25;MQ=34.63;MQ0=2;QD=0.24;SB=-12.60	GT:AD:DP:GL:GQ	0/1:76,19:32:-15.27,-9.65,-107.66:56.27
+chr1	2612572	rs61765712	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=119.88;MQ=29.64;MQ0=12;OQ=136.28;QD=1.57;SB=-70.93	GT:AD:DP:GL:GQ	0/1:30,56:22:-23.54,-6.63,-51.28:99
+chr1	2612576	.	C	G	19.60	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=117.65;MQ=28.19;MQ0=14;QD=0.19;SB=-14.55	GT:AD:DP:GL:GQ	0/1:68,14:25:-20.23,-14.99,-84.25:52.39
+chr1	2612600	.	A	C	31.76	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=221;Dels=0.00;HRun=4;HaplotypeScore=156.76;MQ=23.41;MQ0=28;QD=0.14;SB=30.15	GT:AD:DP:GL:GQ	0/1:163,45:61:-27.98,-21.52,-181.64:64.60
+chr1	2612627	.	A	C	39.29	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=0;HaplotypeScore=198.32;MQ=23.30;MQ0=41;QD=0.16;SB=-11.41	GT:AD:DP:GL:GQ	0/1:198,41:66:-27.09,-19.88,-204.81:72.12
+chr1	2612682	.	A	C	10.13	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=3;HaplotypeScore=52.92;MQ=47.05;MQ0=0;QD=0.24;SB=14.06	GT:AD:DP:GL:GQ	0/1:27,14:23:-11.18,-6.93,-67.83:42.53
+chr1	2612696	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=17.87;MQ=44.37;MQ0=2;OQ=127.11;QD=2.08;SB=-25.83	GT:AD:DP:GL:GQ	0/1:32,29:31:-25.34,-9.35,-104.60:99
+chr1	2612737	rs61765713	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=31.73;MQ=37.37;MQ0=1;OQ=431.17;QD=5.01;SB=-153.88	GT:AD:DP:GL:GQ	0/1:41,45:46:-60.27,-13.87,-108.65:99
+chr1	2612767	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=55.42;MQ=39.20;MQ0=1;OQ=525.18;QD=6.48;SB=-145.82	GT:AD:DP:GL:GQ	0/1:30,49:46:-69.66,-13.86,-97.51:99
+chr1	2612773	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=50.07;MQ=38.87;MQ0=1;OQ=424.50;QD=5.31;SB=-154.37	GT:AD:DP:GL:GQ	0/1:53,27:45:-59.30,-13.57,-131.50:99
+chr1	2612799	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=27.45;MQ=41.43;MQ0=1;OQ=164.57;QD=2.70;SB=-62.57	GT:AD:DP:GL:GQ	0/1:27,34:35:-30.28,-10.54,-94.10:99
+chr1	2612844	rs55724072	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=94.30;MQ=38.07;MQ0=8;OQ=665.81;QD=9.12;SB=-251.98	GT:AD:DP:GL:GQ	0/1:45,26:28:-81.79,-11.92,-21.81:98.87
+chr1	2612950	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=0;HaplotypeScore=255.70;MQ=27.55;MQ0=15;OQ=78.72;QD=0.37;SB=19.51	GT:AD:DP:GL:GQ	0/1:145,61:50:-33.24,-22.08,-169.61:99
+chr1	2612958	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=205;Dels=0.05;HRun=2;HaplotypeScore=345.72;MQ=28.14;MQ0=11;OQ=268.77;QD=1.31;SB=-87.58	GT:AD:DP:GL:GQ	0/1:82,113:44:-43.44,-13.28,-132.37:99
+chr1	2612962	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=206;Dels=0.01;HRun=1;HaplotypeScore=293.73;MQ=28.22;MQ0=11;OQ=53.07;QD=0.26;SB=-7.29	GT:AD:DP:GL:GQ	0/1:160,36:46:-29.48,-20.89,-140.25:85.91
+chr1	2612982	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=0;HaplotypeScore=272.98;MQ=28.95;MQ0=11;OQ=81.29;QD=0.49;SB=23.09	GT:AD:DP:GL:GQ	0/1:43,117:27:-19.56,-8.14,-70.61:99
+chr1	2612988	rs28729890	C	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=157;Dels=0.00;HRun=1;HaplotypeScore=282.08;MQ=29.13;MQ0=10;OQ=1088.24;QD=6.93;SB=-426.67	GT:AD:DP:GL:GQ	1/1:3,146:27:-116.69,-11.76,-4.28:74.86
+chr1	2613013	.	G	A	31.52	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=131;Dels=0.00;HRun=1;HaplotypeScore=164.33;MQ=32.03;MQ0=7;QD=0.24;SB=26.10	GT:AD:DP:GL:GQ	0/1:117,14:35:-16.98,-10.54,-112.15:64.35
+chr1	2613017	.	T	C	180.98	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=137.52;MQ=33.34;MQ0=7;QD=1.65;SB=26.11	GT:AD:DP:GL:GQ	0/1:27,81:34:-31.63,-10.24,-97.73:99
+chr1	2613018	rs28484972	G	C	140.73	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=110;Dels=0.00;HRun=0;HaplotypeScore=137.35;MQ=33.34;MQ0=7;QD=1.28;SB=31.01	GT:AD:DP:GL:GQ	0/1:28,44:35:-37.27,-19.91,-118.50:99
+chr1	2613040	rs55713073	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=61.60;MQ=39.34;MQ0=3;OQ=876.14;QD=14.13;SB=-413.05	GT:AD:DP:GL:GQ	0/1:33,24:31:-100.24,-9.35,-30.73:99
+chr1	2613043	.	T	C	38.29	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=3;HaplotypeScore=55.65;MQ=43.83;MQ0=2;QD=0.78;SB=29.13	GT:AD:DP:GL:GQ	0/1:25,20:28:-15.55,-8.44,-93.33:71.12
+chr1	2613090	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=62.85;MQ=32.34;MQ0=20;OQ=113.77;QD=0.92;SB=20.02	GT:AD:DP:GL:GQ	0/1:89,34:35:-25.22,-10.56,-90.70:99
+chr1	2613132	.	T	C	17.83	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=135.62;MQ=34.15;MQ0=7;QD=0.19;SB=20.93	GT:AD:DP:GL:GQ	0/1:49,17:34:-18.39,-13.34,-109.40:50.59
+chr1	2613155	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=54.50;MQ=36.94;MQ0=5;OQ=56.13;QD=0.85;SB=-8.31	GT:AD:DP:GL:GQ	0/1:26,40:25:-16.44,-7.54,-66.14:88.97
+chr1	2613166	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=54;Dels=0.04;HRun=0;HaplotypeScore=39.25;MQ=40.07;MQ0=1;OQ=108.06;QD=2.00;SB=-13.35	GT:AD:DP:GL:GQ	0/1:25,27:25:-21.62,-7.53,-86.20:99
+chr1	2613178	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=39.82;MQ=40.42;MQ0=1;OQ=87.18;QD=1.53;SB=-9.45	GT:AD:DP:GL:GQ	0/1:38,18:28:-20.44,-8.44,-74.35:99
+chr1	2613186	rs28398452	A	T	0.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=19.52;MQ=46.06;MQ0=0;OQ=818.22;QD=19.96;SB=-414.28	GT:AD:DP:GL:GQ	1/1:0,40:23:-85.41,-6.93,-0.01:69.21
+chr1	2613234	.	C	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=40.12;MQ=46.29;MQ0=1;OQ=1357.25;QD=31.56;SB=-584.52	GT:AD:DP:GL:GQ	1/1:1,41:32:-139.32,-9.64,-0.01:96.32
+chr1	2613318	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=61.23;MQ=29.57;MQ0=14;OQ=124.73;QD=1.48;SB=-14.36	GT:AD:DP:GL:GQ	0/1:67,16:36:-26.61,-10.86,-123.23:99
+chr1	2613323	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=0;HaplotypeScore=72.34;MQ=25.61;MQ0=20;OQ=95.66;QD=0.62;SB=33.80	GT:AD:DP:GL:GQ	0/1:133,12:61:-34.86,-22.01,-226.45:99
+chr1	2613370	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=400;Dels=0.00;HRun=0;HaplotypeScore=293.23;MQ=21.10;MQ0=61;OQ=714.05;QD=1.79;SB=-288.95	GT:AD:DP:GL:GQ	0/1:327,73:124:-112.05,-37.36,-344.59:99
+chr1	2613374	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=416;Dels=0.00;HRun=0;HaplotypeScore=328.46;MQ=20.95;MQ0=62;OQ=571.93;QD=1.37;SB=-114.36	GT:AD:DP:GL:GQ	0/1:288,118:123:-97.54,-37.07,-375.44:99
+chr1	2613385	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=437;Dels=0.00;HRun=0;HaplotypeScore=225.97;MQ=20.17;MQ0=68;OQ=628.49;QD=1.44;SB=-284.83	GT:AD:DP:GL:GQ	0/1:363,65:125:-113.05,-46.91,-348.87:99
+chr1	2613405	rs61765715	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=430;Dels=0.00;HRun=0;HaplotypeScore=214.90;MQ=20.78;MQ0=65;OQ=1559.54;QD=3.63;SB=-415.95	GT:AD:DP:GL:GQ	0/1:296,132:120:-195.39,-36.15,-225.88:99
+chr1	2613406	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=428;Dels=0.00;HRun=0;HaplotypeScore=190.35;MQ=20.81;MQ0=64;OQ=96.31;QD=0.23;SB=35.50	GT:AD:DP:GL:GQ	0/1:369,32:113:-77.37,-64.46,-359.74:99
+chr1	2613418	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=358;Dels=0.00;HRun=0;HaplotypeScore=49.55;MQ=21.34;MQ0=50;OQ=281.60;QD=0.79;SB=32.81	GT:AD:DP:GL:GQ	0/1:313,45:98:-60.98,-29.53,-359.08:99
+chr1	2613432	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=200;Dels=0.00;HRun=2;HaplotypeScore=59.86;MQ=23.20;MQ0=28;OQ=127.98;QD=0.64;SB=-77.60	GT:AD:DP:GL:GQ	0/1:175,24:60:-37.72,-21.64,-201.76:99
+chr1	2613443	rs61765716	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=4;HaplotypeScore=21.82;MQ=28.33;MQ0=15;OQ=129.32;QD=1.54;SB=2.14	GT:AD:DP:GL:GQ	0/1:37,47:28:-24.65,-8.44,-74.06:99
+chr1	2613523	rs61765738	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=4;HaplotypeScore=30.76;MQ=30.14;MQ0=9;OQ=85.37;QD=1.61;SB=5.05	GT:AD:DP:GL:GQ	0/1:23,13:17:-22.76,-10.94,-45.61:99
+chr1	2613566	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=71;Dels=0.04;HRun=3;HaplotypeScore=57.78;MQ=26.34;MQ0=13;OQ=54.80;QD=0.77;SB=8.05	GT:AD:DP:GL:GQ	0/1:32,29:23:-15.40,-6.63,-70.44:87.64
+chr1	2613630	.	G	A	0.07	PASS	AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=13.24;MQ=22.14;MQ0=5;OQ=193.82;QD=10.20;SB=-82.32	GT:AD:DP:GL:GQ	1/1:2,17:6:-22.96,-1.81,-0.00:18.06
+chr1	2613635	.	G	A	0.05	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=13.88;MQ=20.75;MQ0=5;OQ=116.09;QD=7.26;SB=-82.32	GT:AD:DP:GL:GQ	1/1:1,15:4:-15.15,-1.21,-0.00:12.04
+chr1	2613646	.	G	C	10.99	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.07;HRun=2;HaplotypeScore=14.02;MQ=19.81;MQ0=4;QD=0.79;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,8:1:-4.35,-0.30,-0.00:1.76
+chr1	2613690	.	T	C	13.23	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=116.33;MQ=18.38;MQ0=8;QD=0.19;SB=-10.00	GT:AD:DP:GL:GQ	0/1:49,18:4:-5.79,-1.21,-8.34:45.86
+chr1	2613693	.	G	C	35.94	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=149.70;MQ=18.45;MQ0=8;QD=0.45;SB=-10.00	GT:AD:DP:GL:GQ	0/1:76,3:6:-8.69,-1.81,-15.69:68.78
+chr1	2613698	.	T	G	15.64	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=2;HaplotypeScore=190.59;MQ=18.98;MQ0=9;QD=0.16;SB=-10.00	GT:AD:DP:GL:GQ	0/1:64,7:8:-12.71,-7.87,-20.94:48.35
+chr1	2613700	.	G	A	196.12	SnpCluster	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=236.20;MQ=18.98;MQ0=9;QD=2.06;SB=-10.00	GT:AD:DP:GL:GQ	0/1:6,83:8:-25.29,-2.41,-3.47:10.61
+chr1	2613710	.	G	A	290.78	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=258.37;MQ=18.71;MQ0=19;QD=1.88;SB=-45.65	GT:AD:DP:GL:GQ	0/1:71,77:15:-43.35,-10.99,-17.24:62.53
+chr1	2613712	.	A	G	19.12	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=1;HaplotypeScore=303.47;MQ=18.88;MQ0=19;QD=0.12;SB=-3.98	GT:AD:DP:GL:GQ	0/1:153,6:17:-10.32,-5.13,-49.10:51.90
+chr1	2613717	.	C	G	26.91	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=0;HaplotypeScore=408.47;MQ=18.72;MQ0=23;QD=0.14;SB=-6.99	GT:AD:DP:GL:GQ	0/1:167,10:18:-16.44,-10.47,-59.87:59.74
+chr1	2613725	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=210;Dels=0.00;HRun=0;HaplotypeScore=344.41;MQ=18.80;MQ0=26;OQ=51.69;QD=0.25;SB=-6.99	GT:AD:DP:GL:GQ	0/1:188,19:21:-17.15,-8.70,-57.87:84.53
+chr1	2613732	.	A	C	62.04	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=212;Dels=0.00;HRun=0;HaplotypeScore=339.87;MQ=19.08;MQ0=26;QD=0.29;SB=-6.99	GT:AD:DP:GL:GQ	0/1:184,21:14:-13.71,-4.22,-32.30:94.88
+chr1	2613741	.	C	T	167.14	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=1;HaplotypeScore=432.19;MQ=19.10;MQ0=22;QD=0.81;SB=-10.00	GT:AD:DP:GL:GQ	0/1:175,24:13:-27.15,-7.15,-25.74:99
+chr1	2613742	.	T	A	554.18	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=437.29;MQ=19.15;MQ0=21;QD=2.73;SB=-10.00	GT:AD:DP:GL:GQ	1/1:10,159:27:-96.09,-42.87,-37.09:57.79
+chr1	2613744	.	C	T	234.43	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=208;Dels=0.00;HRun=0;HaplotypeScore=584.09;MQ=19.37;MQ0=21;QD=1.13;SB=-10.00	GT:AD:DP:GL:GQ	0/1:171,26:22:-36.59,-9.87,-49.51:99
+chr1	2613745	.	C	G	76.87	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=0;HaplotypeScore=579.63;MQ=19.38;MQ0=20;QD=0.37;SB=-10.00	GT:AD:DP:GL:GQ	0/1:148,19:15:-15.49,-4.52,-49.92:99
+chr1	2613750	.	G	A	306.03	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=1;HaplotypeScore=658.57;MQ=19.32;MQ0=20;QD=1.48;SB=-7.01	GT:AD:DP:GL:GQ	0/1:99,104:19:-39.62,-5.73,-26.69:99
+chr1	2613754	.	C	A	11.17	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=223;Dels=0.00;HRun=1;HaplotypeScore=578.78;MQ=19.04;MQ0=24;QD=0.05;SB=-7.00	GT:AD:DP:GL:GQ	0/1:199,19:23:-11.29,-6.93,-65.57:43.66
+chr1	2613765	.	C	A	112.66	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=230;Dels=0.00;HRun=0;HaplotypeScore=358.32;MQ=18.80;MQ0=30;QD=0.49;SB=-6.99	GT:AD:DP:GL:GQ	0/1:192,30:26:-22.38,-7.83,-66.37:99
+chr1	2613766	.	C	G	145.08	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=229;Dels=0.00;HRun=0;HaplotypeScore=340.83;MQ=18.60;MQ0=30;QD=0.63;SB=-3.99	GT:AD:DP:GL:GQ	0/1:197,20:34:-28.04,-10.25,-119.31:99
+chr1	2613770	.	T	C	33.51	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=219;Dels=0.00;HRun=0;HaplotypeScore=286.65;MQ=18.56;MQ0=29;QD=0.15;SB=-3.99	GT:AD:DP:GL:GQ	0/1:176,33:38:-18.09,-11.45,-126.83:66.35
+chr1	2613772	.	A	G	57.20	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=1;HaplotypeScore=261.18;MQ=18.59;MQ0=29;QD=0.26;SB=-0.97	GT:AD:DP:GL:GQ	0/1:199,13:41:-24.12,-15.12,-140.12:90.03
+chr1	2613796	.	G	C	177.04	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=135;Dels=0.04;HRun=2;HaplotypeScore=330.87;MQ=18.33;MQ0=22;QD=1.31;SB=-45.45	GT:AD:DP:GL:GQ	0/1:71,48:21:-34.21,-13.22,-61.82:99
+chr1	2613800	.	G	A	69.22	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=111;Dels=0.04;HRun=0;HaplotypeScore=218.43;MQ=17.88;MQ0=19;QD=0.62;SB=-7.00	GT:AD:DP:GL:GQ	0/1:92,15:13:-14.13,-3.92,-31.45:99
+chr1	2613801	.	C	G	13.55	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=246.51;MQ=18.17;MQ0=17;QD=0.12;SB=-7.00	GT:AD:DP:GL:GQ	0/1:104,4:15:-12.67,-8.05,-55.30:46.19
+chr1	2613803	.	C	A	151.29	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=1;HaplotypeScore=241.51;MQ=18.66;MQ0=17;QD=1.36;SB=-3.98	GT:AD:DP:GL:GQ	0/1:89,19:17:-27.02,-8.61,-39.19:99
+chr1	2613805	.	C	T	87.71	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=208.83;MQ=18.81;MQ0=15;QD=0.80;SB=-0.98	GT:AD:DP:GL:GQ	0/1:93,15:13:-15.97,-3.92,-32.68:99
+chr1	2613807	.	C	T	57.07	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=165.36;MQ=18.87;MQ0=15;QD=0.53;SB=-3.99	GT:AD:DP:GL:GQ	0/1:93,9:11:-12.30,-3.31,-28.01:89.90
+chr1	2613812	.	G	A	29.24	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=106.13;MQ=18.30;MQ0=14;QD=0.32;SB=-3.99	GT:AD:DP:GL:GQ	0/1:75,16:5:-7.71,-1.51,-10.06:62.07
+chr1	2613813	.	T	C	74.94	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=91.21;MQ=18.35;MQ0=14;QD=0.88;SB=-6.99	GT:AD:DP:GL:GQ	0/1:16,66:5:-12.29,-1.51,-3.76:22.52
+chr1	2613826	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=1;HaplotypeScore=36.04;MQ=20.56;MQ0=13;OQ=192.78;QD=2.30;SB=-28.63	GT:AD:DP:GL:GQ	0/1:21,57:13:-29.99,-7.43,-22.77:99
+chr1	2613831	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=1;HaplotypeScore=23.92;MQ=20.73;MQ0=14;OQ=180.38;QD=2.20;SB=-29.94	GT:AD:DP:GL:GQ	0/1:21,61:13:-25.24,-3.92,-19.14:99
+chr1	2613859	.	G	T	41.43	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=24.92;MQ=20.48;MQ0=13;QD=0.62;SB=-43.38	GT:AD:DP:GL:GQ	0/1:19,47:11:-10.74,-3.32,-20.71:74.26
+chr1	2613869	rs28391329	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=60.53;MQ=21.20;MQ0=15;OQ=293.59;QD=2.94;SB=-0.98	GT:AD:DP:GL:GQ	0/1:82,18:19:-38.38,-5.73,-37.90:99
+chr1	2613889	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=1;HaplotypeScore=72.75;MQ=25.64;MQ0=15;OQ=180.19;QD=1.96;SB=-114.68	GT:AD:DP:GL:GQ	0/1:18,61:28:-47.05,-25.75,-76.38:99
+chr1	2613903	rs11486068	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=48.68;MQ=24.40;MQ0=19;OQ=50.76;QD=0.51;SB=-13.14	GT:AD:DP:GL:GQ	0/1:40,15:30:-30.07,-21.71,-94.96:83.60
+chr1	2613959	rs61765741	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=30.66;MQ=19.75;MQ0=50;OQ=129.32;QD=0.85;SB=-3.99	GT:AD:DP:GL:GQ	0/1:135,11:45:-36.43,-20.22,-129.55:99
+chr1	2613977	rs61765742	T	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=20.51;MQ=18.10;MQ0=36;OQ=631.54;QD=6.19;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,87:32:-76.08,-9.64,-40.58:99
+chr1	2614061	.	C	G	47.32	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=9.70;MQ=18.60;MQ0=18;QD=1.05;SB=-42.45	GT:AD:DP:GL:GQ	0/1:29,16:12:-11.64,-3.62,-36.27:80.16
+chr1	2614087	rs61765744	A	C	20.16	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=3;HaplotypeScore=20.71;MQ=12.14;MQ0=19;QD=0.63;SB=-6.99	GT:AD:DP:GL:GQ	0/1:25,7:6:-7.10,-1.81,-13.92:52.96
+chr1	2614090	.	A	G	19.51	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=1;HaplotypeScore=20.91;MQ=12.88;MQ0=18;QD=0.59;SB=-6.99	GT:AD:DP:GL:GQ	0/1:21,12:7:-7.34,-2.11,-20.39:52.30
+chr1	2614091	.	G	C	37.94	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=1;HaplotypeScore=21.91;MQ=12.37;MQ0=20;QD=1.05;SB=-6.99	GT:AD:DP:GL:GQ	0/1:28,8:7:-9.19,-2.11,-21.58:70.77
+chr1	2614114	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=32.88;MQ=18.47;MQ0=36;OQ=121.42;QD=1.52;SB=-36.64	GT:AD:DP:GL:GQ	0/1:36,44:20:-21.46,-6.03,-44.98:99
+chr1	2614128	.	T	C	13.34	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=4;HaplotypeScore=47.41;MQ=18.72;MQ0=40;QD=0.11;SB=-2.29	GT:AD:DP:GL:GQ	0/1:78,34:26:-19.39,-14.79,-91.44:45.97
+chr1	2614209	.	G	A	41.24	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=1;HaplotypeScore=24.29;MQ=22.02;MQ0=31;QD=0.45;SB=-24.59	GT:AD:DP:GL:GQ	0/1:55,36:29:-16.14,-8.74,-87.91:74.08
+chr1	2614364	rs28730517	A	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=4;HaplotypeScore=28.46;MQ=18.26;MQ0=16;OQ=311.67;QD=6.23;SB=-151.28	GT:AD:DP:GL:GQ	1/1:14,32:12:-37.44,-3.62,-2.80:8.16
+chr1	2614590	rs28497985	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=34.12;MQ=28.69;MQ0=18;OQ=755.20;QD=6.74;SB=-383.20	GT:AD:DP:GL:GQ	0/1:87,25:65:-98.40,-19.59,-181.93:99
+chr1	2614771	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=1;HaplotypeScore=33.03;MQ=8.84;MQ0=54;OQ=63.99;QD=0.94;SB=-10.00	GT:AD:DP:GL:GQ	0/1:54,14:6:-11.49,-1.81,-12.10:96.82
+chr1	2614794	.	A	C	36.23	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=12.63;MQ=15.22;MQ0=54;QD=0.39;SB=8.03	GT:AD:DP:GL:GQ	0/1:56,38:25:-14.44,-7.53,-71.85:69.07
+chr1	2614835	rs61765748	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=146;Dels=0.00;HRun=0;HaplotypeScore=67.43;MQ=23.43;MQ0=43;OQ=134.71;QD=0.92;SB=83.23	GT:AD:DP:GL:GQ	0/1:105,39:61:-35.15,-18.40,-166.15:99
+chr1	2615014	.	A	G	45.47	PASS	AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=21.27;MQ0=3;OQ=106.85;QD=8.90;SB=-34.66	GT:AD:DP:GL:GQ	1/1:0,12:5:-14.25,-1.51,-0.01:15.01
+chr1	2615159	.	C	A	49.14	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=220;Dels=0.00;HRun=2;HaplotypeScore=142.59;MQ=8.79;MQ0=169;QD=0.22;SB=-7.86	GT:AD:DP:GL:GQ	0/1:185,31:17:-13.32,-5.12,-43.12:81.98
+chr1	2615230	.	C	G	11.72	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=1;HaplotypeScore=6.15;MQ=11.52;MQ0=52;QD=0.14;SB=-26.39	GT:AD:DP:GL:GQ	0/1:72,12:14:-8.65,-4.23,-47.78:44.25
+chr1	2615372	.	G	A	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=85;Dels=0.00;HRun=1;HaplotypeScore=29.65;MQ=17.03;MQ0=60;OQ=691.36;QD=8.13;SB=-292.88	GT:AD:DP:GL:GQ	1/1:59,24:18:-72.73,-5.42,-0.01:54.18
+chr1	2615442	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=52.99;MQ=12.22;MQ0=96;OQ=368.66;QD=2.38;SB=-99.96	GT:AD:DP:GL:GQ	0/1:30,125:25:-47.68,-7.53,-41.84:99
+chr1	2615466	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=61.50;MQ=14.17;MQ0=69;OQ=112.35;QD=0.77;SB=-18.60	GT:AD:DP:GL:GQ	0/1:116,29:31:-23.86,-9.34,-81.69:99
+chr1	2615470	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=0;HaplotypeScore=63.31;MQ=14.07;MQ0=68;OQ=351.94;QD=2.53;SB=-90.74	GT:AD:DP:GL:GQ	0/1:65,72:34:-48.72,-10.24,-70.14:99
+chr1	2615502	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=32.33;MQ=16.10;MQ0=38;OQ=288.56;QD=3.65;SB=2.03	GT:AD:DP:GL:GQ	0/1:49,30:24:-39.38,-7.24,-59.32:99
+chr1	2615515	.	T	G	27.54	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=32.70;MQ=13.65;MQ0=43;QD=0.37;SB=-0.98	GT:AD:DP:GL:GQ	0/1:31,13:15:-18.30,-12.26,-45.52:60.37
+chr1	2615553	.	G	A	21.44	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=1;HaplotypeScore=33.08;MQ=9.60;MQ0=74;QD=0.23;SB=-3.99	GT:AD:DP:GL:GQ	0/1:70,24:9:-8.14,-2.71,-26.22:54.25
+chr1	2615563	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=52.83;MQ=8.09;MQ0=76;OQ=64.78;QD=0.70;SB=-10.00	GT:AD:DP:GL:GQ	0/1:82,10:5:-11.27,-1.51,-6.24:47.31
+chr1	2615689	.	T	C	30.94	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=62.56;MQ=10.13;MQ0=88;QD=0.28;SB=-3.98	GT:AD:DP:GL:GQ	0/1:18,89:9:-9.09,-2.71,-22.98:63.77
+chr1	2615717	rs61765669	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=37.80;MQ=10.99;MQ0=80;OQ=103.09;QD=0.95;SB=-3.99	GT:AD:DP:GL:GQ	0/1:26,83:10:-16.61,-3.01,-17.76:99
+chr1	2615757	.	C	A	39.74	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=1;HaplotypeScore=30.17;MQ=13.18;MQ0=60;QD=0.43;SB=0.17	GT:AD:DP:GL:GQ	0/1:71,20:17:-15.95,-8.69,-48.17:72.57
+chr1	2615837	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=39.99;MQ=26.86;MQ0=21;OQ=73.19;QD=1.33;SB=-36.22	GT:AD:DP:GL:GQ	0/1:29,26:20:-16.63,-6.03,-56.46:99
+chr1	2615892	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=3;HaplotypeScore=44.02;MQ=30.58;MQ0=2;OQ=63.96;QD=1.12;SB=26.10	GT:AD:DP:GL:GQ	0/1:25,32:26:-17.51,-7.83,-73.92:96.79
+chr1	2615945	rs28619423	T	C	0.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=8.32;MQ=22.59;MQ0=1;OQ=99.94;QD=5.26;SB=-76.91	GT:AD:DP:GL:GQ	1/1:3,15:4:-13.53,-1.21,-0.00:12.03
+chr1	2615949	rs28373809	G	A	10.26	LowQual	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=9.32;MQ=19.47;MQ0=1;QD=0.68;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,14:1:-4.27,-0.30,-0.00:1.76
+chr1	2615990	.	C	G	0.11	PASS	AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=8.97;MQ=20.31;MQ0=1;OQ=58.76;QD=6.53;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,9:2:-9.28,-0.60,-0.00:6.02
+chr1	2615997	.	G	A	36.46	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=29.63;MQ=20.63;MQ0=6;QD=1.35;SB=-7.00	GT:AD:DP:GL:GQ	0/1:18,9:5:-8.44,-1.51,-10.16:69.30
+chr1	2616009	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=2;HaplotypeScore=37.74;MQ=29.64;MQ0=6;OQ=112.90;QD=3.53;SB=-3.99	GT:AD:DP:GL:GQ	0/1:15,17:12:-18.19,-3.62,-24.59:99
+chr1	2616012	.	A	C	43.77	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=39.70;MQ=31.56;MQ0=5;QD=1.41;SB=-0.98	GT:AD:DP:GL:GQ	0/1:13,18:11:-10.97,-3.31,-27.78:76.61
+chr1	2616021	.	C	A	30.19	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=71.42;MQ=30.54;MQ0=5;QD=0.70;SB=-0.98	GT:AD:DP:GL:GQ	0/1:37,6:16:-11.12,-4.82,-46.67:63.02
+chr1	2616048	.	A	C	104.33	Indel	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=256.69;MQ=33.48;MQ0=5;QD=1.53;SB=-0.98	GT:AD:DP:GL:GQ	0/1:26,38:27:-21.85,-8.13,-76.79:99
+chr1	2616053	.	A	C	36.21	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=80;Dels=0.06;HRun=3;HaplotypeScore=159.99;MQ=31.20;MQ0=8;QD=0.45;SB=-3.99	GT:AD:DP:GL:GQ	0/1:43,32:27:-15.04,-8.13,-81.51:69.04
+chr1	2616066	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=127.16;MQ=28.37;MQ0=17;OQ=116.17;QD=0.90;SB=11.03	GT:AD:DP:GL:GQ	0/1:64,41:40:-43.16,-28.26,-112.08:99
+chr1	2616091	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=152;Dels=0.02;HRun=3;HaplotypeScore=245.31;MQ=26.01;MQ0=24;OQ=74.30;QD=0.49;SB=8.05	GT:AD:DP:GL:GQ	0/1:77,30:40:-32.83,-22.11,-117.91:99
+chr1	2616098	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=238.65;MQ=25.86;MQ0=23;OQ=203.33;QD=1.36;SB=8.03	GT:AD:DP:GL:GQ	0/1:83,65:39:-35.37,-11.76,-97.26:99
+chr1	2616121	rs28707614	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=109;Dels=0.00;HRun=1;HaplotypeScore=348.16;MQ=25.38;MQ0=21;OQ=754.79;QD=6.92;SB=-132.69	GT:AD:DP:GL:GQ	0/1:14,95:27:-86.90,-8.14,-12.11:39.77
+chr1	2616201	rs28495110	G	T	0.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=18.82;MQ=45.96;MQ0=6;OQ=1088.68;QD=25.92;SB=-422.58	GT:AD:DP:GL:GQ	1/1:8,34:31:-112.47,-9.34,-0.01:93.25
+chr1	2616235	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=22.81;MQ=34.27;MQ0=9;OQ=189.73;QD=2.67;SB=-88.83	GT:AD:DP:GL:GQ	0/1:28,43:31:-31.59,-9.34,-82.55:99
+chr1	2616250	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=198;Dels=0.00;HRun=1;HaplotypeScore=98.35;MQ=24.83;MQ0=26;OQ=53.95;QD=0.27;SB=-52.26	GT:AD:DP:GL:GQ	0/1:175,16:77:-39.01,-30.33,-235.94:86.79
+chr1	2616284	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=316;Dels=0.00;HRun=0;HaplotypeScore=207.75;MQ=22.41;MQ0=34;OQ=472.89;QD=1.50;SB=-261.05	GT:AD:DP:GL:GQ	0/1:280,35:108:-83.11,-32.54,-299.84:99
+chr1	2616291	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=308;Dels=0.00;HRun=0;HaplotypeScore=168.73;MQ=22.17;MQ0=35;OQ=503.17;QD=1.63;SB=-147.25	GT:AD:DP:GL:GQ	0/1:228,77:110:-86.74,-33.14,-306.67:99
+chr1	2616303	rs61765755	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=285;Dels=0.00;HRun=0;HaplotypeScore=48.79;MQ=22.14;MQ0=36;OQ=3893.80;QD=13.66;SB=-1294.80	GT:AD:DP:GL:GQ	0/1:13,240:102:-388.38,-54.71,-62.45:77.36
+chr1	2616333	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=234;Dels=0.00;HRun=0;HaplotypeScore=268.36;MQ=23.38;MQ0=29;OQ=127.30;QD=0.54;SB=-30.73	GT:AD:DP:GL:GQ	0/1:215,16:95:-44.63,-28.62,-299.60:99
+chr1	2616354	rs7544898	A	C	1854.66	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=113;Dels=0.00;HRun=1;HaplotypeScore=61.29;MQ=28.89;MQ0=15;QD=16.41;SB=-484.04	GT:AD:DP:GL:GQ	1/1:2,105:53:-193.02,-19.43,-3.97:99
+chr1	2616358	.	A	G	865.25	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=1;HaplotypeScore=46.74;MQ=30.83;MQ0=11;QD=8.83;SB=-6.56	GT:AD:DP:GL:GQ	0/1:29,69:51:-105.17,-15.36,-93.21:99
+chr1	2616363	.	G	C	842.15	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=1;HaplotypeScore=46.38;MQ=31.26;MQ0=12;QD=8.68;SB=-14.79	GT:AD:DP:GL:GQ	0/1:55,42:53:-103.48,-15.98,-115.82:99
+chr1	2616398	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=48.31;MQ=34.63;MQ0=12;OQ=554.46;QD=5.84;SB=10.29	GT:AD:DP:GL:GQ	0/1:66,29:54:-75.00,-16.28,-154.28:99
+chr1	2616612	.	G	C	20.97	LowQual	AC=1;AF=0.50;AN=2;DP=70;Dels=0.01;HRun=0;HaplotypeScore=165.26;MQ=30.37;MQ0=2;QD=0.30;SB=-32.74	GT:AD:DP:GL:GQ	0/1:19,45:24:-19.94,-14.57,-91.68:53.77
+chr1	2616615	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=3;HaplotypeScore=70.16;MQ=28.36;MQ0=2;OQ=89.21;QD=1.29;SB=-14.35	GT:AD:DP:GL:GQ	0/1:26,38:19:-17.94,-5.74,-58.45:99
+chr1	2616647	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=0;HaplotypeScore=217.54;MQ=24.00;MQ0=30;OQ=94.92;QD=0.69;SB=35.11	GT:AD:DP:GL:GQ	0/1:84,43:37:-23.93,-11.16,-103.88:99
+chr1	2616654	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=1;HaplotypeScore=223.04;MQ=23.83;MQ0=42;OQ=359.87;QD=1.99;SB=35.13	GT:AD:DP:GL:GQ	0/1:140,35:44:-52.54,-13.27,-92.39:99
+chr1	2616670	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=198;Dels=0.00;HRun=0;HaplotypeScore=299.99;MQ=23.86;MQ0=44;OQ=60.86;QD=0.31;SB=35.11	GT:AD:DP:GL:GQ	0/1:127,67:50:-24.46,-15.09,-137.52:93.69
+chr1	2616692	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=167;Dels=0.00;HRun=0;HaplotypeScore=231.37;MQ=26.06;MQ0=26;OQ=91.62;QD=0.55;SB=35.13	GT:AD:DP:GL:GQ	0/1:91,73:56:-32.64,-20.19,-183.88:99
+chr1	2616713	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=1;HaplotypeScore=98.28;MQ=31.06;MQ0=12;OQ=565.06;QD=6.81;SB=-40.25	GT:AD:DP:GL:GQ	0/1:27,50:40:-78.76,-18.97,-82.14:99
+chr1	2616803	.	G	C	11.63	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=76;Dels=0.01;HRun=0;HaplotypeScore=115.33;MQ=32.59;MQ0=10;QD=0.15;SB=23.09	GT:AD:DP:GL:GQ	0/1:27,42:23:-11.36,-6.95,-79.45:44.16
+chr1	2616826	.	T	C	18.72	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=39.74;MQ=39.24;MQ0=2;QD=0.38;SB=20.09	GT:AD:DP:GL:GQ	0/1:24,24:22:-11.78,-6.63,-68.52:51.50
+chr1	2616954	rs28486014	C	A	1246.57	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=172;Dels=0.00;HRun=0;HaplotypeScore=118.85;MQ=19.01;MQ0=19;QD=7.25;SB=-604.12	GT:AD:DP:GL:GQ	1/1:2,165:36:-131.25,-13.77,-3.01:99
+chr1	2616962	.	A	G	25.32	DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=218;Dels=0.00;HRun=0;HaplotypeScore=150.59;MQ=18.32;MQ0=25;QD=0.12;SB=17.48	GT:AD:DP:GL:GQ	0/1:179,39:39:-17.57,-11.75,-132.90:58.14
+chr1	2616963	.	C	G	90.14	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=0;HaplotypeScore=167.60;MQ=18.42;MQ0=25;QD=0.41;SB=8.17	GT:AD:DP:GL:GQ	0/1:182,34:40:-27.79,-15.49,-139.11:99
+chr1	2616976	.	C	A	13.99	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=267;Dels=0.00;HRun=0;HaplotypeScore=283.46;MQ=18.62;MQ0=35;QD=0.05;SB=55.93	GT:AD:DP:GL:GQ	0/1:236,26:51:-20.03,-15.36,-160.20:46.65
+chr1	2616982	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=280;Dels=0.00;HRun=0;HaplotypeScore=251.51;MQ=19.64;MQ0=37;OQ=486.76;QD=1.74;SB=8.99	GT:AD:DP:GL:GQ	0/1:187,73:54:-71.97,-20.01,-131.66:99
+chr1	2617013	.	A	C	16.86	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=5;HaplotypeScore=227.22;MQ=22.36;MQ0=34;QD=0.07;SB=14.07	GT:AD:DP:GL:GQ	0/1:208,22:59:-25.00,-20.04,-187.42:49.60
+chr1	2617015	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=0;HaplotypeScore=200.07;MQ=22.66;MQ0=33;OQ=161.89;QD=0.73;SB=20.10	GT:AD:DP:GL:GQ	0/1:186,27:59:-43.12,-23.65,-203.21:99
+chr1	2617028	rs61765757	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=178;Dels=0.00;HRun=0;HaplotypeScore=111.43;MQ=24.75;MQ0=28;OQ=1236.03;QD=6.94;SB=-23.31	GT:AD:DP:GL:GQ	0/1:36,141:55:-143.45,-16.57,-61.22:99
+chr1	2617033	rs61765759	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=173;Dels=0.00;HRun=0;HaplotypeScore=123.68;MQ=24.76;MQ0=29;OQ=945.67;QD=5.47;SB=-60.88	GT:AD:DP:GL:GQ	0/1:19,129:49:-112.61,-14.76,-62.28:99
+chr1	2617058	rs28585375	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=236;Dels=0.00;HRun=0;HaplotypeScore=112.06;MQ=22.97;MQ0=54;OQ=357.80;QD=1.52;SB=-120.52	GT:AD:DP:GL:GQ	0/1:214,20:72:-60.76,-21.69,-192.59:99
+chr1	2617101	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=1;HaplotypeScore=89.01;MQ=23.73;MQ0=48;OQ=1884.44;QD=9.10;SB=-387.68	GT:AD:DP:GL:GQ	0/1:34,172:76:-214.63,-22.90,-42.31:99
+chr1	2617123	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=48.50;MQ=26.08;MQ0=56;OQ=129.18;QD=0.64;SB=-72.20	GT:AD:DP:GL:GQ	0/1:185,17:80:-40.33,-24.13,-284.57:99
+chr1	2617151	.	G	C	42.86	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=2;HaplotypeScore=97.11;MQ=23.22;MQ0=69;QD=0.22;SB=-10.77	GT:AD:DP:GL:GQ	0/1:167,21:55:-24.18,-16.61,-193.30:75.70
+chr1	2617160	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=1;HaplotypeScore=68.35;MQ=20.95;MQ0=76;OQ=103.39;QD=0.57;SB=17.08	GT:AD:DP:GL:GQ	0/1:148,32:50:-28.69,-15.07,-157.59:99
+chr1	2617178	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.01;HRun=4;HaplotypeScore=67.98;MQ=19.71;MQ0=69;OQ=224.46;QD=1.59;SB=-23.83	GT:AD:DP:GL:GQ	0/1:56,82:32:-35.39,-9.66,-90.46:99
+chr1	2617216	.	T	C	14.18	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=2;HaplotypeScore=54.33;MQ=16.92;MQ0=58;QD=0.13;SB=5.04	GT:AD:DP:GL:GQ	0/1:54,55:21:-11.01,-6.33,-70.16:46.85
+chr1	2617218	.	C	G	13.85	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=0;HaplotypeScore=69.57;MQ=15.97;MQ0=58;QD=0.13;SB=5.05	GT:AD:DP:GL:GQ	0/1:87,20:21:-10.98,-6.33,-76.68:46.51
+chr1	2617261	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=41.53;MQ=20.71;MQ0=16;OQ=109.26;QD=1.79;SB=-48.91	GT:AD:DP:GL:GQ	0/1:26,35:19:-19.93,-5.73,-46.91:99
+chr1	2617273	rs61466658	T	C	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=31.65;MQ=19.33;MQ0=33;OQ=744.68;QD=8.97;SB=-307.99	GT:AD:DP:GL:GQ	1/1:6,73:24:-80.83,-7.23,-2.78:44.58
+chr1	2617320	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=383;Dels=0.00;HRun=2;HaplotypeScore=179.89;MQ=20.12;MQ0=69;OQ=511.87;QD=1.34;SB=-192.93	GT:AD:DP:GL:GQ	0/1:271,102:88:-80.98,-26.51,-240.14:99
+chr1	2617333	.	A	C	189.16	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=412;Dels=0.00;HRun=1;HaplotypeScore=324.51;MQ=20.25;MQ0=68;QD=0.46;SB=-46.42	GT:AD:DP:GL:GQ	0/1:362,48:102:-52.93,-30.73,-310.85:99
+chr1	2617334	.	C	T	347.52	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=413;Dels=0.00;HRun=0;HaplotypeScore=315.80;MQ=20.22;MQ0=68;QD=0.84;SB=-93.66	GT:AD:DP:GL:GQ	0/1:367,35:98:-67.59,-29.55,-258.47:99
+chr1	2617338	.	C	G	222.34	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=432;Dels=0.00;HRun=0;HaplotypeScore=396.78;MQ=20.69;MQ0=66;QD=0.51;SB=19.38	GT:AD:DP:GL:GQ	0/1:381,42:103:-66.44,-40.92,-386.05:99
+chr1	2617341	.	G	T	154.66	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=435;Dels=0.00;HRun=1;HaplotypeScore=393.28;MQ=20.73;MQ0=66;QD=0.36;SB=-27.31	GT:AD:DP:GL:GQ	0/1:377,44:114:-56.17,-37.42,-341.25:99
+chr1	2617354	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=456;Dels=0.00;HRun=0;HaplotypeScore=284.18;MQ=21.50;MQ0=65;OQ=410.45;QD=0.90;SB=-157.97	GT:AD:DP:GL:GQ	0/1:367,88:128:-86.24,-41.91,-394.71:99
+chr1	2617375	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=397;Dels=0.00;HRun=0;HaplotypeScore=286.33;MQ=23.04;MQ0=37;OQ=238.47;QD=0.60;SB=-127.61	GT:AD:DP:GL:GQ	0/1:316,80:131:-66.59,-39.46,-400.07:99
+chr1	2617377	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=393;Dels=0.00;HRun=0;HaplotypeScore=264.38;MQ=23.09;MQ0=38;OQ=52.53;QD=0.13;SB=34.31	GT:AD:DP:GL:GQ	0/1:349,42:132:-48.29,-39.76,-421.34:85.37
+chr1	2617406	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=150.38;MQ=24.81;MQ0=30;OQ=1026.09;QD=4.44;SB=-81.56	GT:AD:DP:GL:GQ	0/1:71,150:85:-131.52,-25.63,-230.33:99
+chr1	2617434	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=111.67;MQ=24.27;MQ0=28;OQ=290.81;QD=2.02;SB=-29.80	GT:AD:DP:GL:GQ	0/1:61,70:56:-59.33,-26.96,-156.98:99
+chr1	2617463	rs56282610	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=58.94;MQ=24.92;MQ0=20;OQ=411.11;QD=4.42;SB=-153.67	GT:AD:DP:GL:GQ	0/1:29,63:36:-55.25,-10.85,-76.21:99
+chr1	2617490	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=85.26;MQ=28.92;MQ0=14;OQ=93.54;QD=0.96;SB=32.09	GT:AD:DP:GL:GQ	0/1:84,12:39:-24.38,-11.75,-112.74:99
+chr1	2617496	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=107.91;MQ=30.31;MQ0=12;OQ=102.53;QD=1.11;SB=32.10	GT:AD:DP:GL:GQ	0/1:79,12:38:-24.98,-11.44,-111.78:99
+chr1	2617505	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=81.67;MQ=32.33;MQ0=11;OQ=247.78;QD=2.69;SB=-60.73	GT:AD:DP:GL:GQ	0/1:40,39:40:-40.11,-12.05,-107.49:99
+chr1	2617521	rs56279030	G	C	42.50	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.00;HRun=0;HaplotypeScore=51.30;MQ=31.83;MQ0=12;QD=0.40;SB=0.26	GT:AD:DP:GL:GQ	0/1:94,13:44:-20.79,-13.26,-170.49:75.34
+chr1	2617526	rs28536771	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=63.55;MQ=32.40;MQ0=9;OQ=160.23;QD=1.53;SB=-3.57	GT:AD:DP:GL:GQ	0/1:45,55:37:-30.46,-11.15,-113.20:99
+chr1	2617584	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=87.31;MQ=28.18;MQ0=10;OQ=524.04;QD=3.59;SB=-151.92	GT:AD:DP:GL:GQ	0/1:49,97:62:-74.37,-18.69,-162.12:99
+chr1	2617611	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=154;Dels=0.01;HRun=0;HaplotypeScore=176.05;MQ=27.08;MQ0=16;OQ=81.66;QD=0.53;SB=-0.83	GT:AD:DP:GL:GQ	0/1:126,24:59:-29.22,-17.77,-179.32:99
+chr1	2617617	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=177.05;MQ=27.20;MQ0=14;OQ=126.07;QD=0.84;SB=8.21	GT:AD:DP:GL:GQ	0/1:125,25:58:-33.36,-17.47,-170.99:99
+chr1	2617626	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=140;Dels=0.00;HRun=0;HaplotypeScore=162.52;MQ=28.40;MQ0=11;OQ=508.32;QD=3.63;SB=-161.48	GT:AD:DP:GL:GQ	0/1:40,77:57:-73.89,-19.78,-125.32:99
+chr1	2617630	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=1;HaplotypeScore=122.08;MQ=28.20;MQ0=11;OQ=734.14;QD=5.13;SB=-361.31	GT:AD:DP:GL:GQ	0/1:73,47:61:-98.65,-21.95,-111.48:99
+chr1	2617659	rs55801140	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=159;Dels=0.00;HRun=0;HaplotypeScore=125.08;MQ=27.55;MQ0=12;OQ=175.93;QD=1.11;SB=23.11	GT:AD:DP:GL:GQ	0/1:141,12:44:-34.15,-13.27,-148.76:99
+chr1	2617668	rs28535687	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=0;HaplotypeScore=255.63;MQ=27.99;MQ0=8;OQ=172.40;QD=1.28;SB=-72.12	GT:AD:DP:GL:GQ	0/1:31,69:32:-40.65,-20.12,-107.26:99
+chr1	2617672	.	G	T	32.81	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=132;Dels=0.00;HRun=0;HaplotypeScore=245.46;MQ=28.29;MQ0=7;QD=0.25;SB=11.06	GT:AD:DP:GL:GQ	0/1:84,46:25:-14.10,-7.54,-64.41:65.64
+chr1	2617713	.	C	T	25.50	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=0;HaplotypeScore=235.92;MQ=23.71;MQ0=16;QD=0.15;SB=11.61	GT:AD:DP:GL:GQ	0/1:80,75:31:-15.18,-9.35,-88.30:58.32
+chr1	2617737	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=1;HaplotypeScore=196.10;MQ=25.34;MQ0=20;OQ=242.18;QD=1.19;SB=-124.57	GT:AD:DP:GL:GQ	0/1:154,44:50:-42.56,-15.06,-131.92:99
+chr1	2617767	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=115.66;MQ=29.10;MQ0=18;OQ=374.38;QD=2.92;SB=-46.69	GT:AD:DP:GL:GQ	0/1:37,72:41:-53.07,-12.35,-97.04:99
+chr1	2617781	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=110.28;MQ=28.42;MQ0=22;OQ=65.20;QD=0.50;SB=26.12	GT:AD:DP:GL:GQ	0/1:110,18:43:-22.77,-12.97,-156.99:98.03
+chr1	2617809	rs28698520	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.01;HRun=1;HaplotypeScore=154.47;MQ=26.46;MQ0=29;OQ=544.53;QD=4.54;SB=20.07	GT:AD:DP:GL:GQ	0/1:74,45:37:-68.88,-11.15,-59.02:99
+chr1	2617834	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=1;HaplotypeScore=142.69;MQ=25.75;MQ0=33;OQ=247.39;QD=1.66;SB=-8.79	GT:AD:DP:GL:GQ	0/1:101,20:44:-48.54,-20.52,-132.57:99
+chr1	2617846	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=163;Dels=0.00;HRun=0;HaplotypeScore=110.83;MQ=27.45;MQ0=31;OQ=574.67;QD=3.53;SB=-169.29	GT:AD:DP:GL:GQ	0/1:34,98:52:-84.16,-23.41,-106.75:99
+chr1	2617859	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=258;Dels=0.00;HRun=0;HaplotypeScore=189.65;MQ=26.24;MQ0=36;OQ=661.11;QD=2.56;SB=-188.93	GT:AD:DP:GL:GQ	0/1:183,74:74:-91.72,-22.32,-216.13:99
+chr1	2617878	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=308;Dels=0.00;HRun=0;HaplotypeScore=214.86;MQ=26.40;MQ0=36;OQ=1364.14;QD=4.43;SB=-695.16	GT:AD:DP:GL:GQ	0/1:245,61:100:-169.82,-30.12,-204.71:99
+chr1	2617913	rs61766463	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=276;Dels=0.00;HRun=0;HaplotypeScore=33.34;MQ=34.26;MQ0=23;OQ=345.85;QD=1.25;SB=54.43	GT:AD:DP:GL:GQ	0/1:130,145:134:-78.24,-40.37,-397.42:99
+chr1	2617929	rs61766464	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=313;Dels=0.00;HRun=0;HaplotypeScore=209.86;MQ=34.59;MQ0=24;OQ=2475.95;QD=7.91;SB=-469.20	GT:AD:DP:GL:GQ	0/1:207,106:147:-295.16,-44.28,-232.82:99
+chr1	2617945	rs61766465	G	A	678.02	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=327;Dels=0.00;HRun=0;HaplotypeScore=293.41;MQ=35.76;MQ0=33;QD=2.07;SB=57.72	GT:AD:DP:GL:GQ	0/1:285,42:156:-118.09,-47.00,-457.61:99
+chr1	2617948	.	A	T	1515.78	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=339;Dels=0.00;HRun=0;HaplotypeScore=339.78;MQ=35.84;MQ0=34;QD=4.47;SB=-315.59	GT:AD:DP:GL:GQ	0/1:267,71:155:-201.56,-46.69,-377.16:99
+chr1	2617953	rs61766466	C	A	621.95	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=348;Dels=0.00;HRun=0;HaplotypeScore=257.70;MQ=36.09;MQ0=43;QD=1.79;SB=55.33	GT:AD:DP:GL:GQ	0/1:287,49:168:-116.08,-50.61,-483.68:99
+chr1	2618063	rs28379532	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=143;Dels=0.02;HRun=0;HaplotypeScore=36.25;MQ=31.70;MQ0=29;OQ=1863.52;QD=13.03;SB=-253.52	GT:AD:DP:GL:GQ	0/1:27,111:85:-215.25,-25.61,-83.05:99
+chr1	2618135	rs28499404	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=183;Dels=0.00;HRun=0;HaplotypeScore=48.32;MQ=27.35;MQ0=42;OQ=347.83;QD=1.90;SB=-174.55	GT:AD:DP:GL:GQ	0/1:162,21:105:-69.72,-31.65,-366.58:99
+chr1	2618152	rs61766467	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=192;Dels=0.00;HRun=1;HaplotypeScore=85.82;MQ=26.36;MQ0=44;OQ=458.63;QD=2.39;SB=-15.83	GT:AD:DP:GL:GQ	0/1:151,41:104:-80.48,-31.33,-290.41:99
+chr1	2618186	rs28655771	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=193;Dels=0.00;HRun=1;HaplotypeScore=114.84;MQ=21.49;MQ0=56;OQ=2645.92;QD=13.71;SB=-1050.69	GT:AD:DP:GL:GQ	1/1:5,188:77:-268.22,-23.20,-0.04:99
+chr1	2618191	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=161.00;MQ=22.90;MQ0=57;OQ=50.10;QD=0.25;SB=39.02	GT:AD:DP:GL:GQ	0/1:173,30:86:-34.21,-25.91,-268.48:82.93
+chr1	2618226	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=268;Dels=0.00;HRun=0;HaplotypeScore=192.42;MQ=33.49;MQ0=36;OQ=337.18;QD=1.26;SB=-53.39	GT:AD:DP:GL:GQ	0/1:227,40:152:-82.80,-45.80,-457.42:99
+chr1	2618254	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=296;Dels=0.00;HRun=0;HaplotypeScore=166.54;MQ=37.41;MQ0=24;OQ=808.97;QD=2.73;SB=-397.12	GT:AD:DP:GL:GQ	0/1:225,67:181:-140.83,-56.65,-515.36:99
+chr1	2618301	.	C	A	998.94	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=292;Dels=0.00;HRun=0;HaplotypeScore=277.61;MQ=43.53;MQ0=9;QD=3.42;SB=-458.03	GT:AD:DP:GL:GQ	0/1:215,74:195:-161.93,-58.75,-524.06:99
+chr1	2618303	.	C	A	591.91	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=295;Dels=0.00;HRun=0;HaplotypeScore=301.39;MQ=43.31;MQ0=10;QD=2.01;SB=-293.38	GT:AD:DP:GL:GQ	0/1:236,56:205:-124.23,-61.75,-600.14:99
+chr1	2618307	.	G	A	971.72	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=283;Dels=0.00;HRun=0;HaplotypeScore=193.14;MQ=43.47;MQ0=11;QD=3.43;SB=-273.43	GT:AD:DP:GL:GQ	0/1:228,48:199:-160.42,-59.96,-556.19:99
+chr1	2618320	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=309;Dels=0.00;HRun=0;HaplotypeScore=150.76;MQ=41.04;MQ0=29;OQ=452.34;QD=1.46;SB=-151.56	GT:AD:DP:GL:GQ	0/1:223,31:184:-121.13,-72.62,-509.07:99
+chr1	2618366	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=558;Dels=0.00;HRun=0;HaplotypeScore=219.65;MQ=26.44;MQ0=134;OQ=289.23;QD=0.52;SB=167.70	GT:AD:DP:GL:GQ	0/1:454,69:221:-105.97,-73.77,-728.70:99
+chr1	2618375	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=585;Dels=0.00;HRun=0;HaplotypeScore=337.36;MQ=25.16;MQ0=141;OQ=507.21;QD=0.87;SB=196.74	GT:AD:DP:GL:GQ	0/1:487,75:227:-128.47,-74.47,-700.80:99
+chr1	2618378	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=594;Dels=0.00;HRun=0;HaplotypeScore=307.01;MQ=24.92;MQ0=142;OQ=386.51;QD=0.65;SB=-74.59	GT:AD:DP:GL:GQ	0/1:524,66:225:-115.59,-73.65,-670.89:99
+chr1	2618414	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=573;Dels=0.00;HRun=1;HaplotypeScore=206.56;MQ=24.36;MQ0=140;OQ=719.44;QD=1.26;SB=-72.20	GT:AD:DP:GL:GQ	0/1:439,119:210:-138.50,-63.27,-592.09:99
+chr1	2618418	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=531;Dels=0.00;HRun=0;HaplotypeScore=181.25;MQ=24.54;MQ0=131;OQ=939.27;QD=1.77;SB=-76.38	GT:AD:DP:GL:GQ	0/1:427,103:204:-158.68,-61.47,-574.55:99
+chr1	2618432	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=412;Dels=0.00;HRun=0;HaplotypeScore=70.50;MQ=25.62;MQ0=105;OQ=877.24;QD=2.13;SB=-428.33	GT:AD:DP:GL:GQ	0/1:368,44:152:-136.86,-45.86,-364.87:99
+chr1	2618444	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=352;Dels=0.00;HRun=1;HaplotypeScore=46.24;MQ=26.18;MQ0=89;OQ=1301.34;QD=3.70;SB=170.58	GT:AD:DP:GL:GQ	0/1:167,181:143:-176.57,-43.15,-394.32:99
+chr1	2618459	rs61766471	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=309;Dels=0.00;HRun=0;HaplotypeScore=122.77;MQ=27.15;MQ0=60;OQ=430.68;QD=1.39;SB=-167.89	GT:AD:DP:GL:GQ	0/1:283,25:135:-87.04,-40.69,-380.50:99
+chr1	2618482	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=0;HaplotypeScore=91.95;MQ=32.62;MQ0=31;OQ=752.10;QD=3.36;SB=-248.53	GT:AD:DP:GL:GQ	0/1:115,107:101:-108.92,-30.43,-254.35:99
+chr1	2618501	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=234;Dels=0.01;HRun=4;HaplotypeScore=341.35;MQ=30.82;MQ0=33;OQ=155.62;QD=0.67;SB=92.01	GT:AD:DP:GL:GQ	0/1:155,66:98:-53.97,-35.12,-329.58:99
+chr1	2618530	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=168.93;MQ=32.32;MQ0=29;OQ=236.35;QD=1.02;SB=-122.19	GT:AD:DP:GL:GQ	0/1:211,19:107:-59.16,-32.24,-318.05:99
+chr1	2618557	rs28411025	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=156;Dels=0.00;HRun=0;HaplotypeScore=133.44;MQ=39.19;MQ0=9;OQ=2883.82;QD=18.49;SB=-1383.19	GT:AD:DP:GL:GQ	0/1:27,128:92:-319.41,-27.74,-64.72:99
+chr1	2618577	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=228;Dels=0.01;HRun=1;HaplotypeScore=243.04;MQ=34.35;MQ0=14;OQ=206.46;QD=0.91;SB=-125.59	GT:AD:DP:GL:GQ	0/1:119,105:92:-51.66,-27.73,-260.87:99
+chr1	2618590	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=341;Dels=0.00;HRun=0;HaplotypeScore=269.37;MQ=32.40;MQ0=23;OQ=694.60;QD=2.04;SB=-10.03	GT:AD:DP:GL:GQ	0/1:206,129:134:-115.74,-43.00,-326.10:99
+chr1	2618603	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=385;Dels=0.00;HRun=0;HaplotypeScore=742.67;MQ=32.24;MQ0=20;OQ=374.09;QD=0.97;SB=-84.54	GT:AD:DP:GL:GQ	0/1:213,140:157:-94.37,-53.68,-577.68:99
+chr1	2618613	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=414;Dels=0.00;HRun=1;HaplotypeScore=803.50;MQ=31.66;MQ0=23;OQ=626.38;QD=1.51;SB=181.82	GT:AD:DP:GL:GQ	0/1:349,58:175:-118.68,-52.76,-621.84:99
+chr1	2618617	.	A	C	34.85	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=417;Dels=0.00;HRun=1;HaplotypeScore=645.23;MQ=31.22;MQ0=23;QD=0.08;SB=-15.32	GT:AD:DP:GL:GQ	0/1:232,176:163:-62.01,-55.24,-512.02:67.68
+chr1	2618648	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=485;Dels=0.00;HRun=0;HaplotypeScore=582.18;MQ=29.51;MQ0=32;OQ=1313.91;QD=2.71;SB=163.03	GT:AD:DP:GL:GQ	0/1:367,113:208:-197.35,-62.68,-695.38:99
+chr1	2618651	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=487;Dels=0.00;HRun=0;HaplotypeScore=686.95;MQ=29.46;MQ0=33;OQ=108.10;QD=0.22;SB=256.13	GT:AD:DP:GL:GQ	0/1:431,46:211:-84.08,-69.98,-671.09:99
+chr1	2618685	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=500;Dels=0.00;HRun=1;HaplotypeScore=291.67;MQ=27.86;MQ0=33;OQ=4318.30;QD=8.64;SB=-761.47	GT:AD:DP:GL:GQ	0/1:182,284:216:-430.83,-67.58,-458.35:99
+chr1	2618707	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=462;Dels=0.01;HRun=4;HaplotypeScore=721.39;MQ=29.06;MQ0=34;OQ=2615.02;QD=5.66;SB=-699.35	GT:AD:DP:GL:GQ	0/1:165,282:202:-327.27,-62.48,-383.70:99
+chr1	2618711	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=464;Dels=0.00;HRun=0;HaplotypeScore=458.70;MQ=28.79;MQ0=35;OQ=1658.43;QD=3.57;SB=-180.55	GT:AD:DP:GL:GQ	0/1:156,178:185:-246.74,-77.62,-433.93:99
+chr1	2618743	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=565;Dels=0.00;HRun=1;HaplotypeScore=594.08;MQ=28.52;MQ0=39;OQ=195.57;QD=0.35;SB=27.58	GT:AD:DP:GL:GQ	0/1:503,58:268:-103.62,-80.78,-771.76:99
+chr1	2618776	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=541;Dels=0.00;HRun=0;HaplotypeScore=502.52;MQ=30.93;MQ0=35;OQ=5244.83;QD=9.69;SB=-856.66	GT:AD:DP:GL:GQ	0/1:182,353:279:-523.48,-84.06,-514.94:99
+chr1	2618784	.	C	T	23.85	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=542;Dels=0.00;HRun=0;HaplotypeScore=612.02;MQ=31.33;MQ0=33;QD=0.04;SB=67.53	GT:AD:DP:GL:GQ	0/1:386,152:218:-71.34,-65.68,-703.92:56.67
+chr1	2618799	rs61766473	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=520;Dels=0.00;HRun=1;HaplotypeScore=456.03;MQ=31.14;MQ0=35;OQ=4809.01;QD=9.25;SB=-828.34	GT:AD:DP:GL:GQ	0/1:169,328:274:-479.90,-94.56,-523.76:99
+chr1	2618813	rs28570043	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=586;Dels=0.00;HRun=0;HaplotypeScore=299.20;MQ=30.92;MQ0=47;OQ=1856.68;QD=3.17;SB=-717.31	GT:AD:DP:GL:GQ	0/1:501,75:250:-270.75,-81.80,-777.18:99
+chr1	2618823	rs61766474	A	T	4860.03	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=562;Dels=0.00;HRun=0;HaplotypeScore=709.32;MQ=30.48;MQ0=44;QD=8.65;SB=-560.15	GT:AD:DP:GL:GQ	0/1:287,273:277:-485.00,-83.44,-550.46:99
+chr1	2618832	.	C	G	1479.75	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=512;Dels=0.00;HRun=2;HaplotypeScore=411.64;MQ=30.81;MQ0=42;QD=2.89;SB=-17.36	GT:AD:DP:GL:GQ	0/1:367,94:241:-231.26,-80.00,-778.36:99
+chr1	2618833	.	G	C	375.40	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=513;Dels=0.00;HRun=1;HaplotypeScore=505.52;MQ=30.67;MQ0=42;QD=0.73;SB=152.53	GT:AD:DP:GL:GQ	0/1:466,47:236:-112.05,-71.23,-847.97:99
+chr1	2618853	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=470;Dels=0.00;HRun=0;HaplotypeScore=742.82;MQ=31.02;MQ0=40;OQ=917.98;QD=1.95;SB=-4.91	GT:AD:DP:GL:GQ	0/1:336,89:211:-236.75,-141.67,-586.15:99
+chr1	2618854	rs61766475	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=465;Dels=0.00;HRun=1;HaplotypeScore=675.66;MQ=31.14;MQ0=39;OQ=3030.86;QD=6.52;SB=-170.15	GT:AD:DP:GL:GQ	0/1:129,210:216:-470.96,-164.59,-497.24:99
+chr1	2618865	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=505;Dels=0.00;HRun=0;HaplotypeScore=338.61;MQ=30.47;MQ0=44;OQ=342.56;QD=0.68;SB=-14.42	GT:AD:DP:GL:GQ	0/1:439,53:231:-117.83,-80.29,-726.19:99
+chr1	2618904	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=499;Dels=0.00;HRun=4;HaplotypeScore=608.12;MQ=29.15;MQ0=44;OQ=1769.15;QD=3.55;SB=89.28	GT:AD:DP:GL:GQ	0/1:280,197:227:-252.16,-71.97,-553.68:99
+chr1	2618905	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=514;Dels=0.00;HRun=0;HaplotypeScore=596.36;MQ=29.03;MQ0=46;OQ=337.81;QD=0.66;SB=-30.28	GT:AD:DP:GL:GQ	0/1:424,43:227:-138.22,-101.16,-705.27:99
+chr1	2618928	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=624;Dels=0.00;HRun=2;HaplotypeScore=323.04;MQ=29.42;MQ0=49;OQ=696.10;QD=1.12;SB=42.74	GT:AD:DP:GL:GQ	0/1:499,120:322:-169.90,-97.01,-976.27:99
+chr1	2618942	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=632;Dels=0.00;HRun=0;HaplotypeScore=427.92;MQ=29.57;MQ0=51;OQ=1430.20;QD=2.26;SB=-6.35	GT:AD:DP:GL:GQ	0/1:441,177:340:-255.05,-108.75,-1027.84:99
+chr1	2618944	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=660;Dels=0.01;HRun=1;HaplotypeScore=381.00;MQ=29.09;MQ0=58;OQ=94.18;QD=0.14;SB=-52.32	GT:AD:DP:GL:GQ	0/1:544,51:336:-209.60,-196.90,-1072.15:99
+chr1	2619010	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=979;Dels=0.00;HRun=0;HaplotypeScore=447.29;MQ=26.60;MQ0=70;OQ=796.25;QD=0.81;SB=-92.06	GT:AD:DP:GL:GQ	0/1:864,98:425:-220.34,-137.43,-1275.90:99
+chr1	2619053	rs28733941	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=909;Dels=0.00;HRun=0;HaplotypeScore=595.79;MQ=27.09;MQ0=60;OQ=13631.67;QD=15.00;SB=-2975.80	GT:AD:DP:GL:GQ	0/1:104,553:419:-1362.17,-600.80,-836.54:99
+chr1	2619065	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1083;Dels=0.00;HRun=0;HaplotypeScore=883.09;MQ=27.27;MQ0=55;OQ=741.35;QD=0.68;SB=-174.53	GT:AD:DP:GL:GQ	0/1:939,125:552:-281.40,-203.98,-1716.07:99
+chr1	2619068	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1124;Dels=0.00;HRun=1;HaplotypeScore=958.29;MQ=27.28;MQ0=55;OQ=693.79;QD=0.62;SB=-203.14	GT:AD:DP:GL:GQ	0/1:985,132:593:-257.34,-184.67,-1827.88:99
+chr1	2619088	rs28368434	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=1328;Dels=0.00;HRun=2;HaplotypeScore=334.46;MQ=28.00;MQ0=46;OQ=7035.59;QD=5.30;SB=-1628.81	GT:AD:DP:GL:GQ	0/1:1024,295:793:-702.56,-254.86,-2119.90:99
+chr1	2619105	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=1330;Dels=0.00;HRun=0;HaplotypeScore=932.09;MQ=28.23;MQ0=29;OQ=2367.59;QD=1.78;SB=-1159.72	GT:AD:DP:GL:GQ	0/1:991,151:799:-779.65,-539.60,-2921.50:99
+chr1	2619148	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=990;Dels=0.00;HRun=0;HaplotypeScore=340.48;MQ=27.70;MQ0=55;OQ=2332.09;QD=2.36;SB=-739.43	GT:AD:DP:GL:GQ	0/1:796,178:558:-439.22,-202.73,-1989.78:99
+chr1	2619186	.	A	C	371.93	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=419;Dels=0.00;HRun=2;HaplotypeScore=464.28;MQ=28.43;MQ0=32;QD=0.89;SB=-209.63	GT:AD:DP:GL:GQ	0/1:320,97:190:-97.71,-57.24,-585.62:99
+chr1	2619187	.	A	C	430.91	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=400;Dels=0.00;HRun=1;HaplotypeScore=324.16;MQ=28.26;MQ0=30;QD=1.08;SB=-112.57	GT:AD:DP:GL:GQ	0/1:310,88:169:-97.29,-50.91,-502.75:99
+chr1	2619196	rs61766477	C	T	639.34	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=339;Dels=0.00;HRun=0;HaplotypeScore=406.21;MQ=29.84;MQ0=24;QD=1.89;SB=-240.09	GT:AD:DP:GL:GQ	0/1:283,37:141:-134.06,-66.84,-411.36:99
+chr1	2619205	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=257;Dels=0.00;HRun=0;HaplotypeScore=259.69;MQ=32.70;MQ0=16;OQ=1928.35;QD=7.50;SB=-426.10	GT:AD:DP:GL:GQ	0/1:80,173:106:-228.05,-31.94,-159.03:99
+chr1	2619218	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=235;Dels=0.00;HRun=1;HaplotypeScore=278.38;MQ=35.10;MQ0=10;OQ=372.83;QD=1.59;SB=-167.14	GT:AD:DP:GL:GQ	0/1:174,58:82:-65.27,-24.71,-216.22:99
+chr1	2619230	.	G	A	206.96	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=238;Dels=0.00;HRun=1;HaplotypeScore=422.57;MQ=34.96;MQ0=8;QD=0.87;SB=86.30	GT:AD:DP:GL:GQ	0/1:192,38:100:-59.43,-35.45,-312.61:99
+chr1	2619232	.	T	C	831.94	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=232;Dels=0.00;HRun=0;HaplotypeScore=355.75;MQ=35.18;MQ0=8;QD=3.59;SB=-351.57	GT:AD:DP:GL:GQ	0/1:163,64:87:-112.72,-26.24,-194.80:99
+chr1	2619238	.	G	T	230.19	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=214;Dels=0.00;HRun=0;HaplotypeScore=374.27;MQ=36.67;MQ0=6;QD=1.08;SB=104.29	GT:AD:DP:GL:GQ	0/1:105,106:92:-54.02,-27.71,-267.56:99
+chr1	2619244	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=0;HaplotypeScore=269.42;MQ=37.21;MQ0=7;OQ=1921.19;QD=9.56;SB=-479.90	GT:AD:DP:GL:GQ	0/1:57,142:93:-223.42,-28.02,-104.14:99
+chr1	2619306	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=2;HaplotypeScore=23.50;MQ=42.95;MQ0=2;OQ=983.37;QD=8.48;SB=-151.45	GT:AD:DP:GL:GQ	0/1:49,66:80:-128.94,-27.32,-178.83:99
+chr1	2619313	.	T	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=14.58;MQ=45.37;MQ0=2;OQ=717.70;QD=7.40;SB=-61.81	GT:AD:DP:GL:GQ	0/1:47,50:71:-96.45,-21.40,-150.45:99
+chr1	2619324	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=29.83;MQ=44.91;MQ0=2;OQ=606.68;QD=6.74;SB=-59.89	GT:AD:DP:GL:GQ	0/1:45,45:58:-81.45,-17.50,-117.39:99
+chr1	2619346	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=198;Dels=0.01;HRun=2;HaplotypeScore=304.95;MQ=34.96;MQ0=2;OQ=1893.09;QD=9.56;SB=62.22	GT:AD:DP:GL:GQ	0/1:48,144:92:-224.02,-31.43,-163.64:99
+chr1	2619351	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=249;Dels=0.00;HRun=1;HaplotypeScore=417.56;MQ=32.10;MQ0=4;OQ=1347.04;QD=5.41;SB=71.23	GT:AD:DP:GL:GQ	0/1:80,143:111:-171.44,-33.46,-209.78:99
+chr1	2619360	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=388;Dels=0.00;HRun=1;HaplotypeScore=438.87;MQ=28.93;MQ0=6;OQ=112.12;QD=0.29;SB=98.35	GT:AD:DP:GL:GQ	0/1:301,77:156:-68.00,-53.51,-526.40:99
+chr1	2619395	rs61766478	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=748;Dels=0.00;HRun=0;HaplotypeScore=964.64;MQ=26.94;MQ0=26;OQ=5287.26;QD=7.07;SB=128.59	GT:AD:DP:GL:GQ	0/1:216,518:288:-527.73,-89.49,-471.13:99
+chr1	2619416	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=775;Dels=0.00;HRun=0;HaplotypeScore=727.49;MQ=27.55;MQ0=26;OQ=6889.43;QD=8.89;SB=178.09	GT:AD:DP:GL:GQ	0/1:249,511:342:-687.94,-103.01,-497.11:99
+chr1	2619432	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=738;Dels=0.01;HRun=0;HaplotypeScore=785.98;MQ=28.56;MQ0=15;OQ=287.49;QD=0.39;SB=162.31	GT:AD:DP:GL:GQ	0/1:586,116:299:-161.89,-129.86,-1001.87:99
+chr1	2619446	rs61766479	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=555;Dels=0.00;HRun=1;HaplotypeScore=580.47;MQ=30.08;MQ0=12;OQ=4833.38;QD=8.71;SB=183.30	GT:AD:DP:GL:GQ	0/1:214,317:283:-482.34,-118.04,-540.99:99
+chr1	2619465	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=306;Dels=0.02;HRun=1;HaplotypeScore=404.44;MQ=32.23;MQ0=6;OQ=129.50;QD=0.42;SB=102.00	GT:AD:DP:GL:GQ	0/1:203,74:120:-64.50,-48.27,-416.86:99
+chr1	2619467	rs61766480	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=303;Dels=0.02;HRun=1;HaplotypeScore=363.13;MQ=31.91;MQ0=6;OQ=4502.12;QD=14.86;SB=-1253.39	GT:AD:DP:GL:GQ	0/1:40,252:153:-449.21,-45.80,-111.82:99
+chr1	2619477	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=335.87;MQ=32.02;MQ0=7;OQ=542.66;QD=1.95;SB=122.33	GT:AD:DP:GL:GQ	0/1:161,107:129:-96.42,-38.87,-351.57:99
+chr1	2619489	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=268;Dels=0.00;HRun=1;HaplotypeScore=215.67;MQ=32.52;MQ0=8;OQ=1128.11;QD=4.21;SB=95.32	GT:AD:DP:GL:GQ	0/1:114,145:131:-166.02,-49.92,-331.55:99
+chr1	2619505	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=305.81;MQ=31.15;MQ0=10;OQ=135.21;QD=0.50;SB=68.22	GT:AD:DP:GL:GQ	0/1:237,31:129:-55.67,-38.86,-389.56:99
+chr1	2619511	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=262;Dels=0.00;HRun=0;HaplotypeScore=356.76;MQ=30.03;MQ0=11;OQ=250.01;QD=0.95;SB=47.18	GT:AD:DP:GL:GQ	0/1:212,49:118:-63.84,-35.55,-351.09:99
+chr1	2619524	rs34081960	A	G	343.80	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=216;Dels=0.00;HRun=1;HaplotypeScore=217.57;MQ=30.42;MQ0=7;QD=1.59;SB=47.18	GT:AD:DP:GL:GQ	0/1:179,33:102:-68.39,-30.73,-325.69:99
+chr1	2619526	.	C	A	23.86	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=205;Dels=0.00;HRun=1;HaplotypeScore=236.96;MQ=30.18;MQ0=8;QD=0.12;SB=44.17	GT:AD:DP:GL:GQ	0/1:190,11:95:-34.28,-28.61,-300.58:56.68
+chr1	2619527	.	A	C	538.74	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=197;Dels=0.00;HRun=1;HaplotypeScore=224.55;MQ=30.05;MQ0=8;QD=2.73;SB=-87.11	GT:AD:DP:GL:GQ	0/1:122,73:87:-83.37,-26.21,-226.60:99
+chr1	2619530	.	T	G	866.27	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=215.21;MQ=31.06;MQ0=6;QD=4.84;SB=12.12	GT:AD:DP:GL:GQ	0/1:87,85:86:-126.63,-36.72,-179.70:99
+chr1	2619534	.	A	G	264.68	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=1;HaplotypeScore=280.66;MQ=30.98;MQ0=7;QD=1.54;SB=41.16	GT:AD:DP:GL:GQ	0/1:139,33:74:-52.04,-22.29,-233.98:99
+chr1	2619544	.	C	T	108.85	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=155;Dels=0.06;HRun=0;HaplotypeScore=267.97;MQ=31.40;MQ0=5;QD=0.70;SB=38.12	GT:AD:DP:GL:GQ	0/1:124,16:57:-34.75,-20.58,-177.62:99
+chr1	2619546	.	C	G	37.35	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=251.96;MQ=31.91;MQ0=5;QD=0.25;SB=38.15	GT:AD:DP:GL:GQ	0/1:138,7:61:-25.40,-18.38,-245.36:70.19
+chr1	2619553	.	A	G	821.41	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=113.41;MQ=33.54;MQ0=5;QD=6.96;SB=23.10	GT:AD:DP:GL:GQ	0/1:33,83:56:-102.29,-16.87,-105.73:99
+chr1	2619570	rs12757527	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=61.91;MQ=39.68;MQ0=1;OQ=223.25;QD=2.51;SB=41.15	GT:AD:DP:GL:GQ	0/1:39,49:45:-39.17,-13.56,-132.69:99
+chr1	2619576	rs11516512	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=85.98;MQ=40.41;MQ0=1;OQ=1215.90;QD=15.59;SB=-537.94	GT:AD:DP:GL:GQ	0/1:9,69:47:-139.03,-14.16,-23.39:92.31
+chr1	2619644	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=167.24;MQ=38.77;MQ0=11;OQ=65.21;QD=0.53;SB=59.09	GT:AD:DP:GL:GQ	0/1:83,36:47:-23.99,-14.18,-125.75:98.05
+chr1	2619667	rs12757684	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=110;Dels=0.02;HRun=3;HaplotypeScore=150.20;MQ=38.48;MQ0=2;OQ=87.98;QD=0.80;SB=-4.94	GT:AD:DP:GL:GQ	0/1:62,46:39:-23.84,-11.75,-110.18:99
+chr1	2619672	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=2;HaplotypeScore=165.55;MQ=38.18;MQ0=2;OQ=67.69;QD=0.61;SB=56.21	GT:AD:DP:GL:GQ	0/1:58,23:45:-37.64,-27.58,-156.78:99
+chr1	2619717	rs35537872	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=158.55;MQ=37.91;MQ0=1;OQ=82.21;QD=0.81;SB=12.47	GT:AD:DP:GL:GQ	0/1:41,55:41:-23.87,-12.36,-127.50:99
+chr1	2619725	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=160.68;MQ=38.53;MQ0=0;OQ=110.57;QD=1.00;SB=59.22	GT:AD:DP:GL:GQ	0/1:96,15:49:-29.10,-14.76,-154.28:99
+chr1	2619755	rs35198281	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=135.67;MQ=40.63;MQ0=1;OQ=77.36;QD=0.78;SB=-26.15	GT:AD:DP:GL:GQ	0/1:44,49:41:-23.37,-12.36,-121.95:99
+chr1	2619802	.	G	A	11.69	LowQual	AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=1;HaplotypeScore=127.16;MQ=33.63;MQ0=4;QD=0.12;SB=-22.48	GT:AD:DP:GL:GQ	0/1:79,20:38:-15.87,-11.45,-120.55:44.22
+chr1	2619811	rs11516513	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=1;HaplotypeScore=94.34;MQ=31.96;MQ0=5;OQ=1057.97;QD=11.02;SB=-282.04	GT:AD:DP:GL:GQ	0/1:29,63:37:-120.23,-11.15,-15.87:47.21
+chr1	2619844	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=163.21;MQ=35.54;MQ0=9;OQ=150.26;QD=1.60;SB=-85.59	GT:AD:DP:GL:GQ	0/1:35,58:32:-27.96,-9.65,-83.83:99
+chr1	2619873	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=1;HaplotypeScore=84.94;MQ=33.03;MQ0=22;OQ=528.32;QD=3.80;SB=-259.93	GT:AD:DP:GL:GQ	0/1:45,94:55:-72.69,-16.57,-137.30:99
+chr1	2619885	rs4648686	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=143;Dels=0.00;HRun=0;HaplotypeScore=76.46;MQ=34.20;MQ0=29;OQ=72.77;QD=0.51;SB=-32.15	GT:AD:DP:GL:GQ	0/1:107,35:58:-28.03,-17.47,-178.69:99
+chr1	2619907	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=129;Dels=0.02;HRun=0;HaplotypeScore=75.23;MQ=35.05;MQ0=37;OQ=78.76;QD=0.61;SB=20.08	GT:AD:DP:GL:GQ	0/1:80,29:48:-28.88,-17.72,-148.42:99
+chr1	2619934	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=0;HaplotypeScore=66.32;MQ=35.85;MQ0=29;OQ=172.74;QD=1.52;SB=-28.24	GT:AD:DP:GL:GQ	0/1:48,66:48:-35.03,-14.47,-147.33:99
+chr1	2619955	rs6604996	C	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=63.40;MQ=33.93;MQ0=36;OQ=1440.37;QD=13.21;SB=-479.54	GT:AD:DP:GL:GQ	1/1:0,108:38:-147.67,-11.48,-0.04:99
+chr1	2620070	rs12740972	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=47.55;MQ=45.30;MQ0=8;OQ=554.48;QD=5.72;SB=-255.88	GT:AD:DP:GL:GQ	0/1:70,21:53:-74.72,-15.98,-142.31:99
+chr1	2620085	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=54.16;MQ=39.71;MQ0=11;OQ=120.34;QD=1.02;SB=-33.16	GT:AD:DP:GL:GQ	0/1:69,45:56:-32.19,-16.87,-164.99:99
+chr1	2620124	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=63.81;MQ=34.92;MQ0=3;OQ=525.60;QD=3.65;SB=47.19	GT:AD:DP:GL:GQ	0/1:42,93:57:-80.08,-24.23,-172.63:99
+chr1	2620133	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=151;Dels=0.00;HRun=1;HaplotypeScore=107.36;MQ=34.37;MQ0=3;OQ=432.59;QD=2.86;SB=-11.69	GT:AD:DP:GL:GQ	0/1:52,96:55:-63.12,-16.58,-172.84:99
+chr1	2620148	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=3;HaplotypeScore=138.11;MQ=33.81;MQ0=6;OQ=406.05;QD=2.39;SB=-68.70	GT:AD:DP:GL:GQ	0/1:52,113:57:-61.06,-17.17,-159.71:99
+chr1	2620167	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=206;Dels=0.00;HRun=1;HaplotypeScore=129.33;MQ=31.98;MQ0=15;OQ=238.76;QD=1.16;SB=-5.73	GT:AD:DP:GL:GQ	0/1:136,68:69:-47.94,-20.78,-212.90:99
+chr1	2620268	rs12741311	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=74.94;MQ=48.87;MQ0=0;OQ=615.93;QD=7.90;SB=-166.53	GT:AD:DP:GL:GQ	0/1:39,39:52:-80.54,-15.66,-101.64:99
+chr1	2620338	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=0;HaplotypeScore=10.27;MQ=42.72;MQ0=7;OQ=159.57;QD=1.60;SB=-79.74	GT:AD:DP:GL:GQ	0/1:47,53:53:-35.21,-15.97,-154.39:99
+chr1	2620373	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=37.37;MQ=38.59;MQ0=9;OQ=479.31;QD=3.40;SB=-63.47	GT:AD:DP:GL:GQ	0/1:49,92:64:-70.51,-19.30,-148.48:99
+chr1	2620382	.	G	A	119.16	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=95.95;MQ=37.22;MQ0=9;QD=0.82;SB=68.14	GT:AD:DP:GL:GQ	0/1:86,59:65:-34.81,-19.61,-177.00:99
+chr1	2620388	.	A	C	105.30	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=1;HaplotypeScore=83.57;MQ=35.41;MQ0=9;QD=0.69;SB=-45.48	GT:AD:DP:GL:GQ	0/1:132,21:67:-34.00,-20.19,-204.42:99
+chr1	2620390	rs28376921	A	C	238.82	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=3;HaplotypeScore=84.30;MQ=34.68;MQ0=9;QD=1.57;SB=-137.48	GT:AD:DP:GL:GQ	0/1:57,64:66:-69.75,-42.59,-188.12:99
+chr1	2620438	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=39.76;MQ=41.64;MQ0=7;OQ=388.27;QD=3.70;SB=-212.33	GT:AD:DP:GL:GQ	0/1:46,59:60:-60.19,-18.08,-149.44:99
+chr1	2620448	.	T	C	36.03	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=55.60;MQ=44.75;MQ0=3;QD=0.36;SB=59.63	GT:AD:DP:GL:GQ	0/1:72,27:62:-25.58,-18.69,-209.22:68.86
+chr1	2620451	rs28507126	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=42.59;MQ=44.33;MQ0=4;OQ=207.39;QD=2.07;SB=-2.70	GT:AD:DP:GL:GQ	0/1:56,44:55:-40.61,-16.58,-162.04:99
+chr1	2620498	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=117.30;MQ=35.77;MQ0=21;OQ=96.72;QD=0.68;SB=-10.89	GT:AD:DP:GL:GQ	0/1:119,24:63:-31.93,-18.98,-196.03:99
+chr1	2620509	.	C	A	44.02	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=149.75;MQ=36.71;MQ0=19;QD=0.28;SB=8.48	GT:AD:DP:GL:GQ	0/1:122,32:70:-28.77,-21.09,-215.81:76.85
+chr1	2620530	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.01;HRun=0;HaplotypeScore=86.24;MQ=39.02;MQ0=10;OQ=202.63;QD=1.69;SB=-58.78	GT:AD:DP:GL:GQ	0/1:60,45:53:-46.29,-22.74,-131.05:99
+chr1	2620553	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=4;HaplotypeScore=12.66;MQ=42.96;MQ0=4;OQ=154.29;QD=1.66;SB=6.59	GT:AD:DP:GL:GQ	0/1:47,46:55:-35.28,-16.57,-164.62:99
+chr1	2620589	rs4648687	C	A	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=19.10;MQ=49.13;MQ0=2;OQ=495.80;QD=9.01;SB=-265.29	GT:AD:DP:GL:GQ	0/1:36,19:38:-64.31,-11.45,-69.99:99
+chr1	2620786	rs12742092	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=51.45;MQ=48.85;MQ0=1;OQ=289.75;QD=5.57;SB=-99.04	GT:AD:DP:GL:GQ	0/1:36,16:30:-41.30,-9.04,-64.97:99
+chr1	2620835	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=99.62;MQ=36.59;MQ0=7;OQ=441.17;QD=4.64;SB=-224.20	GT:AD:DP:GL:GQ	0/1:74,18:36:-60.73,-13.33,-87.56:99
+chr1	2620875	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=107.69;MQ=35.97;MQ0=15;OQ=95.46;QD=0.71;SB=-26.90	GT:AD:DP:GL:GQ	0/1:113,19:59:-30.61,-17.78,-174.51:99
+chr1	2620960	.	T	A	14.94	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=17.98;MQ=48.66;MQ0=1;QD=0.38;SB=38.15	GT:AD:DP:GL:GQ	0/1:35,4:38:-16.21,-11.45,-119.38:47.63
+chr1	2621024	.	C	A	47.37	LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=15.73;MQ=45.56;MQ0=1;QD=1.18;SB=-9.87	GT:AD:DP:GL:GQ	0/1:33,7:35:-18.56,-10.54,-104.34:80.21
+chr1	2621154	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=51.59;MQ=53.22;MQ0=2;OQ=488.50;QD=9.77;SB=-206.66	GT:AD:DP:GL:GQ	0/1:29,19:38:-63.61,-11.47,-88.44:99
+chr1	2621346	rs12746691	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=78.63;MQ=48.13;MQ0=0;OQ=876.62;QD=14.61;SB=-440.96	GT:AD:DP:GL:GQ	0/1:34,26:44:-104.20,-13.26,-62.31:99
+chr1	2621414	rs12746841	C	G	50.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=5.31;MQ=55.95;MQ0=0;OQ=526.83;QD=11.97;SB=-219.19	GT:AD:DP:GL:GQ	0/1:24,20:36:-66.82,-10.85,-82.62:99
+chr1	2621575	rs61766505	T	A	0.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=9.78;MQ=51.58;MQ0=2;OQ=514.79;QD=12.26;SB=-105.13	GT:AD:DP:GL:GQ	0/1:24,18:33:-64.70,-9.94,-57.89:99
+chr1	2621592	rs11516514	C	A	2.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=7.05;MQ=51.18;MQ0=2;OQ=412.67;QD=8.78;SB=-93.77	GT:AD:DP:GL:GQ	0/1:31,16:35:-55.10,-10.55,-68.38:99
+chr1	2621664	rs12743419	G	A	126.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=54.07;MQ0=3;OQ=805.45;QD=17.14;SB=-279.82	GT:AD:DP:GL:GQ	0/1:16,31:40:-95.89,-12.06,-46.66:99
+chr1	2621957	rs12751643	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.02;HRun=1;HaplotypeScore=33.34;MQ=53.32;MQ0=0;OQ=1019.18;QD=17.27;SB=-299.66	GT:AD:DP:GL:GQ	0/1:24,34:54:-121.47,-16.27,-70.01:99
+chr1	2622417	.	C	G	34.36	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=22.88;MQ0=7;QD=1.01;SB=-10.00	GT:AD:DP:GL:GQ	0/1:28,6:20:-12.75,-6.03,-74.77:67.20
+chr1	2622422	rs11488613	G	T	0.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=6.76;MQ=21.77;MQ0=7;OQ=525.32;QD=15.45;SB=-10.00	GT:AD:DP:GL:GQ	1/1:3,31:16:-56.12,-4.82,-0.00:48.14
+chr1	2622433	rs12752340	C	A	26.89	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=20.67;MQ0=10;QD=0.75;SB=-10.00	GT:AD:DP:GL:GQ	0/1:30,6:16:-10.79,-4.82,-42.41:59.72
+chr1	2674088	.	C	G	42.96	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=0;HaplotypeScore=11.98;MQ=19.55;MQ0=6;QD=3.91;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,3:5:-9.09,-1.51,-12.64:75.79
+chr1	2674094	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=17.86;MQ=18.47;MQ0=6;OQ=64.31;QD=4.95;SB=-10.00	GT:AD:DP:GL:GQ	0/1:10,3:4:-10.92,-1.20,-3.26:20.53
+chr1	2674111	.	T	A	27.07	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=32.32;MQ0=6;QD=1.80;SB=-6.99	GT:AD:DP:GL:GQ	0/1:12,3:7:-8.10,-2.11,-18.86:59.90
+chr1	2674112	.	A	G	16.12	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=32.32;MQ0=6;QD=1.07;SB=-6.99	GT:AD:DP:GL:GQ	0/1:12,3:7:-6.99,-2.11,-20.42:48.85
+chr1	2674407	.	A	G	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=13.44;MQ=45.39;MQ0=5;OQ=445.12;QD=11.41;SB=-215.68	GT:AD:DP:GL:GQ	0/1:16,22:32:-57.44,-9.65,-56.21:99
+chr1	2674852	rs61766513	G	A	450.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=13.17;MQ0=18;OQ=519.69;QD=10.39;SB=-286.88	GT:AD:DP:GL:GQ	1/1:0,50:14:-55.56,-4.22,-0.00:42.14
+chr1	2676124	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=1;HaplotypeScore=15.64;MQ=24.04;MQ0=14;OQ=178.81;QD=2.03;SB=-90.56	GT:AD:DP:GL:GQ	0/1:59,29:40:-33.21,-12.05,-114.97:99
+chr1	2676150	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=19.23;MQ=23.09;MQ0=22;OQ=221.70;QD=2.33;SB=-83.88	GT:AD:DP:GL:GQ	0/1:54,41:38:-36.91,-11.46,-90.41:99
+chr1	2676190	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=39.71;MQ=18.24;MQ0=31;OQ=65.56;QD=0.85;SB=-25.50	GT:AD:DP:GL:GQ	0/1:64,13:22:-16.48,-6.63,-57.54:98.40
+chr1	2676191	.	G	A	29.02	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=39.71;MQ=17.81;MQ0=31;QD=0.39;SB=26.10	GT:AD:DP:GL:GQ	0/1:60,14:18:-11.61,-5.43,-50.51:61.85
+chr1	2676208	.	G	A	16.39	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=4.26;MQ=15.36;MQ0=32;QD=0.30;SB=-24.49	GT:AD:DP:GL:GQ	0/1:43,10:12:-8.53,-3.62,-33.94:49.13
+chr1	2676293	rs11486072	G	T	42.12	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.44;MQ0=18;QD=0.68;SB=83.26	GT:AD:DP:GL:GQ	0/1:53,9:41:-19.85,-12.35,-121.85:74.96
+chr1	2676409	.	C	G	16.08	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=0;HaplotypeScore=24.91;MQ=14.80;MQ0=58;QD=0.16;SB=-10.00	GT:AD:DP:GL:GQ	0/1:83,17:12:-8.50,-3.62,-44.92:48.81
+chr1	2677515	.	G	T	19.05	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=14.46;MQ=8.37;MQ0=110;QD=0.16;SB=-10.00	GT:AD:DP:GL:GQ	0/1:117,3:8:-7.59,-2.41,-19.90:51.83
+chr1	2677525	.	C	T	16.29	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=1;HaplotypeScore=20.34;MQ=9.26;MQ0=102;QD=0.14;SB=-10.00	GT:AD:DP:GL:GQ	0/1:110,4:10:-7.91,-3.01,-27.95:49.02
+chr1	2677552	.	A	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=12.35;MQ=15.52;MQ0=82;OQ=53.71;QD=0.48;SB=0.32	GT:AD:DP:GL:GQ	0/1:89,18:28:-23.83,-15.18,-91.71:86.54
+chr1	2677675	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=15.33;MQ=33.22;MQ0=25;OQ=57.19;QD=0.55;SB=35.14	GT:AD:DP:GL:GQ	0/1:87,15:66:-28.89,-19.89,-231.82:90.03
+chr1	2677743	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=0;HaplotypeScore=4.26;MQ=19.03;MQ0=67;OQ=90.19;QD=0.78;SB=-10.00	GT:AD:DP:GL:GQ	0/1:98,17:39:-24.05,-11.75,-110.96:99
+chr1	2677829	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=23.79;MQ=23.13;MQ0=70;OQ=279.18;QD=2.18;SB=-0.99	GT:AD:DP:GL:GQ	0/1:107,21:47:-45.38,-14.18,-109.88:99
+chr1	2677890	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=41.46;MQ=39.72;MQ0=24;OQ=334.00;QD=2.24;SB=-111.40	GT:AD:DP:GL:GQ	0/1:125,24:98:-66.21,-29.53,-281.36:99
+chr1	2677918	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=22.75;MQ=42.78;MQ0=7;OQ=406.29;QD=3.01;SB=-222.57	GT:AD:DP:GL:GQ	0/1:111,24:99:-73.74,-29.83,-281.76:99
+chr1	2678023	rs4601526	G	T	43.97	LowQual	AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=8.77;MQ=39.66;MQ0=3;QD=0.46;SB=-45.56	GT:AD:DP:GL:GQ	0/1:69,27:71:-29.07,-21.39,-211.74:76.81
+chr1	2678153	rs4287119	C	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=21.76;MQ=40.92;MQ0=5;OQ=2547.58;QD=22.75;SB=-1076.65	GT:AD:DP:GL:GQ	0/1:21,91:87:-284.26,-26.22,-47.57:99
+chr1	2679458	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=42.73;MQ=34.12;MQ0=11;OQ=188.41;QD=2.36;SB=-47.79	GT:AD:DP:GL:GQ	0/1:51,29:31:-31.49,-9.36,-91.42:99
+chr1	2679642	.	C	G	45.83	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=7.58;MQ=33.48;MQ0=11;QD=0.45;SB=71.27	GT:AD:DP:GL:GQ	0/1:93,9:79:-31.68,-23.81,-299.21:78.67
+chr1	2679803	rs56221638	T	A	49.73	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=28.41;MQ=20.22;MQ0=17;QD=0.80;SB=-24.63	GT:AD:DP:GL:GQ	0/1:36,25:21:-14.59,-6.33,-59.48:82.57
+chr1	2679816	rs4648571	G	A	0.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=13.76;MQ=19.63;MQ0=17;OQ=484.56;QD=8.35;SB=18.94	GT:AD:DP:GL:GQ	1/1:9,49:16:-54.94,-4.82,-2.91:19.19
+chr1	2680538	rs58288263	C	A	0.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=19.45;MQ0=42;OQ=235.18;QD=2.28;SB=-135.60	GT:AD:DP:GL:GQ	0/1:70,33:45:-40.37,-13.56,-115.16:99
+chr1	2681143	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=43.31;MQ=7.59;MQ0=129;OQ=216.62;QD=1.54;SB=-10.00	GT:AD:DP:GL:GQ	0/1:128,12:8:-27.36,-2.41,-6.90:44.81
+chr1	2681205	.	C	T	16.27	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=11.46;MQ=9.18;MQ0=122;QD=0.12;SB=-10.00	GT:AD:DP:GL:GQ	0/1:130,4:11:-8.21,-3.31,-32.22:49.01
+chr1	2681386	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=85;Dels=0.02;HRun=1;HaplotypeScore=17.33;MQ=40.82;MQ0=2;OQ=547.52;QD=6.44;SB=26.11	GT:AD:DP:GL:GQ	0/1:58,25:71:-78.82,-20.79,-186.55:99
+chr1	2681420	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=13.55;MQ=31.27;MQ0=32;OQ=249.95;QD=2.34;SB=17.08	GT:AD:DP:GL:GQ	0/1:90,15:70:-49.36,-21.09,-234.22:99
+chr1	2681440	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=2;HaplotypeScore=12.17;MQ=28.00;MQ0=51;OQ=57.67;QD=0.49;SB=-0.98	GT:AD:DP:GL:GQ	0/1:103,11:57:-26.23,-17.18,-176.09:90.51
+chr1	2681463	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=17.45;MQ=24.10;MQ0=61;OQ=86.42;QD=0.77;SB=-10.00	GT:AD:DP:GL:GQ	0/1:104,8:47:-26.08,-14.16,-135.23:99
+chr1	2681473	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=11.36;MQ=22.15;MQ0=63;OQ=86.11;QD=0.79;SB=-10.00	GT:AD:DP:GL:GQ	0/1:101,7:42:-24.54,-12.65,-127.26:99
+chr1	2681679	rs61766519	A	T	2.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=3.86;MQ=46.07;MQ0=2;OQ=403.94;QD=3.71;SB=-208.28	GT:AD:DP:GL:GQ	0/1:86,23:102:-74.40,-30.73,-305.98:99
+chr1	2681697	.	C	G	10.09	PASS	AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=45.11;MQ0=2;OQ=843.38;QD=7.21;SB=-230.77	GT:AD:DP:GL:GQ	0/1:84,33:113:-121.68,-34.06,-367.48:99
+chr1	2681715	rs4430271	G	A	32.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=112;Dels=0.00;HRun=1;HaplotypeScore=3.54;MQ=44.60;MQ0=4;OQ=4104.48;QD=36.65;SB=-1313.32	GT:AD:DP:GL:GQ	1/1:1,111:104:-409.45,-31.34,-0.04:99
+chr1	2681869	.	T	C	23.42	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=42.88;MQ0=2;QD=0.35;SB=71.26	GT:AD:DP:GL:GQ	0/1:51,15:54:-21.90,-16.27,-186.51:56.24
+chr1	2681986	rs11586212	G	A	7.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.27;MQ=47.82;MQ0=3;OQ=510.08;QD=6.80;SB=56.19	GT:AD:DP:GL:GQ	0/1:53,22:70:-75.38,-21.09,-180.91:99
+chr1	2682337	.	G	A	7.34	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=27.22;MQ0=23;OQ=345.10;QD=8.03;SB=-10.00	GT:AD:DP:GL:GQ	0/1:20,23:16:-42.61,-4.82,-16.65:99
+chr1	2682347	.	G	T	0.70	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=19.93;MQ0=26;OQ=183.77;QD=4.59;SB=-10.00	GT:AD:DP:GL:GQ	0/1:20,20:10:-24.67,-3.01,-11.27:82.62
+chr1	2682645	.	C	A	19.07	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=2.93;MQ=11.47;MQ0=37;QD=0.33;SB=-0.98	GT:AD:DP:GL:GQ	0/1:31,27:8:-7.60,-2.41,-19.17:51.85
+chr1	2683816	rs10909957	C	T	271.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.42;MQ=46.26;MQ0=0;OQ=686.46;QD=13.46;SB=-268.23	GT:AD:DP:GL:GQ	0/1:24,27:45:-85.49,-13.56,-81.02:99
+chr1	2684356	rs6424062	G	A	144.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.15;MQ0=0;OQ=655.97;QD=13.39;SB=-112.11	GT:AD:DP:GL:GQ	0/1:26,23:46:-82.76,-13.88,-73.01:99
+chr1	2687573	rs4648459	G	T	323.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=991.84;QD=18.37;SB=-411.82	GT:AD:DP:GL:GQ	0/1:20,34:49:-117.23,-14.76,-57.58:99
+chr1	2689509	rs4648499	A	C	571.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=812.32;QD=13.32;SB=-346.80	GT:AD:DP:GL:GQ	0/1:31,30:60:-102.59,-18.07,-113.17:99
+chr1	2689977	rs4648502	C	G	37.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=4.68;MQ=58.83;MQ0=0;OQ=362.80;QD=11.34;SB=-98.64	GT:AD:DP:GL:GQ	0/1:15,17:26:-47.41,-7.85,-58.24:99
+chr1	2691287	rs10909982	A	C	5.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=1.88;MQ=58.74;MQ0=0;OQ=1314.76;QD=31.30;SB=-536.04	GT:AD:DP:GL:GQ	1/1:0,42:39:-135.08,-11.75,-0.02:99
+chr1	2691405	.	T	C	26.51	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.83;MQ=54.55;MQ0=0;QD=0.72;SB=1.18	GT:AD:DP:GL:GQ	0/1:31,6:36:-16.78,-10.85,-121.87:59.34
+chr1	2691676	rs1456462	C	G	51.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=3.07;MQ=56.36;MQ0=0;OQ=806.36;QD=17.53;SB=-304.60	GT:AD:DP:GL:GQ	0/1:21,25:41:-96.28,-12.36,-77.64:99
+chr1	2694331	rs12748553	C	T	3.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=8.78;MQ=58.48;MQ0=0;OQ=835.97;QD=17.06;SB=-250.13	GT:AD:DP:GL:GQ	0/1:21,26:46:-100.74,-13.86,-71.99:99
+chr1	2694778	rs55972083	G	T	162.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.66;MQ0=0;OQ=915.47;QD=16.64;SB=-316.68	GT:AD:DP:GL:GQ	0/1:25,30:54:-111.10,-16.27,-82.95:99
+chr1	2697298	rs7526311	A	T	117.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.01;MQ0=0;OQ=185.29;QD=9.75;SB=-41.37	GT:AD:DP:GL:GQ	0/1:12,7:18:-27.23,-5.42,-39.59:99
+chr1	2697760	.	G	T	0.81	PASS	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=2;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=344.69;QD=12.77;SB=-29.36	GT:AD:DP:GL:GQ	0/1:13,14:25:-45.29,-7.54,-35.79:99
+chr1	2697817	rs57572926	T	A	7.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.48;MQ0=0;OQ=773.03;QD=21.47;SB=-134.51	GT:AD:DP:GL:GQ	0/1:11,25:35:-91.13,-10.54,-41.10:99
+chr1	2699252	rs12044475	G	A	223.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=59.73;MQ0=0;OQ=1184.05;QD=17.41;SB=-586.14	GT:AD:DP:GL:GQ	0/1:32,36:66:-141.59,-19.90,-99.06:99
+chr1	2699436	rs12024170	C	T	193.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.75;MQ0=0;OQ=1445.81;QD=19.54;SB=-655.75	GT:AD:DP:GL:GQ	0/1:31,43:72:-169.56,-21.69,-100.95:99
+chr1	2699862	rs6687680	G	A	230.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.28;MQ0=0;OQ=1732.28;QD=19.25;SB=-761.79	GT:AD:DP:GL:GQ	0/1:40,50:89:-203.33,-26.82,-125.78:99
+chr1	2700237	.	G	A	246.23	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1343.35;QD=18.92;SB=-523.75	GT:AD:DP:GL:GQ	0/1:31,40:71:-159.02,-21.40,-102.65:99
+chr1	2702030	rs12731995	A	G	434.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=677.81;QD=11.11;SB=-347.04	GT:AD:DP:GL:GQ	0/1:33,28:60:-89.15,-18.08,-132.37:99
+chr1	2703187	rs2377041	C	T	502.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=621.61;QD=15.54;SB=-277.29	GT:AD:DP:GL:GQ	0/1:21,19:39:-77.20,-11.76,-63.03:99
+chr1	2704632	.	T	C	38.02	LowQual	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=4;HaplotypeScore=7.59;MQ=52.48;MQ0=0;QD=2.38;SB=-19.89	GT:AD:DP:GL:GQ	0/1:10,6:12:-10.71,-3.62,-29.51:70.86
+chr1	2704685	.	G	A	22.35	LowQual	AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=7.62;MQ=56.04;MQ0=0;QD=1.86;SB=-34.51	GT:AD:DP:GL:GQ	0/1:9,2:7:-7.63,-2.11,-16.67:55.16
+chr1	2704950	.	A	G	2.25	PASS	AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=48.87;MQ0=0;OQ=588.34;QD=32.69;SB=-143.72	GT:AD:DP:GL:GQ	1/1:0,18:17:-62.42,-5.12,-0.01:51.15
+chr1	2705371	.	T	C	47.74	LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=3.65;MQ=60.80;MQ0=0;QD=2.51;SB=-6.99	GT:AD:DP:GL:GQ	0/1:12,6:14:-12.28,-4.22,-38.37:80.58
+chr1	2705380	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=2;HaplotypeScore=2.68;MQ=59.93;MQ0=0;OQ=62.82;QD=3.31;SB=-3.98	GT:AD:DP:GL:GQ	0/1:14,5:17:-14.69,-5.13,-40.99:95.66
+chr1	2706146	.	A	G	47.67	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=5;HaplotypeScore=3.46;MQ=57.94;MQ0=0;QD=1.40;SB=47.18	GT:AD:DP:GL:GQ	0/1:26,7:27:-16.19,-8.14,-86.26:80.50
+chr1	2706767	rs751358	G	C	35.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=240.08;QD=16.01;SB=-112.68	GT:AD:DP:GL:GQ	0/1:7,8:15:-31.82,-4.53,-27.47:99
+chr1	2708350	rs897627	T	C	68.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.23;MQ0=0;OQ=241.23;QD=8.04;SB=-88.78	GT:AD:DP:GL:GQ	0/1:18,12:26:-35.25,-7.84,-56.33:99
+chr1	2709162	rs897626	T	C	124.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.89;MQ=58.50;MQ0=0;OQ=297.67;QD=9.60;SB=-169.49	GT:AD:DP:GL:GQ	0/1:13,16:23:-39.99,-6.94,-39.26:99
+chr1	2709764	rs12725202	C	A	209.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=59.58;MQ0=0;OQ=806.35;QD=14.66;SB=-275.34	GT:AD:DP:GL:GQ	0/1:27,28:48:-98.38,-14.47,-61.56:99
+chr1	2711436	rs897623	A	G	190.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=58.98;MQ0=0;OQ=627.29;QD=15.30;SB=-199.45	GT:AD:DP:GL:GQ	0/1:15,26:39:-77.77,-11.76,-60.17:99
+chr1	2712708	rs6692145	C	T	11.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=7.75;MQ=59.11;MQ0=0;OQ=873.72;QD=16.80;SB=-440.44	GT:AD:DP:GL:GQ	0/1:21,31:48:-105.13,-14.48,-65.51:99
+chr1	2713074	rs4648450	C	A	220.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.19;MQ0=0;OQ=931.32;QD=16.34;SB=-352.41	GT:AD:DP:GL:GQ	0/1:24,33:49:-111.18,-14.76,-58.95:99
+chr1	2713205	rs4648360	C	T	362.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.64;MQ0=0;OQ=808.14;QD=12.63;SB=-348.52	GT:AD:DP:GL:GQ	0/1:38,26:64:-103.39,-19.29,-126.27:99
+chr1	2713822	rs11588256	T	C	179.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.44;MQ0=0;OQ=1164.73;QD=28.41;SB=-522.80	GT:AD:DP:GL:GQ	1/1:0,40:39:-122.64,-14.15,-2.58:99
+chr1	2715335	rs7537581	C	A	258.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=59.30;MQ0=0;OQ=476.92;QD=14.45;SB=-256.43	GT:AD:DP:GL:GQ	0/1:16,17:32:-60.62,-9.64,-51.47:99
+chr1	2715367	rs56038961	C	T	199.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.45;MQ0=0;OQ=479.64;QD=15.99;SB=-264.20	GT:AD:DP:GL:GQ	0/1:12,18:27:-59.39,-8.14,-35.88:99
+chr1	2716724	rs17387572	C	G	92.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=2.10;MQ=58.95;MQ0=0;OQ=183.11;QD=8.32;SB=-57.73	GT:AD:DP:GL:GQ	0/1:14,8:19:-27.33,-5.74,-48.15:99
+chr1	2717498	rs10909879	G	A	568.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=638.90;QD=14.20;SB=-321.91	GT:AD:DP:GL:GQ	0/1:24,21:43:-80.13,-12.96,-77.89:99
+chr1	2717664	rs10909880	C	T	111.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=3.85;MQ=58.20;MQ0=0;OQ=901.98;QD=16.40;SB=-412.72	GT:AD:DP:GL:GQ	0/1:27,27:53:-109.45,-15.96,-95.84:99
+chr1	2718581	rs2290583	C	T	466.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.90;MQ0=0;OQ=858.25;QD=15.60;SB=-364.54	GT:AD:DP:GL:GQ	0/1:27,28:51:-104.48,-15.37,-82.61:99
+chr1	2720957	rs56242447	T	C	191.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=60.00;MQ0=0;OQ=720.09;QD=11.43;SB=-266.23	GT:AD:DP:GL:GQ	0/1:29,34:60:-93.39,-18.10,-112.64:99
+chr1	2725957	rs4648454	C	A	155.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=59.23;MQ0=0;OQ=2137.84;QD=35.63;SB=-968.57	GT:AD:DP:GL:GQ	1/1:0,60:60:-217.39,-18.07,-0.02:99
+chr1	2727346	rs4515734	C	T	401.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=1193.72;QD=37.30;SB=-333.34	GT:AD:DP:GL:GQ	1/1:0,32:32:-122.97,-9.64,-0.01:96.30
+chr1	2728125	rs11584658	C	T	220.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=58.92;MQ0=0;OQ=363.72;QD=9.33;SB=-203.89	GT:AD:DP:GL:GQ	0/1:25,14:38:-51.11,-11.46,-81.85:99
+chr1	2728509	.	C	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=2;HaplotypeScore=7.07;MQ=57.48;MQ0=0;OQ=153.44;QD=5.48;SB=38.15	GT:AD:DP:GL:GQ	0/1:17,11:22:-25.28,-6.65,-60.78:99
+chr1	2728983	rs12025517	T	C	254.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.46;MQ0=0;OQ=692.09;QD=16.10;SB=-320.61	GT:AD:DP:GL:GQ	0/1:17,25:42:-87.78,-15.29,-69.40:99
+chr1	2731560	rs897622	T	C	5.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=1.40;MQ=59.38;MQ0=0;OQ=1158.40;QD=31.31;SB=-281.53	GT:AD:DP:GL:GQ	1/1:0,37:35:-119.44,-10.55,-0.02:99
+chr1	2734276	rs56400103	G	A	253.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=949.71;QD=17.92;SB=-409.46	GT:AD:DP:GL:GQ	0/1:24,29:51:-113.64,-15.38,-67.18:99
+chr1	2734570	rs12747919	T	C	241.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=59.34;MQ0=0;OQ=778.48;QD=12.36;SB=-342.05	GT:AD:DP:GL:GQ	0/1:32,31:63:-100.12,-18.99,-128.39:99
+chr1	2734737	rs12125787	G	A	71.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.70;MQ=57.83;MQ0=0;OQ=2028.15;QD=37.56;SB=-957.98	GT:AD:DP:GL:GQ	1/1:0,54:53:-206.42,-15.97,-0.02:99
+chr1	2735743	rs4609377	C	T	266.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=58.76;MQ0=0;OQ=803.58;QD=14.35;SB=-286.83	GT:AD:DP:GL:GQ	0/1:31,25:54:-99.92,-16.28,-93.51:99
+chr1	2735926	rs1001620	G	C	451.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=58.61;MQ0=0;OQ=977.15;QD=12.69;SB=-354.56	GT:AD:DP:GL:GQ	0/1:46,31:77:-124.21,-23.21,-202.34:99
+chr1	2739474	rs10797389	G	A	308.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=60.00;MQ0=0;OQ=750.99;QD=15.65;SB=-309.79	GT:AD:DP:GL:GQ	0/1:23,25:47:-92.55,-14.16,-81.12:99
+chr1	2739576	rs4648481	G	T	368.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=60.00;MQ0=0;OQ=793.99;QD=14.70;SB=-305.02	GT:AD:DP:GL:GQ	0/1:26,28:52:-98.35,-15.67,-82.42:99
+chr1	2739781	rs4648482	T	C	14.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=4.29;MQ=58.44;MQ0=0;OQ=365.14;QD=8.69;SB=-69.92	GT:AD:DP:GL:GQ	0/1:24,18:40:-51.86,-12.06,-91.45:99
+chr1	2740297	rs1563471	C	T	85.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=5.94;MQ=59.22;MQ0=0;OQ=682.02;QD=11.56;SB=-286.79	GT:AD:DP:GL:GQ	0/1:33,26:55:-88.08,-16.60,-99.20:99
+chr1	2740756	rs12132067	G	A	288.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=59.52;MQ0=0;OQ=623.21;QD=12.98;SB=-250.12	GT:AD:DP:GL:GQ	0/1:27,21:48:-80.07,-14.46,-95.69:99
+chr1	2742125	rs7511879	A	G	408.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.68;MQ0=0;OQ=942.16;QD=16.24;SB=-438.99	GT:AD:DP:GL:GQ	0/1:24,34:55:-114.07,-16.57,-91.14:99
+chr1	2742553	rs10797390	C	T	146.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.59;MQ0=0;OQ=1057.36;QD=18.88;SB=-301.83	GT:AD:DP:GL:GQ	0/1:24,32:56:-125.89,-16.87,-83.67:99
+chr1	2743097	rs12031493	A	G	99.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=5.23;MQ=59.34;MQ0=0;OQ=647.93;QD=9.26;SB=-314.90	GT:AD:DP:GL:GQ	0/1:40,29:67:-88.27,-20.19,-156.45:99
+chr1	2743232	rs11803074	T	C	136.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.52;MQ0=0;OQ=450.58;QD=9.39;SB=-159.47	GT:AD:DP:GL:GQ	0/1:26,22:43:-61.31,-12.96,-94.61:99
+chr1	2743923	rs2377040	G	A	85.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.57;MQ0=0;OQ=1679.85;QD=39.07;SB=-699.34	GT:AD:DP:GL:GQ	1/1:0,43:43:-171.58,-12.96,-0.02:99
+chr1	2744048	rs6691019	A	G	253.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=599.61;QD=12.24;SB=-315.28	GT:AD:DP:GL:GQ	0/1:24,25:46:-77.11,-13.87,-86.95:99
+chr1	2744266	rs729045	A	G	494.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=550.14;QD=10.19;SB=-251.93	GT:AD:DP:GL:GQ	0/1:30,24:53:-74.27,-15.97,-120.98:99
+chr1	2744372	rs6680471	C	T	188.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=58.81;MQ0=0;OQ=743.73;QD=13.52;SB=-388.16	GT:AD:DP:GL:GQ	0/1:30,25:50:-92.73,-15.07,-87.39:99
+chr1	2744840	rs7541827	T	G	3.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=3.30;MQ=53.60;MQ0=0;OQ=317.87;QD=7.95;SB=-163.88	GT:AD:DP:GL:GQ	0/1:27,13:38:-46.52,-11.45,-85.79:99
+chr1	2745157	rs10909938	C	G	278.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.10;MQ0=0;OQ=946.24;QD=11.98;SB=-426.32	GT:AD:DP:GL:GQ	0/1:47,32:78:-121.44,-23.53,-202.08:99
+chr1	2745633	rs10909941	A	G	382.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.59;MQ0=0;OQ=1890.77;QD=33.76;SB=-793.15	GT:AD:DP:GL:GQ	1/1:0,56:54:-192.68,-16.26,-0.02:99
+chr1	2746148	rs4648382	C	T	75.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=4.95;MQ=58.25;MQ0=0;OQ=1103.18;QD=17.24;SB=-437.97	GT:AD:DP:GL:GQ	0/1:30,34:62:-132.29,-18.69,-91.91:99
+chr1	2746257	rs4648383	C	T	112.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=59.45;MQ0=0;OQ=1198.75;QD=17.63;SB=-573.37	GT:AD:DP:GL:GQ	0/1:33,35:67:-143.34,-20.18,-115.97:99
+chr1	2746481	rs4648384	C	A	147.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=2.23;MQ=58.55;MQ0=0;OQ=974.97;QD=15.98;SB=-482.87	GT:AD:DP:GL:GQ	0/1:29,32:59:-118.55,-17.77,-93.40:99
+chr1	2746667	rs7516014	G	T	183	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=60.00;MQ0=0;OQ=529.64;QD=10.81;SB=-238.43	GT:AD:DP:GL:GQ	0/1:28,20:47:-70.41,-14.16,-95.06:99
+chr1	2746749	rs7548023	T	G	93.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=3.08;MQ=57.92;MQ0=0;OQ=762.24;QD=14.12;SB=-346.84	GT:AD:DP:GL:GQ	0/1:27,27:54:-95.77,-16.26,-99.72:99
+chr1	2747056	rs4648495	T	C	0.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=4;HaplotypeScore=4.04;MQ=53.57;MQ0=0;OQ=334.06;QD=9.83;SB=-158.61	GT:AD:DP:GL:GQ	0/1:15,19:25:-44.23,-7.54,-43.47:99
+chr1	2747271	rs4648496	A	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=20.04;MQ=49.89;MQ0=0;OQ=70.38;QD=0.95;SB=-47.55	GT:AD:DP:GL:GQ	0/1:64,10:68:-30.81,-20.49,-219.78:99
+chr1	2747291	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=65;Dels=0.03;HRun=0;HaplotypeScore=32.13;MQ=46.89;MQ0=0;OQ=444.72;QD=6.84;SB=-168.12	GT:AD:DP:GL:GQ	0/1:44,19:62:-65.84,-18.08,-149.47:99
+chr1	2747315	.	A	T	0.07	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=12.70;MQ=47.25;MQ0=0;OQ=757.92;QD=13.53;SB=-390.15	GT:AD:DP:GL:GQ	0/1:29,27:49:-93.84,-14.77,-85.21:99
+chr1	2747334	rs36040910	C	G	1014.60	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.02;HRun=0;HaplotypeScore=10.13;MQ=46.42;MQ0=0;QD=19.14;SB=-531.73	GT:AD:DP:GL:GQ	0/1:24,28:52:-120.42,-15.67,-100.79:99
+chr1	2747338	.	G	C	826.30	SnpCluster	AC=1;AF=0.50;AN=2;DP=48;Dels=0.02;HRun=0;HaplotypeScore=9.97;MQ=47.26;MQ0=0;QD=17.21;SB=-358.43	GT:AD:DP:GL:GQ	0/1:23,24:47:-99.78,-13.86,-101.33:99
+chr1	2747339	.	A	T	752.39	SnpCluster	AC=1;AF=0.50;AN=2;DP=48;Dels=0.02;HRun=0;HaplotypeScore=3.00;MQ=47.26;MQ0=0;QD=15.67;SB=-313.68	GT:AD:DP:GL:GQ	0/1:23,24:47:-92.38,-13.86,-82.64:99
+chr1	2747369	.	A	T	3.22	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=5.95;MQ=49.16;MQ0=0;OQ=703.99;QD=14.37;SB=-261.27	GT:AD:DP:GL:GQ	0/1:25,24:47:-87.84,-14.16,-92.00:99
+chr1	2747375	rs61766530	T	A	10.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=7.95;MQ=48.99;MQ0=0;OQ=615.25;QD=13.37;SB=-274.62	GT:AD:DP:GL:GQ	0/1:24,22:43:-77.76,-12.95,-81.15:99
+chr1	2747387	rs34464542	A	T	0.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.05;HRun=0;HaplotypeScore=17.99;MQ=50.33;MQ0=0;OQ=475.32;QD=10.80;SB=-181.51	GT:AD:DP:GL:GQ	0/1:25,17:43:-63.16,-12.35,-94.24:99
+chr1	2747397	rs12739189	C	T	56.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=5.47;MQ=51.77;MQ0=0;OQ=606.36;QD=14.44;SB=-321.86	GT:AD:DP:GL:GQ	0/1:23,19:42:-76.58,-12.66,-74.78:99
+chr1	2747562	rs35401657	A	G	338.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=54.94;MQ0=0;OQ=916.49;QD=12.73;SB=-443.41	GT:AD:DP:GL:GQ	0/1:37,34:70:-119.52,-24.59,-154.08:99
+chr1	2747592	rs34262355	G	A	349.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=54.28;MQ0=0;OQ=1032.22;QD=12.74;SB=-451.44	GT:AD:DP:GL:GQ	0/1:45,35:78:-130.02,-23.51,-145.95:99
+chr1	2747610	rs34202711	A	G	414.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.97;MQ0=0;OQ=1011.04;QD=11.89;SB=-504.68	GT:AD:DP:GL:GQ	0/1:42,43:82:-129.10,-24.71,-172.46:99
+chr1	2747660	rs1456461	C	T	603.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.82;MQ0=0;OQ=891.16;QD=15.63;SB=-457.95	GT:AD:DP:GL:GQ	0/1:30,27:57:-109.57,-17.17,-111.30:99
+chr1	2748044	rs12740180	C	A	413.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=606.44;QD=10.83;SB=-262.28	GT:AD:DP:GL:GQ	0/1:33,23:54:-80.19,-16.26,-114.41:99
+chr1	2748753	rs2889541	G	A	337.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.41;MQ0=0;OQ=1139.69;QD=16.05;SB=-477.50	GT:AD:DP:GL:GQ	0/1:37,34:70:-138.35,-21.10,-115.20:99
+chr1	2749666	rs12037615	A	T	1.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=5;HaplotypeScore=1.16;MQ=59.20;MQ0=0;OQ=1128.99;QD=14.86;SB=-549.41	GT:AD:DP:GL:GQ	0/1:40,36:76:-139.07,-22.89,-148.90:99
+chr1	2749715	rs12047690	C	T	131.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=816.13;QD=12.95;SB=-150.20	GT:AD:DP:GL:GQ	0/1:36,27:60:-102.99,-18.09,-107.52:99
+chr1	2751235	rs12049543	C	A	405.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.56;MQ0=0;OQ=1060.86;QD=12.63;SB=-512.22	GT:AD:DP:GL:GQ	0/1:47,37:84:-134.67,-25.30,-168.73:99
+chr1	2751390	rs1840738	T	C	158.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=56.95;MQ0=0;OQ=466.03;QD=9.14;SB=-238.28	GT:AD:DP:GL:GQ	0/1:29,21:47:-64.06,-14.17,-105.57:99
+chr1	2751392	rs1840737	T	C	150.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=56.89;MQ0=0;OQ=432.09;QD=8.64;SB=-211.35	GT:AD:DP:GL:GQ	0/1:30,20:46:-60.36,-13.87,-105.49:99
+chr1	2751468	rs1840736	C	T	225.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=58.99;MQ0=0;OQ=538.81;QD=11.71;SB=-284.82	GT:AD:DP:GL:GQ	0/1:28,18:46:-71.04,-13.87,-86.92:99
+chr1	2751723	rs1456460	G	T	356.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=57.19;MQ0=0;OQ=1157.64;QD=13.31;SB=-342.38	GT:AD:DP:GL:GQ	0/1:48,39:87:-145.25,-26.21,-162.75:99
+chr1	2753129	rs6424080	T	C	316.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.51;MQ0=0;OQ=966.99;QD=12.24;SB=-274.18	GT:AD:DP:GL:GQ	0/1:43,36:77:-123.19,-23.21,-165.41:99
+chr1	2753241	rs6424081	G	C	7.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=4;HaplotypeScore=2.76;MQ=58.85;MQ0=0;OQ=855.86;QD=17.47;SB=-443.74	GT:AD:DP:GL:GQ	0/1:25,24:49:-103.64,-14.77,-108.86:99
+chr1	2753928	rs10909950	G	C	275.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.98;MQ0=0;OQ=738.28;QD=13.67;SB=-369.83	GT:AD:DP:GL:GQ	0/1:27,27:50:-92.19,-15.07,-120.46:99
+chr1	2754032	rs7553697	T	C	122.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=50.90;MQ0=0;OQ=845.37;QD=27.27;SB=-371.38	GT:AD:DP:GL:GQ	1/1:0,31:28:-88.15,-8.45,-0.03:84.18
+chr1	2754183	rs6424082	A	G	8.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=5.05;MQ=58.51;MQ0=0;OQ=416.20;QD=9.46;SB=-192.43	GT:AD:DP:GL:GQ	0/1:23,21:40:-56.97,-12.06,-83.18:99
+chr1	2754298	rs6424083	C	G	173.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=55.35;MQ0=0;OQ=1296.80;QD=37.05;SB=-603.86	GT:AD:DP:GL:GQ	1/1:0,35:33:-133.29,-9.95,-0.02:99
+chr1	2754773	.	G	A	0.64	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=3.22;MQ=60.00;MQ0=0;OQ=1109.61;QD=18.81;SB=-280.74	GT:AD:DP:GL:GQ	0/1:25,34:58:-131.72,-17.47,-86.47:99
+chr1	2754949	rs34133714	C	T	67.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=57.50;MQ0=0;OQ=577.42;QD=16.98;SB=-168.27	GT:AD:DP:GL:GQ	0/1:16,18:34:-71.28,-10.25,-51.84:99
+chr1	2755031	rs34352177	T	C	19.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=7.41;MQ=59.06;MQ0=0;OQ=899.29;QD=13.03;SB=-455.95	GT:AD:DP:GL:GQ	0/1:36,31:67:-116.13,-22.92,-145.73:99
+chr1	2755403	rs11806141	T	G	18.81	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=6.77;MQ=51.89;MQ0=9;QD=0.27;SB=74.23	GT:AD:DP:GL:GQ	0/1:49,20:51:-20.52,-15.36,-159.70:51.59
+chr1	2755508	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=79;Dels=0.06;HRun=2;HaplotypeScore=38.09;MQ=49.34;MQ0=4;OQ=65.07;QD=0.82;SB=71.26	GT:AD:DP:GL:GQ	0/1:58,15:62:-27.57,-17.78,-196.95:97.90
+chr1	2755529	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=65.45;MQ=46.51;MQ0=7;OQ=513.73;QD=7.04;SB=-185.79	GT:AD:DP:GL:GQ	0/1:43,30:51:-70.02,-15.37,-107.03:99
+chr1	2755532	.	A	G	42.46	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=67.89;MQ=46.23;MQ0=7;QD=0.57;SB=41.14	GT:AD:DP:GL:GQ	0/1:61,13:50:-22.60,-15.07,-170.16:75.29
+chr1	2755579	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=21.20;MQ=45.33;MQ0=9;OQ=157.48;QD=2.02;SB=-23.25	GT:AD:DP:GL:GQ	0/1:60,12:47:-33.22,-14.19,-119.56:99
+chr1	2755596	rs11806928	A	G	0.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=12.62;MQ=45.10;MQ0=9;OQ=205.66;QD=2.78;SB=-15.21	GT:AD:DP:GL:GQ	0/1:58,16:54:-40.13,-16.28,-162.81:99
+chr1	2755612	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=11.17;MQ=46.38;MQ0=5;OQ=126.58;QD=1.73;SB=14.62	GT:AD:DP:GL:GQ	0/1:63,10:57:-33.13,-17.19,-158.30:99
+chr1	2755632	rs10909952	C	T	0.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=10.73;MQ=46.85;MQ0=3;OQ=64.17;QD=0.87;SB=26.06	GT:AD:DP:GL:GQ	0/1:61,13:47:-23.87,-14.17,-131.74:97
+chr1	2755643	.	C	T	0.06	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=7.11;MQ=46.66;MQ0=2;OQ=370.42;QD=5.22;SB=-83.91	GT:AD:DP:GL:GQ	0/1:46,20:49:-55.11,-14.78,-108.17:99
+chr1	2755657	rs61763677	G	T	0.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=8.88;MQ=44.97;MQ0=5;OQ=282.63;QD=3.29;SB=-9.61	GT:AD:DP:GL:GQ	0/1:69,17:72:-53.24,-21.69,-193.61:99
+chr1	2755674	rs61763678	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=23.01;MQ=44.47;MQ0=7;OQ=292.56;QD=2.76;SB=-24.23	GT:AD:DP:GL:GQ	0/1:76,27:79:-56.37,-23.83,-203.58:99
+chr1	2755706	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=0;HaplotypeScore=46.46;MQ=43.46;MQ0=6;OQ=100.65;QD=1.01;SB=48.33	GT:AD:DP:GL:GQ	0/1:73,19:68:-33.86,-20.51,-216.35:99
+chr1	2755733	rs10909953	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=134.56;MQ=44.60;MQ0=11;OQ=218.03;QD=1.83;SB=-68.77	GT:AD:DP:GL:GQ	0/1:91,18:82:-72.98,-47.89,-237.50:99
+chr1	2755738	rs10909954	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=94.54;MQ=44.07;MQ0=12;OQ=119.63;QD=1.01;SB=15.66	GT:AD:DP:GL:GQ	0/1:86,29:80:-42.04,-26.79,-256.64:99
+chr1	2755753	.	G	A	11.77	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=1;HaplotypeScore=33.32;MQ=44.33;MQ0=10;QD=0.09;SB=66.29	GT:AD:DP:GL:GQ	0/1:116,10:95:-33.05,-28.62,-308.21:44.31
+chr1	2755755	rs57067996	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=130;Dels=0.00;HRun=1;HaplotypeScore=39.46;MQ=44.65;MQ0=10;OQ=1208.64;QD=9.30;SB=-349.24	GT:AD:DP:GL:GQ	0/1:72,52:91:-151.57,-27.42,-186.87:99
+chr1	2755787	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=209;Dels=0.00;HRun=0;HaplotypeScore=9.86;MQ=44.22;MQ0=18;OQ=212.29;QD=1.02;SB=84.79	GT:AD:DP:GL:GQ	0/1:175,28:147:-68.83,-44.32,-479.03:99
+chr1	2755816	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=1;HaplotypeScore=62.94;MQ=43.89;MQ0=23;OQ=172.99;QD=0.80;SB=63.05	GT:AD:DP:GL:GQ	0/1:192,24:159:-68.50,-47.92,-487.91:99
+chr1	2755844	rs4991850	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=164;Dels=0.00;HRun=0;HaplotypeScore=53.96;MQ=43.72;MQ0=16;OQ=1135.99;QD=6.93;SB=-394.17	GT:AD:DP:GL:GQ	0/1:112,52:121:-153.35,-36.47,-275.01:99
+chr1	2755847	rs57868894	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=161;Dels=0.00;HRun=1;HaplotypeScore=64.38;MQ=43.84;MQ0=16;OQ=859.67;QD=5.34;SB=-128.73	GT:AD:DP:GL:GQ	0/1:103,58:122:-126.01,-36.76,-296.17:99
+chr1	2755864	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=0;HaplotypeScore=32.56;MQ=44.46;MQ0=14;OQ=96.62;QD=0.70;SB=30.17	GT:AD:DP:GL:GQ	0/1:117,20:102:-43.73,-30.78,-282.87:99
+chr1	2755889	rs4991849	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=114;Dels=0.04;HRun=2;HaplotypeScore=40.28;MQ=47.08;MQ0=9;OQ=2321.13;QD=20.36;SB=-1120.12	GT:AD:DP:GL:GQ	0/1:18,92:93:-262.51,-27.11,-65.29:99
+chr1	2755910	rs12728224	T	G	16.56	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=1;HaplotypeScore=2.13;MQ=49.38;MQ0=5;QD=0.17;SB=88.35	GT:AD:DP:GL:GQ	0/1:84,11:79:-28.73,-23.80,-253.95:49.30
+chr1	2755924	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=18.40;MQ=49.90;MQ0=6;OQ=1394.92;QD=15.16;SB=-476.13	GT:AD:DP:GL:GQ	0/1:39,53:66:-162.68,-19.90,-75.57:99
+chr1	2755992	.	G	A	33.66	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=19.55;MQ=45.20;MQ0=8;QD=0.40;SB=27.48	GT:AD:DP:GL:GQ	0/1:73,12:61:-25.05,-18.40,-176.14:66.50
+chr1	2756013	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=17.90;MQ=45.32;MQ0=5;OQ=157.50;QD=2.67;SB=-33.78	GT:AD:DP:GL:GQ	0/1:38,21:37:-30.19,-11.15,-106.30:99
+chr1	2756025	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=4.66;MQ=45.60;MQ0=4;OQ=63.13;QD=1.15;SB=26.12	GT:AD:DP:GL:GQ	0/1:45,10:38:-21.07,-11.48,-129.01:95.97
+chr1	2756051	rs4992290	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=36.34;MQ=44.26;MQ0=6;OQ=205.91;QD=3.38;SB=35.13	GT:AD:DP:GL:GQ	0/1:37,24:36:-34.74,-10.86,-87.18:99
+chr1	2756088	rs6676347	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=50.22;MQ=41.73;MQ0=14;OQ=1315.11;QD=15.29;SB=-568.14	GT:AD:DP:GL:GQ	0/1:37,49:48:-149.26,-14.46,-35.10:99
+chr1	2756101	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=1;HaplotypeScore=21.36;MQ=40.87;MQ0=15;OQ=73.71;QD=0.88;SB=47.17	GT:AD:DP:GL:GQ	0/1:64,20:51:-26.02,-15.36,-158.57:99
+chr1	2756151	rs4648513	T	C	97.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=4.14;MQ=50.77;MQ0=9;OQ=1380.54;QD=20.92;SB=-651.39	GT:AD:DP:GL:GQ	1/1:9,57:48:-150.01,-14.48,-8.38:61.01
+chr1	2756174	rs59048447	G	A	70.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=5.41;MQ=56.28;MQ0=2;OQ=675.24;QD=12.74;SB=-328.31	GT:AD:DP:GL:GQ	0/1:26,27:46:-84.67,-13.86,-86.53:99
+chr1	2756831	rs4648515	C	T	238.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=59.11;MQ0=0;OQ=2661.31;QD=39.14;SB=-1337.11	GT:AD:DP:GL:GQ	1/1:1,67:68:-272.30,-20.49,-2.59:99
+chr1	2757061	rs4648518	A	G	438.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1894.09;QD=32.66;SB=-719.10	GT:AD:DP:GL:GQ	1/1:0,58:55:-193.02,-16.57,-0.02:99
+chr1	2757563	rs4648519	C	T	617.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=2063.43;QD=38.21;SB=-1058.93	GT:AD:DP:GL:GQ	1/1:0,54:53:-209.94,-15.97,-0.02:99
+chr1	2758482	.	C	T	0.54	PASS	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=50.17;MQ0=3;OQ=191.27;QD=4.25;SB=-120.51	GT:AD:DP:GL:GQ	0/1:31,14:38:-33.86,-11.45,-100.08:99
+chr1	2758751	.	T	G	48.69	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=34.31;MQ0=7;QD=1.62;SB=-11.91	GT:AD:DP:GL:GQ	0/1:21,9:22:-14.78,-6.63,-62.96:81.53
+chr1	2758819	.	A	G	182.25	PASS	AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=42.84;MQ0=2;OQ=868.67;QD=27.15;SB=-395.30	GT:AD:DP:GL:GQ	1/1:1,31:28:-90.48,-8.45,-0.03:84.20
+chr1	2758861	.	T	C	30.75	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=1;HaplotypeScore=1.14;MQ=44.85;MQ0=1;QD=0.90;SB=29.12	GT:AD:DP:GL:GQ	0/1:26,7:26:-14.19,-7.84,-86.43:63.58
+chr1	2758882	.	G	A	6.14	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=35.37;MQ0=5;OQ=748.79;QD=17.41;SB=-255.79	GT:AD:DP:GL:GQ	0/1:14,29:29:-86.90,-8.74,-21.14:99
+chr1	2758933	.	T	C	5.05	PASS	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=4.40;MQ=30.24;MQ0=6;OQ=270.13;QD=7.50;SB=-156.34	GT:AD:DP:GL:GQ	0/1:9,26:16:-35.12,-4.83,-17.51:99
+chr1	2758959	.	T	G	27.66	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=27.02;MQ0=8;QD=0.92;SB=-23.52	GT:AD:DP:GL:GQ	0/1:24,6:11:-9.36,-3.32,-25.67:60.48
+chr1	2759011	.	T	G	0.06	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=3.83;MQ=18.26;MQ0=23;OQ=314.04;QD=4.42;SB=-69.87	GT:AD:DP:GL:GQ	0/1:37,34:26:-42.52,-7.83,-50.68:99
+chr1	2759038	.	G	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=15.13;MQ=25.49;MQ0=29;OQ=89.07;QD=0.97;SB=-9.29	GT:AD:DP:GL:GQ	0/1:85,7:35:-22.74,-10.55,-90.79:99
+chr1	2759090	.	G	T	15.10	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=11.61;MQ=28.51;MQ0=10;QD=0.35;SB=-6.99	GT:AD:DP:GL:GQ	0/1:32,11:16:-9.61,-4.83,-35.57:47.80
+chr1	2759130	rs61763686	T	C	37.28	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.78;MQ0=1;QD=12.43;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:2:-7.14,-0.60,-0.00:6.02
+chr1	2759142	.	G	A	1.53	PASS	AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=-0.12;MQ=18.78;MQ0=2;OQ=80.16;QD=13.36;SB=-10.00	GT:AD:DP:GL:GQ	0/1:3,3:4:-12.50,-1.21,-3.10:18.91
+chr1	2759167	.	G	T	2.82	PASS	AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=26.71;MQ0=4;OQ=151.71;QD=6.90;SB=-6.99	GT:AD:DP:GL:GQ	0/1:16,6:14:-22.67,-4.22,-28.76:99
+chr1	2759193	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=15.10;MQ=26.07;MQ0=10;OQ=142.00;QD=2.90;SB=-61.29	GT:AD:DP:GL:GQ	0/1:38,11:32:-27.13,-9.65,-83.88:99
+chr1	2759219	.	G	T	0.58	PASS	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.57;MQ=27.42;MQ0=13;OQ=233.66;QD=3.03;SB=-10.31	GT:AD:DP:GL:GQ	0/1:59,18:48:-41.11,-14.46,-126.09:99
+chr1	2759237	rs10909961	G	A	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=9.56;MQ=30.14;MQ0=15;OQ=68.31;QD=0.77;SB=29.11	GT:AD:DP:GL:GQ	0/1:82,7:55:-26.69,-16.57,-172.16:99
+chr1	2759271	.	G	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=31.60;MQ0=17;OQ=103.26;QD=1.09;SB=14.07	GT:AD:DP:GL:GQ	0/1:79,16:53:-29.57,-15.96,-157.88:99
+chr1	2759402	rs10752737	G	A	706.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.81;MQ0=0;OQ=3330.93;QD=38.29;SB=-1475.63	GT:AD:DP:GL:GQ	1/1:0,87:84:-332.09,-25.31,-0.03:99
+chr1	2759793	rs6665646	C	T	285.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.67;MQ0=0;OQ=1210.11;QD=17.54;SB=-511.14	GT:AD:DP:GL:GQ	0/1:33,36:69:-145.09,-20.79,-106.44:99
+chr1	2760042	rs6679343	A	T	0.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=6;HaplotypeScore=1.76;MQ=59.01;MQ0=0;OQ=2240.29;QD=33.94;SB=-793.89	GT:AD:DP:GL:GQ	1/1:0,66:63:-227.64,-18.99,-0.03:99
+chr1	2761186	.	C	G	0.63	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=4;HaplotypeScore=1.71;MQ=59.37;MQ0=0;OQ=541.38;QD=12.30;SB=-216.32	GT:AD:DP:GL:GQ	0/1:26,18:41:-69.78,-12.36,-101.99:99
+chr1	2761364	rs12743952	G	A	204.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=59.65;MQ0=0;OQ=611.70;QD=11.33;SB=-279.20	GT:AD:DP:GL:GQ	0/1:32,22:50:-79.52,-15.07,-100.94:99
+chr1	2761375	rs12743965	G	A	240.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.65;MQ0=0;OQ=726.42;QD=13.45;SB=-307.80	GT:AD:DP:GL:GQ	0/1:31,23:53:-91.89,-15.96,-108.39:99
+chr1	2761483	rs34161193	G	A	219.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=58.78;MQ0=0;OQ=505.10;QD=13.29;SB=-258.15	GT:AD:DP:GL:GQ	0/1:20,17:37:-64.94,-11.15,-70.90:99
+chr1	2761516	rs35134901	G	C	42.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=0.79;MQ=58.89;MQ0=0;OQ=485.26;QD=11.55;SB=-253.13	GT:AD:DP:GL:GQ	0/1:25,17:38:-63.28,-11.47,-90.46:99
+chr1	2761538	rs35767265	C	A	434.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=663.44;QD=13.54;SB=-277.32	GT:AD:DP:GL:GQ	0/1:26,23:47:-83.79,-14.16,-83.28:99
+chr1	2761907	rs35313744	A	C	3.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=4;HaplotypeScore=1.29;MQ=59.00;MQ0=0;OQ=545.25;QD=12.98;SB=-173.29	GT:AD:DP:GL:GQ	0/1:20,22:40:-69.86,-12.05,-71.88:99
+chr1	2762054	rs6694484	G	A	356.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.79;MQ0=0;OQ=715.90;QD=13.26;SB=-315.29	GT:AD:DP:GL:GQ	0/1:29,25:51:-90.24,-15.37,-99.20:99
+chr1	2762207	rs6675221	C	A	216.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.45;MQ0=0;OQ=527.73;QD=12.57;SB=-249.28	GT:AD:DP:GL:GQ	0/1:21,20:39:-67.80,-11.75,-71.40:99
+chr1	2762658	rs12727394	T	C	169.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=60.00;MQ0=0;OQ=383.94;QD=11.63;SB=-133.29	GT:AD:DP:GL:GQ	0/1:17,15:29:-50.42,-8.74,-57.72:99
+chr1	2763115	rs12729596	C	T	224.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.16;MQ0=0;OQ=609.66;QD=12.19;SB=-271.12	GT:AD:DP:GL:GQ	0/1:30,20:50:-79.31,-15.06,-107.78:99
+chr1	2763349	rs6660680	C	G	206.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.16;MQ=59.65;MQ0=0;OQ=809.85;QD=15.28;SB=-407.93	GT:AD:DP:GL:GQ	0/1:28,25:49:-99.04,-14.78,-104.68:99
+chr1	2763426	rs6660759	C	T	169.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.89;MQ0=0;OQ=778.20;QD=18.53;SB=-350.90	GT:AD:DP:GL:GQ	0/1:15,27:38:-92.57,-11.46,-40.16:99
+chr1	2763555	rs6674204	A	G	358.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1244.75;QD=33.64;SB=-466.51	GT:AD:DP:GL:GQ	1/1:0,37:36:-128.07,-10.85,-0.01:99
+chr1	2763913	rs7529000	A	G	539.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=590.27;QD=13.73;SB=-268.99	GT:AD:DP:GL:GQ	0/1:19,24:38:-73.77,-11.46,-59.16:99
+chr1	2765576	.	A	G	299.17	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.30;MQ0=1;OQ=708.87;QD=14.18;SB=-362.49	GT:AD:DP:GL:GQ	0/1:25,25:46:-88.03,-13.85,-86.85:99
+chr1	2765703	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=40;Dels=0.03;HRun=1;HaplotypeScore=65.65;MQ=34.06;MQ0=6;OQ=224.51;QD=5.61;SB=-69.85	GT:AD:DP:GL:GQ	0/1:16,18:20:-31.76,-6.02,-57.23:99
+chr1	2765716	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=2;HaplotypeScore=45.86;MQ=31.67;MQ0=6;OQ=473.81;QD=11.56;SB=-227.60	GT:AD:DP:GL:GQ	0/1:7,34:22:-57.29,-6.63,-24.20:99
+chr1	2765718	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=49.51;MQ=31.73;MQ0=6;OQ=139.31;QD=3.48;SB=14.07	GT:AD:DP:GL:GQ	0/1:34,6:18:-22.64,-5.42,-43.65:99
+chr1	2765729	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=2;HaplotypeScore=101.24;MQ=39.70;MQ0=5;OQ=348.53;QD=8.30;SB=-73.03	GT:AD:DP:GL:GQ	0/1:25,16:29:-48.99,-10.85,-57.39:99
+chr1	2765740	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=21.54;MQ=47.97;MQ0=0;OQ=288.34;QD=9.94;SB=-104.59	GT:AD:DP:GL:GQ	0/1:16,13:26:-39.95,-7.84,-58.99:99
+chr1	2765813	.	A	G	11.29	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=3.58;MQ=51.84;MQ0=0;OQ=780.70;QD=15.61;SB=-390.27	GT:AD:DP:GL:GQ	0/1:21,28:48:-95.81,-14.46,-83.37:99
+chr1	2765894	.	A	C	0.06	PASS	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=11.31;MQ=45.14;MQ0=0;OQ=337.42;QD=9.37;SB=-140.89	GT:AD:DP:GL:GQ	0/1:21,15:33:-46.96,-9.94,-71.34:99
+chr1	2765910	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=53;Dels=0.02;HRun=1;HaplotypeScore=33.31;MQ=38.51;MQ0=0;OQ=588.92;QD=11.11;SB=23.11	GT:AD:DP:GL:GQ	0/1:28,24:46:-75.73,-13.55,-102.75:99
+chr1	2765957	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=2;HaplotypeScore=176.91;MQ=27.98;MQ0=17;OQ=352.77;QD=3.12;SB=2.45	GT:AD:DP:GL:GQ	0/1:85,28:53:-54.54,-15.98,-142.28:99
+chr1	2765968	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=1;HaplotypeScore=118.45;MQ=28.99;MQ0=17;OQ=151.04;QD=1.26;SB=-15.93	GT:AD:DP:GL:GQ	0/1:95,25:59:-36.17,-17.78,-173.10:99
+chr1	2765995	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=52.19;MQ=34.85;MQ0=7;OQ=128.24;QD=1.78;SB=-51.69	GT:AD:DP:GL:GQ	0/1:61,11:54:-32.38,-16.27,-203.82:99
+chr1	2765996	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=51.72;MQ=35.05;MQ0=7;OQ=180.10;QD=2.54;SB=-41.96	GT:AD:DP:GL:GQ	0/1:59,12:54:-37.57,-16.27,-158.22:99
+chr1	2766902	rs34376289	C	T	393.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.48;MQ0=0;OQ=811.67;QD=17.64;SB=-367.51	GT:AD:DP:GL:GQ	0/1:20,26:45:-98.01,-13.56,-71.88:99
+chr1	2768626	rs10909992	C	T	335.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.57;MQ0=0;OQ=811.02;QD=12.48;SB=-416.42	GT:AD:DP:GL:GQ	0/1:35,29:62:-103.08,-18.70,-112.11:99
+chr1	2768752	rs12409918	A	C	74.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.55;MQ=59.57;MQ0=0;OQ=965.61;QD=17.88;SB=-402.66	GT:AD:DP:GL:GQ	0/1:20,34:50:-114.91,-15.06,-60.43:99
+chr1	2768903	rs12409348	T	C	172.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.28;MQ=60.00;MQ0=0;OQ=398.89;QD=10.50;SB=-78.75	GT:AD:DP:GL:GQ	0/1:20,17:35:-53.71,-10.54,-80.33:99
+chr1	2769019	rs10909995	C	G	17.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=58.48;MQ0=0;OQ=1462.05;QD=36.55;SB=-653.43	GT:AD:DP:GL:GQ	1/1:0,40:35:-149.81,-10.55,-0.02:99
+chr1	2769620	rs28600853	C	T	67.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=57.53;MQ0=0;OQ=1091.29;QD=28.72;SB=-540.63	GT:AD:DP:GL:GQ	0/1:4,33:36:-123.26,-10.85,-13.62:27.66
+chr1	2769674	rs4648542	G	A	90.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=3.80;MQ=51.80;MQ0=1;OQ=271.91;QD=9.71;SB=-148.61	GT:AD:DP:GL:GQ	0/1:13,15:21:-36.80,-6.33,-39.42:99
+chr1	2769679	rs28367217	C	G	36.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=51.80;MQ0=1;OQ=209.26;QD=8.37;SB=2.04	GT:AD:DP:GL:GQ	0/1:15,10:18:-29.64,-5.43,-44.14:99
+chr1	2769692	rs28478242	A	G	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=4;HaplotypeScore=0.82;MQ=53.88;MQ0=1;OQ=89.42;QD=4.26;SB=5.05	GT:AD:DP:GL:GQ	0/1:15,6:17:-17.35,-5.12,-46.13:99
+chr1	2769752	rs7542593	T	C	75.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=56.77;MQ0=0;OQ=136.56;QD=6.21;SB=-67.76	GT:AD:DP:GL:GQ	0/1:10,12:17:-22.07,-5.13,-38.52:99
+chr1	2769805	rs4648543	T	G	0.02	FDRtranche1.00to2.00	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=4;HaplotypeScore=2.68;MQ=55.12;MQ0=0;OQ=754.89;QD=29.03;SB=-110.69	GT:AD:DP:GL:GQ	1/1:0,26:23:-79.08,-6.93,-0.01:69.18
+chr1	2770855	rs729178	T	G	35.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=57.97;MQ0=0;OQ=332.17;QD=14.44;SB=-62.09	GT:AD:DP:GL:GQ	0/1:7,16:18:-41.92,-5.42,-18.71:99
+chr1	2770856	rs729177	T	C	47.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=57.97;MQ0=0;OQ=319.36;QD=13.89;SB=-53.86	GT:AD:DP:GL:GQ	0/1:7,16:20:-41.25,-6.03,-26.63:99
+chr1	2772453	rs12119163	G	A	585.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1388.32;QD=37.52;SB=-625.84	GT:AD:DP:GL:GQ	1/1:0,37:36:-142.43,-10.85,-0.01:99
+chr1	2772603	rs7551868	T	C	19.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=3.77;MQ=58.92;MQ0=0;OQ=1140.34;QD=29.24;SB=-578.97	GT:AD:DP:GL:GQ	1/1:0,39:37:-117.66,-11.16,-0.04:99
+chr1	2772900	rs4648402	T	C	156.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.00;MQ0=0;OQ=994.66;QD=28.42;SB=-468.49	GT:AD:DP:GL:GQ	1/1:0,35:33:-103.09,-9.96,-0.03:99
+chr1	2773675	rs12752112	G	C	9.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.95;MQ0=0;OQ=859.11;QD=39.05;SB=-325.45	GT:AD:DP:GL:GQ	1/1:0,22:21:-89.50,-6.33,-0.01:63.21
+chr1	2776554	rs1563470	T	C	23.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.69;MQ=60.00;MQ0=0;OQ=1838.24;QD=33.42;SB=-908.03	GT:AD:DP:GL:GQ	1/1:0,55:52:-187.42,-15.66,-0.02:99
+chr1	2777013	rs897616	C	G	7.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=3;HaplotypeScore=1.07;MQ=58.26;MQ0=0;OQ=1193.61;QD=34.10;SB=-446.20	GT:AD:DP:GL:GQ	1/1:0,35:30:-122.96,-9.05,-0.02:90.29
+chr1	2777567	rs897620	C	G	317.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1920.95;QD=42.69;SB=-716.92	GT:AD:DP:GL:GQ	1/1:0,45:44:-195.69,-13.26,-0.01:99
+chr1	2778573	rs56273341	A	G	89.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.42;MQ0=0;OQ=1164.73;QD=29.12;SB=-590.57	GT:AD:DP:GL:GQ	1/1:0,40:37:-120.09,-11.16,-0.03:99
+chr1	2779035	rs12569164	T	C	119.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=49.75;MQ0=0;OQ=1623.80;QD=28.49;SB=-755.66	GT:AD:DP:GL:GQ	1/1:0,57:53:-166.02,-15.99,-0.06:99
+chr1	2779347	.	T	C	140.90	Indel	AC=1;AF=0.50;AN=2;DP=70;Dels=0.03;HRun=0;HaplotypeScore=53.64;MQ=31.59;MQ0=1;QD=2.01;SB=-93.61	GT:AD:DP:GL:GQ	0/1:59,9:55:-33.34,-15.96,-177.98:99
+chr1	2779357	rs55740077	T	C	137.39	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=61.84;MQ=29.83;MQ0=1;QD=1.99;SB=-25.89	GT:AD:DP:GL:GQ	0/1:28,41:15:-21.54,-4.52,-37.07:99
+chr1	2779361	rs55927204	T	C	380.25	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=52.10;MQ=29.71;MQ0=1;QD=5.51;SB=-184.74	GT:AD:DP:GL:GQ	0/1:7,62:16:-46.13,-4.82,-12.60:77.76
+chr1	2779365	.	T	C	528.78	SnpCluster	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=50.77;MQ=30.92;MQ0=1;QD=7.24;SB=-289.59	GT:AD:DP:GL:GQ	0/1:6,67:20:-62.19,-6.02,-12.60:65.71
+chr1	2779369	.	T	C	809.75	SnpCluster	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=40.71;MQ=31.11;MQ0=1;QD=10.52;SB=-337.36	GT:AD:DP:GL:GQ	0/1:9,68:31:-93.60,-9.34,-19.91:99
+chr1	2779373	rs56012041	T	C	260.44	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=37.08;MQ=32.24;MQ0=1;QD=3.38;SB=-116.63	GT:AD:DP:GL:GQ	0/1:28,49:21:-35.65,-6.33,-44.87:99
+chr1	2779421	rs5023660	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.02;HRun=3;HaplotypeScore=23.36;MQ=40.90;MQ0=1;OQ=1397.64;QD=21.18;SB=-647.72	GT:AD:DP:GL:GQ	0/1:24,41:55:-159.31,-16.27,-52.10:99
+chr1	2779423	rs56155638	T	C	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.02;HRun=0;HaplotypeScore=20.03;MQ=40.90;MQ0=1;OQ=1243.01;QD=18.83;SB=-541.02	GT:AD:DP:GL:GQ	0/1:23,42:56:-144.15,-16.57,-59.53:99
+chr1	2779766	rs2124661	C	G	42.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=49.71;MQ0=0;OQ=2767.03;QD=41.92;SB=-1222.51	GT:AD:DP:GL:GQ	1/1:0,66:63:-280.30,-18.98,-0.02:99
+chr1	2779832	rs2168531	C	T	260.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.21;MQ=50.55;MQ0=0;OQ=2553.68;QD=38.69;SB=-1139.52	GT:AD:DP:GL:GQ	1/1:0,66:66:-258.98,-19.89,-0.03:99
+chr1	2780005	.	G	C	32.52	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=15.63;MQ=58.92;MQ0=0;QD=0.76;SB=44.18	GT:AD:DP:GL:GQ	0/1:33,10:29:-15.29,-8.76,-103.60:65.36
+chr1	2781003	rs10910023	C	T	121.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.11;MQ0=0;OQ=1930.80;QD=37.13;SB=-708.95	GT:AD:DP:GL:GQ	1/1:0,52:49:-196.68,-14.76,-0.01:99
+chr1	2781813	rs12131393	C	T	195.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=701.85;QD=13.76;SB=-265.19	GT:AD:DP:GL:GQ	0/1:28,23:44:-86.73,-13.26,-75.43:99
+chr1	2781975	rs12131450	C	T	0.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=915.40;QD=20.80;SB=-418.48	GT:AD:DP:GL:GQ	0/1:17,27:44:-108.08,-13.26,-61.20:99
+chr1	2784004	rs10909791	C	T	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=18.57;MQ=55.20;MQ0=0;OQ=554.87;QD=8.95;SB=-141.63	GT:AD:DP:GL:GQ	0/1:38,21:51:-74.16,-15.38,-99.65:99
+chr1	2784009	rs6673503	T	C	0.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=15.72;MQ=55.44;MQ0=0;OQ=828.36;QD=14.04;SB=-284.66	GT:AD:DP:GL:GQ	0/1:19,40:49:-100.91,-14.79,-59.84:99
+chr1	2784113	rs6658584	G	A	324.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.61;MQ0=0;OQ=573.55;QD=11.95;SB=-252.51	GT:AD:DP:GL:GQ	0/1:29,19:42:-73.29,-12.65,-86.05:99
+chr1	2784397	rs6668620	C	T	83.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.97;MQ0=0;OQ=989.63;QD=21.99;SB=-434.99	GT:AD:DP:GL:GQ	0/1:12,32:41:-114.60,-12.35,-43.77:99
+chr1	2784411	rs10909793	G	T	285.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=987.49;QD=22.44;SB=-485.97	GT:AD:DP:GL:GQ	0/1:11,33:43:-114.99,-12.95,-39.80:99
+chr1	2785397	rs6679954	T	C	177.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=57.39;MQ0=0;OQ=162.89;QD=9.05;SB=-99.99	GT:AD:DP:GL:GQ	0/1:9,8:15:-24.09,-4.52,-32.21:99
+chr1	2785861	rs10797340	G	C	110.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=2067.39;QD=39.01;SB=-1035.13	GT:AD:DP:GL:GQ	1/1:0,53:49:-210.35,-14.77,-0.02:99
+chr1	2786415	rs10752722	A	G	154.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.07;MQ0=0;OQ=1517.85;QD=30.36;SB=-724.72	GT:AD:DP:GL:GQ	1/1:0,50:49:-155.42,-14.78,-0.05:99
+chr1	2786479	rs4648406	T	C	92.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.34;MQ0=0;OQ=883.04;QD=25.23;SB=-376.38	GT:AD:DP:GL:GQ	1/1:0,35:29:-91.92,-8.75,-0.03:87.18
+chr1	2787126	rs6424057	T	G	92.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=59.46;MQ0=0;OQ=1311.97;QD=30.51;SB=-464.84	GT:AD:DP:GL:GQ	1/1:0,43:41:-134.82,-12.36,-0.04:99
+chr1	2787716	rs10797342	C	T	575.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=717.10;QD=14.63;SB=-344.49	GT:AD:DP:GL:GQ	0/1:27,22:49:-89.77,-14.77,-84.62:99
+chr1	2788065	rs2124662	G	C	9.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=5.21;MQ=57.80;MQ0=0;OQ=437.50;QD=13.67;SB=-215.17	GT:AD:DP:GL:GQ	0/1:15,17:26:-54.88,-7.85,-48.57:99
+chr1	2788136	rs1563472	G	A	261.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.38;MQ0=0;OQ=469.47;QD=12.69;SB=-131.12	GT:AD:DP:GL:GQ	0/1:19,18:28:-58.68,-8.45,-41.51:99
+chr1	2788195	rs1563473	T	G	178.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=57.45;MQ0=0;OQ=577.74;QD=12.56;SB=-216.84	GT:AD:DP:GL:GQ	0/1:19,27:43:-74.02,-12.96,-66.19:99
+chr1	2788317	rs1563474	G	A	94.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=3.84;MQ=58.45;MQ0=0;OQ=661.75;QD=14.71;SB=-298.81	GT:AD:DP:GL:GQ	0/1:21,24:41:-81.83,-12.37,-60.24:99
+chr1	2788572	rs4373707	T	C	44.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=5.22;MQ=58.97;MQ0=0;OQ=526.05;QD=11.69;SB=-185.63	GT:AD:DP:GL:GQ	0/1:22,23:42:-68.55,-12.66,-84.21:99
+chr1	2788907	rs2377038	A	G	118.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.81;MQ=59.09;MQ0=0;OQ=482.56;QD=10.49;SB=-194.43	GT:AD:DP:GL:GQ	0/1:24,21:41:-63.90,-12.36,-79.61:99
+chr1	2789039	rs729965	G	C	149.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=2442.19;QD=42.11;SB=-956.71	GT:AD:DP:GL:GQ	1/1:0,58:57:-247.82,-17.18,-0.02:99
+chr1	2789321	rs897629	T	C	12.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=3.68;MQ=58.87;MQ0=0;OQ=1220.90;QD=29.78;SB=-560.89	GT:AD:DP:GL:GQ	1/1:0,40:39:-125.71,-11.76,-0.03:99
+chr1	2789340	rs11580768	C	T	285.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.21;MQ=58.92;MQ0=0;OQ=699.84;QD=16.28;SB=-316.84	GT:AD:DP:GL:GQ	0/1:20,23:40:-85.33,-12.06,-59.14:99
+chr1	2789623	rs729419	G	T	32.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=4.03;MQ=56.89;MQ0=0;OQ=1157.82;QD=30.47;SB=-604.54	GT:AD:DP:GL:GQ	1/1:0,38:33:-119.38,-9.94,-0.01:99
+chr1	2789978	rs4233022	T	C	8.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=58.32;MQ0=0;OQ=1306.00;QD=33.49;SB=-393.50	GT:AD:DP:GL:GQ	1/1:0,38:38:-137.49,-14.36,-3.31:99
+chr1	2790214	rs61763695	G	T	159.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=59.41;MQ0=0;OQ=678.47;QD=17.40;SB=-357.12	GT:AD:DP:GL:GQ	0/1:15,24:37:-82.28,-11.15,-45.69:99
+chr1	2790614	rs2061229	A	G	424.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=1321.60;QD=28.73;SB=-492.17	GT:AD:DP:GL:GQ	1/1:0,46:43:-135.79,-12.97,-0.04:99
+chr1	2791688	rs4648429	A	G	0.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.02;HRun=3;HaplotypeScore=3.60;MQ=59.05;MQ0=0;OQ=1300.58;QD=29.56;SB=-615.14	GT:AD:DP:GL:GQ	1/1:0,43:39:-133.67,-11.76,-0.03:99
+chr1	2791895	rs10737188	A	G	0.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=3;HaplotypeScore=11.58;MQ=57.39;MQ0=0;OQ=1158.45;QD=32.18;SB=-423.17	GT:AD:DP:GL:GQ	1/1:0,36:33:-119.44,-9.94,-0.01:99
+chr1	2791912	rs12127835	C	T	0.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=15.40;MQ=57.73;MQ0=0;OQ=440.23;QD=14.20;SB=-189.24	GT:AD:DP:GL:GQ	0/1:15,16:28:-55.74,-8.44,-48.73:99
+chr1	2791917	rs12124890	G	A	0.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=10.20;MQ=56.96;MQ0=0;OQ=462.23;QD=14.91;SB=-204.21	GT:AD:DP:GL:GQ	0/1:14,16:28:-57.95,-8.44,-40.79:99
+chr1	2792072	rs10752725	T	C	491.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=1748.59;QD=30.68;SB=-570.96	GT:AD:DP:GL:GQ	1/1:0,57:55:-178.49,-16.59,-0.05:99
+chr1	2792208	rs7552943	A	G	158.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.00;MQ0=0;OQ=672.02;QD=16.00;SB=-219.52	GT:AD:DP:GL:GQ	0/1:13,29:36:-81.33,-10.85,-44.36:99
+chr1	2792422	.	G	A	42.68	PASS	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=59.28;MQ0=0;OQ=1176.82;QD=18.39;SB=-377.70	GT:AD:DP:GL:GQ	0/1:28,36:64:-140.25,-19.29,-99.03:99
+chr1	2793407	rs3001793	G	A	9.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=57.81;MQ0=0;OQ=925.83;QD=30.86;SB=-281.35	GT:AD:DP:GL:GQ	1/1:0,30:25:-96.18,-7.54,-0.02:75.22
+chr1	2793666	rs2377039	C	T	77.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=60.00;MQ0=0;OQ=452.51;QD=18.10;SB=-252.58	GT:AD:DP:GL:GQ	0/1:10,15:20:-54.56,-6.03,-20.77:99
+chr1	2794138	rs3001794	C	G	65.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=352.40;QD=13.05;SB=-39.43	GT:AD:DP:GL:GQ	0/1:15,12:26:-46.37,-7.84,-60.81:99
+chr1	2800878	rs2842928	T	C	235.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=901.11;QD=33.37;SB=-249.77	GT:AD:DP:GL:GQ	1/1:0,27:26:-93.71,-7.83,-0.01:78.23
+chr1	2802104	rs10909834	G	C	0.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=3;HaplotypeScore=3.91;MQ=59.36;MQ0=0;OQ=721.69;QD=20.05;SB=-360.48	GT:AD:DP:GL:GQ	0/1:15,21:32:-85.11,-9.65,-46.55:99
+chr1	2803334	rs10909835	C	A	282.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.29;MQ0=0;OQ=1113.78;QD=16.14;SB=-524.88	GT:AD:DP:GL:GQ	0/1:32,37:69:-135.44,-20.78,-115.35:99
+chr1	2809215	.	C	A	24.19	LowQual	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=33.87;MQ0=3;QD=0.67;SB=-3.99	GT:AD:DP:GL:GQ	0/1:32,3:16:-10.52,-4.82,-48.73:57.01
+chr1	2812608	rs12091184	T	C	225.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.35;MQ0=0;OQ=707.81;QD=11.06;SB=-307.08	GT:AD:DP:GL:GQ	0/1:33,31:62:-92.76,-18.69,-131.04:99
+chr1	2813319	rs12035436	G	T	336.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.54;MQ0=0;OQ=779.74;QD=15.59;SB=-317.29	GT:AD:DP:GL:GQ	0/1:23,27:47:-95.42,-14.16,-69.60:99
+chr1	2815014	rs880724	C	T	302.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.57;MQ0=0;OQ=894.47;QD=16.56;SB=-357.16	GT:AD:DP:GL:GQ	0/1:25,29:52:-108.41,-15.68,-73.43:99
+chr1	2816229	rs34114281	G	A	56.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=59.49;MQ0=0;OQ=818.99;QD=18.20;SB=-240.71	GT:AD:DP:GL:GQ	0/1:20,25:44:-98.44,-13.25,-71.30:99
+chr1	2816447	rs12738063	G	A	183.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=436.36;QD=11.79;SB=-199.90	GT:AD:DP:GL:GQ	0/1:21,16:33:-56.87,-9.95,-58.54:99
+chr1	2819411	rs1869970	A	G	323.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=58.68;MQ0=0;OQ=562.16;QD=12.22;SB=-263.95	GT:AD:DP:GL:GQ	0/1:23,23:46:-73.37,-13.87,-93.65:99
+chr1	2819722	rs10797359	G	A	80.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=58.97;MQ0=0;OQ=661.62;QD=14.70;SB=-329.32	GT:AD:DP:GL:GQ	0/1:24,21:45:-83.00,-13.56,-85.88:99
+chr1	2819782	rs10797360	T	C	62.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=58.11;MQ0=0;OQ=276.31;QD=7.47;SB=-143.57	GT:AD:DP:GL:GQ	0/1:22,15:35:-41.46,-10.55,-86.74:99
+chr1	2821229	rs2606408	T	C	106.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=3.39;MQ=59.56;MQ0=0;OQ=598.54;QD=11.51;SB=-201.20	GT:AD:DP:GL:GQ	0/1:29,23:50:-78.20,-15.07,-111.31:99
+chr1	2821448	rs1563475	G	T	119.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=513.38;QD=12.83;SB=-112.67	GT:AD:DP:GL:GQ	0/1:19,21:38:-66.07,-11.45,-67.04:99
+chr1	2821650	rs11590100	A	G	136.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.60;MQ0=0;OQ=943.28;QD=10.14;SB=-480.61	GT:AD:DP:GL:GQ	0/1:51,42:88:-124.13,-26.52,-198.52:99
+chr1	2822111	rs3001796	T	C	212.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.85;MQ=55.14;MQ0=0;OQ=802.13;QD=11.80;SB=-349.06	GT:AD:DP:GL:GQ	0/1:33,34:64:-102.79,-19.29,-127.57:99
+chr1	2822273	rs3001797	G	A	0.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=14.80;MQ=58.82;MQ0=1;OQ=1009.61;QD=19.42;SB=-317.35	GT:AD:DP:GL:GQ	0/1:22,30:49:-119.01,-14.77,-60.02:99
+chr1	2822628	rs6696129	C	T	18.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=6.89;MQ=57.91;MQ0=1;OQ=832.22;QD=14.35;SB=-326.29	GT:AD:DP:GL:GQ	0/1:32,26:55:-103.07,-16.57,-105.26:99
+chr1	2823020	rs1869971	C	T	374.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=57.94;MQ0=0;OQ=535.79;QD=14.48;SB=-291.84	GT:AD:DP:GL:GQ	0/1:19,18:35:-67.42,-10.56,-54.80:99
+chr1	2823154	rs7339944	G	A	129.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=59.45;MQ0=0;OQ=957.99;QD=19.16;SB=-392.16	GT:AD:DP:GL:GQ	0/1:19,31:48:-113.55,-14.46,-66.11:99
+chr1	2823192	rs7340016	A	G	29.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=3.35;MQ=59.34;MQ0=0;OQ=422.29;QD=10.05;SB=-179.53	GT:AD:DP:GL:GQ	0/1:21,21:36:-56.37,-10.85,-73.83:99
+chr1	2823287	rs2124663	C	T	42.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.59;MQ0=0;OQ=634.70;QD=14.10;SB=-71.85	GT:AD:DP:GL:GQ	0/1:24,21:45:-80.32,-13.56,-82.96:99
+chr1	2823310	rs1563466	T	C	23.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.63;MQ=58.92;MQ0=0;OQ=514.85;QD=13.20;SB=-114.69	GT:AD:DP:GL:GQ	0/1:19,20:38:-66.22,-11.45,-76.59:99
+chr1	2823513	rs11587665	C	T	40.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=6.13;MQ=59.14;MQ0=0;OQ=737.31;QD=13.65;SB=-373.35	GT:AD:DP:GL:GQ	0/1:29,25:51:-92.39,-15.38,-90.11:99
+chr1	2823603	rs1563468	T	C	458.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.00;MQ0=0;OQ=947.27;QD=14.14;SB=-372.60	GT:AD:DP:GL:GQ	0/1:28,39:64:-117.31,-19.30,-107.37:99
+chr1	2823870	rs11809099	C	T	295.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.56;MQ0=0;OQ=690.45;QD=13.28;SB=-256.23	GT:AD:DP:GL:GQ	0/1:28,23:49:-87.09,-14.76,-98.54:99
+chr1	2823885	rs2842926	G	A	181.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=59.53;MQ0=0;OQ=786.09;QD=16.04;SB=-320.86	GT:AD:DP:GL:GQ	0/1:23,26:46:-95.76,-13.86,-71.19:99
+chr1	2825347	rs897633	A	C	527.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=683.77;QD=14.86;SB=-280.84	GT:AD:DP:GL:GQ	0/1:21,25:45:-85.22,-13.56,-75.45:99
+chr1	2825552	rs897634	T	C	95.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1172.99;QD=30.08;SB=-560.88	GT:AD:DP:GL:GQ	1/1:0,39:37:-120.91,-11.16,-0.03:99
+chr1	2825769	rs2606409	A	G	32.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=5.74;MQ=57.77;MQ0=0;OQ=329.46;QD=7.84;SB=-164.95	GT:AD:DP:GL:GQ	0/1:25,16:40:-48.29,-12.06,-98.69:99
+chr1	2825959	rs2606410	C	T	311.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.19;MQ=59.57;MQ0=0;OQ=951.03;QD=17.61;SB=-434.47	GT:AD:DP:GL:GQ	0/1:25,29:51:-113.75,-15.36,-82.67:99
+chr1	2827304	rs55855166	G	A	337.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.37;MQ0=0;OQ=391.24;QD=9.10;SB=-201.88	GT:AD:DP:GL:GQ	0/1:27,16:41:-54.76,-12.35,-93.92:99
+chr1	2828084	rs35844499	A	C	0.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=8.95;MQ=33.58;MQ0=13;OQ=215.00;QD=4.89;SB=-66.98	GT:AD:DP:GL:GQ	0/1:23,20:16:-29.61,-4.82,-23.59:99
+chr1	2831038	.	C	T	212.41	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=614.63;QD=14.29;SB=-239.55	GT:AD:DP:GL:GQ	0/1:23,20:43:-77.70,-12.96,-79.28:99
+chr1	2833249	.	C	T	39.44	LowQual	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=2.90;MQ=56.74;MQ0=0;QD=1.36;SB=-41.03	GT:AD:DP:GL:GQ	0/1:24,4:19:-12.96,-5.74,-47.17:72.28
+chr1	2833472	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=11.49;MQ=58.05;MQ0=0;OQ=54.69;QD=1.52;SB=-45.69	GT:AD:DP:GL:GQ	0/1:28,8:19:-14.49,-5.74,-59.79:87.52
+chr1	2837348	rs2606411	T	C	351.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=583.14;QD=14.58;SB=-128.66	GT:AD:DP:GL:GQ	0/1:14,26:36:-72.45,-10.85,-55.84:99
+chr1	2838116	rs35880479	G	A	202.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=58.64;MQ0=0;OQ=848.27;QD=13.05;SB=-379.33	GT:AD:DP:GL:GQ	0/1:37,28:62:-106.79,-18.68,-116.44:99
+chr1	2844321	rs12120163	C	T	361.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.44;MQ0=0;OQ=1226.99;QD=16.58;SB=-528.52	GT:AD:DP:GL:GQ	0/1:36,38:72:-147.69,-21.70,-111.75:99
+chr1	2849584	rs2842909	C	T	85.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=5.45;MQ=57.20;MQ0=0;OQ=445.80;QD=10.87;SB=-188.84	GT:AD:DP:GL:GQ	0/1:22,19:36:-58.71,-10.85,-74.85:99
+chr1	2850791	rs2925499	C	T	367.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.73;MQ0=0;OQ=1163.55;QD=17.11;SB=-509.17	GT:AD:DP:GL:GQ	0/1:33,35:67:-139.83,-20.19,-105.50:99
+chr1	2856184	.	C	T	37.47	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=14.17;MQ0=11;QD=1.63;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,10:4:-8.24,-1.21,-6.09:48.87
+chr1	2856380	rs3010827	T	C	18.54	LowQual	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=21.91;MQ0=3;QD=0.66;SB=-6.99	GT:AD:DP:GL:GQ	0/1:20,8:5:-6.64,-1.51,-11.98:51.31
+chr1	2865080	rs2788089	G	A	618.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2745.57;QD=39.79;SB=-1234.70	GT:AD:DP:GL:GQ	1/1:0,69:69:-278.16,-20.78,-0.02:99
+chr1	2866385	rs10909845	T	C	68.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=1.49;MQ=58.86;MQ0=0;OQ=1786.40;QD=31.34;SB=-680.16	GT:AD:DP:GL:GQ	1/1:0,57:53:-182.25,-15.97,-0.03:99
+chr1	2866462	rs6663830	A	G	10.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.42;MQ=57.19;MQ0=0;OQ=455.20;QD=23.96;SB=-149.73	GT:AD:DP:GL:GQ	1/1:1,18:16:-49.13,-4.83,-0.02:48.09
+chr1	2866480	rs12132266	C	G	0.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=2;HaplotypeScore=2.31;MQ=54.22;MQ0=2;OQ=483.83;QD=32.26;SB=-138.40	GT:AD:DP:GL:GQ	1/1:2,13:12:-51.97,-3.62,-0.01:36.12
+chr1	2866511	rs12129394	G	A	181.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.76;MQ0=0;OQ=82.01;QD=27.34;SB=-47.56	GT:AD:DP:GL:GQ	1/1:0,3:3:-11.69,-0.90,-0.00:9.03
+chr1	2866552	rs11582761	G	A	15.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=47.10;MQ0=0;OQ=87.13;QD=17.43;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,4:3:-12.20,-0.90,-0.00:9.03
+chr1	2868226	rs11583804	G	A	591.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.37;MQ0=0;OQ=1019.85;QD=15.45;SB=-422.44	GT:AD:DP:GL:GQ	0/1:35,31:65:-124.85,-19.58,-125.50:99
+chr1	2872997	rs10909848	G	T	338.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=59.67;MQ0=0;OQ=904.50;QD=15.87;SB=-468.05	GT:AD:DP:GL:GQ	0/1:25,32:54:-110.00,-16.27,-78.02:99
+chr1	2873890	.	G	C	11.21	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=4;HaplotypeScore=5.27;MQ=55.45;MQ0=0;QD=0.59;SB=14.08	GT:AD:DP:GL:GQ	0/1:10,9:11:-7.69,-3.32,-38.19:43.71
+chr1	2874116	rs2993507	T	C	16.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=3;HaplotypeScore=1.05;MQ=58.76;MQ0=0;OQ=1405.38;QD=31.23;SB=-680.25	GT:AD:DP:GL:GQ	1/1:0,45:40:-144.14,-12.05,-0.01:99
+chr1	2876216	rs2842925	A	G	411.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=1144.93;QD=30.13;SB=-502.20	GT:AD:DP:GL:GQ	1/1:0,38:36:-118.11,-10.86,-0.03:99
+chr1	2876326	rs12752801	C	T	372.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.51;MQ0=0;OQ=555.75;QD=11.82;SB=-279.71	GT:AD:DP:GL:GQ	0/1:29,18:46:-72.72,-13.86,-94.69:99
+chr1	2876664	rs1104934	C	T	153.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.11;MQ0=0;OQ=873.37;QD=18.58;SB=-376.40	GT:AD:DP:GL:GQ	0/1:19,28:45:-104.19,-13.57,-58.40:99
+chr1	2876848	rs4072769	G	A	397.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.29;MQ0=0;OQ=569.53;QD=13.56;SB=-264.25	GT:AD:DP:GL:GQ	0/1:22,20:41:-72.60,-12.36,-71.89:99
+chr1	2877278	rs12731895	T	A	88.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.47;MQ0=0;OQ=1142.36;QD=32.64;SB=-433.66	GT:AD:DP:GL:GQ	1/1:0,35:33:-117.84,-9.95,-0.02:99
+chr1	2877329	rs12727338	A	G	1.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=6.87;MQ=57.26;MQ0=0;OQ=1138.52;QD=25.30;SB=-341.40	GT:AD:DP:GL:GQ	1/1:0,45:36:-117.47,-10.86,-0.03:99
+chr1	2877535	rs4648443	G	C	93.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=59.43;MQ0=0;OQ=1023.89;QD=31.03;SB=-246.78	GT:AD:DP:GL:GQ	1/1:0,33:28:-106.01,-8.47,-0.04:84.26
+chr1	2878321	rs10797371	T	C	561.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=1137.37;QD=29.16;SB=-576.99	GT:AD:DP:GL:GQ	1/1:0,39:37:-117.36,-11.16,-0.04:99
+chr1	2878374	rs10797372	A	G	151.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.80;MQ0=0;OQ=958.51;QD=27.39;SB=-485.14	GT:AD:DP:GL:GQ	1/1:0,35:31:-99.47,-9.35,-0.03:93.21
+chr1	2878478	rs57027760	G	T	756.85	Indel	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=16.93;MQ=60.84;MQ0=0;QD=20.46;SB=-136.60	GT:AD:DP:GL:GQ	0/1:7,30:29:-87.69,-8.74,-9.78:10.36
+chr1	2879008	rs56619891	G	A	46.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=58.68;MQ0=0;OQ=1774.48;QD=38.58;SB=-601.31	GT:AD:DP:GL:GQ	1/1:0,46:45:-181.04,-13.56,-0.01:99
+chr1	2879409	rs2495273	T	A	230.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=58.81;MQ0=0;OQ=1962.54;QD=35.68;SB=-1002.53	GT:AD:DP:GL:GQ	1/1:0,55:54:-199.86,-16.27,-0.02:99
+chr1	2879437	rs12044030	C	T	157.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.24;MQ=58.72;MQ0=0;OQ=1987.31;QD=38.97;SB=-989.84	GT:AD:DP:GL:GQ	1/1:0,51:51:-202.33,-15.37,-0.02:99
+chr1	2880205	rs4648445	G	A	0.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=7.53;MQ=59.36;MQ0=0;OQ=1380.04;QD=38.33;SB=-528.20	GT:AD:DP:GL:GQ	1/1:1,35:35:-141.60,-10.54,-0.01:99
+chr1	2880574	rs4648446	C	T	93.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=58.80;MQ0=0;OQ=2154.57;QD=37.15;SB=-942.74	GT:AD:DP:GL:GQ	1/1:0,58:56:-219.07,-16.88,-0.03:99
+chr1	2880814	rs35060945	G	T	115.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.36;MQ0=0;OQ=1511.10;QD=32.85;SB=-647.26	GT:AD:DP:GL:GQ	1/1:0,46:43:-154.71,-12.95,-0.02:99
+chr1	2880975	rs9661752	C	T	171.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.26;MQ=57.35;MQ0=0;OQ=1967.63;QD=36.44;SB=-881.18	GT:AD:DP:GL:GQ	1/1:0,54:51:-200.37,-15.37,-0.02:99
+chr1	2880988	rs35377179	C	A	115.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=57.03;MQ0=0;OQ=1298.02;QD=29.50;SB=-650.95	GT:AD:DP:GL:GQ	1/1:1,43:37:-133.40,-11.15,-0.01:99
+chr1	2881030	.	C	A	0.40	PASS	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=3.41;MQ=54.52;MQ0=1;OQ=214.49;QD=8.25;SB=26.09	GT:AD:DP:GL:GQ	0/1:17,8:22:-34.34,-9.60,-47.09:99
+chr1	2881446	rs12046122	C	A	164.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=56.73;MQ0=0;OQ=1555.86;QD=34.57;SB=-803.87	GT:AD:DP:GL:GQ	1/1:0,45:44:-159.18,-13.25,-0.01:99
+chr1	2881573	rs12046158	C	T	78.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=1075.02;QD=38.39;SB=-495.01	GT:AD:DP:GL:GQ	1/1:0,28:28:-111.09,-8.43,-0.01:84.27
+chr1	2882784	rs12096719	A	G	679.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.77;MQ0=0;OQ=1529.67;QD=33.99;SB=-756.19	GT:AD:DP:GL:GQ	1/1:0,45:44:-156.57,-13.25,-0.01:99
+chr1	2883117	rs34709641	C	A	0.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=10.20;MQ=27.00;MQ0=0;OQ=541.23;QD=24.60;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,21:16:-57.72,-4.82,-0.01:48.13
+chr1	2883336	.	T	C	0.07	PASS	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=2.02;MQ=28.41;MQ0=1;OQ=55.83;QD=2.15;SB=35.13	GT:AD:DP:GL:GQ	0/1:19,7:19:-14.60,-5.73,-55.04:88.67
+chr1	2883474	.	C	T	16.42	PASS	AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=1;HaplotypeScore=1.15;MQ=19.09;MQ0=3;OQ=91.28;QD=9.13;SB=-10.00	GT:AD:DP:GL:GQ	1/1:6,3:4:-15.26,-3.77,-2.60:11.70
+chr1	2883529	.	A	G	32.82	LowQual	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=16.58;MQ0=2;QD=4.69;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,7:2:-6.69,-0.60,-0.00:6.01
+chr1	2883801	.	G	C	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=4.62;MQ=34.13;MQ0=1;OQ=549.05;QD=22.88;SB=-205.68	GT:AD:DP:GL:GQ	0/1:3,21:17:-63.31,-5.13,-9.19:40.68
+chr1	2883821	.	C	G	1.10	PASS	AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=5.35;MQ=22.36;MQ0=5;OQ=186.32;QD=8.47;SB=-39.88	GT:AD:DP:GL:GQ	0/1:7,15:10:-24.93,-3.02,-15.34:99
+chr1	2883940	.	C	G	0.08	PASS	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=7.32;MQ=24.85;MQ0=3;OQ=119.37;QD=7.02;SB=-3.99	GT:AD:DP:GL:GQ	0/1:4,13:7:-17.34,-2.12,-7.20:50.86
+chr1	2883991	.	G	A	9.80	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=39.91;MQ0=4;OQ=393.88;QD=7.16;SB=-196.17	GT:AD:DP:GL:GQ	0/1:36,19:38:-54.13,-11.46,-77.08:99
+chr1	2884111	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=5.45;MQ=48.57;MQ0=0;OQ=67.53;QD=1.73;SB=-58.84	GT:AD:DP:GL:GQ	0/1:29,10:26:-17.87,-7.84,-79.49:99
+chr1	2884204	.	C	G	13.82	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=48;Dels=0.02;HRun=0;HaplotypeScore=10.52;MQ=37.87;MQ0=5;QD=0.29;SB=17.09	GT:AD:DP:GL:GQ	0/1:44,3:31:-13.69,-9.05,-110.48:46.47
+chr1	2884224	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=7.14;MQ=33.65;MQ0=6;OQ=99.62;QD=2.69;SB=-73.89	GT:AD:DP:GL:GQ	0/1:22,14:21:-19.58,-6.34,-62.85:99
+chr1	2884275	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=8.64;MQ=43.29;MQ0=0;OQ=54.38;QD=1.36;SB=23.10	GT:AD:DP:GL:GQ	0/1:34,6:34:-18.98,-10.26,-119.97:87.22
+chr1	2884325	.	G	C	41.80	PASS	AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=49.14;MQ0=0;OQ=1253.36;QD=33.87;SB=-646.42	GT:AD:DP:GL:GQ	1/1:0,37:34:-128.97,-10.28,-0.05:99
+chr1	2885060	rs63721360	G	T	452.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=1106.85;QD=29.13;SB=-549.16	GT:AD:DP:GL:GQ	1/1:0,38:32:-114.28,-9.64,-0.01:96.27
+chr1	2885413	rs34183832	C	T	53.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=60.00;MQ0=0;OQ=1297.32;QD=37.07;SB=-499.18	GT:AD:DP:GL:GQ	1/1:0,35:34:-133.33,-10.25,-0.01:99
+chr1	2885666	rs12746525	C	T	345.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=771.21;QD=35.05;SB=-307.40	GT:AD:DP:GL:GQ	1/1:0,22:21:-80.72,-6.33,-0.01:63.20
+chr1	2885725	rs12731464	G	A	43.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=59.36;MQ0=0;OQ=1296.44;QD=36.01;SB=-473.63	GT:AD:DP:GL:GQ	1/1:0,36:34:-133.24,-10.25,-0.01:99
+chr1	2885912	rs12746985	C	T	116.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.54;MQ0=0;OQ=1570.34;QD=38.30;SB=-739.01	GT:AD:DP:GL:GQ	1/1:0,40:40:-160.63,-12.05,-0.01:99
+chr1	2886057	rs12747179	C	G	228.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1558.47;QD=39.96;SB=-692.89	GT:AD:DP:GL:GQ	1/1:0,39:37:-159.45,-11.15,-0.01:99
+chr1	2886368	rs7519674	G	T	104.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.51;MQ=58.92;MQ0=0;OQ=1251.61;QD=32.09;SB=-486.26	GT:AD:DP:GL:GQ	1/1:0,39:37:-128.76,-11.15,-0.02:99
+chr1	2886595	rs7533362	A	G	145.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=59.61;MQ0=0;OQ=2108.67;QD=35.74;SB=-1026.73	GT:AD:DP:GL:GQ	1/1:0,59:59:-214.47,-17.77,-0.02:99
+chr1	2886944	rs10909849	A	G	437.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.80;MQ0=0;OQ=1258.82;QD=27.97;SB=-649.76	GT:AD:DP:GL:GQ	1/1:0,45:41:-129.52,-12.37,-0.05:99
+chr1	2886953	rs2788088	G	A	571.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.80;MQ0=0;OQ=615.00;QD=13.67;SB=-320.48	GT:AD:DP:GL:GQ	0/1:23,22:41:-77.15,-12.37,-67.43:99
+chr1	2887315	rs3001801	T	C	293.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.55;MQ0=0;OQ=285.37;QD=12.41;SB=-113.63	GT:AD:DP:GL:GQ	0/1:11,12:22:-38.45,-6.63,-44.08:99
+chr1	2887325	rs2495272	A	G	0.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=3;HaplotypeScore=1.25;MQ=56.85;MQ0=0;OQ=451.51;QD=25.08;SB=-251.59	GT:AD:DP:GL:GQ	1/1:0,18:15:-48.75,-4.52,-0.01:45.11
+chr1	2887439	.	A	G	0.37	PASS	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=2;HaplotypeScore=3.88;MQ=55.21;MQ0=0;OQ=257.68;QD=9.20;SB=-92.00	GT:AD:DP:GL:GQ	0/1:17,11:26:-36.89,-7.84,-61.45:99
+chr1	2887454	.	A	G	0.28	PASS	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=2;HaplotypeScore=5.31;MQ=55.54;MQ0=0;OQ=380.48;QD=12.68;SB=-84.99	GT:AD:DP:GL:GQ	0/1:15,15:27:-49.47,-8.14,-52.46:99
+chr1	2887461	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=56.64;MQ0=0;OQ=82.14;QD=2.65;SB=-24.50	GT:AD:DP:GL:GQ	0/1:26,5:30:-20.54,-9.04,-87.21:99
+chr1	2887469	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=10.99;MQ=56.64;MQ0=0;OQ=56.39;QD=1.82;SB=-10.59	GT:AD:DP:GL:GQ	0/1:26,5:30:-17.96,-9.04,-99.17:89.23
+chr1	2887476	rs61763639	G	A	1.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=10.80;MQ=56.85;MQ0=0;OQ=400.87;QD=12.15;SB=-209.95	GT:AD:DP:GL:GQ	0/1:19,13:29:-55.44,-12.07,-58.42:99
+chr1	2887567	rs61763640	G	C	352.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=547.00;QD=15.63;SB=-239.40	GT:AD:DP:GL:GQ	0/1:19,16:35:-68.53,-10.55,-82.14:99
+chr1	2887764	rs35529252	C	G	80.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.06;MQ=57.39;MQ0=0;OQ=226.67;QD=8.40;SB=2.03	GT:AD:DP:GL:GQ	0/1:18,9:23:-32.89,-6.94,-62.31:99
+chr1	2887828	rs56335850	C	G	110.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=4.16;MQ=58.45;MQ0=0;OQ=748.06;QD=17.40;SB=-393.99	GT:AD:DP:GL:GQ	0/1:21,22:42:-90.75,-12.66,-91.15:99
+chr1	2888083	rs56195961	C	T	7.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=2.95;MQ=60.00;MQ0=0;OQ=1112.19;QD=20.22;SB=-391.16	GT:AD:DP:GL:GQ	0/1:22,33:55:-131.08,-16.58,-71.48:99
+chr1	2888354	rs17391563	T	C	531.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=612.67;QD=11.56;SB=-261.21	GT:AD:DP:GL:GQ	0/1:27,26:52:-80.22,-15.67,-108.53:99
+chr1	2888416	rs6681331	C	T	397.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=59.62;MQ0=0;OQ=831.46;QD=13.63;SB=-416.81	GT:AD:DP:GL:GQ	0/1:34,27:59:-104.22,-17.79,-102.21:99
+chr1	2888820	rs6681741	C	T	399.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=60.00;MQ0=0;OQ=909.46;QD=13.78;SB=-406.91	GT:AD:DP:GL:GQ	0/1:37,29:64:-113.53,-19.30,-110.49:99
+chr1	2889209	rs12043738	C	T	43	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=2.99;MQ=59.70;MQ0=0;OQ=782.92;QD=12.63;SB=-392.82	GT:AD:DP:GL:GQ	0/1:36,26:56:-98.47,-16.89,-96.75:99
+chr1	2889348	rs12046140	T	C	210.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.64;MQ=58.78;MQ0=0;OQ=758.51;QD=11.67;SB=-309.09	GT:AD:DP:GL:GQ	0/1:33,31:62:-97.83,-18.69,-124.67:99
+chr1	2891988	rs1572657	C	T	224.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=58.69;MQ0=0;OQ=1966.14;QD=39.32;SB=-982.30	GT:AD:DP:GL:GQ	1/1:0,50:49:-200.21,-14.76,-0.01:99
+chr1	2893019	rs16823303	A	G	473.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1016.72;QD=15.17;SB=-513.96	GT:AD:DP:GL:GQ	0/1:31,36:67:-125.14,-20.19,-125.83:99
+chr1	2893437	rs4350139	T	C	494.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=627.58;QD=13.35;SB=-219.43	GT:AD:DP:GL:GQ	0/1:23,24:46:-79.90,-13.86,-93.15:99
+chr1	2893916	rs10797373	G	A	257.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.18;MQ=59.61;MQ0=0;OQ=845.53;QD=14.33;SB=-302.29	GT:AD:DP:GL:GQ	0/1:31,28:56:-104.72,-16.88,-95.11:99
+chr1	2895465	rs10909852	T	C	196.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=3.24;MQ=59.46;MQ0=0;OQ=1273.07;QD=16.32;SB=-516.27	GT:AD:DP:GL:GQ	0/1:36,42:76:-153.48,-22.89,-141.76:99
+chr1	2897295	rs7546695	C	A	472.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.44;MQ0=0;OQ=1069.83;QD=15.97;SB=-543.65	GT:AD:DP:GL:GQ	0/1:30,37:66:-130.15,-19.88,-106.29:99
+chr1	2897527	rs12411019	T	C	97.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.42;MQ0=0;OQ=164.92;QD=5.15;SB=-60.30	GT:AD:DP:GL:GQ	0/1:21,11:29:-28.52,-8.74,-78.99:99
+chr1	2897840	rs58882615	A	T	78.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=58.81;MQ0=0;OQ=696.78;QD=12.67;SB=-96.85	GT:AD:DP:GL:GQ	0/1:28,27:52:-88.62,-15.66,-107.99:99
+chr1	2897930	rs10909854	A	G	302.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=59.44;MQ0=0;OQ=922.43;QD=11.25;SB=-327.10	GT:AD:DP:GL:GQ	0/1:45,37:81:-119.94,-24.41,-179.92:99
+chr1	2898248	rs10909855	C	T	438.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.39;MQ0=0;OQ=1131.76;QD=16.40;SB=-432.83	GT:AD:DP:GL:GQ	0/1:34,35:68:-136.95,-20.49,-112.64:99
+chr1	2898666	.	G	A	72.98	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=60.00;MQ0=0;OQ=1136.24;QD=18.33;SB=-578.42	GT:AD:DP:GL:GQ	0/1:27,35:58:-134.38,-17.48,-83.03:99
+chr1	2898708	rs56000855	G	T	262.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=393.56;QD=10.09;SB=-213.51	GT:AD:DP:GL:GQ	0/1:23,16:38:-54.09,-11.45,-79.61:99
+chr1	2899110	rs16823315	A	G	251.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.58;MQ=58.82;MQ0=0;OQ=851.48;QD=14.43;SB=-403.32	GT:AD:DP:GL:GQ	0/1:28,31:58:-105.90,-17.47,-115.59:99
+chr1	2899231	rs17391750	G	A	437.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=1161.97;QD=13.51;SB=-467.04	GT:AD:DP:GL:GQ	0/1:50,36:85:-145.10,-25.62,-160.28:99
+chr1	2899576	rs4335321	A	G	105.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=58.00;MQ0=0;OQ=946.55;QD=13.52;SB=-144.87	GT:AD:DP:GL:GQ	0/1:37,33:68:-118.42,-20.48,-143.93:99
+chr1	2899597	.	A	T	1.69	PASS	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=3.60;MQ=57.30;MQ0=0;OQ=711.73;QD=11.67;SB=-108.79	GT:AD:DP:GL:GQ	0/1:34,27:58:-91.93,-17.47,-124.49:99
+chr1	2899698	.	C	A	3.06	PASS	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=964.27;QD=14.39;SB=-495.28	GT:AD:DP:GL:GQ	0/1:34,33:65:-119.29,-19.58,-112.82:99
+chr1	2899893	.	T	C	127.63	PASS	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.77;MQ=59.43;MQ0=0;OQ=700.47;QD=10.61;SB=-280.59	GT:AD:DP:GL:GQ	0/1:36,30:65:-92.92,-19.59,-144.88:99
+chr1	2900185	rs57720952	A	G	235.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=59.13;MQ0=0;OQ=624.52;QD=11.78;SB=-194.60	GT:AD:DP:GL:GQ	0/1:27,26:53:-81.72,-15.98,-107.90:99
+chr1	2900204	rs58538272	A	G	481.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=755.97;QD=13.50;SB=-350.98	GT:AD:DP:GL:GQ	0/1:26,30:55:-95.46,-16.58,-99.09:99
+chr1	2900256	rs60017523	T	C	269.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.37;MQ0=0;OQ=740.61;QD=11.22;SB=-378.62	GT:AD:DP:GL:GQ	0/1:33,33:62:-96.04,-18.69,-126.33:99
+chr1	2901217	rs58445466	T	C	331.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=47.93;MQ0=0;OQ=860.37;QD=15.36;SB=-212.50	GT:AD:DP:GL:GQ	0/1:26,30:54:-105.58,-16.26,-101.98:99
+chr1	2901454	rs56337009	G	A	18.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=49.33;MQ0=1;OQ=975.13;QD=34.83;SB=-240.32	GT:AD:DP:GL:GQ	1/1:2,26:25:-101.11,-7.53,-0.01:75.24
+chr1	2902060	rs12022594	C	T	230.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=53.29;MQ0=0;OQ=1320.21;QD=14.67;SB=-682.37	GT:AD:DP:GL:GQ	0/1:48,42:84:-160.62,-25.31,-148.07:99
+chr1	2902087	rs12059864	C	T	220.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=4.77;MQ=55.08;MQ0=0;OQ=1120.96;QD=14.95;SB=-477.46	GT:AD:DP:GL:GQ	0/1:41,34:69:-136.16,-20.78,-131.24:99
+chr1	2902707	rs10909856	T	C	237.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=59.08;MQ0=0;OQ=1121.38;QD=13.04;SB=-473.58	GT:AD:DP:GL:GQ	0/1:47,39:85:-141.02,-25.60,-190.53:99
+chr1	2902862	rs12401989	C	A	536.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=929.32;QD=11.47;SB=-426.42	GT:AD:DP:GL:GQ	0/1:49,32:81:-120.61,-24.40,-176.66:99
+chr1	2903095	rs60435231	A	G	179.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=2.39;MQ=59.67;MQ0=0;OQ=920.63;QD=13.15;SB=-378.56	GT:AD:DP:GL:GQ	0/1:39,31:70:-116.43,-21.08,-161.00:99
+chr1	2903159	rs59407673	T	C	419.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=752.64;QD=11.07;SB=-260.51	GT:AD:DP:GL:GQ	0/1:41,27:66:-98.43,-19.88,-155.58:99
+chr1	2903756	.	C	T	100.01	PASS	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=59.38;MQ0=0;OQ=1160.57;QD=15.47;SB=-488.46	GT:AD:DP:GL:GQ	0/1:41,34:75:-141.93,-22.59,-152.72:99
+chr1	2903757	.	C	T	97.23	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=59.38;MQ0=0;OQ=1040.83;QD=14.07;SB=-405.37	GT:AD:DP:GL:GQ	0/1:41,33:72:-129.05,-21.68,-151.62:99
+chr1	2903785	.	C	T	13.14	PASS	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=3;HaplotypeScore=0.97;MQ=59.68;MQ0=0;OQ=1201.38;QD=16.69;SB=-623.18	GT:AD:DP:GL:GQ	0/1:36,36:71:-144.81,-21.39,-125.25:99
+chr1	2904148	rs34909435	G	C	261.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.06;MQ0=0;OQ=923.50;QD=16.20;SB=-375.83	GT:AD:DP:GL:GQ	0/1:30,27:56:-112.51,-16.88,-128.89:99
+chr1	2904478	rs34453862	G	T	153.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.73;MQ=59.34;MQ0=0;OQ=843.87;QD=14.80;SB=-424.19	GT:AD:DP:GL:GQ	0/1:29,28:55:-104.24,-16.57,-85.73:99
+chr1	2904922	.	G	A	6.65	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=986.03;QD=18.26;SB=-298.76	GT:AD:DP:GL:GQ	0/1:24,30:53:-117.86,-15.97,-81.07:99
+chr1	2904988	.	G	T	192.75	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.69;MQ0=0;OQ=850.19;QD=14.17;SB=-430.19	GT:AD:DP:GL:GQ	0/1:30,30:56:-105.17,-16.87,-90.14:99
+chr1	2905123	rs12049173	C	A	190.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.62;MQ0=0;OQ=810.47;QD=14.22;SB=-367.40	GT:AD:DP:GL:GQ	0/1:30,27:57:-101.50,-17.17,-107.52:99
+chr1	2905133	rs12046411	G	A	347.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.57;MQ0=0;OQ=1037.17;QD=16.73;SB=-437.83	GT:AD:DP:GL:GQ	0/1:30,32:59:-124.78,-17.78,-92.83:99
+chr1	2905422	rs12049274	C	T	603.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=930.71;QD=16.05;SB=-490.47	GT:AD:DP:GL:GQ	0/1:30,28:58:-113.82,-17.47,-110.72:99
+chr1	2905744	.	G	A	180.07	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=873.90;QD=13.87;SB=-441.80	GT:AD:DP:GL:GQ	0/1:36,27:62:-109.35,-18.68,-126.71:99
+chr1	2905997	rs12239064	T	G	232.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=59.60;MQ0=0;OQ=846.38;QD=14.85;SB=-338.82	GT:AD:DP:GL:GQ	0/1:27,30:56:-104.79,-16.87,-99.38:99
+chr1	2906020	rs12240128	G	A	259.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=59.61;MQ0=0;OQ=950.01;QD=16.10;SB=-410.72	GT:AD:DP:GL:GQ	0/1:30,29:59:-116.06,-17.77,-109.83:99
+chr1	2906205	.	C	T	60.99	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=59.51;MQ0=0;OQ=509.22;QD=13.40;SB=-258.23	GT:AD:DP:GL:GQ	0/1:18,20:34:-64.46,-10.25,-58.74:99
+chr1	2906216	rs59653178	T	C	119.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.26;MQ=59.54;MQ0=0;OQ=444.86;QD=10.85;SB=-210.25	GT:AD:DP:GL:GQ	0/1:22,19:37:-58.92,-11.15,-79.90:99
+chr1	2906318	.	G	C	294.79	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=687.54;QD=14.03;SB=-349.42	GT:AD:DP:GL:GQ	0/1:28,21:48:-86.50,-14.46,-122.06:99
+chr1	2906331	.	T	C	64.13	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=486.38;QD=9.01;SB=-239.89	GT:AD:DP:GL:GQ	0/1:34,20:53:-67.89,-15.97,-133.79:99
+chr1	2906530	rs16823325	A	G	170.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=627.60;QD=14.26;SB=-219.26	GT:AD:DP:GL:GQ	0/1:22,22:44:-79.30,-13.26,-90.47:99
+chr1	2906541	rs57711454	A	G	139.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.54;MQ0=0;OQ=394.78;QD=7.90;SB=-84.54	GT:AD:DP:GL:GQ	0/1:29,20:47:-56.93,-14.17,-116.48:99
+chr1	2906996	rs10909857	T	C	66.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.62;MQ=57.79;MQ0=0;OQ=652.62;QD=12.31;SB=-287.16	GT:AD:DP:GL:GQ	0/1:27,26:51:-83.92,-15.38,-97.87:99
+chr1	2907051	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=17;HaplotypeScore=24.33;MQ=55.91;MQ0=0;OQ=72.31;QD=0.98;SB=54.68	GT:AD:DP:GL:GQ	0/1:56,17:51:-25.89,-15.37,-146.19:99
+chr1	2907237	rs12025260	T	C	432.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.22;MQ0=0;OQ=586.66;QD=11.73;SB=-318.24	GT:AD:DP:GL:GQ	0/1:25,25:46:-75.82,-13.87,-89.45:99
+chr1	2907320	rs10797374	C	G	183.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=56.79;MQ0=0;OQ=866.79;QD=16.35;SB=-401.99	GT:AD:DP:GL:GQ	0/1:26,27:47:-104.13,-14.17,-96.80:99
+chr1	2907323	rs10797375	C	T	107.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=56.36;MQ0=0;OQ=897.14;QD=16.31;SB=-320.30	GT:AD:DP:GL:GQ	0/1:27,28:53:-108.97,-15.97,-91.39:99
+chr1	2907332	rs10797376	A	G	569.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.97;MQ0=0;OQ=769.31;QD=13.26;SB=-314.20	GT:AD:DP:GL:GQ	0/1:28,30:54:-96.49,-16.28,-97.60:99
+chr1	2907425	rs17389607	C	T	13.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=8.86;MQ=57.83;MQ0=0;OQ=822.69;QD=15.82;SB=-373.37	GT:AD:DP:GL:GQ	0/1:24,28:48:-100.02,-14.47,-70.94:99
+chr1	2907558	rs10909859	C	T	467.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=759.55;QD=17.26;SB=-317.87	GT:AD:DP:GL:GQ	0/1:21,23:40:-91.30,-12.06,-54.32:99
+chr1	2907881	rs56008028	A	G	101.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.69;MQ=60.00;MQ0=0;OQ=314.58;QD=9.83;SB=-73.78	GT:AD:DP:GL:GQ	0/1:16,16:27:-42.88,-8.14,-52.46:99
+chr1	2908045	rs12562237	C	T	38.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=3.04;MQ=57.73;MQ0=0;OQ=402.69;QD=12.99;SB=-180.26	GT:AD:DP:GL:GQ	0/1:14,17:26:-51.39,-7.84,-42.83:99
+chr1	2908055	rs3924055	G	A	76.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=57.57;MQ0=0;OQ=483.15;QD=16.66;SB=-242.76	GT:AD:DP:GL:GQ	0/1:13,16:26:-59.44,-7.84,-34.72:99
+chr1	2908089	rs16823330	C	T	124.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.14;MQ0=0;OQ=508.46;QD=18.83;SB=-215.91	GT:AD:DP:GL:GQ	0/1:11,16:27:-62.27,-8.14,-34.10:99
+chr1	2908371	.	G	A	74.23	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.57;MQ0=0;OQ=788.94;QD=18.35;SB=-397.93	GT:AD:DP:GL:GQ	0/1:18,24:36:-93.03,-10.85,-43.26:99
+chr1	2908432	.	T	C	8.81	PASS	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=56.92;MQ0=0;OQ=358.32;QD=15.58;SB=-114.66	GT:AD:DP:GL:GQ	0/1:9,14:19:-44.84,-5.73,-23.69:99
+chr1	2908471	.	G	A	46.40	LowQual	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=4.79;MQ=51.77;MQ0=0;QD=1.93;SB=-32.97	GT:AD:DP:GL:GQ	0/1:20,4:22:-14.55,-6.63,-62.87:79.23
+chr1	2908486	.	G	A	26.78	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=9.20;MQ=53.95;MQ0=0;QD=1.12;SB=-23.58	GT:AD:DP:GL:GQ	0/1:21,3:20:-11.99,-6.02,-60.39:59.60
+chr1	2908487	.	G	A	23.81	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=9.20;MQ=53.95;MQ0=0;QD=0.99;SB=-23.59	GT:AD:DP:GL:GQ	0/1:21,3:20:-11.69,-6.03,-57.69:56.63
+chr1	2908489	rs7413322	A	G	127.27	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=7.20;MQ=53.67;MQ0=0;QD=5.53;SB=-41.81	GT:AD:DP:GL:GQ	0/1:15,7:21:-22.34,-6.33,-53.28:99
+chr1	2908502	.	G	A	0.58	PASS	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=3.89;MQ=54.56;MQ0=0;OQ=132.59;QD=4.28;SB=-84.55	GT:AD:DP:GL:GQ	0/1:22,9:26:-24.37,-7.83,-71.82:99
+chr1	2908503	.	G	A	2.61	PASS	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=3.89;MQ=54.56;MQ0=0;OQ=189.68;QD=6.12;SB=-101.89	GT:AD:DP:GL:GQ	0/1:22,9:28:-30.69,-8.44,-70.32:99
+chr1	2908532	.	T	C	3.50	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.76;MQ=54.67;MQ0=0;OQ=250.55;QD=6.77;SB=-66.91	GT:AD:DP:GL:GQ	0/1:24,13:35:-38.89,-10.55,-92.28:99
+chr1	2908533	.	G	A	0.93	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=4.66;MQ=54.15;MQ0=0;OQ=217.08;QD=5.71;SB=-54.22	GT:AD:DP:GL:GQ	0/1:25,13:33:-34.93,-9.94,-84.25:99
+chr1	2908644	.	G	A	90.84	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.24;MQ=55.47;MQ0=0;OQ=799.27;QD=15.67;SB=-377.10	GT:AD:DP:GL:GQ	0/1:25,26:51:-98.58,-15.37,-88.82:99
+chr1	2908650	.	T	C	65.40	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=55.56;MQ0=0;OQ=744.55;QD=14.32;SB=-322.26	GT:AD:DP:GL:GQ	0/1:26,26:52:-93.41,-15.67,-101.68:99
+chr1	2908671	.	T	C	96.67	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=55.57;MQ0=0;OQ=663.38;QD=13.01;SB=-328.92	GT:AD:DP:GL:GQ	0/1:26,25:50:-84.69,-15.07,-101.18:99
+chr1	2908691	rs7524813	A	G	287.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.53;MQ0=0;OQ=655.21;QD=13.10;SB=-352.07	GT:AD:DP:GL:GQ	0/1:22,28:47:-82.98,-14.17,-84.04:99
+chr1	2908767	.	C	T	11.79	PASS	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=50.29;MQ0=0;OQ=630.57;QD=18.02;SB=-203.89	GT:AD:DP:GL:GQ	0/1:14,21:32:-75.99,-9.65,-40.87:99
+chr1	2908798	rs7520336	C	T	363.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=53.82;MQ0=0;OQ=459.08;QD=13.12;SB=-219.69	GT:AD:DP:GL:GQ	0/1:20,15:31:-58.54,-9.34,-53.07:99
+chr1	2909329	rs6424067	A	G	0.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=4;HaplotypeScore=3.24;MQ=54.59;MQ0=0;OQ=434.74;QD=9.88;SB=-243.29	GT:AD:DP:GL:GQ	0/1:26,18:41:-59.12,-12.36,-92.44:99
+chr1	2909490	rs12025062	C	T	390.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.85;MQ0=0;OQ=616.92;QD=11.64;SB=-324.31	GT:AD:DP:GL:GQ	0/1:32,21:52:-80.64,-15.67,-112.78:99
+chr1	2909802	rs12022429	G	A	318.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=605.69;QD=12.36;SB=-271.15	GT:AD:DP:GL:GQ	0/1:27,22:47:-78.02,-14.16,-93.88:99
+chr1	2909879	rs12025167	C	T	200.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.12;MQ=58.32;MQ0=0;OQ=594.51;QD=15.24;SB=-283.81	GT:AD:DP:GL:GQ	0/1:20,19:35:-73.29,-10.56,-48.45:99
+chr1	2909902	rs12022456	G	A	164.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.51;MQ=58.51;MQ0=0;OQ=722.60;QD=16.42;SB=-335.48	GT:AD:DP:GL:GQ	0/1:20,24:41:-87.91,-12.37,-56.64:99
+chr1	2910018	rs16823332	C	T	243.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=942.08;QD=19.23;SB=-418.46	GT:AD:DP:GL:GQ	0/1:20,28:45:-111.06,-13.56,-54.54:99
+chr1	2910291	rs12066017	A	G	366.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=575.67;QD=14.76;SB=-270.53	GT:AD:DP:GL:GQ	0/1:19,20:38:-72.30,-11.45,-69.20:99
+chr1	2911142	.	G	A	41.67	PASS	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.51;MQ=59.36;MQ0=0;OQ=1099.50;QD=16.92;SB=-501.68	GT:AD:DP:GL:GQ	0/1:32,33:61:-131.61,-18.38,-102.89:99
+chr1	2911277	.	C	G	44.53	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.86;MQ=58.95;MQ0=0;OQ=436.44;QD=10.91;SB=-233.06	GT:AD:DP:GL:GQ	0/1:26,14:40:-58.99,-12.06,-109.38:99
+chr1	2911306	.	G	C	234.71	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.10;MQ0=0;OQ=519.44;QD=14.04;SB=-251.08	GT:AD:DP:GL:GQ	0/1:21,16:36:-66.08,-10.85,-90.14:99
+chr1	2911720	rs16823335	G	A	261.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=2.20;MQ=59.20;MQ0=0;OQ=681.92;QD=11.76;SB=-297.82	GT:AD:DP:GL:GQ	0/1:33,24:53:-87.45,-15.98,-100.90:99
+chr1	2912187	rs12028094	C	T	355.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.31;MQ0=0;OQ=839.47;QD=15.55;SB=-427.81	GT:AD:DP:GL:GQ	0/1:28,26:51:-102.60,-15.37,-81.01:99
+chr1	2912604	rs10797377	G	A	324.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=59.31;MQ0=0;OQ=1121.19;QD=18.38;SB=-566.38	GT:AD:DP:GL:GQ	0/1:27,34:59:-133.18,-17.78,-89.26:99
+chr1	2913061	.	G	A	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=14.44;MQ=58.67;MQ0=0;OQ=1557.84;QD=18.11;SB=-803.34	GT:AD:DP:GL:GQ	0/1:39,47:82:-183.77,-24.70,-131.16:99
+chr1	2913244	rs12063869	T	A	356.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.21;MQ0=0;OQ=1259.24;QD=16.35;SB=-327.01	GT:AD:DP:GL:GQ	0/1:37,40:76:-152.10,-22.89,-141.13:99
+chr1	2913685	.	T	A	78.15	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=72;Dels=0.01;HRun=7;HaplotypeScore=10.99;MQ=58.04;MQ0=0;QD=1.09;SB=89.27	GT:AD:DP:GL:GQ	0/1:54,17:56:-27.67,-16.57,-168.58:99
+chr1	2914586	rs2889476	T	C	86.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=59.50;MQ0=0;OQ=1018.41;QD=13.58;SB=-348.57	GT:AD:DP:GL:GQ	0/1:38,37:73:-127.11,-21.99,-156.39:99
+chr1	2915216	.	C	A	133.06	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=840.99;QD=15.57;SB=-328.03	GT:AD:DP:GL:GQ	0/1:26,28:54:-103.65,-16.27,-91.36:99
+chr1	2915282	rs946175	A	G	382.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.34;MQ0=0;OQ=951.27;QD=13.59;SB=-404.30	GT:AD:DP:GL:GQ	0/1:37,33:69:-119.20,-20.78,-144.79:99
+chr1	2915357	rs946176	C	T	193.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=2.81;MQ=60.00;MQ0=0;OQ=877.87;QD=15.14;SB=-352.31	GT:AD:DP:GL:GQ	0/1:30,28:58:-108.55,-17.48,-106.40:99
+chr1	2915382	rs946177	A	G	311.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=60.00;MQ0=0;OQ=696.00;QD=12.21;SB=-254.19	GT:AD:DP:GL:GQ	0/1:29,28:55:-89.46,-16.58,-112.38:99
+chr1	2916239	rs2027262	T	C	443.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=530.92;QD=9.65;SB=-168.92	GT:AD:DP:GL:GQ	0/1:28,27:51:-71.75,-15.38,-111.87:99
+chr1	2916397	rs2027263	A	G	6.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=4.33;MQ=58.92;MQ0=0;OQ=1007.60;QD=17.99;SB=-520.31	GT:AD:DP:GL:GQ	0/1:22,34:54:-120.31,-16.27,-82.47:99
+chr1	2916415	rs2027264	G	A	412.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=890.12;QD=17.45;SB=-464.45	GT:AD:DP:GL:GQ	0/1:23,27:49:-107.06,-14.77,-75.59:99
+chr1	2916645	.	C	T	34.34	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=56.98;MQ0=0;OQ=878.75;QD=16.90;SB=-242.23	GT:AD:DP:GL:GQ	0/1:24,28:50:-106.23,-15.07,-83.70:99
+chr1	2916833	rs11802804	T	G	172.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=53.08;MQ0=1;OQ=929.71;QD=12.91;SB=-466.74	GT:AD:DP:GL:GQ	0/1:38,34:69:-117.04,-20.78,-128.73:99
+chr1	2916871	.	T	G	0.62	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=5.93;MQ=46.04;MQ0=1;OQ=612.93;QD=10.57;SB=-101.87	GT:AD:DP:GL:GQ	0/1:33,25:54:-80.84,-16.27,-108.92:99
+chr1	2916874	.	G	A	4.25	PASS	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=3.93;MQ=45.85;MQ0=1;OQ=812.26;QD=13.32;SB=-234.49	GT:AD:DP:GL:GQ	0/1:33,28:56:-101.38,-16.87,-110.18:99
+chr1	2917035	rs12028439	A	G	6.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=4.28;MQ=54.23;MQ0=0;OQ=1040.90;QD=18.93;SB=-369.97	GT:AD:DP:GL:GQ	0/1:20,35:53:-123.34,-15.97,-76.66:99
+chr1	2917114	rs12024879	G	A	187.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=55.08;MQ0=0;OQ=934.32;QD=17.30;SB=-362.51	GT:AD:DP:GL:GQ	0/1:25,29:52:-112.38,-15.67,-83.45:99
+chr1	2917331	rs12027818	C	T	143.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=58.15;MQ0=1;OQ=1252.97;QD=20.21;SB=-536.07	GT:AD:DP:GL:GQ	0/1:25,37:61:-146.97,-18.38,-79.78:99
+chr1	2917538	rs12027883	C	T	346.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=58.55;MQ0=0;OQ=1081.24;QD=14.42;SB=-345.82	GT:AD:DP:GL:GQ	0/1:42,33:74:-133.70,-22.29,-151.25:99
+chr1	2918836	rs6681651	C	T	64.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=454.13;QD=15.66;SB=-29.51	GT:AD:DP:GL:GQ	0/1:13,16:27:-56.83,-8.14,-47.37:99
+chr1	2921187	rs6691208	C	A	92.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=715.52;QD=11.36;SB=-355.27	GT:AD:DP:GL:GQ	0/1:37,26:61:-93.21,-18.38,-116.36:99
+chr1	2921274	rs4357486	G	C	320.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=59.45;MQ0=0;OQ=673.44;QD=16.03;SB=-361.79	GT:AD:DP:GL:GQ	0/1:20,22:41:-83.00,-12.37,-84.03:99
+chr1	2921300	rs4486390	C	T	182.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=3.96;MQ=59.45;MQ0=0;OQ=737.41;QD=17.56;SB=-360.43	GT:AD:DP:GL:GQ	0/1:18,24:38:-88.48,-11.46,-48.81:99
+chr1	2922007	rs59869348	T	C	59.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=2.22;MQ=59.22;MQ0=0;OQ=864.59;QD=16.01;SB=-414.28	GT:AD:DP:GL:GQ	0/1:23,31:52:-105.41,-15.67,-90.49:99
+chr1	2922076	rs59041920	C	T	58.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=4.59;MQ=59.36;MQ0=0;OQ=1222.53;QD=18.81;SB=-446.93	GT:AD:DP:GL:GQ	0/1:26,38:58:-143.01,-17.47,-78.18:99
+chr1	2922420	.	C	T	142.55	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=58.20;MQ0=0;OQ=828.62;QD=13.81;SB=-355.45	GT:AD:DP:GL:GQ	0/1:34,26:58:-103.62,-17.47,-119.28:99
+chr1	2922927	.	A	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=1;HaplotypeScore=3.70;MQ=45.44;MQ0=1;OQ=81.65;QD=2.92;SB=-41.94	GT:AD:DP:GL:GQ	0/1:20,8:20:-17.47,-6.02,-59.35:99
+chr1	2923073	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=21;Dels=0.05;HRun=1;HaplotypeScore=30.97;MQ=45.34;MQ0=0;OQ=111.92;QD=5.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,8:13:-18.39,-3.92,-26.21:99
+chr1	2923110	.	A	C	47.42	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=28.91;MQ=36.30;MQ0=0;QD=3.65;SB=5.05	GT:AD:DP:GL:GQ	0/1:6,4:10:-13.77,-5.74,-26.81:80.25
+chr1	2923762	rs6680573	C	G	6.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=3.37;MQ=60.00;MQ0=0;OQ=313.93;QD=10.46;SB=-109.66	GT:AD:DP:GL:GQ	0/1:20,10:28:-43.13,-8.46,-67.50:99
+chr1	2924595	rs56200661	C	T	138.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.81;MQ0=0;OQ=702.85;QD=18.02;SB=-315.84	GT:AD:DP:GL:GQ	0/1:17,22:37:-84.72,-11.16,-50.65:99
+chr1	2924706	.	G	A	66.14	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.09;MQ0=0;OQ=681.79;QD=16.63;SB=-295.78	GT:AD:DP:GL:GQ	0/1:19,22:39:-83.22,-11.75,-60.51:99
+chr1	2926246	rs12564456	C	G	10.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=2.61;MQ=58.69;MQ0=0;OQ=646.12;QD=12.92;SB=-206.63	GT:AD:DP:GL:GQ	0/1:26,24:45:-81.49,-13.60,-94.41:99
+chr1	2926340	rs10752732	T	C	133.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.12;MQ=58.78;MQ0=0;OQ=1282.63;QD=33.75;SB=-620.25	GT:AD:DP:GL:GQ	1/1:0,38:38:-131.87,-11.45,-0.02:99
+chr1	2926606	rs55949537	A	T	46.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=3.14;MQ=59.67;MQ0=0;OQ=1017.41;QD=14.13;SB=-469.52	GT:AD:DP:GL:GQ	0/1:36,35:69:-125.81,-20.79,-130.04:99
+chr1	2926614	rs55784203	G	T	254.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=59.65;MQ0=0;OQ=972.92;QD=14.31;SB=-412.15	GT:AD:DP:GL:GQ	0/1:33,35:66:-120.46,-19.89,-108.03:99
+chr1	2926663	rs56091202	A	G	268.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=59.60;MQ0=0;OQ=738.64;QD=12.74;SB=-307.21	GT:AD:DP:GL:GQ	0/1:29,29:57:-94.32,-17.18,-112.23:99
+chr1	2926891	.	A	G	0.34	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=3;HaplotypeScore=3.44;MQ=59.42;MQ0=0;OQ=538.71;QD=11.22;SB=-143.63	GT:AD:DP:GL:GQ	0/1:27,21:47:-71.31,-14.16,-109.92:99
+chr1	2927088	rs61266721	G	A	167.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=3.88;MQ=59.23;MQ0=0;OQ=1016.77;QD=16.95;SB=-453.45	GT:AD:DP:GL:GQ	0/1:30,30:57:-122.14,-17.18,-86.53:99
+chr1	2927410	rs12033927	A	G	358.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.45;MQ=59.13;MQ0=0;OQ=706.05;QD=14.71;SB=-368.25	GT:AD:DP:GL:GQ	0/1:23,25:48:-88.35,-14.46,-94.54:99
+chr1	2927411	rs12034794	T	G	337.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.45;MQ=59.15;MQ0=0;OQ=614.57;QD=12.54;SB=-294.80	GT:AD:DP:GL:GQ	0/1:24,25:47:-78.90,-14.16,-89.23:99
+chr1	2928125	rs4576609	C	T	277.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=4.12;MQ=57.60;MQ0=0;OQ=875.52;QD=14.35;SB=-423.82	GT:AD:DP:GL:GQ	0/1:31,30:59:-108.62,-17.78,-98.44:99
+chr1	2928429	rs35806103	C	T	10.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.15;MQ=59.80;MQ0=0;OQ=886.08;QD=19.69;SB=-315.84	GT:AD:DP:GL:GQ	0/1:17,27:42:-104.54,-12.65,-59.38:99
+chr1	2928557	rs3795262	T	G	88	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.78;MQ0=0;OQ=296.95;QD=7.81;SB=-58.83	GT:AD:DP:GL:GQ	0/1:21,17:33:-42.92,-9.94,-74.02:99
+chr1	2928784	.	T	G	4.50	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=2;HaplotypeScore=2.61;MQ=58.98;MQ0=0;OQ=615.11;QD=15.00;SB=-301.85	GT:AD:DP:GL:GQ	0/1:17,24:38:-76.24,-11.45,-59.09:99
+chr1	2929872	rs55873718	A	G	218.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.73;MQ0=0;OQ=845.74;QD=10.07;SB=-404.66	GT:AD:DP:GL:GQ	0/1:48,36:83:-112.88,-25.02,-189.40:99
+chr1	2930858	rs56176404	A	G	226.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.44;MQ0=0;OQ=1022.49;QD=13.82;SB=-491.10	GT:AD:DP:GL:GQ	0/1:38,36:73:-127.52,-21.99,-154.69:99
+chr1	2932289	rs55885250	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.04;HRun=0;HaplotypeScore=32.21;MQ=45.88;MQ0=1;OQ=148.06;QD=1.90;SB=104.37	GT:AD:DP:GL:GQ	0/1:58,16:68:-38.29,-20.20,-216.63:99
+chr1	2932299	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=92;Dels=0.02;HRun=0;HaplotypeScore=97.52;MQ=43.85;MQ0=0;OQ=59.90;QD=0.65;SB=104.31	GT:AD:DP:GL:GQ	0/1:78,12:69:-29.77,-20.49,-208.32:92.74
+chr1	2932325	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=91;Dels=0.02;HRun=1;HaplotypeScore=195.32;MQ=42.40;MQ0=0;OQ=612.63;QD=6.73;SB=-162.19	GT:AD:DP:GL:GQ	0/1:51,38:73:-86.24,-21.70,-183.14:99
+chr1	2932341	.	A	G	250.48	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=1;HaplotypeScore=40.55;MQ=40.81;MQ0=0;QD=2.04;SB=89.32	GT:AD:DP:GL:GQ	0/1:96,27:107:-60.57,-32.24,-364.33:99
+chr1	2932343	.	G	A	487.06	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=123;Dels=0.01;HRun=0;HaplotypeScore=44.00;MQ=40.81;MQ0=0;QD=3.96;SB=58.75	GT:AD:DP:GL:GQ	0/1:99,23:108:-84.22,-32.23,-314.56:99
+chr1	2932349	.	G	A	708.07	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=1;HaplotypeScore=35.72;MQ=40.62;MQ0=0;QD=5.80;SB=89.29	GT:AD:DP:GL:GQ	0/1:95,27:119:-109.94,-35.84,-335.64:99
+chr1	2932354	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=0;HaplotypeScore=77.99;MQ=40.25;MQ0=0;OQ=691.65;QD=5.49;SB=86.28	GT:AD:DP:GL:GQ	0/1:97,29:123:-109.51,-37.06,-349.27:99
+chr1	2932376	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=2;HaplotypeScore=11.36;MQ=39.42;MQ0=0;OQ=679.31;QD=5.27;SB=92.31	GT:AD:DP:GL:GQ	0/1:96,32:117:-106.47,-35.26,-303.35:99
+chr1	2932379	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=125;Dels=0.01;HRun=1;HaplotypeScore=36.27;MQ=39.15;MQ0=0;OQ=716.76;QD=5.73;SB=92.27	GT:AD:DP:GL:GQ	0/1:94,28:121:-111.11,-36.16,-333.12:99
+chr1	2932387	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=36.67;MQ=38.20;MQ0=0;OQ=140.95;QD=1.25;SB=77.24	GT:AD:DP:GL:GQ	0/1:93,19:101:-47.83,-30.45,-304.67:99
+chr1	2932417	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=80.35;MQ=36.74;MQ0=0;OQ=291.45;QD=2.83;SB=86.26	GT:AD:DP:GL:GQ	0/1:76,27:77:-55.63,-23.21,-217.09:99
+chr1	2932437	.	G	A	14.74	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=80.96;MQ=35.05;MQ0=0;QD=0.16;SB=80.26	GT:AD:DP:GL:GQ	0/1:79,12:67:-24.93,-20.19,-214.14:47.43
+chr1	2932441	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=78.31;MQ=34.28;MQ0=0;OQ=251.61;QD=2.83;SB=77.24	GT:AD:DP:GL:GQ	0/1:70,19:66:-48.33,-19.89,-185.59:99
+chr1	2932450	rs55992205	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=52.98;MQ=32.53;MQ0=0;OQ=616.18;QD=7.16;SB=92.26	GT:AD:DP:GL:GQ	0/1:64,22:76:-87.80,-22.90,-186.06:99
+chr1	2932474	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=98;Dels=0.05;HRun=0;HaplotypeScore=121.87;MQ=31.47;MQ0=0;OQ=770.86;QD=7.87;SB=104.31	GT:AD:DP:GL:GQ	0/1:66,27:80:-104.48,-24.11,-189.46:99
+chr1	2932495	.	A	G	458.76	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=1;HaplotypeScore=104.10;MQ=35.05;MQ0=0;QD=4.59;SB=98.32	GT:AD:DP:GL:GQ	0/1:77,23:78:-72.67,-23.51,-220.09:99
+chr1	2932498	.	G	A	771.99	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=0;HaplotypeScore=85.95;MQ=35.28;MQ0=0;QD=8.04;SB=59.63	GT:AD:DP:GL:GQ	0/1:70,26:76:-103.38,-22.90,-174.72:99
+chr1	2932501	.	G	A	15.55	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=78.10;MQ=36.15;MQ0=0;QD=0.16;SB=-7.88	GT:AD:DP:GL:GQ	0/1:82,13:64:-24.12,-19.29,-198.59:48.26
+chr1	2932516	.	A	G	437.11	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=100;Dels=0.02;HRun=2;HaplotypeScore=90.55;MQ=38.01;MQ0=0;QD=4.37;SB=68.24	GT:AD:DP:GL:GQ	0/1:78,20:76:-69.30,-22.30,-207.20:99
+chr1	2932519	.	A	G	420.64	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=1;HaplotypeScore=127.72;MQ=37.64;MQ0=1;QD=3.72;SB=86.29	GT:AD:DP:GL:GQ	0/1:90,23:88:-71.87,-26.52,-261.50:99
+chr1	2932522	.	A	G	354.05	SnpCluster	AC=1;AF=0.50;AN=2;DP=116;Dels=0.02;HRun=1;HaplotypeScore=155.74;MQ=37.22;MQ0=2;QD=3.05;SB=-178.30	GT:AD:DP:GL:GQ	0/1:89,24:100:-68.22,-29.53,-308.19:99
+chr1	2932531	.	G	A	40.28	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=127;Dels=0.02;HRun=0;HaplotypeScore=95.96;MQ=37.07;MQ0=3;QD=0.32;SB=-35.75	GT:AD:DP:GL:GQ	0/1:114,11:85:-32.32,-25.01,-255.84:73.11
+chr1	2932543	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=125;Dels=0.00;HRun=0;HaplotypeScore=90.42;MQ=36.51;MQ0=3;OQ=448.17;QD=3.59;SB=-29.75	GT:AD:DP:GL:GQ	0/1:94,23:99:-91.60,-43.50,-272.82:99
+chr1	2932549	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=1;HaplotypeScore=106.24;MQ=36.58;MQ0=3;OQ=776.41;QD=6.81;SB=20.21	GT:AD:DP:GL:GQ	0/1:80,34:91:-108.36,-27.43,-223.52:99
+chr1	2932558	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=87.01;MQ=36.91;MQ0=2;OQ=55.94;QD=0.53;SB=50.16	GT:AD:DP:GL:GQ	0/1:89,16:77:-32.08,-23.20,-238.58:88.78
+chr1	2932594	.	A	G	95.90	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=101;Dels=0.01;HRun=2;HaplotypeScore=79.79;MQ=37.41;MQ0=0;QD=0.95;SB=41.16	GT:AD:DP:GL:GQ	0/1:85,15:78:-36.37,-23.50,-267.93:99
+chr1	2932595	.	G	T	858.77	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=99;Dels=0.01;HRun=0;HaplotypeScore=92.92;MQ=37.56;MQ0=0;QD=8.67;SB=50.17	GT:AD:DP:GL:GQ	0/1:57,41:82:-113.86,-24.70,-181.24:99
+chr1	2932597	.	A	G	613.75	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=100;Dels=0.01;HRun=2;HaplotypeScore=83.48;MQ=37.85;MQ0=0;QD=6.14;SB=53.19	GT:AD:DP:GL:GQ	0/1:69,29:84:-89.97,-25.31,-224.02:99
+chr1	2932647	.	A	G	424.25	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=1;HaplotypeScore=36.34;MQ=40.26;MQ0=1;QD=3.82;SB=65.23	GT:AD:DP:GL:GQ	0/1:87,24:95:-74.33,-28.62,-285.65:99
+chr1	2932650	.	G	A	15.47	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=0;HaplotypeScore=35.26;MQ=39.92;MQ0=1;QD=0.13;SB=83.21	GT:AD:DP:GL:GQ	0/1:106,9:104:-36.16,-31.34,-318.46:48.18
+chr1	2932656	.	G	A	597.61	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=0;HaplotypeScore=41.23;MQ=39.70;MQ0=1;QD=5.24;SB=83.24	GT:AD:DP:GL:GQ	0/1:85,29:104:-94.39,-31.34,-268.84:99
+chr1	2932671	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=1;HaplotypeScore=55.64;MQ=38.11;MQ0=1;OQ=790.23;QD=6.17;SB=74.25	GT:AD:DP:GL:GQ	0/1:94,34:113:-116.34,-34.04,-292.03:99
+chr1	2932680	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=32.69;MQ=37.68;MQ0=1;OQ=1237.37;QD=9.67;SB=74.20	GT:AD:DP:GL:GQ	0/1:85,43:122:-163.79,-36.76,-270.86:99
+chr1	2932682	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=26.80;MQ=37.61;MQ0=1;OQ=704.94;QD=5.42;SB=71.27	GT:AD:DP:GL:GQ	0/1:103,27:122:-110.54,-36.77,-411.49:99
+chr1	2932721	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=36.50;MQ=39.93;MQ0=0;OQ=181.45;QD=1.51;SB=92.30	GT:AD:DP:GL:GQ	0/1:93,27:104:-52.76,-31.33,-321.47:99
+chr1	2932727	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=27.86;MQ=40.16;MQ0=0;OQ=588.52;QD=5.35;SB=83.30	GT:AD:DP:GL:GQ	0/1:83,27:109:-94.97,-32.83,-329.92:99
+chr1	2932738	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=39.11;MQ=39.53;MQ0=0;OQ=873.00;QD=7.94;SB=74.25	GT:AD:DP:GL:GQ	0/1:74,36:108:-123.12,-32.54,-289.99:99
+chr1	2932769	.	G	A	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=7.13;MQ=40.78;MQ0=0;OQ=619.13;QD=6.59;SB=56.17	GT:AD:DP:GL:GQ	0/1:71,23:91:-92.61,-27.42,-231.77:99
+chr1	2933043	rs7412983	A	C	563.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=861.61;QD=12.67;SB=-438.69	GT:AD:DP:GL:GQ	0/1:37,31:65:-109.02,-19.58,-126.93:99
+chr1	2933258	rs58265521	C	A	261.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.67;MQ0=0;OQ=928.26;QD=16.29;SB=-439.21	GT:AD:DP:GL:GQ	0/1:24,33:53:-112.08,-15.97,-65.68:99
+chr1	2933528	rs60287244	A	G	23.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=7.04;MQ=58.03;MQ0=0;OQ=739.69;QD=12.98;SB=-372.23	GT:AD:DP:GL:GQ	0/1:30,27:55:-93.82,-16.57,-116.71:99
+chr1	2933898	rs12034766	A	G	35.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=1.69;MQ=58.27;MQ0=0;OQ=600.73;QD=11.12;SB=-275.56	GT:AD:DP:GL:GQ	0/1:26,28:51:-78.73,-15.38,-104.98:99
+chr1	2933946	rs12033401	C	T	155.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.82;MQ=57.46;MQ0=0;OQ=525.20;QD=14.19;SB=-282.22	GT:AD:DP:GL:GQ	0/1:16,21:31:-65.15,-9.35,-44.32:99
+chr1	2934531	rs57893585	T	A	124.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.24;MQ0=0;OQ=372.99;QD=15.54;SB=-168.83	GT:AD:DP:GL:GQ	0/1:10,14:21:-46.91,-6.33,-28.06:99
+chr1	2935764	rs12035292	C	T	0.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=10.18;MQ=43.51;MQ0=2;OQ=248.84;QD=4.70;SB=-149.59	GT:AD:DP:GL:GQ	0/1:30,23:31:-37.51,-9.34,-74.68:99
+chr1	2935800	rs6693975	G	A	0.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=6.49;MQ=45.50;MQ0=1;OQ=189.85;QD=4.75;SB=-111.56	GT:AD:DP:GL:GQ	0/1:24,16:23:-29.21,-6.94,-45.54:99
+chr1	2935836	rs6693982	G	A	38.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.48;MQ=49.72;MQ0=2;OQ=286.18;QD=6.36;SB=-139.13	GT:AD:DP:GL:GQ	0/1:25,20:29:-40.65,-8.75,-58.79:99
+chr1	2936586	rs12038530	T	A	386.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=538.23;QD=11.21;SB=-193.51	GT:AD:DP:GL:GQ	0/1:29,19:46:-70.96,-13.86,-104.56:99
+chr1	2937616	rs12037307	C	A	453.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=785.06;QD=15.10;SB=-326.01	GT:AD:DP:GL:GQ	0/1:25,27:52:-97.46,-15.67,-88.48:99
+chr1	2937769	rs12039548	T	C	374.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.69;MQ=59.62;MQ0=0;OQ=1018.45;QD=16.97;SB=-485.32	GT:AD:DP:GL:GQ	0/1:25,35:58:-122.60,-17.48,-90.45:99
+chr1	2937880	rs12034573	G	A	539.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=601.18;QD=13.36;SB=-263.26	GT:AD:DP:GL:GQ	0/1:25,20:44:-76.67,-13.27,-77.09:99
+chr1	2938038	rs10909864	T	C	31.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=3.17;MQ=58.15;MQ0=0;OQ=603.85;QD=12.58;SB=-301.61	GT:AD:DP:GL:GQ	0/1:20,28:44:-76.94,-13.27,-79.42:99
+chr1	2938888	rs1890338	C	T	331.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=59.50;MQ0=0;OQ=622.92;QD=13.54;SB=-315.86	GT:AD:DP:GL:GQ	0/1:22,23:40:-77.64,-12.06,-61.98:99
+chr1	2939215	rs12039132	C	T	18.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=58.67;MQ0=0;OQ=590.59;QD=16.87;SB=-94.60	GT:AD:DP:GL:GQ	0/1:16,19:32:-71.99,-9.65,-41.59:99
+chr1	2939467	rs7514166	G	C	161.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=58.11;MQ0=0;OQ=380.76;QD=10.29;SB=-57.73	GT:AD:DP:GL:GQ	0/1:23,14:34:-51.61,-10.25,-87.39:99
+chr1	2939859	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=9;HaplotypeScore=3.75;MQ=51.46;MQ0=0;OQ=333.21;QD=11.49;SB=-54.83	GT:AD:DP:GL:GQ	0/1:17,12:25:-44.15,-7.55,-58.82:99
+chr1	2939927	rs34408665	T	C	431.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.91;MQ0=0;OQ=752.79;QD=11.76;SB=-348.05	GT:AD:DP:GL:GQ	0/1:32,32:61:-96.95,-18.39,-123.70:99
+chr1	2939954	rs58052947	T	C	258.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=58.84;MQ0=0;OQ=891.02;QD=13.92;SB=-428.88	GT:AD:DP:GL:GQ	0/1:28,36:63:-111.38,-19.00,-108.25:99
+chr1	2940097	rs56398543	G	A	185.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=57.77;MQ0=0;OQ=622.10;QD=14.81;SB=-266.78	GT:AD:DP:GL:GQ	0/1:21,21:40:-77.55,-12.06,-68.06:99
+chr1	2940194	rs6661908	G	A	424.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=1140.17;QD=20.00;SB=-442.95	GT:AD:DP:GL:GQ	0/1:24,33:57:-134.47,-17.17,-86.30:99
+chr1	2940230	rs41334845	G	T	113.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.36;MQ0=0;OQ=1373.67;QD=21.13;SB=-590.07	GT:AD:DP:GL:GQ	0/1:21,44:63:-159.63,-18.98,-64.63:99
+chr1	2940454	rs6679678	T	C	216.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=522.35;QD=9.16;SB=-250.32	GT:AD:DP:GL:GQ	0/1:31,26:48:-69.99,-14.47,-101.54:99
+chr1	2940732	rs12042403	T	C	312.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=888.06;QD=12.51;SB=-433.91	GT:AD:DP:GL:GQ	0/1:39,32:70:-113.18,-21.09,-157.81:99
+chr1	2940746	rs12041583	A	G	452.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=809.95;QD=12.27;SB=-418.24	GT:AD:DP:GL:GQ	0/1:35,31:63:-103.26,-18.98,-134.35:99
+chr1	2940894	rs12041634	A	T	208.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=886.35;QD=14.77;SB=-371.51	GT:AD:DP:GL:GQ	0/1:30,30:60:-110.00,-18.08,-114.34:99
+chr1	2940901	rs12040299	C	T	487.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=953.57;QD=15.63;SB=-409.79	GT:AD:DP:GL:GQ	0/1:31,30:60:-116.73,-18.09,-97.56:99
+chr1	2941104	rs10489589	T	C	232.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.67;MQ0=0;OQ=498.13;QD=8.90;SB=-202.46	GT:AD:DP:GL:GQ	0/1:33,23:54:-69.37,-16.27,-132.36:99
+chr1	2941207	.	G	A	104.13	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.25;MQ0=0;OQ=904.38;QD=16.15;SB=-378.12	GT:AD:DP:GL:GQ	0/1:27,29:55:-110.29,-16.57,-94.24:99
+chr1	2941209	.	T	C	102.69	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.25;MQ0=0;OQ=663.66;QD=11.85;SB=-280.62	GT:AD:DP:GL:GQ	0/1:26,30:53:-85.63,-15.98,-103.85:99
+chr1	2941371	rs12408197	C	T	428.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=717.16;QD=12.36;SB=-246.23	GT:AD:DP:GL:GQ	0/1:33,25:52:-90.68,-15.68,-91.34:99
+chr1	2941666	.	T	C	142.44	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.70;MQ0=0;OQ=433.61;QD=8.50;SB=-223.24	GT:AD:DP:GL:GQ	0/1:30,21:49:-61.42,-14.77,-117.95:99
+chr1	2941694	rs10489588	G	A	184.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.01;MQ=58.17;MQ0=0;OQ=458.21;QD=8.98;SB=-152.21	GT:AD:DP:GL:GQ	0/1:34,17:47:-63.28,-14.17,-98.47:99
+chr1	2941849	.	C	T	36.18	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=3.75;MQ=59.44;MQ0=0;OQ=1385.60;QD=18.72;SB=-578.48	GT:AD:DP:GL:GQ	0/1:29,44:70:-162.94,-21.10,-91.88:99
+chr1	2942163	rs2017600	A	C	566.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=2376.48;QD=32.55;SB=-930.21	GT:AD:DP:GL:GQ	1/1:0,72:69:-241.26,-20.78,-0.03:99
+chr1	2942474	rs1005471	T	C	5.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=4;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=441.09;QD=10.02;SB=-191.58	GT:AD:DP:GL:GQ	0/1:27,17:44:-60.65,-13.26,-106.56:99
+chr1	2942683	rs9660819	C	T	0.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=5.17;MQ=58.20;MQ0=0;OQ=155.13;QD=5.97;SB=-65.81	GT:AD:DP:GL:GQ	0/1:19,7:24:-26.03,-7.23,-63.04:99
+chr1	2942700	rs9661525	T	G	36.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=59.11;MQ0=0;OQ=126.09;QD=4.85;SB=-19.97	GT:AD:DP:GL:GQ	0/1:19,7:25:-23.42,-7.53,-64.66:99
+chr1	2943003	.	G	A	0.16	PASS	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.14;MQ0=0;OQ=556.71;QD=20.62;SB=-180.72	GT:AD:DP:GL:GQ	0/1:10,17:27:-67.10,-8.14,-31.23:99
+chr1	2943693	rs16823392	C	G	180.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.22;MQ=57.09;MQ0=0;OQ=626.82;QD=16.07;SB=-312.19	GT:AD:DP:GL:GQ	0/1:21,18:38:-77.42,-11.46,-83.70:99
+chr1	2943891	.	A	G	12.02	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=54.82;MQ0=0;OQ=422.22;QD=8.28;SB=-205.52	GT:AD:DP:GL:GQ	0/1:33,18:49:-60.27,-14.76,-127.83:99
+chr1	2943911	.	C	T	10.41	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.91;MQ=52.84;MQ0=0;QD=0.25;SB=11.05	GT:AD:DP:GL:GQ	0/1:24,17:24:-11.53,-7.24,-65.03:42.84
+chr1	2943915	.	A	G	396.79	SnpCluster	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=3;HaplotypeScore=1.74;MQ=53.20;MQ0=0;QD=9.23;SB=-114.71	GT:AD:DP:GL:GQ	0/1:25,18:39:-54.71,-11.75,-89.79:99
+chr1	2943921	.	G	A	412.53	SnpCluster	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=53.30;MQ0=0;QD=10.31;SB=-110.52	GT:AD:DP:GL:GQ	0/1:23,17:37:-55.69,-11.15,-76.61:99
+chr1	2943983	.	T	C	18.12	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.49;MQ=57.65;MQ0=0;OQ=359.40;QD=9.46;SB=-125.65	GT:AD:DP:GL:GQ	0/1:21,17:36:-50.07,-10.85,-82.05:99
+chr1	2944025	.	C	T	103.45	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.94;MQ0=0;OQ=634.89;QD=13.23;SB=-327.90	GT:AD:DP:GL:GQ	0/1:27,21:45:-80.34,-13.56,-81.81:99
+chr1	2944063	.	C	T	0.51	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=4;HaplotypeScore=2.62;MQ=59.46;MQ0=0;OQ=776.27;QD=15.22;SB=-389.17	GT:AD:DP:GL:GQ	0/1:26,25:47:-95.07,-14.16,-76.30:99
+chr1	2944068	.	G	A	119.57	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.51;MQ=59.46;MQ0=0;OQ=782.48;QD=15.34;SB=-373.90	GT:AD:DP:GL:GQ	0/1:25,26:49:-96.29,-14.76,-89.91:99
+chr1	2944090	.	T	C	3.70	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=2;HaplotypeScore=2.56;MQ=59.48;MQ0=0;OQ=656.17;QD=12.38;SB=-215.36	GT:AD:DP:GL:GQ	0/1:27,26:49:-83.67,-14.77,-97.10:99
+chr1	2944157	.	T	C	29.83	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=59.30;MQ0=0;OQ=936.38;QD=15.61;SB=-205.50	GT:AD:DP:GL:GQ	0/1:27,33:58:-114.40,-17.47,-101.34:99
+chr1	2944208	rs4996810	A	C	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=3.45;MQ=56.26;MQ0=1;OQ=219.14;QD=3.48;SB=-132.81	GT:AD:DP:GL:GQ	0/1:47,15:56:-42.07,-16.87,-150.42:99
+chr1	2944226	.	G	A	136.97	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.40;MQ0=1;OQ=501.67;QD=8.36;SB=-261.69	GT:AD:DP:GL:GQ	0/1:41,19:55:-70.03,-16.58,-122.86:99
+chr1	2944238	.	T	C	5.54	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=54.51;MQ0=0;OQ=327.91;QD=6.43;SB=-156.50	GT:AD:DP:GL:GQ	0/1:37,14:48:-50.53,-14.46,-136.22:99
+chr1	2944239	.	T	C	1.08	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=4.23;MQ=54.83;MQ0=0;OQ=279.86;QD=5.18;SB=-104.43	GT:AD:DP:GL:GQ	0/1:40,14:49:-46.04,-14.77,-139.11:99
+chr1	2945018	rs12036378	G	A	163.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=59.58;MQ0=0;OQ=895.36;QD=16.28;SB=-275.78	GT:AD:DP:GL:GQ	0/1:27,28:53:-108.80,-15.98,-79.65:99
+chr1	2945105	rs55863899	C	G	134.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.52;MQ0=0;OQ=868.77;QD=18.10;SB=-284.96	GT:AD:DP:GL:GQ	0/1:21,27:46:-104.04,-13.88,-85.12:99
+chr1	2945790	.	A	G	4.08	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=57.28;MQ0=0;OQ=318.97;QD=15.19;SB=-83.80	GT:AD:DP:GL:GQ	0/1:8,13:20:-41.21,-6.03,-32.48:99
+chr1	2946023	rs10909865	A	G	147.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.15;MQ=60.00;MQ0=0;OQ=547.73;QD=10.74;SB=-195.64	GT:AD:DP:GL:GQ	0/1:24,27:47:-72.23,-14.17,-93.16:99
+chr1	2946442	.	A	G	66.31	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.61;MQ0=0;OQ=798.37;QD=10.79;SB=-385.01	GT:AD:DP:GL:GQ	0/1:39,35:70:-104.22,-21.10,-152.02:99
+chr1	2946526	rs2993510	T	C	256.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.44;MQ0=0;OQ=807.53;QD=9.73;SB=-328.89	GT:AD:DP:GL:GQ	0/1:47,36:81:-108.45,-24.41,-191.18:99
+chr1	2946859	rs12567620	T	G	251.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.22;MQ0=0;OQ=588.28;QD=9.97;SB=-221.33	GT:AD:DP:GL:GQ	0/1:35,23:57:-79.28,-17.17,-127.60:99
+chr1	2947460	rs12409277	T	C	554.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1261.63;QD=14.67;SB=-598.55	GT:AD:DP:GL:GQ	0/1:39,47:86:-155.36,-25.92,-158.90:99
+chr1	2948421	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=83;Dels=0.02;HRun=17;HaplotypeScore=13.52;MQ=50.26;MQ0=0;OQ=57.24;QD=0.69;SB=67.75	GT:AD:DP:GL:GQ	0/1:69,12:60:-26.49,-17.48,-170.55:90.07
+chr1	2948568	rs12044162	A	G	115.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=57.63;MQ0=0;OQ=498.67;QD=9.23;SB=-105.58	GT:AD:DP:GL:GQ	0/1:33,21:52:-68.82,-15.67,-126.86:99
+chr1	2949062	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=21.05;MQ=49.42;MQ0=0;OQ=103.70;QD=2.53;SB=-31.97	GT:AD:DP:GL:GQ	0/1:35,6:34:-23.91,-10.25,-88.62:99
+chr1	2949076	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=103.01;MQ=49.60;MQ0=0;OQ=345.15;QD=7.50;SB=-146.53	GT:AD:DP:GL:GQ	0/1:33,13:40:-49.87,-12.07,-111.45:99
+chr1	2949080	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=47.15;MQ=49.74;MQ0=0;OQ=115.37;QD=2.35;SB=-79.50	GT:AD:DP:GL:GQ	0/1:37,11:45:-31.37,-16.54,-140.93:99
+chr1	2949088	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=39.37;MQ=50.39;MQ0=0;OQ=395.27;QD=7.60;SB=-176.85	GT:AD:DP:GL:GQ	0/1:38,14:46:-56.68,-13.87,-100.52:99
+chr1	2949107	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=4.13;MQ=51.92;MQ0=0;OQ=58.43;QD=0.96;SB=-33.78	GT:AD:DP:GL:GQ	0/1:53,8:55:-25.70,-16.57,-188.08:91.26
+chr1	2949470	rs6692292	T	C	310.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=58.36;MQ0=0;OQ=1146.89;QD=15.93;SB=-322.30	GT:AD:DP:GL:GQ	0/1:33,39:71:-139.36,-21.39,-132.11:99
+chr1	2949881	rs56213325	G	A	8.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=3.87;MQ=58.97;MQ0=0;OQ=1032.99;QD=16.40;SB=-387.12	GT:AD:DP:GL:GQ	0/1:30,33:61:-124.96,-18.37,-109.42:99
+chr1	2950052	rs12045368	A	G	278.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=53.32;MQ0=0;OQ=936.38;QD=14.41;SB=-275.26	GT:AD:DP:GL:GQ	0/1:28,37:62:-115.61,-18.69,-106.66:99
+chr1	2950232	rs10909866	C	T	182.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=57.68;MQ0=0;OQ=969.99;QD=15.90;SB=-309.81	GT:AD:DP:GL:GQ	0/1:32,29:61:-118.67,-18.38,-109.12:99
+chr1	2950468	rs12046233	A	G	39.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.71;MQ=59.23;MQ0=0;OQ=754.54;QD=12.58;SB=-279.44	GT:AD:DP:GL:GQ	0/1:30,30:55:-95.31,-16.57,-110.00:99
+chr1	2950650	rs12044848	C	T	194.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=59.52;MQ0=0;OQ=784.81;QD=16.35;SB=-285.29	GT:AD:DP:GL:GQ	0/1:24,24:47:-95.92,-14.16,-84.23:99
+chr1	2950883	.	C	A	3.38	PASS	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=1;HaplotypeScore=2.94;MQ=60.00;MQ0=0;OQ=1395.15;QD=16.81;SB=-283.26	GT:AD:DP:GL:GQ	0/1:36,46:82:-170.17,-27.37,-127.09:99
+chr1	2951230	rs56088946	T	C	7.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=59.61;MQ0=0;OQ=1944.95;QD=16.34;SB=-964.49	GT:AD:DP:GL:GQ	0/1:53,66:118:-233.32,-35.54,-213.54:99
+chr1	2951262	rs10909867	G	T	333.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=59.76;MQ0=0;OQ=1581.91;QD=16.48;SB=-612.08	GT:AD:DP:GL:GQ	0/1:44,52:95:-190.09,-28.61,-155.75:99
+chr1	2952067	rs10909868	A	C	183.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=60.00;MQ0=0;OQ=929.11;QD=14.75;SB=-149.21	GT:AD:DP:GL:GQ	0/1:29,34:62:-114.87,-18.67,-108.28:99
+chr1	2952085	rs12048975	T	C	158.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=956.32;QD=14.94;SB=-180.58	GT:AD:DP:GL:GQ	0/1:30,34:62:-117.59,-18.68,-121.18:99
+chr1	2952452	rs2981859	G	A	525.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2597.04;QD=39.95;SB=-874.18	GT:AD:DP:GL:GQ	1/1:0,65:65:-263.30,-19.58,-0.02:99
+chr1	2953353	rs7339938	G	C	184.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1644.05;QD=21.35;SB=-832.89	GT:AD:DP:GL:GQ	0/1:34,43:75:-190.30,-22.61,-128.08:99
+chr1	2954257	rs12044831	A	C	328.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.75;MQ0=0;OQ=969.03;QD=12.75;SB=-480.26	GT:AD:DP:GL:GQ	0/1:35,41:74:-122.48,-22.29,-132.71:99
+chr1	2956899	rs2993479	A	T	39.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=7.90;MQ=58.88;MQ0=0;OQ=639.75;QD=11.85;SB=-334.02	GT:AD:DP:GL:GQ	0/1:32,22:53:-83.22,-15.96,-119.83:99
+chr1	2958839	.	C	T	167.01	PASS	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.03;MQ0=0;OQ=1118.18;QD=16.69;SB=-463.99	GT:AD:DP:GL:GQ	0/1:31,36:62:-133.80,-18.70,-86.01:99
+chr1	2958843	.	G	C	98.75	PASS	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=58.98;MQ0=0;OQ=1122.63;QD=17.54;SB=-409.32	GT:AD:DP:GL:GQ	0/1:29,34:58:-133.03,-17.49,-113.54:99
+chr1	2960143	rs56298939	A	T	308.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.67;MQ0=0;OQ=788.46;QD=14.08;SB=-295.64	GT:AD:DP:GL:GQ	0/1:29,27:56:-99.00,-16.87,-109.64:99
+chr1	2960324	rs717795	T	C	9.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=3;HaplotypeScore=2.74;MQ=59.13;MQ0=0;OQ=443.35;QD=8.37;SB=-240.88	GT:AD:DP:GL:GQ	0/1:32,21:49:-62.39,-14.77,-120.82:99
+chr1	2961312	rs56069604	T	C	18.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=3;HaplotypeScore=0.73;MQ=58.64;MQ0=0;OQ=450.45;QD=14.53;SB=-212.67	GT:AD:DP:GL:GQ	0/1:13,18:29:-57.07,-8.74,-51.18:99
+chr1	2961381	rs2981857	T	C	166.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.57;MQ=60.00;MQ0=0;OQ=428.10;QD=15.29;SB=-207.68	GT:AD:DP:GL:GQ	0/1:10,18:28:-54.54,-8.45,-38.77:99
+chr1	2962384	rs2981856	T	C	282.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=862.73;QD=12.32;SB=-362.96	GT:AD:DP:GL:GQ	0/1:34,36:67:-109.75,-20.19,-134.76:99
+chr1	2963182	rs2993480	C	T	393.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=959.18;QD=15.72;SB=-400.92	GT:AD:DP:GL:GQ	0/1:31,30:60:-117.29,-18.09,-96.43:99
+chr1	2963293	rs2993481	A	T	141.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.01;MQ=59.62;MQ0=0;OQ=743.23;QD=12.39;SB=-349.56	GT:AD:DP:GL:GQ	0/1:34,26:58:-95.08,-17.48,-119.69:99
+chr1	2963436	rs1109251	G	A	197.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=1.34;MQ=60.00;MQ0=0;OQ=932.59;QD=15.04;SB=-469.42	GT:AD:DP:GL:GQ	0/1:34,28:62:-115.22,-18.68,-120.45:99
+chr1	2963924	.	A	G	132.32	PASS	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.54;MQ0=0;OQ=1229.61;QD=13.51;SB=-579.93	GT:AD:DP:GL:GQ	0/1:47,44:90:-153.35,-27.11,-189.83:99
+chr1	2964602	rs1125017	A	C	413.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=60.00;MQ0=0;OQ=773.70;QD=11.90;SB=-364.77	GT:AD:DP:GL:GQ	0/1:35,30:63:-99.63,-18.98,-121.64:99
+chr1	2964712	rs2376821	T	C	458.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=2329.60;QD=30.25;SB=-1071.67	GT:AD:DP:GL:GQ	1/1:0,77:75:-236.63,-22.63,-0.08:99
+chr1	2964979	rs55775305	C	G	191.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=59.60;MQ0=0;OQ=1095.41;QD=18.89;SB=-526.68	GT:AD:DP:GL:GQ	0/1:27,31:56:-129.70,-16.87,-112.36:99
+chr1	2966676	rs1138513	T	C	342.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=60.00;MQ0=0;OQ=1004.23;QD=15.45;SB=-395.31	GT:AD:DP:GL:GQ	0/1:29,36:64:-122.99,-19.29,-112.84:99
+chr1	2967377	rs2981855	A	G	110.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=58.78;MQ0=0;OQ=2017.68;QD=35.40;SB=-766.96	GT:AD:DP:GL:GQ	1/1:0,57:57:-205.37,-17.17,-0.02:99
+chr1	2967903	rs2075969	G	C	175.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.42;MQ0=0;OQ=486.84;QD=12.17;SB=-253.09	GT:AD:DP:GL:GQ	0/1:21,19:36:-62.83,-10.86,-80.92:99
+chr1	2969034	rs41315262	C	T	141.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=432.24;QD=14.90;SB=-163.20	GT:AD:DP:GL:GQ	0/1:14,15:28:-54.95,-8.44,-49.21:99
+chr1	2970137	rs2072732	T	C	36.95	LowQual	AC=1;AF=0.50;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.39;MQ0=0;QD=4.11;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,4:7:-9.09,-2.11,-16.67:69.79
+chr1	2970438	.	C	T	1.69	PASS	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=3.02;MQ=60.00;MQ0=0;OQ=106.79;QD=5.62;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,5:16:-18.78,-4.82,-35.96:99
+chr1	2973178	rs2788091	T	C	354.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=59.56;MQ0=0;OQ=657.96;QD=12.65;SB=-286.58	GT:AD:DP:GL:GQ	0/1:29,23:52:-84.74,-15.66,-115.27:99
+chr1	2973823	rs2297828	G	A	18.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=95.21;QD=3.97;SB=-16.50	GT:AD:DP:GL:GQ	0/1:18,6:22:-19.43,-6.63,-57.66:99
+chr1	2975672	.	C	G	0.31	PASS	AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=1;HaplotypeScore=6.00;MQ=60.00;MQ0=0;OQ=69.47;QD=7.72;SB=-10.00	GT:AD:DP:GL:GQ	1/1:3,6:3:-10.44,-0.91,-0.01:9.02
+chr1	2977743	rs909510	G	C	79.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=3.50;MQ=58.73;MQ0=0;OQ=593.38;QD=17.98;SB=-309.99	GT:AD:DP:GL:GQ	0/1:15,18:31:-71.97,-9.35,-58.08:99
+chr1	2979403	rs1572656	T	G	132.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.39;MQ0=0;OQ=227.87;QD=7.86;SB=-74.87	GT:AD:DP:GL:GQ	0/1:16,12:27:-34.21,-8.14,-59.65:99
+chr1	2982894	rs2981889	T	C	0.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=4;HaplotypeScore=3.40;MQ=59.07;MQ0=0;OQ=530.79;QD=10.62;SB=-197.61	GT:AD:DP:GL:GQ	0/1:25,25:44:-69.63,-13.27,-84.86:99
+chr1	2983498	rs2993486	G	A	189.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.11;MQ0=0;OQ=2009.66;QD=38.65;SB=-804.34	GT:AD:DP:GL:GQ	1/1:0,52:51:-204.56,-15.36,-0.01:99
+chr1	2983667	rs2981888	C	G	249.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=760.63;QD=16.54;SB=-378.87	GT:AD:DP:GL:GQ	0/1:20,26:44:-92.63,-13.28,-85.11:99
+chr1	2984196	rs4648359	G	C	304.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=59.62;MQ0=0;OQ=739.36;QD=15.09;SB=-327.39	GT:AD:DP:GL:GQ	0/1:26,23:45:-90.79,-13.57,-98.24:99
+chr1	2984400	rs2788092	C	G	25.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=59.57;MQ0=0;OQ=997.66;QD=18.48;SB=-280.54	GT:AD:DP:GL:GQ	0/1:23,31:51:-118.43,-15.38,-97.87:99
+chr1	2985122	rs2742689	T	G	341.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=58.79;MQ0=0;OQ=737.00;QD=13.65;SB=-353.07	GT:AD:DP:GL:GQ	0/1:26,28:52:-92.65,-15.66,-91.92:99
+chr1	2985309	rs7515436	G	A	254.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=59.36;MQ0=0;OQ=1107.59;QD=17.04;SB=-525.74	GT:AD:DP:GL:GQ	0/1:30,35:61:-132.42,-18.38,-99.41:99
+chr1	2985493	rs2788093	C	T	164.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=52.54;MQ0=0;OQ=672.12;QD=14.61;SB=-188.18	GT:AD:DP:GL:GQ	0/1:25,21:45:-84.06,-13.57,-76.74:99
+chr1	2985947	.	G	A	42.58	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=2.35;MQ=59.42;MQ0=0;QD=1.06;SB=86.29	GT:AD:DP:GL:GQ	0/1:35,5:38:-18.99,-11.45,-122.25:75.41
+chr1	2986056	rs7525173	C	G	198.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=57.11;MQ0=0;OQ=1235.82;QD=21.68;SB=-610.55	GT:AD:DP:GL:GQ	0/1:22,35:54:-143.14,-16.27,-91.10:99
+chr1	2986416	rs1569420	C	G	131.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.22;MQ0=0;OQ=1047.24;QD=19.39;SB=-356.09	GT:AD:DP:GL:GQ	0/1:24,30:53:-123.98,-15.97,-102.98:99
+chr1	2986462	rs1569419	T	C	443.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1686.91;QD=29.59;SB=-810.28	GT:AD:DP:GL:GQ	1/1:0,57:54:-172.33,-16.29,-0.05:99
+chr1	2988794	rs2742686	T	C	110.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.81;MQ=59.55;MQ0=0;OQ=633.23;QD=12.42;SB=-265.98	GT:AD:DP:GL:GQ	0/1:26,25:48:-81.08,-14.47,-95.70:99
+chr1	2988858	rs10909873	C	G	203.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.25;MQ=59.51;MQ0=0;OQ=629.03;QD=13.38;SB=-304.03	GT:AD:DP:GL:GQ	0/1:24,23:43:-79.16,-12.98,-98.92:99
+chr1	2988928	rs2981886	T	G	27.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=1.77;MQ=60.00;MQ0=0;OQ=713.08;QD=17.39;SB=-342.06	GT:AD:DP:GL:GQ	0/1:16,25:41:-86.94,-12.35,-58.67:99
+chr1	2989062	rs2742685	T	C	91.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.60;MQ=59.38;MQ0=0;OQ=332.13;QD=8.98;SB=-168.61	GT:AD:DP:GL:GQ	0/1:21,16:36:-47.35,-10.86,-77.27:99
+chr1	2989275	rs760570	T	C	183.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.10;MQ=60.00;MQ0=0;OQ=452.99;QD=11.62;SB=-195.61	GT:AD:DP:GL:GQ	0/1:18,21:37:-59.74,-11.16,-71.21:99
+chr1	2989352	rs11580403	C	T	17.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=6.35;MQ=58.51;MQ0=0;OQ=786.31;QD=16.73;SB=-390.18	GT:AD:DP:GL:GQ	0/1:22,25:44:-95.18,-13.26,-64.65:99
+chr1	2989378	rs11581212	A	G	26.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=4.12;MQ=58.01;MQ0=0;OQ=610.70;QD=12.99;SB=-220.27	GT:AD:DP:GL:GQ	0/1:23,24:41:-76.70,-12.35,-80.42:99
+chr1	2989575	rs6674036	G	T	86.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=60.00;MQ0=0;OQ=295.75;QD=8.45;SB=-112.67	GT:AD:DP:GL:GQ	0/1:22,13:32:-42.50,-9.64,-70.40:99
+chr1	2989750	rs6683976	C	G	152.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=58.25;MQ0=0;OQ=588.86;QD=14.72;SB=-197.30	GT:AD:DP:GL:GQ	0/1:21,19:38:-73.63,-11.46,-80.42:99
+chr1	2989984	rs760569	A	G	0.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=3;HaplotypeScore=3.04;MQ=55.35;MQ0=1;OQ=203.26;QD=6.78;SB=-13.61	GT:AD:DP:GL:GQ	0/1:16,14:25:-31.15,-7.54,-61.01:99
+chr1	2990301	rs760568	A	G	305.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=56.76;MQ0=0;OQ=713.37;QD=13.99;SB=-336.34	GT:AD:DP:GL:GQ	0/1:22,29:50:-89.69,-15.07,-88.33:99
+chr1	2990325	rs760567	A	G	357.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=57.34;MQ0=0;OQ=769.95;QD=14.53;SB=-388.67	GT:AD:DP:GL:GQ	0/1:25,28:52:-95.94,-15.67,-100.59:99
+chr1	2990784	rs6695131	T	C	278.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.71;MQ=59.69;MQ0=0;OQ=1038.17;QD=17.02;SB=-324.30	GT:AD:DP:GL:GQ	0/1:25,36:59:-124.87,-17.77,-99.97:99
+chr1	2991113	rs760566	T	C	528.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=1563.77;QD=31.91;SB=-755.58	GT:AD:DP:GL:GQ	1/1:0,49:46:-159.99,-13.86,-0.02:99
+chr1	2991563	rs6690540	C	T	182.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=58.34;MQ0=0;OQ=662.57;QD=14.72;SB=-343.52	GT:AD:DP:GL:GQ	0/1:23,22:42:-82.21,-12.67,-65.85:99
+chr1	2991617	rs2742682	T	C	232.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.38;MQ0=0;OQ=410.76;QD=11.10;SB=-215.29	GT:AD:DP:GL:GQ	0/1:16,19:33:-54.32,-9.96,-57.14:99
+chr1	2991708	rs2742681	T	G	14.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=58.98;MQ0=0;OQ=365.17;QD=8.91;SB=-102.16	GT:AD:DP:GL:GQ	0/1:24,17:38:-51.25,-11.45,-78.22:99
+chr1	2992174	rs2742680	C	G	300.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.13;MQ=58.66;MQ0=0;OQ=934.85;QD=17.98;SB=-447.39	GT:AD:DP:GL:GQ	0/1:22,30:49:-111.56,-14.79,-83.87:99
+chr1	2992195	rs2742679	C	T	269.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=58.13;MQ0=0;OQ=860.87;QD=17.22;SB=-384.13	GT:AD:DP:GL:GQ	0/1:23,27:48:-103.84,-14.47,-74.36:99
+chr1	2992210	rs2742678	G	A	296.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=57.39;MQ0=0;OQ=701.27;QD=15.58;SB=-336.35	GT:AD:DP:GL:GQ	0/1:23,22:43:-86.37,-12.96,-74.58:99
+chr1	2993392	rs11801109	G	A	5.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=59.59;MQ0=0;OQ=759.83;QD=16.52;SB=-91.91	GT:AD:DP:GL:GQ	0/1:23,23:45:-92.82,-13.56,-77.23:99
+chr1	2993874	rs2981883	T	C	12.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.37;MQ=58.95;MQ0=0;OQ=1316.25;QD=29.91;SB=-475.45	GT:AD:DP:GL:GQ	1/1:0,44:39:-135.23,-11.75,-0.02:99
+chr1	2994092	rs2981882	A	G	168.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=59.63;MQ0=0;OQ=1897.54;QD=30.61;SB=-828.34	GT:AD:DP:GL:GQ	1/1:0,62:61:-193.40,-18.40,-0.06:99
+chr1	2994217	rs2981881	T	C	270.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=58.88;MQ0=0;OQ=1946.57;QD=31.40;SB=-838.62	GT:AD:DP:GL:GQ	1/1:1,61:56:-198.26,-16.87,-0.02:99
+chr1	2994648	rs2981880	T	C	6.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.30;MQ=56.36;MQ0=0;OQ=1597.03;QD=34.72;SB=-433.18	GT:AD:DP:GL:GQ	1/1:0,45:44:-163.30,-13.25,-0.01:99
+chr1	2994734	rs2981879	T	C	43.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.75;MQ0=0;OQ=1057.22;QD=35.24;SB=-208.08	GT:AD:DP:GL:GQ	1/1:0,30:30:-109.32,-9.04,-0.01:90.26
+chr1	2994945	rs34014659	G	A	271.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.59;MQ0=1;OQ=187.11;QD=9.85;SB=-73.30	GT:AD:DP:GL:GQ	0/1:11,8:17:-27.12,-5.12,-33.00:99
+chr1	2995445	rs2981878	A	G	132.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=56.06;MQ0=1;OQ=382.82;QD=11.96;SB=-131.28	GT:AD:DP:GL:GQ	0/1:16,16:31:-50.91,-9.34,-62.42:99
+chr1	2995487	rs6676479	G	A	196.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=57.97;MQ0=1;OQ=534.41;QD=14.06;SB=-244.76	GT:AD:DP:GL:GQ	0/1:21,17:34:-66.98,-10.25,-53.48:99
+chr1	2995498	rs34884268	C	T	260.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=626.01;QD=14.90;SB=-317.32	GT:AD:DP:GL:GQ	0/1:22,20:41:-78.24,-12.36,-68.94:99
+chr1	2995610	rs34782467	G	A	183.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.56;MQ0=0;OQ=857.05;QD=16.48;SB=-325.85	GT:AD:DP:GL:GQ	0/1:26,26:50:-104.07,-15.08,-74.92:99
+chr1	2995991	rs926246	T	C	314.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=57.39;MQ0=0;OQ=671.24;QD=12.43;SB=-260.51	GT:AD:DP:GL:GQ	0/1:30,24:53:-86.37,-15.96,-115.93:99
+chr1	2996058	rs926245	C	A	105.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=53.36;MQ0=0;OQ=705.06;QD=12.82;SB=-99.80	GT:AD:DP:GL:GQ	0/1:29,26:52:-89.45,-15.66,-93.51:99
+chr1	2996143	rs926244	A	G	215.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=58.61;MQ0=0;OQ=1978.79;QD=31.92;SB=-947.90	GT:AD:DP:GL:GQ	1/1:0,60:58:-201.49,-17.47,-0.03:99
+chr1	2996175	rs926243	T	G	426.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.31;MQ0=0;OQ=690.75;QD=11.32;SB=-265.78	GT:AD:DP:GL:GQ	0/1:31,30:58:-89.83,-17.48,-108.47:99
+chr1	2996487	rs55932943	C	T	3.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=10.54;MQ=58.03;MQ0=1;OQ=1021.25;QD=14.80;SB=-443.45	GT:AD:DP:GL:GQ	0/1:37,31:63:-124.40,-18.99,-104.76:99
+chr1	2996899	rs2817165	A	G	93.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=58.80;MQ0=0;OQ=288.71;QD=8.25;SB=-166.95	GT:AD:DP:GL:GQ	0/1:21,13:29:-40.90,-8.74,-67.04:99
+chr1	2997535	rs34300623	G	A	185.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=59.69;MQ0=0;OQ=968.84;QD=15.88;SB=-326.31	GT:AD:DP:GL:GQ	0/1:32,29:60:-118.25,-18.08,-106.92:99
+chr1	2997956	rs6693385	C	T	247.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=59.55;MQ0=0;OQ=876.50;QD=17.19;SB=-364.90	GT:AD:DP:GL:GQ	0/1:22,29:45:-104.50,-13.57,-57.88:99
+chr1	2998547	rs2376820	C	G	2318.28	Indel	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=17.39;MQ=51.50;MQ0=0;QD=40.67;SB=-1149.31	GT:AD:DP:GL:GQ	1/1:0,55:56:-238.28,-19.61,-2.86:99
+chr1	3000177	rs760565	A	T	219.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=60.00;MQ0=0;OQ=708.84;QD=15.75;SB=-333.07	GT:AD:DP:GL:GQ	0/1:21,24:41:-86.52,-12.35,-66.91:99
+chr1	3001189	rs2981873	T	C	24.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=57.66;MQ0=0;OQ=381.92;QD=12.73;SB=-154.31	GT:AD:DP:GL:GQ	0/1:16,14:30:-50.52,-9.04,-62.50:99
+chr1	3002186	rs12135325	T	C	1.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=4.32;MQ=58.67;MQ0=0;OQ=210.96;QD=6.03;SB=-111.21	GT:AD:DP:GL:GQ	0/1:22,13:32:-34.02,-9.64,-84.87:99
+chr1	3002840	rs6666748	A	G	255.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.28;MQ=60.00;MQ0=0;OQ=801.41;QD=14.84;SB=-400.31	GT:AD:DP:GL:GQ	0/1:21,33:50:-98.50,-15.08,-74.39:99
+chr1	3003005	rs2788097	A	C	59.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.07;MQ=59.05;MQ0=0;OQ=463.07;QD=10.52;SB=-200.91	GT:AD:DP:GL:GQ	0/1:25,19:39:-61.34,-11.75,-74.66:99
+chr1	3005383	rs2981870	G	A	337.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=59.45;MQ0=0;OQ=532.89;QD=12.69;SB=-258.26	GT:AD:DP:GL:GQ	0/1:23,19:40:-68.63,-12.06,-71.78:99
+chr1	3005452	rs55674255	C	T	63.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.20;MQ=60.00;MQ0=0;OQ=640.76;QD=14.56;SB=-293.19	GT:AD:DP:GL:GQ	0/1:24,20:44:-80.62,-13.26,-82.30:99
+chr1	3005702	rs55784774	G	A	50.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=2.79;MQ=59.56;MQ0=0;OQ=701.05;QD=13.23;SB=-358.53	GT:AD:DP:GL:GQ	0/1:30,23:49:-88.16,-14.77,-89.46:99
+chr1	3005947	.	C	T	228.82	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.77;MQ0=0;OQ=514.40;QD=13.54;SB=-233.73	GT:AD:DP:GL:GQ	0/1:21,17:37:-65.88,-11.16,-63.18:99
+chr1	3005977	.	G	A	25.43	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=57.94;MQ0=0;OQ=561.32;QD=13.69;SB=-151.18	GT:AD:DP:GL:GQ	0/1:21,20:37:-70.56,-11.15,-69.03:99
+chr1	3006143	rs2981869	C	T	155.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=58.84;MQ0=0;OQ=588.68;QD=14.72;SB=-230.75	GT:AD:DP:GL:GQ	0/1:19,21:38:-73.61,-11.45,-64.86:99
+chr1	3007018	.	G	A	13.33	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.77;MQ=59.05;MQ0=0;OQ=465.01;QD=10.57;SB=-225.50	GT:AD:DP:GL:GQ	0/1:25,18:41:-64.52,-14.73,-86.50:99
+chr1	3008086	rs2993492	G	A	197.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.53;MQ0=0;OQ=913.42;QD=18.64;SB=-406.43	GT:AD:DP:GL:GQ	0/1:20,29:46:-108.49,-13.86,-62.00:99
+chr1	3009487	rs12131890	G	A	77.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.17;MQ0=0;OQ=935.16;QD=20.78;SB=-364.90	GT:AD:DP:GL:GQ	0/1:15,30:42:-109.46,-12.66,-48.94:99
+chr1	3010048	rs56029998	T	C	182.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.92;MQ=59.24;MQ0=0;OQ=609.91;QD=11.09;SB=-261.57	GT:AD:DP:GL:GQ	0/1:31,24:54:-80.54,-16.27,-125.83:99
+chr1	3010106	rs2993493	C	A	285.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=59.63;MQ0=0;OQ=789.70;QD=15.48;SB=-315.68	GT:AD:DP:GL:GQ	0/1:25,26:51:-97.62,-15.36,-86.35:99
+chr1	3010923	rs2993494	G	A	362.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.94;MQ0=0;OQ=449.17;QD=13.21;SB=-177.14	GT:AD:DP:GL:GQ	0/1:18,16:33:-58.15,-9.95,-61.38:99
+chr1	3011156	rs55898371	A	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=5;HaplotypeScore=4.00;MQ=58.74;MQ0=0;OQ=420.03;QD=11.35;SB=-193.92	GT:AD:DP:GL:GQ	0/1:18,19:33:-55.23,-9.95,-57.05:99
+chr1	3011412	rs12133978	G	A	162.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=59.34;MQ0=0;OQ=429.68;QD=12.28;SB=-187.26	GT:AD:DP:GL:GQ	0/1:20,15:33:-56.20,-9.95,-61.55:99
+chr1	3011547	rs11808136	C	T	5.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.91;MQ=59.52;MQ0=0;OQ=731.81;QD=18.76;SB=-195.18	GT:AD:DP:GL:GQ	0/1:16,23:36:-87.31,-10.85,-49.60:99
+chr1	3012571	rs2993495	A	G	13.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=549.01;QD=28.90;SB=-194.71	GT:AD:DP:GL:GQ	1/1:0,19:18:-58.50,-5.43,-0.01:54.13
+chr1	3012575	rs2993496	T	C	83.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=58.78;MQ0=0;OQ=196.75;QD=10.36;SB=-98.00	GT:AD:DP:GL:GQ	0/1:9,10:18:-28.39,-5.43,-32.68:99
+chr1	3012992	rs2993497	G	A	7	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=1.90;MQ=59.59;MQ0=0;OQ=932.60;QD=20.72;SB=-424.82	GT:AD:DP:GL:GQ	0/1:16,29:42:-109.20,-12.66,-48.01:99
+chr1	3013111	rs56363358	C	A	42.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=58.28;MQ0=0;OQ=749.52;QD=19.72;SB=-289.38	GT:AD:DP:GL:GQ	0/1:12,26:36:-89.08,-10.85,-37.10:99
+chr1	3013255	rs2993498	T	C	497.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=1211.16;QD=31.87;SB=-545.88	GT:AD:DP:GL:GQ	1/1:0,38:36:-124.72,-10.85,-0.02:99
+chr1	3013565	rs6667850	A	C	171.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.41;MQ0=0;OQ=400.63;QD=10.27;SB=-101.88	GT:AD:DP:GL:GQ	0/1:20,19:37:-54.50,-11.15,-69.04:99
+chr1	3013819	rs1890337	A	G	45.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.68;MQ=58.49;MQ0=0;OQ=1788.78;QD=31.38;SB=-712.22	GT:AD:DP:GL:GQ	1/1:0,56:52:-182.49,-15.67,-0.02:99
+chr1	3014125	rs1890336	A	C	168.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.71;MQ0=0;OQ=1775.96;QD=32.89;SB=-886.08	GT:AD:DP:GL:GQ	1/1:0,54:51:-181.20,-15.36,-0.02:99
+chr1	3014227	rs2993499	T	C	143.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=0.04;MQ=59.50;MQ0=0;OQ=1217.03;QD=32.89;SB=-587.31	GT:AD:DP:GL:GQ	1/1:0,37:36:-125.31,-10.85,-0.02:99
+chr1	3014565	rs2993500	C	T	15.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=4.44;MQ=59.65;MQ0=0;OQ=1234.24;QD=18.99;SB=-544.80	GT:AD:DP:GL:GQ	0/1:29,36:64:-145.99,-19.28,-92.77:99
+chr1	3015706	rs12137954	T	A	122.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.40;MQ0=0;OQ=345.66;QD=6.91;SB=-177.77	GT:AD:DP:GL:GQ	0/1:35,15:48:-52.31,-14.46,-129.85:99
+chr1	3015846	rs2993501	A	C	217.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=57.44;MQ0=0;OQ=1649.50;QD=29.99;SB=-596.80	GT:AD:DP:GL:GQ	1/1:0,55:53:-168.59,-15.98,-0.05:99
+chr1	3015960	rs12135664	C	T	346.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=60.00;MQ0=0;OQ=1146.10;QD=16.85;SB=-550.79	GT:AD:DP:GL:GQ	0/1:34,34:67:-138.08,-20.19,-108.20:99
+chr1	3016120	rs2981868	T	A	119.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=4.10;MQ=59.44;MQ0=0;OQ=1114.65;QD=15.06;SB=-570.99	GT:AD:DP:GL:GQ	0/1:37,36:67:-134.93,-20.18,-118.55:99
+chr1	3016369	rs59909070	G	A	353.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.69;MQ0=0;OQ=434.09;QD=10.10;SB=-171.10	GT:AD:DP:GL:GQ	0/1:27,16:42:-59.35,-12.65,-95.52:99
+chr1	3016502	.	T	C	0.18	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=2;HaplotypeScore=5.91;MQ=44.72;MQ0=3;OQ=351.94;QD=7.65;SB=-166.48	GT:AD:DP:GL:GQ	0/1:25,21:36:-49.33,-10.85,-81.52:99
+chr1	3016606	.	A	C	15.74	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.75;MQ=48.95;MQ0=1;OQ=373.22;QD=9.82;SB=-133.20	GT:AD:DP:GL:GQ	0/1:18,17:27:-48.74,-8.13,-43.17:99
+chr1	3016839	rs56010213	A	T	12.71	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=38.33;MQ0=7;QD=0.33;SB=20.09	GT:AD:DP:GL:GQ	0/1:34,5:23:-11.46,-6.93,-70.69:45.31
+chr1	3017201	rs2993502	C	T	589.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.38;MQ0=0;OQ=2029.57;QD=38.29;SB=-936.75	GT:AD:DP:GL:GQ	1/1:0,53:51:-206.56,-15.36,-0.01:99
+chr1	3017765	.	T	C	156.29	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=257.37;QD=12.26;SB=-133.69	GT:AD:DP:GL:GQ	0/1:7,14:18:-34.45,-5.43,-28.78:99
+chr1	3017780	.	C	T	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=1;HaplotypeScore=2.01;MQ=59.03;MQ0=0;OQ=567.81;QD=23.66;SB=-154.18	GT:AD:DP:GL:GQ	0/1:6,18:22:-66.70,-6.63,-18.59:99
+chr1	3018779	rs11808946	C	T	272.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=781.20;QD=16.62;SB=-355.56	GT:AD:DP:GL:GQ	0/1:22,25:44:-94.67,-13.26,-66.92:99
+chr1	3018847	rs2993503	A	G	82.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=59.16;MQ0=0;OQ=1494.14;QD=27.17;SB=-767.73	GT:AD:DP:GL:GQ	1/1:0,55:49:-153.05,-14.78,-0.05:99
+chr1	3018941	rs2072733	C	T	12.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=2.15;MQ=59.46;MQ0=0;OQ=605.93;QD=14.09;SB=-165.23	GT:AD:DP:GL:GQ	0/1:22,21:41:-76.24,-12.36,-69.17:99
+chr1	3019072	rs10909875	C	T	272.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.03;MQ0=0;OQ=534.00;QD=11.12;SB=-208.44	GT:AD:DP:GL:GQ	0/1:28,20:45:-70.25,-13.56,-92.78:99
+chr1	3019517	rs12136745	G	A	248.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=59.62;MQ0=0;OQ=984.07;QD=16.40;SB=-470.51	GT:AD:DP:GL:GQ	0/1:28,32:55:-118.26,-16.57,-87.88:99
+chr1	3019842	rs58968988	G	A	56.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=4.37;MQ=58.92;MQ0=0;OQ=590.92;QD=13.74;SB=-159.22	GT:AD:DP:GL:GQ	0/1:22,21:39:-74.13,-11.75,-67.01:99
+chr1	3020484	rs2981867	G	C	387.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=547.74;QD=12.17;SB=-190.58	GT:AD:DP:GL:GQ	0/1:29,16:44:-71.32,-13.26,-119.60:99
+chr1	3020597	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=37.34;MQ=39.25;MQ0=1;OQ=144.44;QD=4.25;SB=-87.67	GT:AD:DP:GL:GQ	0/1:24,10:27:-25.87,-8.14,-74.17:99
+chr1	3020599	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=45.49;MQ=39.25;MQ0=1;OQ=360.48;QD=10.60;SB=-127.10	GT:AD:DP:GL:GQ	0/1:21,13:31:-48.68,-9.35,-60.35:99
+chr1	3020611	.	A	G	19.24	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=21.97;MQ=37.81;MQ0=1;QD=0.62;SB=-30.78	GT:AD:DP:GL:GQ	0/1:24,7:24:-12.43,-7.23,-80.13:52.02
+chr1	3020613	rs6691894	A	G	41.97	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=22.61;MQ=37.81;MQ0=1;QD=1.35;SB=-10.86	GT:AD:DP:GL:GQ	0/1:24,7:20:-13.51,-6.02,-64.69:74.80
+chr1	3020615	rs6691895	A	G	400.54	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=24.36;MQ=38.97;MQ0=1;QD=12.92;SB=-173.99	GT:AD:DP:GL:GQ	0/1:14,17:24:-50.58,-7.24,-30.30:99
+chr1	3020629	.	A	G	22.23	LowQual	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=19.42;MQ=38.02;MQ0=1;QD=0.85;SB=-32.78	GT:AD:DP:GL:GQ	0/1:21,5:22:-12.14,-6.63,-70.51:55.04
+chr1	3020688	rs6691996	A	G	381.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.90;MQ0=0;OQ=370.45;QD=11.58;SB=-184.01	GT:AD:DP:GL:GQ	0/1:14,18:30:-49.38,-9.05,-56.94:99
+chr1	3020691	rs6695017	T	C	343.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.28;MQ0=0;OQ=495.78;QD=14.58;SB=-192.66	GT:AD:DP:GL:GQ	0/1:16,18:34:-63.11,-10.25,-58.83:99
+chr1	3020744	rs6687292	C	T	95.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=3.34;MQ=56.56;MQ0=0;OQ=522.71;QD=9.33;SB=-137.11	GT:AD:DP:GL:GQ	0/1:34,22:53:-71.53,-15.97,-120.29:99
+chr1	3020924	rs2981866	G	A	33.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=57.17;MQ0=0;OQ=1933.34;QD=38.67;SB=-489.14	GT:AD:DP:GL:GQ	1/1:0,50:49:-196.94,-14.76,-0.02:99
+chr1	3020982	rs10909876	A	G	347.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=54.47;MQ0=0;OQ=796.80;QD=13.06;SB=-340.94	GT:AD:DP:GL:GQ	0/1:29,32:61:-101.36,-18.40,-112.11:99
+chr1	3020998	rs10909877	T	A	2173.88	Indel	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=54.79;MQ0=0;QD=36.23;SB=-1033.22	GT:AD:DP:GL:GQ	1/1:0,60:59:-220.99,-17.77,-0.02:99
+chr1	3021182	.	G	A	53.76	PASS	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.25;MQ0=0;OQ=405.03;QD=13.07;SB=-180.66	GT:AD:DP:GL:GQ	0/1:18,13:30:-52.83,-9.04,-54.54:99
+chr1	3022425	rs2981865	G	C	1.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=57.81;MQ0=0;OQ=743.56;QD=24.79;SB=-346.46	GT:AD:DP:GL:GQ	0/1:9,21:29:-86.39,-8.75,-34.33:99
+chr1	3024466	rs10909878	A	G	299.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=58.18;MQ0=0;OQ=619.53;QD=13.18;SB=-324.31	GT:AD:DP:GL:GQ	0/1:20,27:45:-78.81,-13.57,-80.16:99
+chr1	3024530	rs12141827	T	C	99.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=53.26;MQ0=0;OQ=329.91;QD=8.25;SB=-169.50	GT:AD:DP:GL:GQ	0/1:24,16:37:-47.43,-11.15,-87.85:99
+chr1	3025087	rs6690373	A	G	254.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.67;MQ0=0;OQ=819.31;QD=14.63;SB=-343.19	GT:AD:DP:GL:GQ	0/1:23,33:54:-101.49,-16.28,-89.82:99
+chr1	3025597	rs2981864	A	G	2.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=59.23;MQ0=0;OQ=762.15;QD=25.41;SB=-232.49	GT:AD:DP:GL:GQ	1/1:0,28:25:-82.46,-10.02,-2.66:73.60
+chr1	3025622	rs12409836	A	G	68.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.74;MQ0=0;OQ=225.89;QD=6.11;SB=-44.83	GT:AD:DP:GL:GQ	0/1:23,14:30:-34.92,-9.04,-72.62:99
+chr1	3025639	rs2472822	C	G	79.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.42;MQ0=0;OQ=1446.74;QD=36.17;SB=-602.98	GT:AD:DP:GL:GQ	1/1:0,40:36:-148.28,-10.86,-0.02:99
+chr1	3027473	rs876740	C	T	271.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=2215.19;QD=38.19;SB=-1128.00	GT:AD:DP:GL:GQ	1/1:0,58:56:-225.12,-16.87,-0.02:99
+chr1	3028483	rs2742672	A	G	23.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.51;MQ0=0;OQ=1087.23;QD=28.61;SB=-502.17	GT:AD:DP:GL:GQ	1/1:0,38:36:-112.35,-10.86,-0.04:99
+chr1	3029008	rs2817171	C	A	191.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=59.65;MQ0=0;OQ=733.04;QD=13.57;SB=-391.11	GT:AD:DP:GL:GQ	0/1:29,25:54:-92.85,-16.26,-102.92:99
+chr1	3030045	rs2981863	G	C	66.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.63;MQ0=0;OQ=889.03;QD=17.78;SB=-256.52	GT:AD:DP:GL:GQ	0/1:23,27:46:-106.06,-13.87,-86.32:99
+chr1	3030624	rs2012731	G	A	16.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=4.70;MQ=59.61;MQ0=0;OQ=1536.02;QD=32.00;SB=-433.32	GT:AD:DP:GL:GQ	1/1:0,48:41:-157.21,-12.36,-0.02:99
+chr1	3031379	rs2817172	T	C	144.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=1381.66;QD=30.70;SB=-636.88	GT:AD:DP:GL:GQ	1/1:0,45:44:-141.79,-13.27,-0.04:99
+chr1	3032241	rs2472820	G	A	108.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=58.74;MQ0=0;OQ=572.26;QD=15.47;SB=-176.66	GT:AD:DP:GL:GQ	0/1:19,18:36:-71.36,-10.85,-60.89:99
+chr1	3032694	.	C	T	55.78	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=60.00;MQ0=0;OQ=546.49;QD=14.77;SB=-205.90	GT:AD:DP:GL:GQ	0/1:19,18:36:-68.78,-10.85,-58.80:99
+chr1	3033426	rs12410830	A	G	6.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=3.60;MQ=59.16;MQ0=0;OQ=614.56;QD=12.29;SB=-235.29	GT:AD:DP:GL:GQ	0/1:27,23:49:-79.50,-14.76,-107.00:99
+chr1	3034041	rs2817174	T	C	277.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.38;MQ0=0;OQ=1499.60;QD=26.78;SB=-664.93	GT:AD:DP:GL:GQ	1/1:0,56:48:-153.59,-14.48,-0.05:99
+chr1	3034512	rs35529420	C	T	72.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.41;MQ=59.18;MQ0=0;OQ=899.04;QD=15.77;SB=-264.19	GT:AD:DP:GL:GQ	0/1:27,29:53:-109.16,-15.97,-86.82:99
+chr1	3034731	rs35951269	T	C	58.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=2.40;MQ=58.97;MQ0=0;OQ=780.41;QD=12.39;SB=-339.30	GT:AD:DP:GL:GQ	0/1:36,27:63:-100.30,-18.98,-146.89:99
+chr1	3035225	rs2742670	A	G	75.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.62;MQ=60.00;MQ0=0;OQ=1811.56;QD=33.55;SB=-920.03	GT:AD:DP:GL:GQ	1/1:0,54:51:-184.76,-15.36,-0.02:99
+chr1	3035475	rs2817175	T	C	135.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=57.17;MQ0=0;OQ=1487.18;QD=29.74;SB=-663.57	GT:AD:DP:GL:GQ	1/1:0,50:49:-152.36,-14.79,-0.06:99
+chr1	3035871	rs2817176	A	G	10.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=4.69;MQ=58.80;MQ0=0;OQ=1642.91;QD=28.33;SB=-799.47	GT:AD:DP:GL:GQ	1/1:0,58:54:-167.94,-16.30,-0.07:99
+chr1	3036323	rs2817177	T	C	492.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=1385.60;QD=34.64;SB=-536.41	GT:AD:DP:GL:GQ	1/1:0,40:39:-142.16,-11.75,-0.01:99
+chr1	3036571	rs35625823	T	G	1.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.02;HRun=1;HaplotypeScore=8.04;MQ=58.17;MQ0=0;OQ=682.10;QD=13.37;SB=-105.91	GT:AD:DP:GL:GQ	0/1:25,25:50:-86.26,-14.76,-86.59:99
+chr1	3036686	rs35201154	G	T	212.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.64;MQ0=0;OQ=542.18;QD=11.30;SB=-157.49	GT:AD:DP:GL:GQ	0/1:27,21:48:-71.97,-14.46,-93.11:99
+chr1	3037032	rs2788086	A	G	87.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.14;MQ0=0;OQ=1440.07;QD=26.67;SB=-745.96	GT:AD:DP:GL:GQ	1/1:1,53:49:-151.81,-14.78,-4.21:99
+chr1	3037112	rs2817178	T	C	138.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.50;MQ=59.01;MQ0=0;OQ=1783.83;QD=33.66;SB=-780.99	GT:AD:DP:GL:GQ	1/1:0,53:51:-182.00,-15.37,-0.03:99
+chr1	3037307	rs10797378	T	C	263.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=57.77;MQ0=0;OQ=673.03;QD=12.02;SB=-270.24	GT:AD:DP:GL:GQ	0/1:24,31:50:-85.66,-15.07,-91.32:99
+chr1	3037312	rs2788087	A	G	5.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=3;HaplotypeScore=4.61;MQ=57.43;MQ0=0;OQ=719.26;QD=12.40;SB=-323.12	GT:AD:DP:GL:GQ	0/1:28,30:54:-91.49,-16.28,-101.63:99
+chr1	3037323	rs10909881	G	A	169.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=4.31;MQ=57.69;MQ0=0;OQ=859.60;QD=14.57;SB=-445.45	GT:AD:DP:GL:GQ	0/1:30,29:55:-105.83,-16.59,-85.38:99
+chr1	3038158	rs2817180	T	C	101.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.60;MQ0=0;OQ=1662.63;QD=29.17;SB=-686.71	GT:AD:DP:GL:GQ	1/1:0,57:52:-169.90,-15.69,-0.05:99
+chr1	3038602	rs35360783	A	G	220.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.65;MQ0=0;OQ=463.18;QD=8.74;SB=-235.89	GT:AD:DP:GL:GQ	0/1:32,21:53:-65.58,-15.98,-127.69:99
+chr1	3039222	rs12024620	C	T	40.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=4.42;MQ=59.20;MQ0=0;OQ=839.66;QD=14.48;SB=-156.21	GT:AD:DP:GL:GQ	0/1:32,26:56:-104.13,-16.88,-98.69:99
+chr1	3039241	rs12021948	G	C	56.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.56;MQ0=0;OQ=946.79;QD=17.86;SB=-223.20	GT:AD:DP:GL:GQ	0/1:25,28:53:-113.94,-15.98,-109.97:99
+chr1	3039433	rs12740389	C	T	216.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.36;MQ0=0;OQ=1244.61;QD=19.15;SB=-628.67	GT:AD:DP:GL:GQ	0/1:28,37:63:-146.73,-18.98,-86.83:99
+chr1	3039715	rs35999894	C	T	445.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1131.40;QD=18.86;SB=-581.12	GT:AD:DP:GL:GQ	0/1:26,34:58:-133.91,-17.48,-78.73:99
+chr1	3039945	rs34733164	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=4;HaplotypeScore=2.38;MQ=59.17;MQ0=0;OQ=103.23;QD=3.69;SB=-48.95	GT:AD:DP:GL:GQ	0/1:18,10:23:-20.53,-6.93,-62.39:99
+chr1	3040081	rs12022170	G	A	254.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.17;MQ0=0;OQ=717.02;QD=15.93;SB=-327.88	GT:AD:DP:GL:GQ	0/1:23,22:43:-87.95,-12.96,-65.92:99
+chr1	3040191	rs12028027	T	C	223.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.03;MQ0=0;OQ=428.68;QD=8.93;SB=-212.28	GT:AD:DP:GL:GQ	0/1:28,20:45:-59.72,-13.57,-97.74:99
+chr1	3040222	rs12027117	A	G	229.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=59.46;MQ0=0;OQ=557.56;QD=12.97;SB=-281.47	GT:AD:DP:GL:GQ	0/1:21,22:42:-71.69,-12.65,-82.66:99
+chr1	3040357	rs10909883	A	G	344.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.62;MQ0=0;OQ=754.58;QD=12.37;SB=-348.58	GT:AD:DP:GL:GQ	0/1:28,33:59:-96.53,-17.79,-109.54:99
+chr1	3040454	rs12120879	C	G	45.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=2.33;MQ=58.92;MQ0=0;OQ=1009.80;QD=18.03;SB=-357.43	GT:AD:DP:GL:GQ	0/1:27,29:53:-120.25,-15.98,-106.43:99
+chr1	3040798	rs35848773	T	C	267.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.65;MQ0=0;OQ=685.07;QD=12.69;SB=-277.27	GT:AD:DP:GL:GQ	0/1:21,33:48:-86.26,-14.47,-82.32:99
+chr1	3040900	rs12731315	G	C	3.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=3;HaplotypeScore=3.13;MQ=60.00;MQ0=0;OQ=656.27;QD=17.74;SB=-310.23	GT:AD:DP:GL:GQ	0/1:18,19:37:-80.07,-11.16,-76.94:99
+chr1	3041210	rs12724921	T	A	454.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=611.82;QD=12.00;SB=-313.55	GT:AD:DP:GL:GQ	0/1:28,23:48:-78.92,-14.46,-101.94:99
+chr1	3041481	rs909509	A	G	48.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=4.12;MQ=59.51;MQ0=0;OQ=373.32;QD=7.94;SB=-138.54	GT:AD:DP:GL:GQ	0/1:28,18:38:-52.08,-11.46,-81.04:99
+chr1	3041609	rs12725529	T	C	111.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=58.62;MQ0=0;OQ=287.04;QD=7.76;SB=-113.62	GT:AD:DP:GL:GQ	0/1:21,16:34:-42.24,-10.25,-81.99:99
+chr1	3042125	rs7535865	A	C	10.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=7.89;MQ=58.97;MQ0=0;OQ=623.66;QD=13.86;SB=-308.90	GT:AD:DP:GL:GQ	0/1:18,27:40:-77.70,-12.05,-63.90:99
+chr1	3042361	rs4648363	C	T	227.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.42;MQ0=0;OQ=413.64;QD=10.34;SB=-159.64	GT:AD:DP:GL:GQ	0/1:26,14:37:-55.80,-11.16,-73.37:99
+chr1	3043023	rs35794895	G	A	293.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=58.64;MQ0=0;OQ=693.50;QD=14.45;SB=-320.87	GT:AD:DP:GL:GQ	0/1:21,26:42:-85.30,-12.67,-60.57:99
+chr1	3043817	rs12741594	A	T	497.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=877.02;QD=14.62;SB=-406.56	GT:AD:DP:GL:GQ	0/1:31,29:60:-109.06,-18.07,-115.07:99
+chr1	3043966	rs2235176	T	C	337.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=677.48;QD=12.55;SB=-208.33	GT:AD:DP:GL:GQ	0/1:27,27:53:-87.00,-15.97,-104.05:99
+chr1	3044349	rs35877876	C	T	270.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.61;MQ0=0;OQ=969.79;QD=16.44;SB=-358.48	GT:AD:DP:GL:GQ	0/1:30,29:59:-118.04,-17.77,-107.71:99
+chr1	3045481	rs10797379	T	C	126.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.62;MQ0=0;OQ=1290.17;QD=29.32;SB=-604.23	GT:AD:DP:GL:GQ	1/1:0,44:42:-132.64,-12.67,-0.04:99
+chr1	3045736	rs10797380	A	G	12.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=4.39;MQ=59.03;MQ0=0;OQ=1384.53;QD=28.84;SB=-697.60	GT:AD:DP:GL:GQ	1/1:0,48:44:-142.08,-13.27,-0.04:99
+chr1	3046509	rs7354964	C	G	181.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.06;MQ0=0;OQ=756.10;QD=18.90;SB=-387.98	GT:AD:DP:GL:GQ	0/1:19,21:40:-90.95,-12.05,-80.97:99
+chr1	3047001	rs2817181	A	G	378.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=2402.64;QD=34.32;SB=-979.90	GT:AD:DP:GL:GQ	1/1:0,70:68:-243.87,-20.48,-0.03:99
+chr1	3047521	rs7538096	T	C	291.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=59.64;MQ0=0;OQ=861.01;QD=13.45;SB=-250.18	GT:AD:DP:GL:GQ	0/1:31,33:64:-108.67,-19.29,-124.47:99
+chr1	3048093	rs2742666	T	C	36.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=6.22;MQ=57.02;MQ0=0;OQ=594.94;QD=12.93;SB=-209.63	GT:AD:DP:GL:GQ	0/1:23,23:42:-75.43,-12.65,-85.93:99
+chr1	3048098	rs2742665	A	C	100.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=57.17;MQ0=0;OQ=617.42;QD=15.44;SB=-256.42	GT:AD:DP:GL:GQ	0/1:17,23:38:-76.47,-11.45,-58.49:99
+chr1	3048109	rs2817183	A	G	380.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.05;MQ0=0;OQ=578.38;QD=14.46;SB=-222.56	GT:AD:DP:GL:GQ	0/1:19,21:39:-72.87,-11.75,-75.47:99
+chr1	3048230	rs2817184	G	A	543.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=743.48;QD=15.82;SB=-334.86	GT:AD:DP:GL:GQ	0/1:23,24:46:-91.50,-13.86,-76.30:99
+chr1	3050041	rs6684093	C	T	40.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=5.68;MQ=58.71;MQ0=0;OQ=937.27;QD=17.36;SB=-475.05	GT:AD:DP:GL:GQ	0/1:24,30:51:-112.38,-15.37,-76.51:99
+chr1	3051143	rs1875449	C	A	6.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=5.78;MQ=59.44;MQ0=0;OQ=367.51;QD=8.96;SB=-206.89	GT:AD:DP:GL:GQ	0/1:23,18:37:-51.19,-11.15,-77.66:99
+chr1	3052735	rs2817187	G	T	176.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.61;MQ0=0;OQ=2057.17;QD=34.87;SB=-1041.53	GT:AD:DP:GL:GQ	1/1:0,59:58:-209.32,-17.47,-0.02:99
+chr1	3066300	.	C	T	85.23	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=59.28;MQ0=0;OQ=957.84;QD=16.51;SB=-344.34	GT:AD:DP:GL:GQ	0/1:29,29:58:-116.54,-17.47,-102.34:99
+chr1	3068821	.	G	A	12.77	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.86;MQ=59.41;MQ0=0;OQ=492.51;QD=12.63;SB=-226.54	GT:AD:DP:GL:GQ	0/1:19,20:34:-62.79,-10.25,-59.33:99
+chr1	3069601	rs34175350	G	C	4.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=15.60;MQ0=24;OQ=307.57;QD=4.16;SB=-10.00	GT:AD:DP:GL:GQ	0/1:61,13:26:-41.87,-7.83,-71.98:99
+chr1	3071991	.	T	C	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=7.33;MQ=54.00;MQ0=2;OQ=261.16;QD=5.02;SB=-67.51	GT:AD:DP:GL:GQ	0/1:33,19:40:-41.45,-12.05,-111.58:99
+chr1	3072015	.	C	T	17.95	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=6.27;MQ=51.72;MQ0=4;QD=0.46;SB=-17.49	GT:AD:DP:GL:GQ	0/1:29,10:20:-11.10,-6.03,-56.69:50.72
+chr1	3077233	rs10909887	A	T	53.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.52;MQ=59.65;MQ0=0;OQ=1671.94;QD=31.55;SB=-810.23	GT:AD:DP:GL:GQ	1/1:0,53:48:-170.81,-14.47,-0.03:99
+chr1	3078302	rs2817127	C	G	3.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=58.92;MQ0=0;OQ=1590.78;QD=40.79;SB=-669.44	GT:AD:DP:GL:GQ	1/1:0,39:38:-162.68,-11.46,-0.02:99
+chr1	3078602	rs2651936	C	T	556.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1763.78;QD=38.34;SB=-617.01	GT:AD:DP:GL:GQ	1/1:0,46:45:-179.97,-13.55,-0.01:99
+chr1	3078803	rs2817128	T	C	41.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=0.92;MQ=58.79;MQ0=0;OQ=1700.76;QD=31.50;SB=-627.85	GT:AD:DP:GL:GQ	1/1:0,54:53:-173.71,-15.98,-0.05:99
+chr1	3078920	rs2817129	G	C	420.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2270.90;QD=42.85;SB=-927.24	GT:AD:DP:GL:GQ	1/1:0,53:53:-230.70,-15.98,-0.02:99
+chr1	3079836	rs3795268	G	A	518.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2012.53;QD=38.70;SB=-765.66	GT:AD:DP:GL:GQ	1/1:0,52:51:-204.85,-15.36,-0.01:99
+chr1	3082486	rs61759169	A	T	0.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=17.96;MQ=49.98;MQ0=1;OQ=467.66;QD=5.85;SB=-63.76	GT:AD:DP:GL:GQ	0/1:57,23:74:-72.34,-22.29,-212.74:99
+chr1	3082576	rs59307218	T	C	89.31	Indel	AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=1;HaplotypeScore=16.28;MQ=58.32;MQ0=0;QD=0.84;SB=-6.84	GT:AD:DP:GL:GQ	0/1:94,12:100:-42.34,-30.13,-353.31:99
+chr1	3082715	rs61759170	T	C	0.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=1;HaplotypeScore=13.70;MQ=54.13;MQ0=0;OQ=433.59;QD=4.61;SB=-120.39	GT:AD:DP:GL:GQ	0/1:66,28:84:-71.95,-25.31,-255.13:99
+chr1	3082724	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=20.17;MQ=53.56;MQ0=0;OQ=265.77;QD=3.09;SB=-1.90	GT:AD:DP:GL:GQ	0/1:64,21:77:-55.36,-25.50,-226.03:99
+chr1	3082730	rs61759171	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=25.02;MQ=53.60;MQ0=0;OQ=115.19;QD=1.46;SB=35.65	GT:AD:DP:GL:GQ	0/1:62,16:69:-35.59,-20.79,-209.49:99
+chr1	3083610	rs2817131	T	C	1.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=7.31;MQ=58.76;MQ0=0;OQ=2679.05;QD=35.25;SB=-1269.49	GT:AD:DP:GL:GQ	1/1:0,76:75:-271.51,-22.59,-0.03:99
+chr1	3086215	rs868718	G	A	224.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.60;MQ0=0;OQ=2257.57;QD=38.92;SB=-929.74	GT:AD:DP:GL:GQ	1/1:0,58:57:-229.36,-17.17,-0.02:99
+chr1	3086338	rs2817132	T	C	256.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=1749.39;QD=34.30;SB=-792.14	GT:AD:DP:GL:GQ	1/1:0,51:49:-178.54,-14.76,-0.01:99
+chr1	3086971	.	G	A	6.54	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.12;MQ=59.63;MQ0=0;OQ=869.92;QD=17.06;SB=-366.15	GT:AD:DP:GL:GQ	0/1:23,28:49:-105.05,-14.78,-70.17:99
+chr1	3087284	rs28576654	G	A	0.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=8.45;MQ=55.21;MQ0=0;OQ=1827.21;QD=37.29;SB=-761.03	GT:AD:DP:GL:GQ	1/1:1,48:47:-186.32,-14.16,-0.02:99
+chr1	3087324	rs36042320	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=36.16;MQ=53.71;MQ0=0;OQ=1199.13;QD=20.32;SB=-596.19	GT:AD:DP:GL:GQ	1/1:10,49:47:-136.03,-14.18,-12.56:16.27
+chr1	3087368	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=62.15;MQ=52.02;MQ0=2;OQ=84.05;QD=0.99;SB=68.22	GT:AD:DP:GL:GQ	0/1:64,20:65:-31.27,-19.58,-199.12:99
+chr1	3087405	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=113.18;MQ=45.62;MQ0=12;OQ=152.20;QD=1.23;SB=83.17	GT:AD:DP:GL:GQ	0/1:93,25:100:-54.91,-36.41,-286.94:99
+chr1	3087421	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=108;Dels=0.01;HRun=1;HaplotypeScore=157.91;MQ=45.44;MQ0=13;OQ=317.87;QD=2.94;SB=62.22	GT:AD:DP:GL:GQ	0/1:65,42:72:-56.46,-21.39,-222.98:99
+chr1	3087430	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=100;Dels=0.09;HRun=0;HaplotypeScore=131.45;MQ=45.35;MQ0=13;OQ=71.40;QD=0.71;SB=68.23	GT:AD:DP:GL:GQ	0/1:57,34:61:-28.82,-18.40,-174.57:99
+chr1	3087432	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=125.43;MQ=44.68;MQ0=16;OQ=349.00;QD=3.39;SB=68.23	GT:AD:DP:GL:GQ	0/1:85,18:67:-58.39,-20.20,-173.08:99
+chr1	3087446	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=34.86;MQ=42.41;MQ0=15;OQ=253.15;QD=2.81;SB=53.16	GT:AD:DP:GL:GQ	0/1:47,43:54:-44.89,-16.29,-135.66:99
+chr1	3087456	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=33.91;MQ=40.94;MQ0=15;OQ=574.41;QD=6.38;SB=41.15	GT:AD:DP:GL:GQ	0/1:47,43:59:-78.52,-17.79,-127.78:99
+chr1	3087469	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=37.75;MQ=38.93;MQ0=14;OQ=420.06;QD=4.94;SB=41.09	GT:AD:DP:GL:GQ	0/1:56,29:63:-64.29,-19.00,-146.93:99
+chr1	3087482	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=75.90;MQ=37.38;MQ0=13;OQ=93.48;QD=1.23;SB=56.14	GT:AD:DP:GL:GQ	0/1:55,21:54:-28.92,-16.29,-150.91:99
+chr1	3087484	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=59.86;MQ=36.69;MQ0=13;OQ=224.49;QD=2.95;SB=47.15	GT:AD:DP:GL:GQ	0/1:64,12:51:-41.12,-15.38,-130.32:99
+chr1	3087496	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.18;HRun=0;HaplotypeScore=92.35;MQ=35.16;MQ0=7;OQ=80.55;QD=1.41;SB=-35.75	GT:AD:DP:GL:GQ	0/1:30,16:29:-20.09,-8.75,-100.50:99
+chr1	3087498	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=70.78;MQ=33.76;MQ0=7;OQ=147.15;QD=2.58;SB=-95.04	GT:AD:DP:GL:GQ	0/1:41,16:33:-27.95,-9.95,-82.07:99
+chr1	3087509	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=61;Dels=0.05;HRun=0;HaplotypeScore=74.81;MQ=32.58;MQ0=5;OQ=64.70;QD=1.06;SB=56.11	GT:AD:DP:GL:GQ	0/1:52,6:35:-20.32,-10.56,-93.36:97.54
+chr1	3087512	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=54.96;MQ=31.97;MQ0=5;OQ=503.11;QD=8.11;SB=-236.10	GT:AD:DP:GL:GQ	0/1:31,31:45:-67.16,-13.57,-94.41:99
+chr1	3087536	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=33.03;MQ=32.40;MQ0=3;OQ=59.37;QD=0.74;SB=89.25	GT:AD:DP:GL:GQ	0/1:72,7:63:-28.22,-18.99,-181.57:92.21
+chr1	3087538	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=37.44;MQ=32.40;MQ0=3;OQ=247.27;QD=3.09;SB=80.25	GT:AD:DP:GL:GQ	0/1:65,15:63:-46.99,-18.98,-180.33:99
+chr1	3087608	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=168;Dels=0.01;HRun=0;HaplotypeScore=54.40;MQ=37.28;MQ0=13;OQ=1887.72;QD=11.24;SB=-729.24	GT:AD:DP:GL:GQ	0/1:104,63:145:-235.47,-43.42,-271.37:99
+chr1	3087617	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=0;HaplotypeScore=53.68;MQ=37.94;MQ0=15;OQ=1635.04;QD=8.84;SB=-493.28	GT:AD:DP:GL:GQ	0/1:114,71:160:-215.01,-48.22,-344.93:99
+chr1	3087664	.	A	G	18.84	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=189;Dels=0.01;HRun=0;HaplotypeScore=131.51;MQ=40.84;MQ0=15;QD=0.10;SB=241.96	GT:AD:DP:GL:GQ	0/1:170,18:163:-53.97,-48.81,-580.79:51.62
+chr1	3087667	.	C	T	165.92	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=188;Dels=0.01;HRun=0;HaplotypeScore=132.64;MQ=41.11;MQ0=15;QD=0.88;SB=179.60	GT:AD:DP:GL:GQ	0/1:167,20:158:-67.18,-47.30,-486.26:99
+chr1	3087668	.	A	G	310.08	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=187;Dels=0.01;HRun=1;HaplotypeScore=124.54;MQ=41.17;MQ0=15;QD=1.66;SB=124.04	GT:AD:DP:GL:GQ	0/1:158,28:160:-82.20,-47.90,-540.31:99
+chr1	3087734	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=1;HaplotypeScore=13.23;MQ=44.53;MQ0=2;OQ=55.34;QD=0.49;SB=-14.90	GT:AD:DP:GL:GQ	0/1:101,11:104:-40.16,-31.34,-369.37:88.18
+chr1	3087747	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=23.95;MQ=43.49;MQ0=2;OQ=1649.29;QD=15.71;SB=-709.98	GT:AD:DP:GL:GQ	0/1:48,57:100:-198.34,-30.13,-180.84:99
+chr1	3087772	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=0;HaplotypeScore=99.40;MQ=37.75;MQ0=7;OQ=762.57;QD=5.73;SB=-239.63	GT:AD:DP:GL:GQ	0/1:102,30:117:-114.83,-35.29,-281.68:99
+chr1	3087833	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=1;HaplotypeScore=261.50;MQ=29.30;MQ0=7;OQ=1486.23;QD=9.78;SB=-676.51	GT:AD:DP:GL:GQ	0/1:100,52:130:-191.07,-39.17,-253.74:99
+chr1	3087850	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=106.63;MQ=29.08;MQ0=7;OQ=1055.92;QD=7.23;SB=-459.23	GT:AD:DP:GL:GQ	0/1:100,46:125:-146.56,-37.68,-289.33:99
+chr1	3087853	.	C	A	11.81	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=84.96;MQ=29.13;MQ0=6;QD=0.08;SB=22.69	GT:AD:DP:GL:GQ	0/1:134,14:133:-44.49,-40.06,-434.86:44.36
+chr1	3087861	.	A	C	168.29	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=23.28;MQ=29.00;MQ0=4;QD=1.25;SB=-17.42	GT:AD:DP:GL:GQ	0/1:115,20:120:-56.26,-36.15,-379.05:99
+chr1	3087900	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=22.94;MQ=28.28;MQ0=1;OQ=423.78;QD=5.81;SB=-214.40	GT:AD:DP:GL:GQ	0/1:51,22:68:-66.15,-20.49,-189.92:99
+chr1	3087911	.	C	T	880.08	SnpCluster	AC=1;AF=0.50;AN=2;DP=69;Dels=0.03;HRun=0;HaplotypeScore=32.89;MQ=28.46;MQ0=0;QD=12.75;SB=-315.83	GT:AD:DP:GL:GQ	0/1:40,27:49:-105.45,-14.16,-69.50:99
+chr1	3087912	.	A	G	1267.81	SnpCluster	AC=1;AF=0.50;AN=2;DP=68;Dels=0.03;HRun=1;HaplotypeScore=32.88;MQ=28.45;MQ0=0;QD=18.64;SB=-474.20	GT:AD:DP:GL:GQ	0/1:22,44:48:-143.92,-13.86,-20.32:64.59
+chr1	3087920	.	G	A	574.31	SnpCluster	AC=1;AF=0.50;AN=2;DP=74;Dels=0.04;HRun=0;HaplotypeScore=182.60;MQ=28.60;MQ0=0;QD=7.76;SB=-289.69	GT:AD:DP:GL:GQ	0/1:50,21:71:-81.21,-20.50,-157.25:99
+chr1	3087952	.	G	A	1075.62	Indel	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=58.78;MQ=31.99;MQ0=0;QD=13.62;SB=-555.39	GT:AD:DP:GL:GQ	0/1:45,34:75:-133.45,-22.61,-136.49:99
+chr1	3087978	.	A	G	38.22	DPFilter;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=109;Dels=0.02;HRun=1;HaplotypeScore=54.40;MQ=36.04;MQ0=0;QD=0.35;SB=94.63	GT:AD:DP:GL:GQ	0/1:93,14:103:-37.54,-30.43,-360.90:71.06
+chr1	3088004	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=30.72;MQ=40.10;MQ0=2;OQ=423.13;QD=3.00;SB=9.29	GT:AD:DP:GL:GQ	0/1:121,20:123:-82.68,-37.08,-335.63:99
+chr1	3088013	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=142;Dels=0.03;HRun=0;HaplotypeScore=47.98;MQ=41.19;MQ0=4;OQ=426.97;QD=3.01;SB=-54.18	GT:AD:DP:GL:GQ	0/1:112,26:133:-84.85,-38.87,-412.97:99
+chr1	3088015	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=42.51;MQ=41.21;MQ0=4;OQ=465.21;QD=3.21;SB=-60.11	GT:AD:DP:GL:GQ	0/1:116,29:131:-89.28,-39.48,-409.01:99
+chr1	3088100	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=132;Dels=0.00;HRun=0;HaplotypeScore=4.53;MQ=40.45;MQ0=11;OQ=130.52;QD=0.99;SB=-31.41	GT:AD:DP:GL:GQ	0/1:119,13:106:-48.30,-31.97,-302.63:99
+chr1	3088101	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=4.53;MQ=40.49;MQ0=10;OQ=71.07;QD=0.55;SB=-5.78	GT:AD:DP:GL:GQ	0/1:117,11:111:-47.37,-36.98,-326.83:99
+chr1	3088217	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=80;Dels=0.01;HRun=0;HaplotypeScore=17.08;MQ=42.86;MQ0=1;OQ=126.54;QD=1.58;SB=-85.23	GT:AD:DP:GL:GQ	0/1:66,13:74:-37.94,-22.00,-241.16:99
+chr1	3088220	rs34886760	A	G	0.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.01;HRun=1;HaplotypeScore=12.97;MQ=43.96;MQ0=1;OQ=1584.16;QD=20.84;SB=-521.89	GT:AD:DP:GL:GQ	0/1:11,64:65:-181.29,-19.59,-39.63:99
+chr1	3088304	rs61759175	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.08;HRun=0;HaplotypeScore=55.59;MQ=46.00;MQ0=11;OQ=251.71;QD=2.13;SB=81.71	GT:AD:DP:GL:GQ	0/1:90,18:102:-58.89,-30.43,-301.97:99
+chr1	3088575	rs2817134	T	C	3.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=5.64;MQ=59.45;MQ0=0;OQ=1472.39;QD=35.06;SB=-604.20	GT:AD:DP:GL:GQ	1/1:0,42:42:-150.84,-12.65,-0.02:99
+chr1	3088745	rs2651931	C	T	32.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.49;MQ=59.44;MQ0=0;OQ=1502.67;QD=36.65;SB=-632.85	GT:AD:DP:GL:GQ	1/1:0,40:38:-153.86,-11.45,-0.01:99
+chr1	3088761	rs2817135	T	C	98.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.39;MQ0=0;OQ=1114.54;QD=29.33;SB=-484.51	GT:AD:DP:GL:GQ	1/1:0,38:36:-115.07,-10.86,-0.04:99
+chr1	3089054	rs950200	A	G	135.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.38;MQ0=0;OQ=1494.35;QD=33.21;SB=-586.20	GT:AD:DP:GL:GQ	1/1:0,45:43:-153.04,-12.95,-0.02:99
+chr1	3091593	rs9660914	G	A	174.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=2157.13;QD=34.24;SB=-1073.97	GT:AD:DP:GL:GQ	1/1:0,63:58:-219.33,-17.49,-0.04:99
+chr1	3093686	rs4233024	C	T	199.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.75;MQ0=0;OQ=1964.65;QD=37.78;SB=-829.97	GT:AD:DP:GL:GQ	1/1:0,52:51:-200.08,-15.37,-0.03:99
+chr1	3094490	rs10752733	A	G	125.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1561.08;QD=30.61;SB=-635.88	GT:AD:DP:GL:GQ	1/1:0,51:49:-159.74,-14.78,-0.04:99
+chr1	3094942	rs2817136	G	A	89.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1690.06;QD=36.74;SB=-568.32	GT:AD:DP:GL:GQ	1/1:0,46:44:-172.61,-13.26,-0.02:99
+chr1	3095136	rs2817138	T	G	4.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=58.92;MQ0=0;OQ=1072.43;QD=24.94;SB=-511.45	GT:AD:DP:GL:GQ	1/1:0,43:37:-110.87,-11.16,-0.04:99
+chr1	3095423	rs2651919	G	T	722.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2110.88;QD=35.78;SB=-952.39	GT:AD:DP:GL:GQ	1/1:0,59:58:-214.69,-17.47,-0.02:99
+chr1	3095697	rs2651918	T	C	14.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=3.68;MQ=59.20;MQ0=0;OQ=1955.56;QD=33.72;SB=-956.98	GT:AD:DP:GL:GQ	1/1:0,58:55:-199.16,-16.57,-0.02:99
+chr1	3095769	rs2817139	A	G	514.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.29;MQ0=0;OQ=1684.86;QD=27.18;SB=-755.66	GT:AD:DP:GL:GQ	1/1:0,62:53:-172.12,-15.99,-0.05:99
+chr1	3095922	rs7530075	G	A	526.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1784.81;QD=39.66;SB=-851.64	GT:AD:DP:GL:GQ	1/1:0,45:45:-182.08,-13.55,-0.01:99
+chr1	3096128	rs2651917	C	G	97.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.80;MQ0=0;OQ=1717.27;QD=36.54;SB=-542.46	GT:AD:DP:GL:GQ	1/1:0,47:42:-175.34,-12.67,-0.03:99
+chr1	3096165	rs7545798	A	G	335.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=1218.45;QD=30.46;SB=-546.04	GT:AD:DP:GL:GQ	1/1:0,40:39:-125.47,-11.76,-0.04:99
+chr1	3096243	rs7545871	A	G	179.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1274.76;QD=30.35;SB=-481.26	GT:AD:DP:GL:GQ	1/1:0,42:39:-131.09,-11.76,-0.02:99
+chr1	3096257	rs2651916	C	T	670.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=1810.18;QD=36.20;SB=-763.02	GT:AD:DP:GL:GQ	1/1:0,50:47:-184.62,-14.16,-0.02:99
+chr1	3096476	rs2817140	A	G	6.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=1038.30;QD=28.84;SB=-515.16	GT:AD:DP:GL:GQ	1/1:0,36:34:-107.45,-10.26,-0.04:99
+chr1	3096661	rs61759179	G	A	1.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=5.55;MQ=53.62;MQ0=2;OQ=1172.74;QD=30.07;SB=-520.65	GT:AD:DP:GL:GQ	1/1:8,31:31:-120.87,-9.34,-0.01:93.29
+chr1	3096814	rs2817141	T	C	22.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=1.30;MQ=59.19;MQ0=0;OQ=1269.17;QD=27.59;SB=-620.79	GT:AD:DP:GL:GQ	1/1:0,46:42:-130.56,-12.68,-0.06:99
+chr1	3097140	rs1875451	C	T	277.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.63;MQ0=0;OQ=1807.86;QD=35.45;SB=-805.30	GT:AD:DP:GL:GQ	1/1:0,51:46:-184.39,-13.86,-0.02:99
+chr1	3098276	rs2651914	T	G	143.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=2148.66;QD=35.22;SB=-1029.38	GT:AD:DP:GL:GQ	1/1:0,61:61:-218.47,-18.37,-0.02:99
+chr1	3098356	rs10737190	G	A	615.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=3298.92;QD=39.75;SB=-1410.68	GT:AD:DP:GL:GQ	1/1:0,83:81:-328.89,-24.40,-0.02:99
+chr1	3098377	rs6685614	G	A	280.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.78;MQ0=0;OQ=3233.06;QD=38.95;SB=-1261.68	GT:AD:DP:GL:GQ	1/1:0,83:82:-327.11,-24.71,-0.03:99
+chr1	3099011	rs7539775	G	A	230.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=59.47;MQ0=0;OQ=1818.76;QD=34.98;SB=-678.01	GT:AD:DP:GL:GQ	1/1:1,51:49:-188.18,-14.77,-2.72:99
+chr1	3100277	rs2651913	C	G	465.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1755.38;QD=41.79;SB=-899.81	GT:AD:DP:GL:GQ	1/1:0,42:41:-179.13,-12.35,-0.01:99
+chr1	3100595	rs2651912	T	C	68.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=4.22;MQ=58.95;MQ0=0;OQ=646.58;QD=10.43;SB=-279.12	GT:AD:DP:GL:GQ	0/1:33,29:56:-84.82,-16.88,-119.30:99
+chr1	3104232	.	G	A	37.52	PASS	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=60.00;MQ0=0;OQ=572.60;QD=16.36;SB=-260.57	GT:AD:DP:GL:GQ	0/1:16,19:33:-70.49,-9.94,-51.89:99
+chr1	3105581	rs950449	C	G	114.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=352.20;QD=14.09;SB=-136.76	GT:AD:DP:GL:GQ	0/1:14,11:24:-45.74,-7.23,-56.39:99
+chr1	3106518	rs2651923	T	C	555.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.18;MQ0=0;OQ=1262.70;QD=28.70;SB=-607.93	GT:AD:DP:GL:GQ	1/1:0,44:40:-129.89,-12.07,-0.04:99
+chr1	3110061	rs2817142	T	C	84.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=58.76;MQ0=0;OQ=950.22;QD=27.95;SB=-463.20	GT:AD:DP:GL:GQ	1/1:1,33:31:-98.64,-9.35,-0.03:93.20
+chr1	3113619	rs2817143	T	C	475.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=1485.25;QD=30.31;SB=-541.01	GT:AD:DP:GL:GQ	1/1:0,49:46:-152.15,-13.87,-0.04:99
+chr1	3119305	.	C	T	6.85	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=482.22;QD=12.06;SB=-197.28	GT:AD:DP:GL:GQ	0/1:23,17:38:-62.96,-11.45,-76.10:99
+chr1	3119433	rs60892783	T	A	341.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.85;MQ0=0;OQ=778.15;QD=15.26;SB=-381.44	GT:AD:DP:GL:GQ	0/1:26,25:51:-96.46,-15.36,-96.60:99
+chr1	3124191	rs12124147	C	T	18.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=4;HaplotypeScore=1.41;MQ=60.00;MQ0=0;OQ=2106.36;QD=38.30;SB=-923.21	GT:AD:DP:GL:GQ	1/1:0,55:54:-214.24,-16.27,-0.02:99
+chr1	3125697	.	G	A	48.02	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=3.90;MQ=59.58;MQ0=0;OQ=894.40;QD=16.26;SB=-426.44	GT:AD:DP:GL:GQ	0/1:28,27:53:-108.70,-15.98,-81.48:99
+chr1	3133804	rs10737191	T	C	216.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.05;MQ0=0;OQ=1310.90;QD=29.79;SB=-629.85	GT:AD:DP:GL:GQ	1/1:0,44:43:-134.73,-12.98,-0.05:99
+chr1	3137939	rs2651921	T	C	31.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.62;MQ=57.88;MQ0=0;OQ=1318.12;QD=31.38;SB=-539.87	GT:AD:DP:GL:GQ	1/1:0,42:38:-135.41,-11.45,-0.01:99
+chr1	3139859	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=4;HaplotypeScore=1.59;MQ=58.84;MQ0=0;OQ=177.35;QD=4.43;SB=56.21	GT:AD:DP:GL:GQ	0/1:24,16:34:-31.27,-10.25,-94.47:99
+chr1	3140395	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=1;HaplotypeScore=11.19;MQ=58.95;MQ0=0;OQ=93.28;QD=2.12;SB=71.27	GT:AD:DP:GL:GQ	0/1:31,13:33:-22.56,-9.95,-125.01:99
+chr1	3146326	rs2455112	A	G	135.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=60.00;MQ0=0;OQ=1096.93;QD=16.88;SB=-503.18	GT:AD:DP:GL:GQ	0/1:28,37:65:-132.56,-19.58,-110.95:99
+chr1	3151094	.	T	G	27.85	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=10.51;MQ=58.72;MQ0=0;QD=0.55;SB=62.22	GT:AD:DP:GL:GQ	0/1:29,22:34:-16.31,-10.24,-101.82:60.68
+chr1	3154977	.	C	T	20.55	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.05;MQ0=0;OQ=960.26;QD=19.60;SB=-359.36	GT:AD:DP:GL:GQ	0/1:20,29:48:-113.77,-14.46,-73.03:99
+chr1	3155966	rs1105111	C	A	740.08	Indel	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=60.39;MQ0=0;QD=13.46;SB=-187.60	GT:AD:DP:GL:GQ	0/1:28,27:54:-93.56,-16.26,-102.62:99
+chr1	3156860	.	C	A	1.29	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=2.70;MQ=59.41;MQ0=0;OQ=714.68;QD=18.33;SB=-335.33	GT:AD:DP:GL:GQ	0/1:15,24:39:-86.50,-11.75,-50.10:99
+chr1	3157063	rs60443258	C	G	197.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.43;MQ0=0;OQ=467.30;QD=14.16;SB=-190.23	GT:AD:DP:GL:GQ	0/1:18,15:33:-59.97,-9.95,-75.73:99
+chr1	3158034	rs11589327	C	T	221.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=55.82;MQ0=0;OQ=602.02;QD=14.68;SB=-226.92	GT:AD:DP:GL:GQ	0/1:22,19:39:-75.24,-11.75,-65.81:99
+chr1	3158063	rs61759183	G	A	105.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.23;MQ=54.25;MQ0=0;OQ=859.64;QD=18.29;SB=-349.39	GT:AD:DP:GL:GQ	0/1:17,30:44:-102.53,-13.28,-49.01:99
+chr1	3158107	rs55987640	G	A	184.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=55.61;MQ0=0;OQ=836.43;QD=16.73;SB=-292.80	GT:AD:DP:GL:GQ	0/1:21,29:42:-99.58,-12.65,-57.74:99
+chr1	3158110	rs10909910	G	C	37.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=55.78;MQ0=0;OQ=2043.92;QD=39.31;SB=-983.24	GT:AD:DP:GL:GQ	1/1:0,52:49:-208.00,-14.77,-0.02:99
+chr1	3158140	rs10797386	A	G	147.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=58.66;MQ0=0;OQ=1752.75;QD=33.71;SB=-820.65	GT:AD:DP:GL:GQ	1/1:0,52:49:-178.87,-14.76,-0.02:99
+chr1	3158322	rs12143201	C	T	107.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=58.81;MQ0=0;OQ=1087.80;QD=19.78;SB=-426.85	GT:AD:DP:GL:GQ	0/1:23,32:54:-128.34,-16.28,-69.54:99
+chr1	3158948	rs7539489	G	A	212.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.64;MQ=59.50;MQ0=0;OQ=701.66;QD=15.25;SB=-203.89	GT:AD:DP:GL:GQ	0/1:22,24:42:-86.11,-12.66,-64.73:99
+chr1	3160428	rs56015432	C	G	319.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=42.71;MQ0=18;OQ=1056.37;QD=11.61;SB=-361.10	GT:AD:DP:GL:GQ	0/1:52,38:68:-131.78,-22.86,-160.18:99
+chr1	3160647	rs2376494	T	C	490.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.54;MQ0=5;OQ=1049.98;QD=13.46;SB=-449.81	GT:AD:DP:GL:GQ	0/1:34,44:69:-129.08,-20.80,-121.01:99
+chr1	3160969	rs61691507	T	C	83.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=3;HaplotypeScore=0.96;MQ=48.88;MQ0=0;OQ=936.08;QD=14.18;SB=-414.90	GT:AD:DP:GL:GQ	0/1:32,34:63:-115.87,-18.98,-126.60:99
+chr1	3161244	rs28883366	T	C	328.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=20.07;MQ0=44;OQ=827.10;QD=11.18;SB=-204.07	GT:AD:DP:GL:GQ	1/1:25,49:28:-86.33,-8.45,-0.03:84.18
+chr1	3161789	rs4648464	G	A	197.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=53.22;MQ0=0;OQ=1078.68;QD=20.35;SB=-414.45	GT:AD:DP:GL:GQ	0/1:21,32:51:-126.53,-15.37,-60.62:99
+chr1	3161922	rs4648465	G	A	93.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=50.73;MQ0=0;OQ=1117.60;QD=22.35;SB=-454.98	GT:AD:DP:GL:GQ	0/1:18,32:50:-130.11,-15.06,-59.43:99
+chr1	3162133	rs2455100	T	C	1.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=5.09;MQ=58.24;MQ0=0;OQ=1353.88;QD=28.21;SB=-366.45	GT:AD:DP:GL:GQ	1/1:0,48:45:-139.02,-13.58,-0.05:99
+chr1	3162911	rs6699624	G	C	272.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.50;MQ0=0;OQ=1093.08;QD=16.07;SB=-449.43	GT:AD:DP:GL:GQ	0/1:32,35:63:-131.59,-19.00,-134.16:99
+chr1	3163088	rs1971330	C	T	114.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=49.78;MQ0=0;OQ=900.72;QD=19.58;SB=-445.49	GT:AD:DP:GL:GQ	0/1:19,27:44:-106.61,-13.25,-68.73:99
+chr1	3163142	rs1971331	A	G	155.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=39.25;MQ0=0;OQ=1400.23;QD=30.44;SB=-715.29	GT:AD:DP:GL:GQ	1/1:0,46:45:-143.65,-13.57,-0.04:99
+chr1	3165231	rs10909912	T	G	383.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.06;MQ0=0;OQ=430.36;QD=10.76;SB=-234.78	GT:AD:DP:GL:GQ	0/1:20,20:39:-58.07,-11.75,-73.52:99
+chr1	3165588	rs2455101	A	G	194.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.36;MQ0=0;OQ=514.34;QD=12.86;SB=-185.55	GT:AD:DP:GL:GQ	0/1:18,22:37:-65.87,-11.15,-65.63:99
+chr1	3165783	.	C	T	13.80	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=427.64;QD=9.30;SB=-160.18	GT:AD:DP:GL:GQ	0/1:30,16:42:-58.70,-12.66,-94.89:99
+chr1	3166230	.	C	G	139.63	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=825.87;QD=15.88;SB=-367.51	GT:AD:DP:GL:GQ	0/1:23,29:49:-100.65,-14.78,-100.14:99
+chr1	3167106	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=181.43;MQ=36.47;MQ0=0;OQ=530.53;QD=4.31;SB=-209.32	GT:AD:DP:GL:GQ	0/1:66,39:92:-95.27,-38.93,-253.94:99
+chr1	3167116	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=174;Dels=0.01;HRun=1;HaplotypeScore=260.94;MQ=34.61;MQ0=0;OQ=942.41;QD=5.42;SB=-369.43	GT:AD:DP:GL:GQ	0/1:66,57:123:-208.12,-110.59,-323.19:99
+chr1	3167119	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=1;HaplotypeScore=217.51;MQ=34.08;MQ0=0;OQ=198.48;QD=1.04;SB=93.36	GT:AD:DP:GL:GQ	0/1:148,42:118:-61.70,-38.57,-398.62:99
+chr1	3167131	.	G	A	38.92	DPFilter;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=0;HaplotypeScore=418.78;MQ=33.67;MQ0=0;QD=0.18;SB=-15.26	GT:AD:DP:GL:GQ	0/1:171,44:118:-42.73,-35.55,-373.47:71.75
+chr1	3167160	.	G	A	609.50	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=190;Dels=0.00;HRun=0;HaplotypeScore=319.28;MQ=32.32;MQ0=1;QD=3.21;SB=-149.32	GT:AD:DP:GL:GQ	0/1:134,56:72:-85.93,-21.70,-173.92:99
+chr1	3167161	.	T	C	245.51	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=0;HaplotypeScore=318.96;MQ=32.30;MQ0=1;QD=1.31;SB=53.20	GT:AD:DP:GL:GQ	0/1:174,14:59:-45.63,-17.79,-171.10:99
+chr1	3167162	.	G	A	200.87	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=0;HaplotypeScore=336.60;MQ=32.32;MQ0=1;QD=1.07;SB=56.18	GT:AD:DP:GL:GQ	0/1:174,10:62:-51.08,-27.71,-180.52:99
+chr1	3167163	.	G	A	107.11	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=184;Dels=0.00;HRun=0;HaplotypeScore=325.93;MQ=32.20;MQ0=1;QD=0.58;SB=-62.93	GT:AD:DP:GL:GQ	0/1:163,18:64:-33.28,-19.29,-195.22:99
+chr1	3167166	.	A	G	243.37	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=314.12;MQ=31.98;MQ0=1;QD=1.36;SB=56.35	GT:AD:DP:GL:GQ	0/1:138,41:62:-46.30,-18.68,-187.52:99
+chr1	3167169	.	A	G	120.84	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=1;HaplotypeScore=387.92;MQ=32.13;MQ0=1;QD=0.65;SB=76.41	GT:AD:DP:GL:GQ	0/1:141,44:79:-39.18,-23.81,-262.75:99
+chr1	3167180	rs57179041	G	A	114.65	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=141;Dels=0.00;HRun=1;HaplotypeScore=408.58;MQ=31.71;MQ0=1;QD=0.81;SB=86.30	GT:AD:DP:GL:GQ	0/1:118,23:43:-27.70,-12.95,-132.25:99
+chr1	3167181	.	A	G	38.85	DPFilter;Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=1;HaplotypeScore=419.93;MQ=31.63;MQ0=1;QD=0.28;SB=86.30	GT:AD:DP:GL:GQ	0/1:108,33:42:-19.82,-12.66,-143.77:71.68
+chr1	3167187	.	T	C	11.48	DPFilter;Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=120;Dels=0.41;HRun=0;HaplotypeScore=330.20;MQ=31.90;MQ0=1;QD=0.10;SB=5.04	GT:AD:DP:GL:GQ	0/1:52,5:44:-17.05,-12.65,-148.02:44
+chr1	3167189	.	G	A	33.08	DPFilter;Indel;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=123;Dels=0.12;HRun=1;HaplotypeScore=208.65;MQ=32.18;MQ0=1;QD=0.27;SB=8.05	GT:AD:DP:GL:GQ	0/1:103,5:46:-20.45,-13.86,-154.58:65.91
+chr1	3167200	rs57648616	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=125.27;MQ=33.30;MQ0=1;OQ=406.22;QD=3.41;SB=39.53	GT:AD:DP:GL:GQ	0/1:44,74:56:-63.73,-19.82,-152.72:99
+chr1	3167205	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=1;HaplotypeScore=95.81;MQ=33.44;MQ0=1;OQ=560.09;QD=4.87;SB=72.41	GT:AD:DP:GL:GQ	0/1:70,45:71:-80.68,-21.39,-190.32:99
+chr1	3167222	rs57879698	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=105.67;MQ=36.94;MQ0=1;OQ=371.38;QD=4.08;SB=65.41	GT:AD:DP:GL:GQ	0/1:54,36:67:-60.61,-20.18,-198.91:99
+chr1	3167226	.	A	G	25.97	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=1;HaplotypeScore=94.17;MQ=37.02;MQ0=1;QD=0.29;SB=104.36	GT:AD:DP:GL:GQ	0/1:77,13:68:-26.37,-20.49,-239.07:58.80
+chr1	3167247	.	A	G	94.62	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=9.30;MQ=43.30;MQ0=0;QD=1.30;SB=66.40	GT:AD:DP:GL:GQ	0/1:60,13:64:-32.03,-19.29,-213.53:99
+chr1	3167248	rs61151413	C	T	166.25	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=15.29;MQ=43.46;MQ0=0;QD=2.31;SB=80.73	GT:AD:DP:GL:GQ	0/1:59,13:65:-39.51,-19.60,-174.44:99
+chr1	3167253	.	A	G	43.60	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=1;HaplotypeScore=18.65;MQ=43.75;MQ0=0;QD=0.56;SB=110.39	GT:AD:DP:GL:GQ	0/1:68,10:69:-28.43,-20.79,-243.20:76.44
+chr1	3167258	.	G	A	29.42	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=1;HaplotypeScore=29.46;MQ=43.75;MQ0=0;QD=0.38;SB=107.33	GT:AD:DP:GL:GQ	0/1:71,7:70:-27.32,-21.09,-225.20:62.25
+chr1	3167340	rs3002685	A	G	235.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=44.86;MQ0=0;OQ=812.94;QD=11.29;SB=-432.88	GT:AD:DP:GL:GQ	0/1:35,37:64:-103.87,-19.29,-131.86:99
+chr1	3167551	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=15;HaplotypeScore=12.64;MQ=52.48;MQ0=0;OQ=368.96;QD=5.95;SB=77.28	GT:AD:DP:GL:GQ	0/1:44,18:52:-55.84,-15.67,-137.44:99
+chr1	3168576	.	C	T	188.74	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.69;MQ0=0;OQ=823.49;QD=13.72;SB=-404.84	GT:AD:DP:GL:GQ	0/1:34,26:58:-103.11,-17.48,-109.21:99
+chr1	3169081	.	C	T	79.34	PASS	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.66;MQ0=0;OQ=1096.77;QD=16.37;SB=-547.56	GT:AD:DP:GL:GQ	0/1:32,35:63:-131.94,-18.98,-108.41:99
+chr1	3169567	rs1501611	G	A	10.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=8.26;MQ=58.29;MQ0=0;OQ=520.16;QD=12.69;SB=-281.22	GT:AD:DP:GL:GQ	0/1:21,20:36:-66.15,-10.85,-62.40:99
+chr1	3169746	rs2455106	G	C	285.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=1036.68;QD=23.56;SB=-535.79	GT:AD:DP:GL:GQ	0/1:15,29:43:-119.91,-12.96,-65.17:99
+chr1	3170018	rs2455107	T	G	277.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.18;MQ=59.50;MQ0=0;OQ=669.75;QD=14.56;SB=-280.87	GT:AD:DP:GL:GQ	0/1:21,25:42:-82.91,-12.65,-66.12:99
+chr1	3170493	rs2455102	A	G	356.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.62;MQ0=0;OQ=653.73;QD=10.21;SB=-205.32	GT:AD:DP:GL:GQ	0/1:37,27:63:-87.64,-18.99,-144.47:99
+chr1	3170958	.	C	T	1.10	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=5.86;MQ=59.55;MQ0=0;OQ=1035.67;QD=20.31;SB=-528.11	GT:AD:DP:GL:GQ	0/1:20,31:50:-121.92,-15.07,-64.72:99
+chr1	3171559	rs2500250	T	C	389.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=559.12;QD=10.55;SB=-252.33	GT:AD:DP:GL:GQ	0/1:30,23:52:-74.86,-15.66,-123.43:99
+chr1	3171782	rs10909913	A	G	116.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=2.90;MQ=59.63;MQ0=0;OQ=1003.48;QD=15.93;SB=-509.29	GT:AD:DP:GL:GQ	0/1:27,35:61:-122.01,-18.38,-106.15:99
+chr1	3172391	rs2455096	A	C	43.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=287.98;QD=8.47;SB=-120.97	GT:AD:DP:GL:GQ	0/1:18,16:31:-41.43,-9.34,-63.22:99
+chr1	3172429	rs56042628	C	T	96.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=60.00;MQ0=0;OQ=280.31;QD=9.34;SB=-80.59	GT:AD:DP:GL:GQ	0/1:19,11:28:-39.76,-8.44,-58.47:99
+chr1	3173020	rs2455094	G	A	166.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=59.53;MQ0=0;OQ=444.07;QD=11.10;SB=-203.69	GT:AD:DP:GL:GQ	0/1:22,17:34:-57.94,-10.25,-64.34:99
+chr1	3173727	rs2455093	A	G	256.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=832.24;QD=16.98;SB=-357.94	GT:AD:DP:GL:GQ	0/1:20,29:47:-100.67,-14.16,-75.12:99
+chr1	3174715	rs2455119	G	T	285.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.49;MQ0=0;OQ=576.42;QD=12.81;SB=-209.45	GT:AD:DP:GL:GQ	0/1:23,22:42:-73.58,-12.65,-77.54:99
+chr1	3176001	.	C	T	83.35	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.70;MQ0=0;OQ=696.01;QD=13.92;SB=-293.84	GT:AD:DP:GL:GQ	0/1:26,23:46:-86.76,-13.88,-73.45:99
+chr1	3176267	.	T	G	76.55	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.02;MQ=60.00;MQ0=0;OQ=841.56;QD=14.76;SB=-394.65	GT:AD:DP:GL:GQ	0/1:27,30:56:-104.31,-16.87,-93.27:99
+chr1	3177045	rs3002687	T	G	225.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.21;MQ=59.59;MQ0=0;OQ=571.62;QD=12.43;SB=-258.88	GT:AD:DP:GL:GQ	0/1:24,22:45:-74.00,-13.56,-84.05:99
+chr1	3177468	.	C	T	3.04	PASS	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=59.42;MQ0=0;OQ=538.59;QD=16.83;SB=-100.92	GT:AD:DP:GL:GQ	0/1:14,18:31:-66.48,-9.34,-49.83:99
+chr1	3177939	rs2500308	A	G	95.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=1.13;MQ=59.39;MQ0=0;OQ=763.00;QD=10.04;SB=-332.88	GT:AD:DP:GL:GQ	0/1:45,31:71:-100.98,-21.39,-171.46:99
+chr1	3178661	.	G	A	33.39	PASS	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=60.00;MQ0=0;OQ=796.34;QD=18.96;SB=-401.21	GT:AD:DP:GL:GQ	0/1:18,24:42:-95.58,-12.66,-58.00:99
+chr1	3178998	rs2455127	A	G	173.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=58.67;MQ0=0;OQ=507.17;QD=14.49;SB=-257.35	GT:AD:DP:GL:GQ	0/1:11,24:30:-63.05,-9.05,-41.23:99
+chr1	3179379	.	A	G	65.56	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=58.32;MQ0=0;OQ=481.41;QD=12.34;SB=-241.93	GT:AD:DP:GL:GQ	0/1:18,21:37:-62.58,-11.16,-65.22:99
+chr1	3179574	rs2455128	A	G	108.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=59.62;MQ0=0;OQ=838.70;QD=13.98;SB=-378.24	GT:AD:DP:GL:GQ	0/1:31,29:59:-104.93,-17.77,-121.27:99
+chr1	3179592	rs2500307	T	A	726.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2101.50;QD=36.23;SB=-987.86	GT:AD:DP:GL:GQ	1/1:0,58:58:-213.75,-17.47,-0.02:99
+chr1	3182386	rs2500304	T	C	246	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.51;MQ0=0;OQ=550.86;QD=11.72;SB=-174.37	GT:AD:DP:GL:GQ	0/1:23,24:45:-71.94,-13.57,-90.75:99
+chr1	3182819	rs2455131	A	G	160.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=53.72;MQ0=0;OQ=380.67;QD=9.28;SB=-185.58	GT:AD:DP:GL:GQ	0/1:26,15:41:-53.71,-12.35,-99.70:99
+chr1	3183091	.	T	G	31.12	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.54;MQ=48.96;MQ0=0;QD=0.80;SB=16.16	GT:AD:DP:GL:GQ	0/1:34,5:37:-17.54,-11.14,-116.34:63.95
+chr1	3183092	.	C	A	30.14	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=9.54;MQ=48.87;MQ0=0;QD=0.74;SB=14.77	GT:AD:DP:GL:GQ	0/1:36,5:37:-17.45,-11.16,-100.79:62.97
+chr1	3183861	rs55923982	G	C	139.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.45;MQ=57.45;MQ0=0;OQ=542.30;QD=11.79;SB=-148.38	GT:AD:DP:GL:GQ	0/1:27,19:44:-70.78,-13.27,-111.52:99
+chr1	3184193	rs2455115	A	G	314.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=53.52;MQ0=0;OQ=598.87;QD=12.22;SB=-281.59	GT:AD:DP:GL:GQ	0/1:25,24:48:-77.64,-14.47,-94.87:99
+chr1	3185401	.	G	T	101.68	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.51;MQ0=0;OQ=440.43;QD=11.59;SB=-233.97	GT:AD:DP:GL:GQ	0/1:19,19:33:-57.27,-9.94,-56.75:99
+chr1	3187015	.	G	A	77.56	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=59.67;MQ0=0;OQ=971.62;QD=17.05;SB=-421.44	GT:AD:DP:GL:GQ	0/1:28,29:55:-117.01,-16.57,-95.93:99
+chr1	3188693	rs905137	A	G	186.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.61;MQ0=0;OQ=484.36;QD=10.09;SB=-266.22	GT:AD:DP:GL:GQ	0/1:25,23:44:-64.98,-13.26,-96.26:99
+chr1	3189244	rs905136	A	G	4.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=4;HaplotypeScore=2.03;MQ=60.00;MQ0=0;OQ=654.87;QD=15.97;SB=-328.31	GT:AD:DP:GL:GQ	0/1:18,23:38:-80.22,-11.45,-60.36:99
+chr1	3189344	rs905135	A	C	1.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=6.41;MQ=59.54;MQ0=0;OQ=215.02;QD=4.30;SB=-100.13	GT:AD:DP:GL:GQ	0/1:35,15:44:-38.04,-13.26,-114.24:99
+chr1	3189859	rs2500302	T	C	241.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.92;MQ0=0;OQ=339.74;QD=8.71;SB=-144.67	GT:AD:DP:GL:GQ	0/1:23,16:37:-48.41,-11.15,-86.58:99
+chr1	3190143	rs56004439	G	A	2.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=8.41;MQ=57.37;MQ0=0;OQ=401.65;QD=8.37;SB=-155.21	GT:AD:DP:GL:GQ	0/1:33,15:46:-57.32,-13.87,-99.82:99
+chr1	3190754	.	G	A	32.75	PASS	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1225.08;QD=18.85;SB=-426.92	GT:AD:DP:GL:GQ	0/1:29,36:64:-145.07,-19.28,-99.09:99
+chr1	3190930	rs6685398	C	A	88.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=4.12;MQ=60.00;MQ0=0;OQ=531.21;QD=13.28;SB=-273.35	GT:AD:DP:GL:GQ	0/1:21,19:39:-68.15,-11.75,-68.57:99
+chr1	3190993	rs6690217	A	C	128.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=1454.60;QD=28.52;SB=-648.68	GT:AD:DP:GL:GQ	1/1:0,51:48:-149.09,-14.47,-0.05:99
+chr1	3192051	.	C	T	11.01	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.25;MQ0=0;OQ=927.90;QD=18.56;SB=-215.90	GT:AD:DP:GL:GQ	0/1:20,30:48:-110.53,-14.46,-70.14:99
+chr1	3192870	rs10797387	A	C	142.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=1.89;MQ=59.80;MQ0=0;OQ=775.82;QD=12.93;SB=-322.85	GT:AD:DP:GL:GQ	0/1:30,30:54:-97.13,-16.27,-96.18:99
+chr1	3193262	.	A	G	27.47	PASS	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=60.00;MQ0=0;OQ=435.09;QD=14.04;SB=-158.61	GT:AD:DP:GL:GQ	0/1:13,18:29:-55.53,-8.74,-48.24:99
+chr1	3193691	rs12024838	G	C	0.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=9.20;MQ=52.13;MQ0=0;OQ=313.95;QD=12.08;SB=-105.65	GT:AD:DP:GL:GQ	0/1:16,10:19:-40.41,-5.73,-35.18:99
+chr1	3193692	rs61759191	C	T	0.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=9.20;MQ=52.13;MQ0=0;OQ=179.56;QD=6.91;SB=-26.50	GT:AD:DP:GL:GQ	0/1:18,8:19:-26.97,-5.73,-38.66:99
+chr1	3193738	rs10909916	C	G	2.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=6.33;MQ=40.46;MQ0=4;OQ=154.87;QD=11.06;SB=-44.90	GT:AD:DP:GL:GQ	0/1:9,5:7:-20.88,-2.11,-8.99:68.77
+chr1	3194086	rs6687930	T	C	3.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=48.01;MQ0=1;OQ=344.21;QD=18.12;SB=-6.99	GT:AD:DP:GL:GQ	0/1:2,17:14:-41.92,-4.22,-8.13:39.10
+chr1	3194355	rs2134119	C	G	59.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=4.23;MQ=54.23;MQ0=0;OQ=781.76;QD=15.95;SB=-353.76	GT:AD:DP:GL:GQ	0/1:22,27:44:-94.74,-13.28,-81.77:99
+chr1	3194394	rs2455117	T	A	339.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=56.31;MQ0=0;OQ=679.10;QD=15.43;SB=-276.72	GT:AD:DP:GL:GQ	0/1:22,22:42:-83.84,-12.65,-73.08:99
+chr1	3197040	rs2250291	C	T	260.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=59.34;MQ0=0;OQ=469.67;QD=13.42;SB=-216.70	GT:AD:DP:GL:GQ	0/1:18,17:34:-60.50,-10.25,-62.96:99
+chr1	3197640	rs55866132	G	A	241.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.46;MQ=60.00;MQ0=0;OQ=793.46;QD=13.45;SB=-307.77	GT:AD:DP:GL:GQ	0/1:34,25:59:-100.40,-17.77,-123.91:99
+chr1	3197902	rs2500297	C	T	238.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=60.00;MQ0=0;OQ=756.06;QD=14.00;SB=-170.24	GT:AD:DP:GL:GQ	0/1:30,24:49:-93.65,-14.77,-87.43:99
+chr1	3198235	rs10909918	A	G	238.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=60.00;MQ0=0;OQ=490.49;QD=8.92;SB=-208.46	GT:AD:DP:GL:GQ	0/1:32,23:51:-67.70,-15.37,-121.94:99
+chr1	3198466	.	G	A	262.64	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=604.73;QD=12.34;SB=-281.22	GT:AD:DP:GL:GQ	0/1:28,21:46:-77.62,-13.87,-86.11:99
+chr1	3199356	rs2500295	T	C	571.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.75;MQ0=0;OQ=1482.44;QD=28.51;SB=-763.58	GT:AD:DP:GL:GQ	1/1:0,52:48:-151.88,-14.48,-0.05:99
+chr1	3199491	rs4648376	G	A	14.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=4.90;MQ=58.90;MQ0=0;OQ=2231.72;QD=37.83;SB=-1015.37	GT:AD:DP:GL:GQ	1/1:0,59:58:-226.79,-17.49,-0.03:99
+chr1	3199627	rs2500294	C	T	622.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=2326.22;QD=38.77;SB=-1091.37	GT:AD:DP:GL:GQ	1/1:0,60:58:-236.22,-17.47,-0.02:99
+chr1	3199783	rs1553291	A	G	564.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=1581.83;QD=29.29;SB=-575.98	GT:AD:DP:GL:GQ	1/1:0,54:51:-161.82,-15.38,-0.05:99
+chr1	3200187	.	C	T	35.88	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.26;MQ=59.60;MQ0=0;OQ=491.30;QD=10.45;SB=-217.71	GT:AD:DP:GL:GQ	0/1:29,18:43:-65.37,-12.96,-91.60:99
+chr1	3200810	rs4648468	A	G	447.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=1398.57;QD=30.40;SB=-596.06	GT:AD:DP:GL:GQ	1/1:0,46:43:-143.47,-12.96,-0.03:99
+chr1	3201105	rs10047257	C	T	220.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=596.34;QD=15.29;SB=-318.86	GT:AD:DP:GL:GQ	0/1:20,19:38:-74.37,-11.45,-63.70:99
+chr1	3201318	rs4648377	A	C	538.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=1615.09;QD=33.65;SB=-661.05	GT:AD:DP:GL:GQ	1/1:0,48:47:-165.11,-14.16,-0.02:99
+chr1	3201410	rs4648469	A	G	202.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1230.36;QD=30.76;SB=-513.23	GT:AD:DP:GL:GQ	1/1:0,39:38:-126.64,-11.45,-0.02:99
+chr1	3201613	rs4648470	C	T	79.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=60.00;MQ0=0;OQ=1081.89;QD=24.59;SB=-515.59	GT:AD:DP:GL:GQ	0/1:12,32:43:-124.44,-12.96,-36.35:99
+chr1	3202053	rs2500292	A	G	471	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=1432.25;QD=32.55;SB=-511.16	GT:AD:DP:GL:GQ	1/1:0,44:41:-146.83,-12.35,-0.02:99
+chr1	3202174	rs2500291	C	T	728.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2429.46;QD=38.56;SB=-1207.61	GT:AD:DP:GL:GQ	1/1:1,62:61:-246.55,-18.37,-0.01:99
+chr1	3202451	rs2500290	G	C	18.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.98;MQ=58.98;MQ0=0;OQ=1616.44;QD=39.43;SB=-797.54	GT:AD:DP:GL:GQ	1/1:0,41:39:-165.25,-11.76,-0.02:99
+chr1	3202782	rs1875452	C	G	157.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.36;MQ=59.54;MQ0=0;OQ=2035.33;QD=40.71;SB=-884.21	GT:AD:DP:GL:GQ	1/1:0,50:48:-207.14,-14.47,-0.02:99
+chr1	3202806	rs2500289	A	G	260.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=59.19;MQ0=0;OQ=1923.10;QD=33.74;SB=-724.29	GT:AD:DP:GL:GQ	1/1:0,57:54:-195.91,-16.27,-0.02:99
+chr1	3203962	rs2500288	T	C	186.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.58;MQ0=0;OQ=1801.36;QD=32.75;SB=-828.32	GT:AD:DP:GL:GQ	1/1:0,55:51:-183.74,-15.36,-0.02:99
+chr1	3204030	rs7553849	T	C	226.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=56.20;MQ0=0;OQ=1684.70;QD=29.05;SB=-851.52	GT:AD:DP:GL:GQ	1/1:0,58:53:-172.10,-15.99,-0.05:99
+chr1	3204380	rs10442593	A	G	67.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=958.98;QD=29.97;SB=-369.57	GT:AD:DP:GL:GQ	1/1:0,32:28:-99.49,-8.43,-0.01:84.24
+chr1	3204592	rs2455144	A	G	617.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=2332.51;QD=29.90;SB=-1027.75	GT:AD:DP:GL:GQ	1/1:0,78:74:-236.91,-22.33,-0.08:99
+chr1	3204835	.	G	A	53.06	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.06;MQ=60.00;MQ0=0;OQ=892.55;QD=15.13;SB=-296.23	GT:AD:DP:GL:GQ	0/1:30,29:55:-109.11,-16.57,-93.52:99
+chr1	3204852	rs2500287	G	T	86	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=60.00;MQ0=0;OQ=2470.97;QD=33.85;SB=-613.02	GT:AD:DP:GL:GQ	1/1:1,71:71:-250.71,-21.39,-0.03:99
+chr1	3205054	.	A	G	35.05	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.07;MQ=60.00;MQ0=0;OQ=563.88;QD=10.44;SB=-299.62	GT:AD:DP:GL:GQ	0/1:29,25:52:-75.34,-15.67,-118.24:99
+chr1	3205180	rs2455143	A	T	124.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=58.71;MQ0=0;OQ=2383.23;QD=36.67;SB=-1091.65	GT:AD:DP:GL:GQ	1/1:0,65:64:-241.93,-19.28,-0.02:99
+chr1	3205492	rs2455142	T	G	512.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.74;MQ0=0;OQ=2083.81;QD=29.77;SB=-759.91	GT:AD:DP:GL:GQ	1/1:0,70:70:-212.03,-21.10,-0.07:99
+chr1	3205734	rs2455141	A	C	27.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=40.69;MQ0=0;OQ=504.37;QD=19.40;SB=-155.27	GT:AD:DP:GL:GQ	1/1:2,24:21:-57.94,-6.33,-3.92:24.11
+chr1	3205761	rs2455140	T	G	0.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=2.39;MQ=22.97;MQ0=1;OQ=235.32;QD=18.10;SB=-39.00	GT:AD:DP:GL:GQ	0/1:2,10:9:-29.50,-2.71,-3.64:9.30
+chr1	3205805	rs12728296	T	C	26.83	LowQual	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=13.68;MQ0=0;QD=1.79;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,15:2:-6.09,-0.60,-0.00:6.01
+chr1	3205846	.	G	A	232.99	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.36;MQ0=0;OQ=538.85;QD=13.47;SB=-237.77	GT:AD:DP:GL:GQ	0/1:19,21:21:-63.50,-6.33,-16.25:99
+chr1	3206300	rs12036713	A	G	35.28	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=14.04;MQ0=4;QD=5.04;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,7:2:-6.94,-0.60,-0.00:6.02
+chr1	3206493	.	T	G	46.28	PASS	AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=17.34;MQ0=4;OQ=70.14;QD=6.38;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,10:3:-10.50,-0.90,-0.00:9.03
+chr1	3206505	.	T	C	3.40	PASS	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=18.66;MQ0=4;OQ=95.85;QD=6.85;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,9:5:-14.37,-1.51,-4.06:25.51
+chr1	3206506	.	A	G	5.49	PASS	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=18.66;MQ0=4;OQ=74.94;QD=5.35;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,9:5:-12.29,-1.51,-3.97:24.63
+chr1	3206538	.	G	A	1.11	PASS	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=18.43;MQ0=3;OQ=73.15;QD=5.23;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,7:4:-11.80,-1.21,-3.10:18.92
+chr1	3206554	rs56276321	T	G	10.51	LowQual	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.60;MQ0=3;QD=0.53;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,5:8:-6.70,-2.41,-21.47:42.94
+chr1	3206566	.	T	C	28.09	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=22.53;MQ0=2;OQ=145.15;QD=6.91;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,9:12:-21.41,-3.62,-22.84:99
+chr1	3206567	.	A	G	6.01	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.53;MQ0=2;OQ=85.83;QD=4.09;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,9:11:-15.19,-3.32,-21.71:99
+chr1	3206577	.	C	T	7.20	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=22.19;MQ0=2;OQ=218.94;QD=10.43;SB=-10.00	GT:AD:DP:GL:GQ	0/1:10,11:11:-28.49,-3.31,-13.17:98.62
+chr1	3206588	.	A	C	10.65	LowQual	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=1;HaplotypeScore=2.88;MQ=22.98;MQ0=0;QD=0.59;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,6:7:-6.42,-2.11,-14.50:43.09
+chr1	3206599	.	G	A	2.11	PASS	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=22.00;MQ0=0;OQ=65.71;QD=4.11;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,9:7:-11.98,-2.12,-8.40:62.78
+chr1	3206700	.	A	G	0.69	PASS	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.64;MQ0=1;OQ=276.82;QD=18.45;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,14:12:-34.36,-3.62,-3.48:2.36
+chr1	3206761	.	A	G	22.65	LowQual	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=26.60;MQ0=1;QD=0.54;SB=-10.00	GT:AD:DP:GL:GQ	0/1:32,10:32:-15.20,-9.65,-103.92:55.47
+chr1	3206926	rs61759194	A	G	113.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=2.49;MQ=46.00;MQ0=0;OQ=649.36;QD=10.82;SB=-346.23	GT:AD:DP:GL:GQ	0/1:29,31:46:-82.08,-13.86,-88.11:99
+chr1	3207011	rs2455137	C	T	379.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=48.62;MQ0=0;OQ=1983.22;QD=35.41;SB=-860.00	GT:AD:DP:GL:GQ	1/1:0,56:50:-201.92,-15.06,-0.01:99
+chr1	3207294	rs2500284	G	A	102.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=58.88;MQ0=0;OQ=2616.26;QD=39.05;SB=-1335.76	GT:AD:DP:GL:GQ	1/1:1,66:66:-265.23,-19.89,-0.02:99
+chr1	3208189	rs2455136	A	T	142.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=2.14;MQ=59.12;MQ0=0;OQ=2529.01;QD=36.65;SB=-1261.52	GT:AD:DP:GL:GQ	1/1:0,69:68:-256.50,-20.48,-0.02:99
+chr1	3208783	rs2500283	G	C	612.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2831.75;QD=42.91;SB=-1184.48	GT:AD:DP:GL:GQ	1/1:0,66:66:-286.78,-19.89,-0.02:99
+chr1	3209357	rs2500282	A	G	594.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1981.22;QD=32.48;SB=-526.13	GT:AD:DP:GL:GQ	1/1:0,61:61:-201.75,-18.39,-0.04:99
+chr1	3209761	rs2455135	A	G	63.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1623.95;QD=30.64;SB=-619.36	GT:AD:DP:GL:GQ	1/1:0,53:46:-165.99,-13.85,-0.01:99
+chr1	3210242	rs2500281	G	A	563.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.01;MQ0=0;OQ=1613.10;QD=35.07;SB=-716.96	GT:AD:DP:GL:GQ	1/1:0,46:42:-164.91,-12.65,-0.01:99
+chr1	3210275	rs2455134	A	G	102.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=34.21;MQ0=0;OQ=983.95;QD=25.89;SB=-399.50	GT:AD:DP:GL:GQ	1/1:0,38:28:-101.99,-8.43,-0.01:84.26
+chr1	3210353	rs2455133	C	G	65.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=35.62;MQ0=2;OQ=1518.72;QD=29.78;SB=-723.73	GT:AD:DP:GL:GQ	1/1:4,47:41:-164.26,-12.36,-8.80:35.57
+chr1	3210943	rs2455132	T	C	34.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=58.65;MQ0=0;OQ=1292.96;QD=28.73;SB=-546.03	GT:AD:DP:GL:GQ	1/1:1,44:43:-137.07,-12.97,-4.19:87.75
+chr1	3211298	rs56357655	G	T	236.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.31;MQ0=0;OQ=570.69;QD=13.59;SB=-286.33	GT:AD:DP:GL:GQ	0/1:20,22:39:-72.10,-11.75,-66.92:99
+chr1	3211481	rs4648378	A	T	264.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1968.99;QD=35.80;SB=-994.60	GT:AD:DP:GL:GQ	1/1:0,55:54:-200.50,-16.27,-0.02:99
+chr1	3212566	rs3923081	A	G	604.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1445.27;QD=30.75;SB=-602.58	GT:AD:DP:GL:GQ	1/1:0,47:46:-148.15,-13.87,-0.04:99
+chr1	3213090	rs4648471	A	G	181.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=58.96;MQ0=0;OQ=1176.67;QD=14.53;SB=-570.90	GT:AD:DP:GL:GQ	0/1:40,41:78:-144.45,-23.50,-149.52:99
+chr1	3213140	rs4233025	C	T	288.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.52;MQ0=0;OQ=3371.29;QD=38.75;SB=-1393.36	GT:AD:DP:GL:GQ	1/1:0,86:84:-336.13,-25.31,-0.03:99
+chr1	3213393	rs4648472	G	A	290.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=58.95;MQ0=0;OQ=2168.73;QD=34.98;SB=-915.32	GT:AD:DP:GL:GQ	1/1:0,61:56:-220.48,-16.87,-0.02:99
+chr1	3213624	rs4648473	A	G	299.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=60.00;MQ0=0;OQ=2351.35;QD=35.09;SB=-1180.73	GT:AD:DP:GL:GQ	1/1:0,67:67:-238.75,-20.18,-0.03:99
+chr1	3213815	rs4145901	A	G	578.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=1913.13;QD=34.78;SB=-765.19	GT:AD:DP:GL:GQ	1/1:0,55:55:-194.92,-16.57,-0.02:99
+chr1	3214070	rs4145900	C	T	633.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.20;MQ0=0;OQ=2312.37;QD=39.87;SB=-883.19	GT:AD:DP:GL:GQ	1/1:0,58:58:-234.84,-17.47,-0.01:99
+chr1	3214663	rs2483258	A	G	141.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.74;MQ=58.20;MQ0=0;OQ=1545.60;QD=32.89;SB=-781.14	GT:AD:DP:GL:GQ	1/1:0,47:45:-158.16,-13.56,-0.02:99
+chr1	3215654	rs2500279	A	G	10.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=3;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1630.84;QD=29.65;SB=-792.65	GT:AD:DP:GL:GQ	1/1:0,55:51:-166.71,-15.38,-0.04:99
+chr1	3215800	rs2500278	C	T	196.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=60.00;MQ0=0;OQ=2097.43;QD=35.55;SB=-1034.29	GT:AD:DP:GL:GQ	1/1:1,57:55:-213.35,-16.58,-0.03:99
+chr1	3216399	rs59127130	T	A	71.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=3.18;MQ=59.01;MQ0=0;OQ=500.47;QD=10.65;SB=-267.66	GT:AD:DP:GL:GQ	0/1:27,19:45:-66.90,-13.56,-91.26:99
+chr1	3218505	.	G	T	13.88	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.49;MQ=59.42;MQ0=0;OQ=562.03;QD=14.05;SB=-143.82	GT:AD:DP:GL:GQ	0/1:17,23:34:-69.73,-10.24,-51.47:99
+chr1	3223491	rs2500277	T	C	605.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1039.56;QD=14.85;SB=-437.57	GT:AD:DP:GL:GQ	0/1:34,36:70:-128.33,-21.09,-137.20:99
+chr1	3227069	rs2500274	G	A	733.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2547.84;QD=38.03;SB=-1230.64	GT:AD:DP:GL:GQ	1/1:0,67:65:-258.39,-19.58,-0.02:99
+chr1	3231689	rs2500271	A	G	65.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=6.09;MQ=58.05;MQ0=0;OQ=618.77;QD=12.89;SB=-326.13	GT:AD:DP:GL:GQ	0/1:22,25:43:-80.91,-15.74,-76.88:99
+chr1	3232314	rs2500270	C	T	276.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=58.93;MQ0=0;OQ=890.12;QD=13.69;SB=-466.96	GT:AD:DP:GL:GQ	0/1:37,28:63:-111.27,-18.97,-132.21:99
+chr1	3232391	rs7521865	T	C	80.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=59.46;MQ0=0;OQ=581.07;QD=12.11;SB=-302.66	GT:AD:DP:GL:GQ	0/1:25,23:45:-74.95,-13.56,-94.63:99
+chr1	3232424	rs11576578	C	T	337.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=583.63;QD=16.21;SB=-245.53	GT:AD:DP:GL:GQ	0/1:18,18:35:-72.19,-10.55,-57.05:99
+chr1	3232513	rs2500268	C	T	2.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.10;MQ0=0;OQ=81.92;QD=2.64;SB=-51.23	GT:AD:DP:GL:GQ	0/1:26,5:28:-19.91,-8.44,-80.68:99
+chr1	3232545	rs7550743	G	C	135.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=204.00;QD=6.18;SB=-89.25	GT:AD:DP:GL:GQ	0/1:25,8:26:-31.53,-7.85,-72.48:99
+chr1	3233210	rs2483268	C	T	55.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.45;MQ0=0;OQ=685.34;QD=20.16;SB=-292.33	GT:AD:DP:GL:GQ	0/1:13,21:31:-81.16,-9.34,-34.58:99
+chr1	3233282	rs2483269	C	T	150.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.51;MQ0=0;OQ=931.05;QD=19.81;SB=-450.84	GT:AD:DP:GL:GQ	0/1:20,27:46:-110.24,-13.86,-67.60:99
+chr1	3234117	rs2483270	T	C	92.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=1.03;MQ=54.48;MQ0=0;OQ=186.80;QD=8.90;SB=-89.99	GT:AD:DP:GL:GQ	0/1:13,8:21:-28.30,-6.33,-49.94:99
+chr1	3235659	rs56368529	T	G	3.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=4.81;MQ=58.01;MQ0=0;OQ=299.04;QD=9.06;SB=-59.90	GT:AD:DP:GL:GQ	0/1:16,17:27:-41.32,-8.14,-54.29:99
+chr1	3236031	rs55929121	A	G	111.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=59.44;MQ0=0;OQ=382.21;QD=9.32;SB=-138.40	GT:AD:DP:GL:GQ	0/1:24,17:41:-53.86,-12.36,-96.85:99
+chr1	3237249	rs2483272	T	C	227.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=58.89;MQ0=0;OQ=695.19;QD=16.55;SB=-364.39	GT:AD:DP:GL:GQ	0/1:17,25:40:-84.86,-12.05,-61.97:99
+chr1	3237696	rs11577229	A	C	60.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.98;MQ=59.46;MQ0=0;OQ=605.90;QD=14.09;SB=-151.87	GT:AD:DP:GL:GQ	0/1:20,23:42:-76.53,-12.66,-70.16:99
+chr1	3237725	rs2483273	C	T	273.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=458.56;QD=11.46;SB=-253.26	GT:AD:DP:GL:GQ	0/1:23,17:37:-60.29,-11.15,-74.02:99
+chr1	3237958	rs2483274	A	G	334.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=489.91;QD=10.42;SB=-162.48	GT:AD:DP:GL:GQ	0/1:24,23:45:-65.84,-13.57,-92.79:99
+chr1	3238582	rs56033677	T	C	21.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=59.43;MQ0=0;OQ=296.91;QD=9.00;SB=-160.33	GT:AD:DP:GL:GQ	0/1:18,15:30:-42.02,-9.04,-67.71:99
+chr1	3238892	rs55807399	G	T	41.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=58.83;MQ0=0;OQ=103.10;QD=6.44;SB=-69.87	GT:AD:DP:GL:GQ	0/1:10,6:13:-17.51,-3.92,-27.55:99
+chr1	3239158	.	C	T	1.04	PASS	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.48;MQ0=0;OQ=666.04;QD=18.50;SB=-35.64	GT:AD:DP:GL:GQ	0/1:16,20:35:-80.44,-10.55,-47.82:99
+chr1	3239323	.	G	A	79.22	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=885.68;QD=16.10;SB=-289.76	GT:AD:DP:GL:GQ	0/1:28,27:52:-107.52,-15.67,-84.40:99
+chr1	3240283	rs1889121	A	G	183.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=58.44;MQ0=0;OQ=423.56;QD=10.86;SB=-163.96	GT:AD:DP:GL:GQ	0/1:18,20:36:-60.24,-14.60,-67.49:99
+chr1	3241019	rs1110307	T	C	317.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.03;MQ0=0;OQ=790.39;QD=11.80;SB=-362.96	GT:AD:DP:GL:GQ	0/1:34,33:66:-102.22,-19.90,-132.82:99
+chr1	3241835	rs4648477	G	A	340.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.63;MQ0=0;OQ=880.63;QD=17.27;SB=-457.99	GT:AD:DP:GL:GQ	0/1:24,27:48:-105.81,-14.46,-75.34:99
+chr1	3241867	rs4648478	C	T	165.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.81;MQ=58.72;MQ0=0;OQ=927.39;QD=18.18;SB=-291.79	GT:AD:DP:GL:GQ	0/1:22,29:49:-110.80,-14.77,-66.95:99
+chr1	3241964	rs2483278	C	T	199.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=4.49;MQ=58.47;MQ0=0;OQ=815.99;QD=11.33;SB=-270.80	GT:AD:DP:GL:GQ	0/1:44,28:65:-104.47,-19.59,-130.43:99
+chr1	3242641	rs10797388	C	T	87.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=59.66;MQ0=0;OQ=1468.23;QD=21.91;SB=-716.28	GT:AD:DP:GL:GQ	0/1:24,43:63:-169.09,-18.98,-69.99:99
+chr1	3243022	rs4648479	C	G	270.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.32;MQ0=0;OQ=1259.62;QD=18.52;SB=-604.54	GT:AD:DP:GL:GQ	0/1:33,35:68:-149.74,-20.49,-145.47:99
+chr1	3243475	rs2500264	A	G	371.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=57.70;MQ0=0;OQ=965.24;QD=13.04;SB=-435.59	GT:AD:DP:GL:GQ	0/1:35,39:72:-121.52,-21.71,-132.46:99
+chr1	3243538	rs2500263	C	T	449.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=59.43;MQ0=0;OQ=1163.15;QD=14.36;SB=-551.30	GT:AD:DP:GL:GQ	0/1:44,37:79:-143.40,-23.80,-157.59:99
+chr1	3243563	rs10909933	A	T	21.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=5.38;MQ=58.82;MQ0=0;OQ=1256.33;QD=15.90;SB=-624.35	GT:AD:DP:GL:GQ	0/1:39,40:77:-152.11,-23.19,-142.90:99
+chr1	3243699	rs7516137	C	G	384.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=58.95;MQ0=1;OQ=1414.58;QD=19.38;SB=-612.10	GT:AD:DP:GL:GQ	0/1:31,42:71:-166.15,-21.41,-133.01:99
+chr1	3243749	rs7516150	C	T	110.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=4.27;MQ=59.28;MQ0=0;OQ=1059.88;QD=16.56;SB=-511.08	GT:AD:DP:GL:GQ	0/1:31,33:63:-128.25,-18.98,-110.55:99
+chr1	3243801	rs7552331	G	A	50.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=3.37;MQ=59.68;MQ0=0;OQ=1395.05;QD=19.38;SB=-586.45	GT:AD:DP:GL:GQ	0/1:31,41:71:-164.18,-21.39,-100.20:99
+chr1	3244201	rs1572038	G	A	223.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=60.00;MQ0=0;OQ=849.89;QD=14.40;SB=-320.28	GT:AD:DP:GL:GQ	0/1:33,26:58:-105.75,-17.48,-105.23:99
+chr1	3244229	rs1572037	T	C	103.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=1.14;MQ=59.74;MQ0=0;OQ=759.65;QD=10.70;SB=-211.19	GT:AD:DP:GL:GQ	0/1:40,31:70:-100.34,-21.09,-160.53:99
+chr1	3245634	.	G	A	2.67	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=2;HaplotypeScore=5.38;MQ=59.21;MQ0=0;OQ=768.53;QD=14.50;SB=-362.88	GT:AD:DP:GL:GQ	0/1:27,25:49:-94.91,-14.77,-78.82:99
+chr1	3245968	rs1999527	C	A	270.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.55;MQ0=0;OQ=832.76;QD=16.33;SB=-309.70	GT:AD:DP:GL:GQ	0/1:20,31:46:-100.42,-13.86,-57.62:99
+chr1	3246110	rs1999526	G	A	145.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.11;MQ=60.00;MQ0=0;OQ=722.36;QD=13.89;SB=-206.02	GT:AD:DP:GL:GQ	0/1:25,26:46:-91.77,-16.25,-79.35:99
+chr1	3247225	rs944819	T	G	210.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=59.73;MQ0=0;OQ=1004.82;QD=11.68;SB=-427.67	GT:AD:DP:GL:GQ	0/1:50,36:86:-129.67,-25.90,-183.72:99
+chr1	3247599	rs2483281	C	T	240.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=58.98;MQ0=0;OQ=504.82;QD=12.31;SB=-180.16	GT:AD:DP:GL:GQ	0/1:24,17:38:-65.21,-11.45,-77.36:99
+chr1	3251376	rs4648379	C	T	354.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=1.15;MQ=59.76;MQ0=0;OQ=1302.21;QD=16.91;SB=-654.31	GT:AD:DP:GL:GQ	0/1:37,40:76:-156.40,-22.89,-133.27:99
+chr1	3251542	rs4415513	C	T	583.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1033.27;QD=16.67;SB=-449.45	GT:AD:DP:GL:GQ	0/1:31,31:61:-125.00,-18.39,-98.88:99
+chr1	3252129	rs12564920	A	G	258.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.38;MQ0=0;OQ=448.15;QD=9.96;SB=-222.39	GT:AD:DP:GL:GQ	0/1:23,22:39:-59.86,-11.76,-74.90:99
+chr1	3253722	.	G	A	5.82	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=951.14;QD=18.65;SB=-376.90	GT:AD:DP:GL:GQ	0/1:22,29:50:-113.46,-15.06,-78.22:99
+chr1	3254050	rs2483289	A	C	189.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=800.56;QD=13.80;SB=-367.58	GT:AD:DP:GL:GQ	0/1:28,30:55:-99.91,-16.57,-92.54:99
+chr1	3254157	rs2500257	A	G	11.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=3.42;MQ=59.13;MQ0=0;OQ=570.29;QD=13.26;SB=-176.97	GT:AD:DP:GL:GQ	0/1:21,22:40:-72.37,-12.05,-79.78:99
+chr1	3257948	.	G	C	98.91	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=35.14;MQ0=0;QD=7.07;SB=14.07	GT:AD:DP:GL:GQ	0/1:10,4:12:-16.79,-3.62,-31.08:99
+chr1	3257994	rs60920916	T	C	0.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=2;HaplotypeScore=2.63;MQ=42.15;MQ0=0;OQ=77.87;QD=4.58;SB=20.08	GT:AD:DP:GL:GQ	0/1:13,4:15:-15.59,-4.52,-39.62:99
+chr1	3258005	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=3;HaplotypeScore=6.10;MQ=42.12;MQ0=0;OQ=65.85;QD=3.29;SB=23.09	GT:AD:DP:GL:GQ	0/1:16,4:17:-15.00,-5.13,-47.65:98.69
+chr1	3258920	.	C	T	2.85	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=553.46;QD=12.87;SB=-213.92	GT:AD:DP:GL:GQ	0/1:24,19:40:-70.69,-12.06,-71.24:99
+chr1	3262401	rs7550526	G	A	60.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=58.89;MQ0=0;OQ=1567.02;QD=37.31;SB=-629.85	GT:AD:DP:GL:GQ	1/1:0,42:40:-160.30,-12.05,-0.01:99
+chr1	3262685	rs946759	C	A	62.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=-0.12;MQ=57.75;MQ0=0;OQ=630.41;QD=19.70;SB=-314.39	GT:AD:DP:GL:GQ	1/1:3,29:21:-69.14,-6.33,-2.51:38.17
+chr1	3262923	rs946758	G	A	287.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=59.58;MQ0=0;OQ=2113.36;QD=38.42;SB=-1046.71	GT:AD:DP:GL:GQ	1/1:0,55:53:-214.93,-15.96,-0.01:99
+chr1	3263976	rs55805251	C	T	94.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.59;MQ0=0;OQ=518.72;QD=15.72;SB=-142.59	GT:AD:DP:GL:GQ	0/1:15,18:30:-64.20,-9.04,-43.17:99
+chr1	3264566	rs2483265	T	C	43.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=868.82;QD=26.33;SB=-460.17	GT:AD:DP:GL:GQ	1/1:0,33:29:-90.50,-8.75,-0.03:87.17
+chr1	3265009	rs12748963	C	T	26.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=5.21;MQ=58.97;MQ0=0;OQ=826.30;QD=18.36;SB=-347.35	GT:AD:DP:GL:GQ	0/1:19,25:43:-98.87,-12.96,-59.86:99
+chr1	3266234	rs12073172	G	A	592.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.50;MQ0=0;OQ=1102.37;QD=35.56;SB=-562.26	GT:AD:DP:GL:GQ	1/1:0,31:30:-113.84,-9.05,-0.02:90.27
+chr1	3266600	rs2500280	G	C	2.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=8.93;MQ=59.31;MQ0=0;OQ=2375.28;QD=38.94;SB=-992.26	GT:AD:DP:GL:GQ	1/1:0,60:56:-241.13,-16.87,-0.02:99
+chr1	3266936	.	G	A	52.38	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.54;MQ=59.62;MQ0=0;OQ=518.77;QD=10.59;SB=-162.22	GT:AD:DP:GL:GQ	0/1:32,17:48:-69.63,-14.47,-101.23:99
+chr1	3267606	rs884308	C	T	94.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1579.42;QD=39.49;SB=-771.63	GT:AD:DP:GL:GQ	1/1:0,40:40:-161.54,-12.05,-0.01:99
+chr1	3268390	rs11583116	G	A	130.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=58.33;MQ0=0;OQ=690.56;QD=13.81;SB=-242.25	GT:AD:DP:GL:GQ	0/1:26,24:43:-85.30,-12.96,-65.77:99
+chr1	3269184	rs7524171	A	G	11.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=5.01;MQ=59.60;MQ0=0;OQ=1781.26;QD=30.71;SB=-880.26	GT:AD:DP:GL:GQ	1/1:0,58:53:-181.75,-15.98,-0.04:99
+chr1	3269881	rs2500262	T	C	201.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.11;MQ0=0;OQ=1534.16;QD=29.50;SB=-546.01	GT:AD:DP:GL:GQ	1/1:0,52:49:-157.05,-14.78,-0.05:99
+chr1	3271322	.	C	T	58.72	PASS	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=59.40;MQ0=0;OQ=375.26;QD=12.11;SB=-208.89	GT:AD:DP:GL:GQ	0/1:17,14:28:-49.26,-8.45,-45.56:99
+chr1	3273388	rs4648485	G	A	602.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2075.89;QD=37.74;SB=-912.72	GT:AD:DP:GL:GQ	1/1:0,55:53:-211.19,-15.97,-0.02:99
+chr1	3275010	rs4648486	C	T	123.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=58.75;MQ0=0;OQ=2039.90;QD=39.23;SB=-914.69	GT:AD:DP:GL:GQ	1/1:0,52:51:-207.59,-15.36,-0.01:99
+chr1	3275164	rs4648487	T	C	21.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=5.20;MQ=59.14;MQ0=0;OQ=1843.56;QD=34.14;SB=-799.67	GT:AD:DP:GL:GQ	1/1:0,54:53:-187.96,-15.97,-0.02:99
+chr1	3275488	rs6424073	G	A	234.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2488.63;QD=39.50;SB=-1214.11	GT:AD:DP:GL:GQ	1/1:0,63:63:-252.47,-18.98,-0.02:99
+chr1	3277411	rs12138292	A	G	1.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.96;MQ=56.17;MQ0=0;OQ=1416.27;QD=24.85;SB=-414.15	GT:AD:DP:GL:GQ	1/1:0,57:48:-145.28,-14.50,-0.07:99
+chr1	3279384	rs12135987	G	A	273.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.39;MQ0=0;OQ=2572.74;QD=37.83;SB=-927.33	GT:AD:DP:GL:GQ	1/1:0,68:65:-260.88,-19.58,-0.02:99
+chr1	3279467	rs6688949	T	C	3.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=2.45;MQ=57.66;MQ0=0;OQ=1297.10;QD=25.94;SB=-450.26	GT:AD:DP:GL:GQ	1/1:0,50:40:-133.33,-12.06,-0.03:99
+chr1	3279589	rs1333190	C	T	668.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=1807.78;QD=36.89;SB=-784.69	GT:AD:DP:GL:GQ	1/1:0,49:46:-184.37,-13.86,-0.01:99
+chr1	3279831	rs1333189	C	T	229.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=57.13;MQ0=0;OQ=1483.34;QD=36.18;SB=-765.52	GT:AD:DP:GL:GQ	1/1:0,40:38:-151.93,-11.45,-0.01:99
+chr1	3280999	rs2249860	A	C	81.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=57.93;MQ0=0;OQ=1454.60;QD=33.83;SB=-752.07	GT:AD:DP:GL:GQ	1/1:0,43:42:-149.06,-12.65,-0.01:99
+chr1	3281067	rs2368593	G	T	64.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.86;MQ=58.09;MQ0=0;OQ=2257.03;QD=31.79;SB=-1064.90	GT:AD:DP:GL:GQ	1/1:0,70:66:-229.32,-19.89,-0.04:99
+chr1	3281249	.	G	A	160.30	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.53;MQ0=0;OQ=717.46;QD=13.54;SB=-318.84	GT:AD:DP:GL:GQ	0/1:27,26:46:-88.90,-13.87,-75.19:99
+chr1	3282736	rs4648488	C	T	347.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.52;MQ0=0;OQ=841.46;QD=17.53;SB=-434.81	GT:AD:DP:GL:GQ	0/1:21,27:46:-101.29,-13.86,-70.83:99
+chr1	3283525	rs4648489	A	G	474.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=1662.64;QD=30.23;SB=-834.46	GT:AD:DP:GL:GQ	1/1:0,55:53:-169.90,-15.99,-0.06:99
+chr1	3284832	rs1538693	G	A	695.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1980.96;QD=38.10;SB=-939.35	GT:AD:DP:GL:GQ	1/1:0,52:51:-201.70,-15.37,-0.02:99
+chr1	3285724	.	G	A	0.22	PASS	AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=1;HaplotypeScore=6.56;MQ=21.51;MQ0=1;OQ=72.03;QD=9.00;SB=-40.54	GT:AD:DP:GL:GQ	0/1:2,5:4:-11.69,-1.21,-3.37:21.64
+chr1	3285990	.	G	A	25.35	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=1;HaplotypeScore=5.35;MQ=15.41;MQ0=12;QD=0.85;SB=-32.52	GT:AD:DP:GL:GQ	0/1:21,9:5:-7.32,-1.51,-9.51:58.18
+chr1	3286144	.	A	G	36.06	LowQual	AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=14.48;MQ0=3;QD=4.51;SB=-6.99	GT:AD:DP:GL:GQ	0/1:4,3:3:-7.79,-0.90,-4.06:31.52
+chr1	3286152	.	A	C	0.09	PASS	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=27.22;MQ0=3;OQ=114.38;QD=16.34;SB=-46.01	GT:AD:DP:GL:GQ	1/1:0,7:4:-14.97,-1.20,-0.00:12.04
+chr1	3286284	.	G	A	36.93	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=3.77;MQ=31.49;MQ0=4;QD=1.27;SB=-29.53	GT:AD:DP:GL:GQ	0/1:22,7:15:-11.50,-4.52,-41.17:69.76
+chr1	3286312	.	G	A	19.94	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=1;HaplotypeScore=9.31;MQ=28.36;MQ0=5;QD=0.59;SB=-24.50	GT:AD:DP:GL:GQ	0/1:27,6:17:-10.40,-5.13,-47.64:52.73
+chr1	3286320	.	C	A	227.39	HARD_TO_VALIDATE;Indel	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=8.75;MQ=31.04;MQ0=4;QD=5.98;SB=-25.91	GT:AD:DP:GL:GQ	0/1:27,11:20:-32.05,-6.03,-35.21:99
+chr1	3286354	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=1;HaplotypeScore=6.21;MQ=33.14;MQ0=5;OQ=87.60;QD=2.92;SB=-62.36	GT:AD:DP:GL:GQ	0/1:22,7:14:-19.10,-7.05,-34.67:99
+chr1	3286558	rs61043152	G	A	1.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=54.01;MQ0=1;OQ=487.76;QD=11.09;SB=-75.56	GT:AD:DP:GL:GQ	0/1:23,21:40:-64.12,-12.06,-79.70:99
+chr1	3286811	.	T	C	44.59	PASS	AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=60.00;MQ0=0;OQ=1964.33;QD=34.46;SB=-944.38	GT:AD:DP:GL:GQ	1/1:0,57:56:-200.04,-16.87,-0.02:99
+chr1	3287141	rs11584942	G	A	391.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.82;MQ0=0;OQ=780.63;QD=15.31;SB=-324.32	GT:AD:DP:GL:GQ	0/1:25,26:47:-95.51,-14.16,-75.83:99
+chr1	3287246	rs11584967	G	A	573.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=877.40;QD=15.67;SB=-384.91	GT:AD:DP:GL:GQ	0/1:28,28:54:-107.29,-16.27,-98.41:99
+chr1	3287659	rs4648490	A	C	117.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.24;MQ=58.26;MQ0=0;OQ=1692.37;QD=33.18;SB=-840.06	GT:AD:DP:GL:GQ	1/1:0,51:50:-172.85,-15.06,-0.02:99
+chr1	3290667	rs868688	C	T	279.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=58.44;MQ0=0;OQ=2018.08;QD=35.40;SB=-933.25	GT:AD:DP:GL:GQ	1/1:0,57:52:-205.41,-15.67,-0.02:99
+chr1	3290990	rs868689	T	G	679.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.27;MQ0=0;OQ=1815.91;QD=31.86;SB=-898.65	GT:AD:DP:GL:GQ	1/1:0,57:52:-185.19,-15.66,-0.02:99
+chr1	3292591	rs11810266	C	G	73.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.54;MQ0=0;OQ=822.36;QD=20.06;SB=-350.43	GT:AD:DP:GL:GQ	0/1:18,23:40:-97.58,-12.06,-74.61:99
+chr1	3293306	rs2245703	T	C	622.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2385.34;QD=35.60;SB=-962.70	GT:AD:DP:GL:GQ	1/1:0,67:67:-242.14,-20.18,-0.02:99
+chr1	3293627	rs6676024	C	T	186.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.97;MQ0=0;OQ=1016.67;QD=17.23;SB=-303.79	GT:AD:DP:GL:GQ	0/1:29,30:58:-122.43,-17.48,-92.51:99
+chr1	3293798	rs2065525	C	G	62.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=58.34;MQ0=0;OQ=2298.73;QD=40.33;SB=-651.91	GT:AD:DP:GL:GQ	1/1:0,56:54:-233.47,-16.27,-0.01:99
+chr1	3294876	rs17399998	C	T	445.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=1142.20;QD=15.23;SB=-563.39	GT:AD:DP:GL:GQ	0/1:40,35:73:-139.51,-22.00,-126.39:99
+chr1	3295312	rs6687463	A	G	1.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=5.24;MQ=59.03;MQ0=0;OQ=1175.21;QD=27.33;SB=-477.09	GT:AD:DP:GL:GQ	1/1:0,42:38:-121.14,-11.46,-0.04:99
+chr1	3295326	.	C	A	16.33	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=58.87;MQ0=0;OQ=469.13;QD=12.68;SB=-130.80	GT:AD:DP:GL:GQ	0/1:19,18:34:-60.44,-10.25,-57.03:99
+chr1	3295820	.	C	T	40.94	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=844.76;QD=17.60;SB=-369.85	GT:AD:DP:GL:GQ	0/1:21,27:46:-101.62,-13.86,-70.72:99
+chr1	3296384	rs6686140	C	A	6.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=6.50;MQ=59.17;MQ0=0;OQ=324.87;QD=11.60;SB=-121.49	GT:AD:DP:GL:GQ	0/1:8,20:20:-41.81,-6.04,-18.74:99
+chr1	3296715	rs2151350	T	G	0.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=4;HaplotypeScore=2.18;MQ=58.99;MQ0=0;OQ=1168.63;QD=25.41;SB=-611.86	GT:AD:DP:GL:GQ	1/1:0,46:39:-120.49,-11.76,-0.04:99
+chr1	3297308	rs2493281	A	G	8.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.21;MQ=58.18;MQ0=1;OQ=1041.73;QD=26.04;SB=-499.54	GT:AD:DP:GL:GQ	1/1:1,39:33:-107.79,-9.95,-0.03:99
+chr1	3297606	rs2493278	T	C	732.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.88;MQ0=0;OQ=2573.66;QD=35.26;SB=-1043.85	GT:AD:DP:GL:GQ	1/1:0,73:73:-260.97,-21.99,-0.02:99
+chr1	3298358	rs2493268	T	C	154.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.44;MQ=58.22;MQ0=0;OQ=1688.23;QD=33.76;SB=-851.05	GT:AD:DP:GL:GQ	1/1:0,50:48:-172.42,-14.46,-0.02:99
+chr1	3298817	rs12139767	G	C	583.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=898.96;QD=13.62;SB=-383.19	GT:AD:DP:GL:GQ	0/1:39,27:65:-112.80,-19.62,-153.47:99
+chr1	3299326	rs35864014	G	A	497.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=1037.02;QD=15.25;SB=-535.48	GT:AD:DP:GL:GQ	0/1:36,32:68:-127.47,-20.48,-131.88:99
+chr1	3301121	rs6702992	C	T	313.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.53;MQ0=0;OQ=194.21;QD=10.22;SB=-113.94	GT:AD:DP:GL:GQ	0/1:12,7:19:-28.43,-5.72,-42.63:99
+chr1	3301284	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=11;HaplotypeScore=19.15;MQ=56.72;MQ0=0;OQ=88.35;QD=1.38;SB=59.21	GT:AD:DP:GL:GQ	0/1:53,11:56:-28.99,-16.87,-158.63:99
+chr1	3301891	rs883678	C	G	91.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.56;MQ0=0;OQ=812.38;QD=19.34;SB=-299.58	GT:AD:DP:GL:GQ	0/1:20,22:42:-97.18,-12.66,-83.21:99
+chr1	3302116	rs17822575	T	G	316.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.54;MQ0=0;OQ=510.49;QD=12.45;SB=-250.83	GT:AD:DP:GL:GQ	0/1:20,21:40:-66.39,-12.05,-67.05:99
+chr1	3302296	rs10909937	C	T	502.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1321.67;QD=36.71;SB=-625.01	GT:AD:DP:GL:GQ	1/1:0,36:34:-135.76,-10.24,-0.01:99
+chr1	3302524	rs56378103	C	T	103.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=58.71;MQ0=0;OQ=1572.33;QD=29.12;SB=-689.92	GT:AD:DP:GL:GQ	1/1:0,52:42:-160.84,-12.66,-0.02:99
+chr1	3302527	.	C	T	6.09	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=5.35;MQ=58.33;MQ0=0;OQ=1011.78;QD=18.07;SB=-471.49	GT:AD:DP:GL:GQ	0/1:25,31:52:-120.14,-15.67,-71.42:99
+chr1	3302823	rs12726710	C	T	452.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=952.26;QD=17.31;SB=-305.83	GT:AD:DP:GL:GQ	0/1:25,30:55:-115.09,-16.58,-80.89:99
+chr1	3303142	rs7535965	G	A	141.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.64;MQ0=0;OQ=1848.10;QD=38.50;SB=-836.62	GT:AD:DP:GL:GQ	1/1:0,48:47:-188.41,-14.16,-0.02:99
+chr1	3304456	rs17822581	A	G	359.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=58.93;MQ0=0;OQ=1113.18;QD=17.13;SB=-574.04	GT:AD:DP:GL:GQ	0/1:27,38:62:-133.28,-18.68,-95.39:99
+chr1	3304922	rs57432749	C	T	181.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=2.15;MQ=59.75;MQ0=0;OQ=993.31;QD=13.07;SB=-496.07	GT:AD:DP:GL:GQ	0/1:41,34:74:-127.49,-24.88,-150.46:99
+chr1	3305219	rs12144338	C	T	131.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=59.67;MQ0=0;OQ=987.68;QD=17.33;SB=-284.79	GT:AD:DP:GL:GQ	0/1:26,31:53:-118.03,-15.98,-72.20:99
+chr1	3305551	.	G	A	103.37	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=59.39;MQ0=0;OQ=1099.92;QD=15.94;SB=-511.04	GT:AD:DP:GL:GQ	0/1:36,33:68:-133.77,-20.49,-112.10:99
+chr1	3305678	rs7542793	G	A	440.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.35;MQ0=0;OQ=1064.35;QD=16.63;SB=-455.47	GT:AD:DP:GL:GQ	0/1:30,34:62:-128.41,-18.69,-93.40:99
+chr1	3305692	rs12737284	G	A	493.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.31;MQ0=0;OQ=901.95;QD=14.79;SB=-398.19	GT:AD:DP:GL:GQ	0/1:31,30:59:-111.27,-17.79,-96.32:99
+chr1	3305845	rs12117228	T	C	284.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=60.00;MQ0=0;OQ=892.28;QD=11.74;SB=-260.21	GT:AD:DP:GL:GQ	0/1:38,38:73:-114.51,-22.00,-150.21:99
+chr1	3305873	rs7551733	C	G	174.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.43;MQ=60.00;MQ0=0;OQ=1089.18;QD=17.02;SB=-530.69	GT:AD:DP:GL:GQ	0/1:32,32:62:-130.89,-18.69,-134.52:99
+chr1	3306535	rs10909939	T	C	528.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=956.73;QD=17.08;SB=-375.64	GT:AD:DP:GL:GQ	0/1:23,33:55:-115.53,-16.57,-90.24:99
+chr1	3306616	rs10909940	G	A	39.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=1181.64;QD=23.63;SB=-497.15	GT:AD:DP:GL:GQ	0/1:15,35:49:-136.22,-14.77,-45.61:99
+chr1	3306995	rs12743248	G	A	92.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=59.54;MQ0=0;OQ=921.67;QD=15.36;SB=-465.48	GT:AD:DP:GL:GQ	0/1:29,31:55:-112.03,-16.58,-86.62:99
+chr1	3307093	rs12747145	G	A	172.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.50;MQ0=0;OQ=526.33;QD=14.23;SB=-229.52	GT:AD:DP:GL:GQ	0/1:18,17:34:-69.44,-13.52,-51.06:99
+chr1	3307640	rs6424074	A	G	354.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.52;MQ0=0;OQ=483.77;QD=10.08;SB=-196.29	GT:AD:DP:GL:GQ	0/1:28,20:48:-66.12,-14.46,-114.20:99
+chr1	3307747	rs6424075	G	T	374.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.24;MQ0=0;OQ=884.55;QD=14.04;SB=-359.35	GT:AD:DP:GL:GQ	0/1:31,32:59:-109.52,-17.78,-88.61:99
+chr1	3308193	rs7551796	G	A	363.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.69;MQ0=0;OQ=1293.28;QD=17.24;SB=-465.48	GT:AD:DP:GL:GQ	0/1:35,40:71:-154.00,-21.39,-119.84:99
+chr1	3308294	rs11576794	C	T	278.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.09;MQ=57.73;MQ0=0;OQ=809.01;QD=14.19;SB=-410.42	GT:AD:DP:GL:GQ	0/1:31,26:56:-101.07,-16.88,-98.51:99
+chr1	3308295	rs11577526	A	G	45.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=4.09;MQ=57.69;MQ0=0;OQ=1861.63;QD=33.24;SB=-741.99	GT:AD:DP:GL:GQ	1/1:0,56:55:-189.77,-16.57,-0.03:99
+chr1	3308392	rs11578011	T	C	195.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=59.80;MQ0=0;OQ=1812.46;QD=30.21;SB=-790.65	GT:AD:DP:GL:GQ	1/1:0,59:59:-188.08,-20.60,-3.25:99
+chr1	3308574	rs5024246	G	A	333.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=876.20;QD=19.47;SB=-325.85	GT:AD:DP:GL:GQ	0/1:19,26:45:-104.46,-13.56,-63.60:99
+chr1	3308629	rs10909942	C	G	63.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.03;HRun=0;HaplotypeScore=2.61;MQ=58.12;MQ0=0;OQ=1384.57;QD=36.44;SB=-590.68	GT:AD:DP:GL:GQ	1/1:0,37:37:-142.07,-10.86,-0.03:99
+chr1	3308702	rs56148282	G	A	636.18	Indel	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.59;MQ0=0;QD=19.28;SB=-248.56	GT:AD:DP:GL:GQ	0/1:12,21:30:-75.94,-9.04,-37.32:99
+chr1	3308921	rs1889124	A	G	16.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.23;MQ=58.83;MQ0=0;OQ=1016.70;QD=28.24;SB=-485.51	GT:AD:DP:GL:GQ	1/1:0,36:33:-105.29,-9.95,-0.03:99
+chr1	3309492	rs4353034	G	A	0.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=16.76;MQ=57.87;MQ0=0;OQ=200.25;QD=6.07;SB=-37.01	GT:AD:DP:GL:GQ	0/1:23,8:31:-40.02,-16.71,-79.20:99
+chr1	3309534	rs12562397	C	T	380.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.05;MQ0=0;OQ=1380.14;QD=38.34;SB=-494.65	GT:AD:DP:GL:GQ	1/1:0,36:35:-141.61,-10.54,-0.01:99
+chr1	3309541	rs12562399	C	G	28.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.39;MQ0=0;OQ=1543.76;QD=40.63;SB=-639.90	GT:AD:DP:GL:GQ	1/1:0,38:37:-157.97,-11.15,-0.01:99
+chr1	3309637	rs4471209	G	A	344.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.51;MQ0=0;OQ=382.91;QD=10.08;SB=-184.19	GT:AD:DP:GL:GQ	0/1:25,13:37:-52.73,-11.16,-73.72:99
+chr1	3309732	rs6664364	C	T	134.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.91;MQ0=0;OQ=1699.09;QD=36.15;SB=-803.59	GT:AD:DP:GL:GQ	1/1:0,47:44:-173.51,-13.26,-0.01:99
+chr1	3309737	rs6664369	C	T	130.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.53;MQ0=0;OQ=1859.42;QD=37.95;SB=-907.23	GT:AD:DP:GL:GQ	1/1:0,49:48:-189.54,-14.46,-0.02:99
+chr1	3309924	rs6669407	A	G	328.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=995.86;QD=29.29;SB=-353.80	GT:AD:DP:GL:GQ	1/1:0,34:32:-103.20,-9.65,-0.03:96.22
+chr1	3310023	rs2493286	G	C	420.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1672.06;QD=40.78;SB=-718.73	GT:AD:DP:GL:GQ	1/1:0,41:40:-170.80,-12.05,-0.01:99
+chr1	3310336	rs6657675	G	A	148.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=58.38;MQ0=0;OQ=936.76;QD=20.36;SB=-332.89	GT:AD:DP:GL:GQ	0/1:17,29:43:-109.92,-12.96,-52.69:99
+chr1	3310582	rs55820208	C	T	260.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=862.76;QD=19.61;SB=-355.48	GT:AD:DP:GL:GQ	0/1:19,25:43:-102.51,-12.95,-64.90:99
+chr1	3311027	rs41315264	C	A	149.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=59.45;MQ0=0;OQ=411.02;QD=12.09;SB=-182.52	GT:AD:DP:GL:GQ	0/1:19,15:31:-53.72,-9.34,-57.20:99
+chr1	3311596	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=4;HaplotypeScore=11.58;MQ=54.22;MQ0=0;OQ=65.40;QD=1.42;SB=47.17	GT:AD:DP:GL:GQ	0/1:36,10:29:-18.61,-8.78,-88.90:98.24
+chr1	3312969	rs2483222	T	C	325.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.04;MQ0=0;OQ=585.55;QD=11.71;SB=-306.07	GT:AD:DP:GL:GQ	0/1:25,25:48:-76.31,-14.47,-93.64:99
+chr1	3313057	rs2483223	T	G	88.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.28;MQ0=0;OQ=1723.37;QD=26.93;SB=-826.52	GT:AD:DP:GL:GQ	1/1:0,64:57:-175.98,-17.18,-0.06:99
+chr1	3313337	rs2493304	A	G	110.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=57.61;MQ0=0;OQ=687.56;QD=10.91;SB=-122.49	GT:AD:DP:GL:GQ	0/1:35,28:61:-90.42,-18.38,-140.37:99
+chr1	3313476	rs2483224	C	T	77.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=3.15;MQ=58.48;MQ0=0;OQ=742.74;QD=16.15;SB=-389.41	GT:AD:DP:GL:GQ	0/1:21,25:42:-90.21,-12.66,-65.08:99
+chr1	3314069	rs2493303	G	C	188.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=4.50;MQ=59.20;MQ0=0;OQ=943.60;QD=16.27;SB=-364.47	GT:AD:DP:GL:GQ	0/1:29,29:57:-114.83,-17.19,-120.69:99
+chr1	3314293	rs2493302	A	T	133.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=59.50;MQ0=0;OQ=1593.32;QD=34.64;SB=-633.61	GT:AD:DP:GL:GQ	1/1:0,46:43:-162.93,-12.95,-0.01:99
+chr1	3314897	rs2483225	T	C	612.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.62;MQ0=0;OQ=1899.06;QD=30.14;SB=-687.73	GT:AD:DP:GL:GQ	1/1:0,63:60:-193.54,-18.10,-0.05:99
+chr1	3315120	rs12063572	A	G	188.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.59;MQ0=0;OQ=550.32;QD=9.83;SB=-278.26	GT:AD:DP:GL:GQ	0/1:32,24:53:-74.29,-15.98,-116.93:99
+chr1	3315180	rs12063579	A	G	62.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=5.22;MQ=57.82;MQ0=1;OQ=599.80;QD=10.91;SB=-262.60	GT:AD:DP:GL:GQ	0/1:27,28:47:-77.44,-14.18,-83.26:99
+chr1	3315190	rs2493301	G	C	0.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=15.61;MQ=57.11;MQ0=1;OQ=860.03;QD=14.83;SB=-355.44	GT:AD:DP:GL:GQ	0/1:31,27:50:-104.37,-15.08,-104.68:99
+chr1	3315194	rs12063613	A	G	1.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=10.46;MQ=56.06;MQ0=1;OQ=577.86;QD=9.47;SB=-271.10	GT:AD:DP:GL:GQ	0/1:30,31:51:-76.46,-15.39,-99.42:99
+chr1	3315219	.	C	T	17.67	DPFilter;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=15.64;MQ=52.76;MQ0=1;QD=0.26;SB=34.67	GT:AD:DP:GL:GQ	0/1:62,6:62:-23.74,-18.70,-180.77:50.43
+chr1	3315354	rs12065021	T	C	254.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.68;MQ0=0;OQ=519.08;QD=13.66;SB=-277.27	GT:AD:DP:GL:GQ	0/1:17,21:38:-66.65,-11.46,-65.47:99
+chr1	3315386	rs2493300	A	G	19.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=60.00;MQ0=0;OQ=1158.12;QD=28.95;SB=-549.05	GT:AD:DP:GL:GQ	1/1:0,40:37:-119.43,-11.16,-0.04:99
+chr1	3315441	rs2493299	A	G	105.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.81;MQ=60.00;MQ0=0;OQ=1355.37;QD=28.24;SB=-603.93	GT:AD:DP:GL:GQ	1/1:0,48:44:-139.17,-13.27,-0.04:99
+chr1	3315528	rs55929648	C	T	143.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=56.18;MQ0=0;OQ=1041.13;QD=18.59;SB=-362.91	GT:AD:DP:GL:GQ	0/1:25,31:52:-123.07,-15.67,-66.96:99
+chr1	3315772	rs2493298	C	A	135.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.28;MQ=60.00;MQ0=0;OQ=850.76;QD=17.72;SB=-447.55	GT:AD:DP:GL:GQ	0/1:19,29:48:-102.82,-14.46,-64.75:99
+chr1	3315954	rs36070715	C	G	3.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.72;MQ=51.04;MQ0=0;OQ=1102.41;QD=21.62;SB=-424.97	GT:AD:DP:GL:GQ	0/1:21,30:46:-127.39,-13.87,-69.58:99
+chr1	3316002	rs60965010	G	A	53.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=53.52;MQ0=0;OQ=683.65;QD=15.19;SB=-341.33	GT:AD:DP:GL:GQ	0/1:23,22:41:-84.00,-12.35,-71.37:99
+chr1	3316048	rs59831144	A	G	16.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=6.55;MQ=58.48;MQ0=0;OQ=584.41;QD=12.70;SB=-233.93	GT:AD:DP:GL:GQ	0/1:24,22:41:-74.08,-12.36,-76.23:99
+chr1	3316091	rs2493297	G	A	148.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.53;MQ0=0;OQ=1649.32;QD=33.66;SB=-643.25	GT:AD:DP:GL:GQ	1/1:0,49:44:-168.54,-13.26,-0.02:99
+chr1	3316251	.	G	A	182.76	SnpCluster	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=43.92;MQ0=0;QD=3.10;SB=-111.51	GT:AD:DP:GL:GQ	0/1:47,12:54:-37.83,-16.27,-156.64:99
+chr1	3316256	.	T	C	219.54	SnpCluster	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=43.18;MQ0=0;QD=3.66;SB=-32.48	GT:AD:DP:GL:GQ	0/1:44,16:55:-41.82,-16.58,-163.02:99
+chr1	3316258	rs7364679	G	T	370	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=43.51;MQ0=0;QD=6.07;SB=-108.68	GT:AD:DP:GL:GQ	0/1:43,18:56:-57.15,-16.87,-140.13:99
+chr1	3316271	.	G	T	44.21	PASS	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.38;MQ=42.99;MQ0=0;OQ=836.87;QD=13.72;SB=-249.23	GT:AD:DP:GL:GQ	0/1:29,32:52:-102.65,-15.68,-71.94:99
+chr1	3316274	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=55.35;MQ=42.03;MQ0=0;OQ=122.20;QD=2.07;SB=-76.97	GT:AD:DP:GL:GQ	0/1:47,12:53:-31.48,-15.98,-148.32:99
+chr1	3316287	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=56;Dels=0.04;HRun=0;HaplotypeScore=28.34;MQ=46.39;MQ0=0;OQ=249.44;QD=4.45;SB=13.22	GT:AD:DP:GL:GQ	0/1:42,12:52:-43.29,-15.07,-133.82:99
+chr1	3316288	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=24.35;MQ=46.92;MQ0=0;OQ=241.94;QD=4.17;SB=40.21	GT:AD:DP:GL:GQ	0/1:44,14:54:-43.75,-16.27,-150.33:99
+chr1	3316304	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=2;HaplotypeScore=31.71;MQ=50.98;MQ0=0;OQ=105.86;QD=1.79;SB=47.12	GT:AD:DP:GL:GQ	0/1:51,8:50:-28.93,-15.06,-145.13:99
+chr1	3316355	.	A	G	40.11	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=6.42;MQ=53.40;MQ0=0;QD=0.79;SB=24.53	GT:AD:DP:GL:GQ	0/1:42,9:48:-21.76,-14.47,-159.00:72.94
+chr1	3316370	.	G	A	1.13	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=7.87;MQ=52.81;MQ0=0;OQ=530.25;QD=10.40;SB=-291.29	GT:AD:DP:GL:GQ	0/1:31,20:45:-69.88,-13.57,-88.85:99
+chr1	3316500	rs4648494	A	G	396.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.41;MQ0=0;OQ=1411.68;QD=27.15;SB=-591.87	GT:AD:DP:GL:GQ	1/1:0,52:46:-144.80,-13.88,-0.05:99
+chr1	3316656	rs6670123	C	G	292.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.36;MQ=56.33;MQ0=0;OQ=1404.84;QD=19.79;SB=-673.50	GT:AD:DP:GL:GQ	0/1:33,38:68:-164.26,-20.49,-128.05:99
+chr1	3316892	rs2493296	C	T	338.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.07;MQ0=0;OQ=702.09;QD=14.04;SB=-332.51	GT:AD:DP:GL:GQ	0/1:27,23:46:-87.37,-13.87,-76.76:99
+chr1	3317409	rs1106270	A	G	118.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.41;MQ0=0;OQ=1192.84;QD=30.59;SB=-537.44	GT:AD:DP:GL:GQ	1/1:0,39:35:-122.88,-10.54,-0.02:99
+chr1	3317462	rs1106271	T	G	1.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=4;HaplotypeScore=1.32;MQ=56.98;MQ0=0;OQ=1224.22;QD=31.39;SB=-406.92	GT:AD:DP:GL:GQ	1/1:0,39:38:-126.04,-11.45,-0.03:99
+chr1	3317665	rs57382922	C	T	121.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.88;MQ=57.50;MQ0=0;OQ=526.20;QD=15.48;SB=-279.22	GT:AD:DP:GL:GQ	0/1:15,19:32:-65.55,-9.65,-47.15:99
+chr1	3318218	rs870124	T	C	46.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=58.35;MQ0=0;OQ=987.47;QD=31.85;SB=-495.44	GT:AD:DP:GL:GQ	1/1:0,30:29:-102.35,-8.74,-0.01:87.24
+chr1	3318519	rs2493292	C	T	35.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=5.38;MQ=58.81;MQ0=0;OQ=410.88;QD=10.54;SB=-213.48	GT:AD:DP:GL:GQ	0/1:22,17:36:-55.22,-10.85,-74.55:99
+chr1	3319244	rs2493291	C	T	128.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=57.07;MQ0=0;OQ=113.91;QD=8.76;SB=-36.64	GT:AD:DP:GL:GQ	0/1:8,5:13:-18.59,-3.92,-28.88:99
+chr1	3319441	.	G	A	108.40	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=283.86;QD=13.52;SB=-108.97	GT:AD:DP:GL:GQ	0/1:11,10:21:-38.00,-6.33,-35.64:99
+chr1	3320120	.	C	T	102.17	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=60.00;MQ0=0;OQ=709.62;QD=14.78;SB=-362.53	GT:AD:DP:GL:GQ	0/1:24,23:45:-87.81,-13.57,-69.77:99
+chr1	3320537	rs2493290	G	A	97.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=2.41;MQ=59.54;MQ0=0;OQ=872.79;QD=17.46;SB=-392.92	GT:AD:DP:GL:GQ	0/1:24,26:48:-105.02,-14.46,-80.60:99
+chr1	3320607	rs11578951	G	A	205.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=56.45;MQ0=0;OQ=183.21;QD=9.16;SB=-114.08	GT:AD:DP:GL:GQ	0/1:13,7:17:-26.73,-5.12,-34.52:99
+chr1	3320622	rs2493289	A	G	29.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=56.62;MQ0=0;OQ=591.39;QD=28.16;SB=-179.75	GT:AD:DP:GL:GQ	1/1:0,20:19:-62.74,-5.73,-0.02:57.13
+chr1	3320744	rs2493288	G	A	319.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.00;MQ0=0;OQ=558.26;QD=13.29;SB=-286.76	GT:AD:DP:GL:GQ	0/1:23,19:41:-71.47,-12.36,-76.00:99
+chr1	3321412	rs60973157	G	C	340.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=59.61;MQ0=0;OQ=1008.01;QD=17.08;SB=-510.27	GT:AD:DP:GL:GQ	0/1:31,28:58:-121.57,-17.48,-125.42:99
+chr1	3321593	rs2483228	T	C	57.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=59.17;MQ0=0;OQ=862.49;QD=30.80;SB=-342.44	GT:AD:DP:GL:GQ	1/1:0,28:27:-89.85,-8.14,-0.02:81.21
+chr1	3321759	rs1999528	A	G	88.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1263.70;QD=30.82;SB=-424.24	GT:AD:DP:GL:GQ	1/1:0,41:41:-129.99,-12.37,-0.04:99
+chr1	3322543	rs2483229	T	C	158.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.98;MQ0=0;OQ=401.83;QD=7.31;SB=-190.61	GT:AD:DP:GL:GQ	0/1:33,22:50:-58.54,-15.08,-123.40:99
+chr1	3322811	rs1889123	T	C	57.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.68;MQ=60.00;MQ0=0;OQ=1553.51;QD=34.52;SB=-743.30	GT:AD:DP:GL:GQ	1/1:0,45:44:-158.95,-13.25,-0.01:99
+chr1	3323101	rs55713431	A	G	0.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=4;HaplotypeScore=1.93;MQ=59.65;MQ0=0;OQ=422.62;QD=7.97;SB=-123.50	GT:AD:DP:GL:GQ	0/1:32,21:47:-59.71,-14.17,-112.42:99
+chr1	3323323	rs2068354	A	G	160.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.65;MQ0=0;OQ=738.34;QD=11.36;SB=-391.91	GT:AD:DP:GL:GQ	0/1:34,31:64:-96.41,-19.29,-135.43:99
+chr1	3324752	rs2483230	A	G	139.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=59.42;MQ0=0;OQ=1229.51;QD=30.74;SB=-406.34	GT:AD:DP:GL:GQ	1/1:0,40:38:-126.56,-11.45,-0.03:99
+chr1	3326060	rs1984069	C	T	66.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=2062.28;QD=37.50;SB=-721.47	GT:AD:DP:GL:GQ	1/1:0,55:53:-209.83,-15.97,-0.02:99
+chr1	3327403	rs1572040	A	G	479.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1561.86;QD=33.95;SB=-803.63	GT:AD:DP:GL:GQ	1/1:0,46:45:-159.79,-13.56,-0.02:99
+chr1	3327481	.	A	G	13.29	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=3.51;MQ=58.78;MQ0=0;OQ=805.84;QD=11.68;SB=-333.16	GT:AD:DP:GL:GQ	0/1:35,34:66:-103.76,-19.89,-136.42:99
+chr1	3327496	rs11579873	G	A	76.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=5.52;MQ=59.07;MQ0=0;OQ=1231.78;QD=17.60;SB=-403.19	GT:AD:DP:GL:GQ	0/1:34,36:67:-146.65,-20.19,-102.53:99
+chr1	3328305	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=2;HaplotypeScore=9.54;MQ=57.05;MQ0=0;OQ=81.44;QD=1.66;SB=56.21	GT:AD:DP:GL:GQ	0/1:35,13:31:-20.79,-9.36,-100.83:99
+chr1	3328931	rs2483231	A	G	0.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=2.58;MQ=57.64;MQ0=0;OQ=961.69;QD=26.71;SB=-96.83	GT:AD:DP:GL:GQ	1/1:0,35:29:-99.77,-8.74,-0.01:87.24
+chr1	3329199	rs10492937	C	A	94.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=591.17;QD=15.16;SB=-220.88	GT:AD:DP:GL:GQ	0/1:18,21:38:-73.85,-11.45,-60.07:99
+chr1	3329740	.	G	T	6.44	PASS	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=1;HaplotypeScore=3.49;MQ=59.36;MQ0=0;OQ=539.79;QD=14.99;SB=-294.29	GT:AD:DP:GL:GQ	0/1:15,21:33:-67.21,-9.94,-47.46:99
+chr1	3329976	rs2483232	A	G	146.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.54;MQ0=0;OQ=1387.79;QD=27.76;SB=-682.70	GT:AD:DP:GL:GQ	1/1:0,49:45:-142.42,-13.58,-0.05:99
+chr1	3330129	rs4648385	C	T	62.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=59.51;MQ0=0;OQ=1421.02;QD=37.40;SB=-712.36	GT:AD:DP:GL:GQ	1/1:0,38:36:-145.70,-10.84,-0.01:99
+chr1	3330207	rs2483233	A	G	536.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1265.03;QD=33.29;SB=-631.30	GT:AD:DP:GL:GQ	1/1:0,38:37:-130.10,-11.15,-0.02:99
+chr1	3330527	rs2483234	A	G	229.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1088.75;QD=27.92;SB=-544.02	GT:AD:DP:GL:GQ	1/1:0,38:35:-112.49,-10.56,-0.04:99
+chr1	3330619	rs2483235	A	G	461.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.29;MQ0=0;OQ=1699.01;QD=28.80;SB=-626.83	GT:AD:DP:GL:GQ	1/1:0,59:55:-173.55,-16.59,-0.06:99
+chr1	3330715	rs4648500	A	C	461.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.69;MQ0=0;OQ=953.20;QD=15.63;SB=-476.30	GT:AD:DP:GL:GQ	0/1:28,33:61:-116.98,-18.37,-104.31:99
+chr1	3331400	rs2483236	C	T	56.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=55.81;MQ0=0;OQ=1168.69;QD=36.52;SB=-534.21	GT:AD:DP:GL:GQ	1/1:0,31:30:-120.46,-9.04,-0.01:90.29
+chr1	3331651	rs1970118	A	G	69.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=50.87;MQ0=0;OQ=938.62;QD=27.61;SB=-452.46	GT:AD:DP:GL:GQ	1/1:0,34:32:-97.49,-9.66,-0.04:96.17
+chr1	3331969	rs41303861	G	T	165.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=56.82;MQ0=0;OQ=610.74;QD=12.99;SB=-193.66	GT:AD:DP:GL:GQ	0/1:23,24:44:-77.62,-13.26,-67.40:99
+chr1	3332390	rs2244013	G	A	343.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.76;MQ=59.53;MQ0=0;OQ=624.83;QD=12.75;SB=-319.81	GT:AD:DP:GL:GQ	0/1:27,22:47:-79.93,-14.16,-96.24:99
+chr1	3332664	rs870171	G	T	453.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=726.05;QD=12.10;SB=-151.13	GT:AD:DP:GL:GQ	0/1:34,26:59:-93.67,-17.78,-105.77:99
+chr1	3333105	rs7549050	A	G	414.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=796.44;QD=10.62;SB=-292.01	GT:AD:DP:GL:GQ	0/1:42,33:74:-105.23,-22.30,-168.30:99
+chr1	3333795	rs55833861	T	C	103.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=2.59;MQ=58.97;MQ0=0;OQ=717.11;QD=11.38;SB=-232.86	GT:AD:DP:GL:GQ	0/1:36,27:59:-92.78,-17.78,-129.42:99
+chr1	3333920	rs56196310	G	T	246.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=59.56;MQ0=0;OQ=564.40;QD=10.65;SB=-293.98	GT:AD:DP:GL:GQ	0/1:32,21:49:-74.48,-14.76,-99.79:99
+chr1	3334336	rs61759212	A	G	99.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=59.13;MQ0=0;OQ=418.37;QD=9.73;SB=-116.62	GT:AD:DP:GL:GQ	0/1:23,20:40:-57.18,-12.06,-85.13:99
+chr1	3334647	rs2483240	A	G	15.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=55.38;MQ0=1;OQ=79.23;QD=3.96;SB=-53.29	GT:AD:DP:GL:GQ	0/1:13,7:16:-16.03,-4.82,-44.27:99
+chr1	3335005	rs2483242	A	T	508.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.64;MQ0=0;OQ=469.82;QD=13.82;SB=-232.91	GT:AD:DP:GL:GQ	0/1:18,16:34:-60.51,-10.24,-69.68:99
+chr1	3335714	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=9.36;MQ=57.49;MQ0=0;OQ=205.84;QD=4.57;SB=56.19	GT:AD:DP:GL:GQ	0/1:25,20:36:-34.71,-10.85,-86.86:99
+chr1	3336208	rs2493277	C	G	559.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=642.22;QD=14.94;SB=-326.21	GT:AD:DP:GL:GQ	0/1:23,20:42:-80.17,-12.66,-97.68:99
+chr1	3336263	rs11583353	C	T	94.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.90;MQ0=0;OQ=708.85;QD=18.65;SB=-324.84	GT:AD:DP:GL:GQ	0/1:17,21:37:-85.32,-11.15,-51.45:99
+chr1	3339994	rs10752734	T	C	155.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.27;MQ0=2;OQ=107.39;QD=6.32;SB=-10.00	GT:AD:DP:GL:GQ	1/1:8,9:4:-14.27,-1.20,-0.00:12.04
+chr1	3342087	rs1537406	T	C	266.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.23;MQ0=0;OQ=2135.99;QD=33.90;SB=-825.32	GT:AD:DP:GL:GQ	1/1:0,63:60:-217.21,-18.07,-0.02:99
+chr1	3342088	rs12735779	G	C	80.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.25;MQ0=0;OQ=2678.31;QD=41.20;SB=-987.13	GT:AD:DP:GL:GQ	1/1:0,65:62:-271.44,-18.68,-0.02:99
+chr1	3342207	rs1537405	T	C	92.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=60.00;MQ0=0;OQ=1223.31;QD=28.45;SB=-485.50	GT:AD:DP:GL:GQ	1/1:0,43:40:-125.96,-12.07,-0.04:99
+chr1	3342363	rs1537404	G	C	0.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=4;HaplotypeScore=2.53;MQ=57.71;MQ0=0;OQ=1605.19;QD=37.33;SB=-574.94	GT:AD:DP:GL:GQ	1/1:0,43:39:-164.12,-11.76,-0.02:99
+chr1	3342401	rs1065247	T	C	218.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=58.89;MQ0=0;OQ=523.80;QD=12.47;SB=-250.33	GT:AD:DP:GL:GQ	0/1:20,21:38:-67.12,-11.46,-67.07:99
+chr1	3342439	rs1537402	T	C	329.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.61;MQ0=0;OQ=1390.94;QD=29.59;SB=-663.80	GT:AD:DP:GL:GQ	1/1:0,47:44:-142.72,-13.27,-0.04:99
+chr1	3342644	rs2493267	A	G	426.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1871.16;QD=31.71;SB=-785.23	GT:AD:DP:GL:GQ	1/1:0,59:54:-190.73,-16.27,-0.03:99
+chr1	3342725	rs35015571	C	T	160.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=59.43;MQ0=0;OQ=266.00;QD=8.06;SB=-157.61	GT:AD:DP:GL:GQ	0/1:23,10:28:-38.32,-8.44,-61.48:99
+chr1	3342732	rs2236518	A	C	16.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=2;HaplotypeScore=2.32;MQ=59.45;MQ0=0;OQ=611.30;QD=17.98;SB=-246.93	GT:AD:DP:GL:GQ	0/1:10,24:30:-73.45,-9.04,-31.78:99
+chr1	3343497	rs35837267	G	A	179.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=1.81;MQ=58.20;MQ0=0;OQ=412.37;QD=12.13;SB=-230.72	GT:AD:DP:GL:GQ	0/1:20,14:34:-54.77,-10.25,-72.54:99
+chr1	3343750	rs2493265	A	G	92.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.09;MQ0=0;OQ=1343.75;QD=27.42;SB=-616.98	GT:AD:DP:GL:GQ	1/1:0,49:43:-138.00,-12.97,-0.04:99
+chr1	3343809	rs2493264	A	G	123.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.40;MQ=58.91;MQ0=0;OQ=1865.11;QD=29.14;SB=-622.24	GT:AD:DP:GL:GQ	1/1:0,64:61:-190.17,-18.41,-0.07:99
+chr1	3344455	rs2483249	T	C	577.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2266.24;QD=31.92;SB=-1078.24	GT:AD:DP:GL:GQ	1/1:0,71:70:-230.26,-21.11,-0.05:99
+chr1	3344475	rs2493263	T	C	726.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2858.56;QD=35.29;SB=-1249.13	GT:AD:DP:GL:GQ	1/1:0,81:80:-289.47,-24.10,-0.03:99
+chr1	3345122	rs55729137	G	A	38.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=59.48;MQ0=0;OQ=807.80;QD=18.36;SB=-199.91	GT:AD:DP:GL:GQ	0/1:20,24:42:-96.73,-12.66,-57.09:99
+chr1	3346265	rs2483250	A	C	12.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=59.52;MQ0=0;OQ=1256.35;QD=32.21;SB=-315.07	GT:AD:DP:GL:GQ	1/1:0,39:37:-129.23,-11.15,-0.01:99
+chr1	3346495	rs2483251	T	C	2.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=2;HaplotypeScore=1.13;MQ=60.00;MQ0=0;OQ=525.69;QD=27.67;SB=-225.75	GT:AD:DP:GL:GQ	1/1:0,19:16:-56.16,-4.82,-0.01:48.13
+chr1	3346655	rs2493262	C	G	18.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=2;HaplotypeScore=2.19;MQ=59.17;MQ0=0;OQ=878.66;QD=31.38;SB=-427.67	GT:AD:DP:GL:GQ	1/1:0,27:23:-91.47,-6.94,-0.02:69.23
+chr1	3346875	rs12745100	C	T	10.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=496.33;QD=18.38;SB=-39.63	GT:AD:DP:GL:GQ	0/1:12,15:27:-61.05,-8.13,-42.91:99
+chr1	3347097	rs55892133	A	G	803.11	Indel	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.17;MQ=58.79;MQ0=0;QD=12.55;SB=-200.20	GT:AD:DP:GL:GQ	0/1:34,30:60:-101.69,-18.09,-118.87:99
+chr1	3347896	rs10797392	T	G	467.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.49;MQ0=1;OQ=720.09;QD=12.20;SB=-372.76	GT:AD:DP:GL:GQ	0/1:27,32:54:-91.57,-16.27,-88.57:99
+chr1	3348782	rs2483252	G	C	20.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=1.07;MQ=58.41;MQ0=0;OQ=1754.48;QD=39.87;SB=-676.45	GT:AD:DP:GL:GQ	1/1:0,43:42:-179.05,-12.66,-0.02:99
+chr1	3348792	rs35536718	C	G	187.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=58.60;MQ0=0;OQ=722.68;QD=14.45;SB=-275.28	GT:AD:DP:GL:GQ	0/1:28,22:46:-89.42,-13.87,-106.46:99
+chr1	3349040	rs2493261	C	G	241.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=2328.68;QD=40.85;SB=-454.11	GT:AD:DP:GL:GQ	1/1:0,57:55:-236.48,-16.59,-0.03:99
+chr1	3349142	rs56009352	G	T	195.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=58.75;MQ0=0;OQ=381.64;QD=9.09;SB=-161.15	GT:AD:DP:GL:GQ	0/1:24,18:38:-52.90,-11.45,-81.46:99
+chr1	3349843	rs11588737	T	C	126.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.70;MQ0=0;OQ=680.83;QD=8.96;SB=-348.93	GT:AD:DP:GL:GQ	0/1:44,32:72:-93.07,-21.70,-169.44:99
+chr1	3349896	rs9424295	C	A	298.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.90;MQ0=0;OQ=883.58;QD=12.27;SB=-371.71	GT:AD:DP:GL:GQ	0/1:40,32:69:-112.42,-20.78,-136.87:99
+chr1	3350654	.	A	G	19.67	PASS	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=4.82;MQ=58.94;MQ0=0;OQ=752.06;QD=11.22;SB=-353.94	GT:AD:DP:GL:GQ	0/1:36,30:64:-97.78,-19.29,-134.25:99
+chr1	3350874	rs2493260	A	T	152.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1881.55;QD=33.01;SB=-813.90	GT:AD:DP:GL:GQ	1/1:0,54:52:-191.76,-15.67,-0.02:99
+chr1	3351164	rs2483254	G	A	165.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.02;MQ=57.99;MQ0=0;OQ=1923.46;QD=34.35;SB=-708.45	GT:AD:DP:GL:GQ	1/1:0,56:52:-195.97,-15.68,-0.04:99
+chr1	3351668	rs61759222	T	C	292.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.16;MQ0=0;OQ=649.71;QD=12.99;SB=-320.27	GT:AD:DP:GL:GQ	0/1:27,23:50:-83.32,-15.07,-104.64:99
+chr1	3351675	rs61759223	T	C	215.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.56;MQ0=0;OQ=453.74;QD=8.73;SB=-214.35	GT:AD:DP:GL:GQ	0/1:31,21:51:-64.03,-15.38,-121.39:99
+chr1	3351951	rs61759224	A	G	132.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=58.69;MQ0=0;OQ=462.74;QD=9.25;SB=-204.32	GT:AD:DP:GL:GQ	0/1:29,21:49:-64.32,-14.77,-119.90:99
+chr1	3352116	rs867814	C	T	338.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.66;MQ0=0;OQ=1015.19;QD=15.15;SB=-259.14	GT:AD:DP:GL:GQ	0/1:34,33:66:-124.69,-19.89,-112.54:99
+chr1	3352233	rs55781247	C	T	0.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=12.27;MQ=55.55;MQ0=1;OQ=438.31;QD=8.59;SB=-227.00	GT:AD:DP:GL:GQ	0/1:27,22:35:-60.74,-13.63,-60.12:99
+chr1	3352662	.	G	C	94.32	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.30;MQ0=0;OQ=750.60;QD=12.94;SB=-224.33	GT:AD:DP:GL:GQ	0/1:34,23:56:-95.22,-16.87,-149.91:99
+chr1	3353096	rs11808277	C	G	337.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.63;MQ0=0;OQ=1053.89;QD=17.00;SB=-489.21	GT:AD:DP:GL:GQ	0/1:30,32:59:-126.45,-17.78,-131.54:99
+chr1	3353132	.	G	A	167.12	PASS	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.73;MQ0=0;OQ=1096.75;QD=16.13;SB=-431.84	GT:AD:DP:GL:GQ	0/1:34,34:67:-133.15,-20.19,-109.37:99
+chr1	3353327	rs10158332	A	T	108.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=58.82;MQ0=0;OQ=1002.21;QD=14.12;SB=-515.47	GT:AD:DP:GL:GQ	0/1:38,33:71:-124.89,-21.39,-148.24:99
+chr1	3353449	rs10157570	G	A	490.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=905.02;QD=15.88;SB=-430.82	GT:AD:DP:GL:GQ	0/1:30,27:56:-110.66,-16.88,-93.98:99
+chr1	3353662	rs2483255	A	T	46.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=4.02;MQ=59.30;MQ0=0;OQ=2470.87;QD=37.44;SB=-912.35	GT:AD:DP:GL:GQ	1/1:0,66:64:-250.68,-19.27,-0.01:99
+chr1	3353786	rs2493258	A	G	307.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.56;MQ0=0;OQ=1182.18;QD=13.91;SB=-595.40	GT:AD:DP:GL:GQ	0/1:39,46:85:-147.12,-25.62,-159.37:99
+chr1	3354380	rs61759225	T	C	235.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=921.81;QD=12.29;SB=-424.06	GT:AD:DP:GL:GQ	0/1:42,33:74:-117.76,-22.29,-166.03:99
+chr1	3354597	rs2263010	T	C	533.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2222.94;QD=35.85;SB=-1114.11	GT:AD:DP:GL:GQ	1/1:0,62:62:-225.90,-18.68,-0.02:99
+chr1	3354829	rs61759226	A	T	251.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.16;MQ0=0;OQ=1748.33;QD=17.48;SB=-874.02	GT:AD:DP:GL:GQ	0/1:46,54:99:-207.93,-29.81,-176.30:99
+chr1	3355107	rs4648386	A	G	12.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=59.31;MQ0=0;OQ=1773.45;QD=34.77;SB=-505.48	GT:AD:DP:GL:GQ	1/1:0,51:51:-180.95,-15.36,-0.02:99
+chr1	3355113	rs61759227	G	A	0.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=6.85;MQ=58.80;MQ0=0;OQ=911.32;QD=18.60;SB=-216.88	GT:AD:DP:GL:GQ	0/1:22,27:48:-108.87,-14.46,-75.78:99
+chr1	3355993	rs55913848	G	T	115.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=58.15;MQ0=0;OQ=1046.84;QD=16.62;SB=-492.93	GT:AD:DP:GL:GQ	0/1:29,34:61:-126.34,-18.38,-91.26:99
+chr1	3356353	rs2096102	C	A	344.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=61.19;MQ0=0;OQ=1204.86;QD=17.21;SB=-565.00	GT:AD:DP:GL:GQ	0/1:30,40:67:-143.95,-20.18,-94.79:99
+chr1	3356461	.	G	A	34.92	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=63.59;MQ=46.78;MQ0=1;QD=0.83;SB=-40.97	GT:AD:DP:GL:GQ	0/1:36,6:34:-17.03,-10.25,-100.31:67.76
+chr1	3356464	.	T	G	27.11	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=13.28;MQ=49.36;MQ0=1;QD=0.85;SB=-38.91	GT:AD:DP:GL:GQ	0/1:28,4:29:-14.73,-8.74,-84.74:59.94
+chr1	3356466	.	G	T	324.76	SnpCluster	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=10.60;MQ=48.57;MQ0=1;QD=10.83;SB=-127.64	GT:AD:DP:GL:GQ	0/1:15,15:26:-43.60,-7.84,-42.90:99
+chr1	3357640	rs2487679	A	G	123.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.76;MQ=59.32;MQ0=0;OQ=2260.98;QD=33.25;SB=-697.21	GT:AD:DP:GL:GQ	1/1:0,68:67:-229.71,-20.18,-0.03:99
+chr1	3357895	rs6697669	T	C	43.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.03;HRun=0;HaplotypeScore=3.79;MQ=57.15;MQ0=0;OQ=335.02;QD=10.15;SB=-38.93	GT:AD:DP:GL:GQ	0/1:18,13:30:-45.82,-9.04,-67.57:99
+chr1	3357991	rs4648501	G	A	122.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.97;MQ0=0;OQ=545.72;QD=10.70;SB=-291.79	GT:AD:DP:GL:GQ	0/1:33,18:50:-72.92,-15.06,-113.74:99
+chr1	3358003	rs2487670	G	A	120.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.77;MQ0=0;OQ=1144.78;QD=22.01;SB=-472.53	GT:AD:DP:GL:GQ	0/1:18,34:50:-132.83,-15.07,-51.40:99
+chr1	3358201	rs55902179	A	G	118.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=60.00;MQ0=0;OQ=620.71;QD=14.78;SB=-241.29	GT:AD:DP:GL:GQ	0/1:20,22:41:-77.71,-12.35,-78.03:99
+chr1	3359613	rs2487668	G	A	227.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=59.61;MQ0=0;OQ=985.10;QD=16.70;SB=-425.79	GT:AD:DP:GL:GQ	0/1:26,32:57:-118.97,-17.18,-94.23:99
+chr1	3359684	rs34681041	A	G	13.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=1.71;MQ=60.00;MQ0=0;OQ=330.72;QD=8.70;SB=-110.60	GT:AD:DP:GL:GQ	0/1:21,17:34:-46.60,-10.25,-79.14:99
+chr1	3361330	.	G	C	0.29	PASS	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=68.48;QD=6.85;SB=-10.00	GT:AD:DP:GL:GQ	0/1:6,4:9:-12.85,-2.72,-22.16:99
+chr1	3361841	rs55858614	G	C	94.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.70;MQ0=0;OQ=503.58;QD=17.36;SB=-238.39	GT:AD:DP:GL:GQ	0/1:14,15:29:-62.38,-8.74,-58.19:99
+chr1	3362331	rs10909946	A	C	12.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=2.71;MQ=58.18;MQ0=0;OQ=655.84;QD=12.15;SB=-228.89	GT:AD:DP:GL:GQ	0/1:26,28:47:-83.03,-14.16,-81.70:99
+chr1	3362529	rs61759232	T	C	1.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=3.67;MQ=58.99;MQ0=0;OQ=549.81;QD=11.95;SB=-107.61	GT:AD:DP:GL:GQ	0/1:22,24:42:-70.93,-12.66,-83.77:99
+chr1	3362717	.	A	G	41.71	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.52;MQ=59.65;MQ0=0;OQ=773.42;QD=14.59;SB=-374.28	GT:AD:DP:GL:GQ	0/1:23,30:49:-95.39,-14.76,-86.55:99
+chr1	3363471	rs56365322	C	G	249.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.24;MQ0=0;OQ=638.66;QD=11.61;SB=-240.06	GT:AD:DP:GL:GQ	0/1:30,25:50:-82.23,-15.08,-125.58:99
+chr1	3363827	rs2493256	A	G	265.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=58.48;MQ0=0;OQ=531.11;QD=12.35;SB=-221.59	GT:AD:DP:GL:GQ	0/1:23,19:42:-71.22,-14.82,-89.22:99
+chr1	3364220	rs12745860	C	T	264.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=58.78;MQ0=0;OQ=718.26;QD=12.60;SB=-212.70	GT:AD:DP:GL:GQ	0/1:33,24:53:-91.09,-15.98,-94.23:99
+chr1	3364244	rs12758368	T	A	250.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.60;MQ=59.27;MQ0=0;OQ=910.80;QD=14.46;SB=-359.58	GT:AD:DP:GL:GQ	0/1:33,30:62:-113.04,-18.68,-119.17:99
+chr1	3364803	rs56242281	A	G	70.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=3.36;MQ=59.30;MQ0=0;OQ=300.82;QD=9.12;SB=-84.67	GT:AD:DP:GL:GQ	0/1:18,14:30:-42.41,-9.04,-64.59:99
+chr1	3365228	rs61759235	A	G	136.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=58.63;MQ0=0;OQ=478.85;QD=9.39;SB=-239.48	GT:AD:DP:GL:GQ	0/1:30,21:48:-65.63,-14.46,-116.95:99
+chr1	3365583	rs61759236	C	G	131.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=835.90;QD=18.58;SB=-383.86	GT:AD:DP:GL:GQ	0/1:22,23:43:-99.85,-12.97,-77.78:99
+chr1	3366053	rs61759237	C	T	131.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=735.43;QD=17.10;SB=-313.83	GT:AD:DP:GL:GQ	0/1:21,22:42:-89.48,-12.65,-70.75:99
+chr1	3366393	rs12059504	T	C	302.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=60.00;MQ0=0;OQ=609.78;QD=12.70;SB=-240.29	GT:AD:DP:GL:GQ	0/1:24,24:48:-78.73,-14.47,-96.53:99
+chr1	3366983	rs59183260	C	T	199.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.76;MQ=59.56;MQ0=0;OQ=586.61;QD=13.97;SB=-272.28	GT:AD:DP:GL:GQ	0/1:22,20:39:-73.71,-11.76,-62.95:99
+chr1	3367203	rs2487681	T	C	222.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=60.00;MQ0=0;OQ=351.40;QD=8.79;SB=-154.93	GT:AD:DP:GL:GQ	0/1:22,18:38:-49.88,-11.46,-85.17:99
+chr1	3372040	rs10909947	G	T	39.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.75;MQ0=0;OQ=1667.04;QD=35.47;SB=-355.84	GT:AD:DP:GL:GQ	1/1:0,47:46:-170.30,-13.86,-0.01:99
+chr1	3372773	.	T	G	28.89	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=4.07;MQ=59.49;MQ0=0;QD=0.64;SB=56.17	GT:AD:DP:GL:GQ	0/1:32,13:34:-16.42,-10.24,-99.13:61.72
+chr1	3372898	rs947351	G	A	372.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.19;MQ0=0;OQ=649.44;QD=12.49;SB=-216.21	GT:AD:DP:GL:GQ	0/1:28,24:49:-83.00,-14.77,-93.12:99
+chr1	3373453	rs3893316	G	T	349.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=441.10;QD=14.70;SB=-201.58	GT:AD:DP:GL:GQ	0/1:13,17:29:-56.13,-8.74,-43.76:99
+chr1	3373525	rs7550948	G	A	64.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.53;MQ0=0;OQ=1066.26;QD=21.76;SB=-418.80	GT:AD:DP:GL:GQ	0/1:18,31:47:-124.08,-14.17,-50.84:99
+chr1	3373758	rs6424078	A	G	63.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=2.28;MQ=58.45;MQ0=0;OQ=303.09;QD=10.10;SB=-109.62	GT:AD:DP:GL:GQ	0/1:15,15:29:-42.34,-8.75,-57.35:99
+chr1	3373912	rs45512802	C	T	115.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.77;MQ=58.81;MQ0=0;OQ=487.90;QD=12.51;SB=-154.65	GT:AD:DP:GL:GQ	0/1:21,18:37:-63.22,-11.15,-77.33:99
+chr1	3374091	rs6667361	A	G	15.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=3;HaplotypeScore=1.91;MQ=58.45;MQ0=0;OQ=441.93;QD=9.82;SB=-196.52	GT:AD:DP:GL:GQ	0/1:26,19:43:-60.43,-12.96,-100.55:99
+chr1	3374466	rs7522513	A	G	114.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.36;MQ0=0;OQ=449.01;QD=11.23;SB=-195.64	GT:AD:DP:GL:GQ	0/1:20,20:37:-59.34,-11.16,-69.75:99
+chr1	3374989	rs2493250	G	A	285.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.52;MQ0=0;OQ=823.07;QD=17.15;SB=-412.42	GT:AD:DP:GL:GQ	0/1:23,25:48:-100.06,-14.47,-73.79:99
+chr1	3374999	rs2487673	G	T	438.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=759.07;QD=16.87;SB=-384.82	GT:AD:DP:GL:GQ	0/1:19,26:45:-92.75,-13.56,-63.83:99
+chr1	3375110	rs1417897	C	A	224.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=57.71;MQ0=0;OQ=613.48;QD=15.73;SB=-271.51	GT:AD:DP:GL:GQ	0/1:18,21:37:-75.78,-11.15,-51.34:99
+chr1	3375116	rs1891143	A	G	122.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=57.71;MQ0=0;OQ=346.85;QD=8.89;SB=-128.27	GT:AD:DP:GL:GQ	0/1:22,17:35:-48.52,-10.55,-81.11:99
+chr1	3375190	rs2493249	T	C	0.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=3;HaplotypeScore=2.59;MQ=59.45;MQ0=0;OQ=889.42;QD=26.16;SB=-381.39	GT:AD:DP:GL:GQ	1/1:0,34:28:-92.55,-8.44,-0.02:84.20
+chr1	3377520	.	G	A	54.48	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=60.00;MQ0=0;OQ=404.10;QD=10.92;SB=-123.57	GT:AD:DP:GL:GQ	0/1:21,16:32:-53.34,-9.65,-57.04:99
+chr1	3379133	rs2298082	T	C	273.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.53;MQ=58.32;MQ0=0;OQ=528.06;QD=13.20;SB=-222.68	GT:AD:DP:GL:GQ	0/1:19,21:37:-67.24,-11.15,-73.98:99
+chr1	3379181	rs2487687	C	T	16.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=60.00;MQ0=0;OQ=545.94;QD=21.00;SB=-232.27	GT:AD:DP:GL:GQ	0/1:9,17:25:-65.41,-7.53,-31.41:99
+chr1	3379587	rs2185639	C	T	119.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=58.13;MQ0=0;OQ=232.01;QD=9.28;SB=-26.61	GT:AD:DP:GL:GQ	0/1:14,10:22:-33.12,-6.63,-45.28:99
+chr1	3380098	rs2493323	T	A	210.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=1873.41;QD=38.23;SB=-364.88	GT:AD:DP:GL:GQ	1/1:0,49:49:-190.94,-14.76,-0.01:99
+chr1	3380882	rs2493322	G	A	155.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.57;MQ0=0;OQ=666.25;QD=12.34;SB=-269.17	GT:AD:DP:GL:GQ	0/1:33,21:52:-85.58,-15.67,-103.39:99
+chr1	3381466	.	A	G	34.09	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.23;MQ=18.93;MQ0=48;QD=0.47;SB=2.04	GT:AD:DP:GL:GQ	0/1:58,15:13:-10.61,-3.92,-40.00:66.92
+chr1	3381536	rs2493320	G	A	66.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=9.35;MQ0=30;OQ=163.18;QD=3.98;SB=-10.00	GT:AD:DP:GL:GQ	1/1:12,29:5:-19.88,-1.51,-0.00:15.05
+chr1	3381776	rs56863381	G	A	0.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=12.80;MQ0=34;OQ=57.75;QD=1.03;SB=5.02	GT:AD:DP:GL:GQ	0/1:40,16:11:-12.38,-3.32,-24.49:90.59
+chr1	3382016	.	A	G	35.80	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=12.28;MQ0=39;QD=0.55;SB=-10.00	GT:AD:DP:GL:GQ	0/1:54,11:16:-11.69,-4.82,-49.41:68.63
+chr1	3382186	rs2493318	A	G	275.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=47.26;MQ0=1;OQ=747.71;QD=13.35;SB=-372.26	GT:AD:DP:GL:GQ	0/1:27,29:52:-93.72,-15.67,-105.01:99
+chr1	3382897	rs12124163	G	T	198.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.56;MQ0=0;OQ=598.86;QD=14.26;SB=-222.53	GT:AD:DP:GL:GQ	0/1:21,21:41:-75.52,-12.35,-66.44:99
+chr1	3383727	rs10797394	G	A	171.07	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=49.26;MQ0=0;QD=13.16;SB=8.03	GT:AD:DP:GL:GQ	0/1:7,6:12:-24.01,-3.62,-19.11:99
+chr1	3383981	rs56341824	G	T	14.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=1.70;MQ=59.25;MQ0=0;OQ=147.62;QD=5.90;SB=-6.99	GT:AD:DP:GL:GQ	0/1:17,8:23:-24.98,-6.93,-50.77:99
+chr1	3384110	rs10909948	C	T	220.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=54.75;MQ0=0;OQ=493.02;QD=17.00;SB=-263.55	GT:AD:DP:GL:GQ	0/1:13,16:28:-61.02,-8.44,-45.99:99
+chr1	3384316	rs4638054	T	C	12.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.07;MQ0=0;OQ=1239.78;QD=27.55;SB=-421.16	GT:AD:DP:GL:GQ	1/1:0,45:41:-127.61,-12.37,-0.05:99
+chr1	3384500	rs4422946	A	G	10.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=2;HaplotypeScore=1.93;MQ=60.00;MQ0=0;OQ=259.70;QD=9.27;SB=-73.94	GT:AD:DP:GL:GQ	0/1:16,12:25:-36.79,-7.54,-56.39:99
+chr1	3384534	rs4534324	T	C	47.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.99;MQ0=0;OQ=674.08;QD=29.31;SB=-343.44	GT:AD:DP:GL:GQ	1/1:0,23:22:-71.01,-6.63,-0.02:66.16
+chr1	3384899	rs10797395	G	A	51.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.52;MQ=59.38;MQ0=0;OQ=712.83;QD=19.27;SB=-338.87	GT:AD:DP:GL:GQ	0/1:16,21:35:-85.11,-10.54,-50.14:99
+chr1	3385089	rs4553117	T	C	310.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=892.31;QD=26.24;SB=-387.26	GT:AD:DP:GL:GQ	1/1:0,34:29:-92.85,-8.75,-0.03:87.19
+chr1	3385248	rs28568519	C	G	124.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=59.45;MQ0=0;OQ=725.71;QD=17.28;SB=-286.30	GT:AD:DP:GL:GQ	0/1:20,22:38:-87.31,-11.46,-71.37:99
+chr1	3386469	rs881978	C	T	144.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=2.64;MQ=59.25;MQ0=0;OQ=1109.69;QD=19.82;SB=-578.43	GT:AD:DP:GL:GQ	0/1:23,33:55:-130.82,-16.57,-79.57:99
+chr1	3386922	rs56309807	G	A	10.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=6.20;MQ=58.23;MQ0=0;OQ=434.23;QD=11.74;SB=-179.25	GT:AD:DP:GL:GQ	0/1:20,16:31:-56.05,-9.34,-54.39:99
+chr1	3387048	rs2487677	T	C	22.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.93;MQ=58.11;MQ0=0;OQ=1498.47;QD=31.88;SB=-723.23	GT:AD:DP:GL:GQ	1/1:0,46:43:-153.45,-12.96,-0.02:99
+chr1	3387315	rs1051515	G	A	124.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=59.55;MQ0=0;OQ=661.19;QD=15.03;SB=-242.52	GT:AD:DP:GL:GQ	0/1:21,23:41:-81.76,-12.36,-69.63:99
+chr1	3387424	rs1051517	C	T	185.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.57;MQ0=0;OQ=722.32;QD=16.80;SB=-358.40	GT:AD:DP:GL:GQ	0/1:21,22:42:-88.17,-12.66,-71.34:99
+chr1	3387765	rs2487676	G	C	0.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=59.56;MQ0=0;OQ=985.55;QD=23.47;SB=-402.96	GT:AD:DP:GL:GQ	0/1:13,29:39:-113.61,-11.77,-48.31:99
+chr1	3387785	rs10797396	G	A	343.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=869.16;QD=19.75;SB=-452.50	GT:AD:DP:GL:GQ	0/1:15,29:41:-102.56,-12.36,-46.08:99
+chr1	3388739	.	G	C	3.92	PASS	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=47.12;MQ0=0;OQ=99.91;QD=7.14;SB=-0.98	GT:AD:DP:GL:GQ	0/1:10,4:13:-17.20,-3.93,-33.90:99
+chr1	3388844	rs11579276	C	T	89.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=228.92;QD=8.80;SB=-0.98	GT:AD:DP:GL:GQ	0/1:16,10:21:-32.51,-6.33,-40.91:99
+chr1	3389315	rs2493316	T	C	332.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=364.79;QD=11.40;SB=-143.65	GT:AD:DP:GL:GQ	0/1:18,14:32:-49.41,-9.65,-68.22:99
+chr1	3390585	rs12124659	C	T	210.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.96;MQ0=0;OQ=1350.80;QD=37.52;SB=-227.30	GT:AD:DP:GL:GQ	1/1:0,36:35:-138.68,-10.55,-0.01:99
+chr1	3391131	rs2487674	A	G	49.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=60.00;MQ0=0;OQ=2482.25;QD=31.82;SB=-1068.16	GT:AD:DP:GL:GQ	1/1:0,78:76:-251.87,-22.92,-0.06:99
+chr1	3392093	rs4648504	C	T	77.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.60;MQ=53.45;MQ0=1;OQ=1952.99;QD=36.17;SB=-850.15	GT:AD:DP:GL:GQ	1/1:1,53:50:-198.90,-15.06,-0.02:99
+chr1	3394087	rs2821041	C	T	330.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=59.75;MQ0=0;OQ=1098.32;QD=14.64;SB=-325.80	GT:AD:DP:GL:GQ	0/1:41,34:73:-135.10,-21.99,-140.04:99
+chr1	3394997	rs61759244	C	G	135	PASS	AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=59.37;MQ0=0;OQ=1716.91;QD=17.88;SB=-792.82	GT:AD:DP:GL:GQ	0/1:43,53:93:-203.04,-28.07,-171.23:99
+chr1	3395156	rs4648505	T	C	309	PASS	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.51;MQ0=0;OQ=921.20;QD=9.70;SB=-319.80	GT:AD:DP:GL:GQ	0/1:57,38:95:-124.03,-28.62,-233.81:99
+chr1	3401826	rs2821034	T	C	25.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=5.69;MQ=57.22;MQ0=0;OQ=336.60;QD=15.30;SB=-157.73	GT:AD:DP:GL:GQ	1/1:0,21:12:-37.26,-3.62,-0.02:36.06
+chr1	3406983	.	G	A	147.34	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=493.27;QD=14.51;SB=-172.20	GT:AD:DP:GL:GQ	0/1:17,17:33:-62.55,-9.94,-60.75:99
+chr1	3408031	rs7516662	A	G	45.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.10;MQ=59.41;MQ0=0;OQ=599.81;QD=15.38;SB=-119.66	GT:AD:DP:GL:GQ	0/1:18,21:37:-74.41,-11.15,-64.16:99
+chr1	3408425	rs2821030	T	C	291.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=44.95;MQ0=0;OQ=775.65;QD=13.61;SB=-335.17	GT:AD:DP:GL:GQ	0/1:17,40:43:-93.82,-12.97,-49.21:99
+chr1	3408438	rs56284135	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=5;HaplotypeScore=43.60;MQ=44.49;MQ0=0;OQ=630.57;QD=9.70;SB=-139.40	GT:AD:DP:GL:GQ	0/1:28,36:49:-81.11,-14.77,-94.33:99
+chr1	3408476	rs57408931	G	C	181.30	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=164;Dels=0.03;HRun=1;HaplotypeScore=218.91;MQ=41.51;MQ0=3;QD=1.11;SB=-63.16	GT:AD:DP:GL:GQ	0/1:117,24:115:-89.58,-68.17,-379.21:99
+chr1	3408478	rs57082253	G	A	513.03	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=180;Dels=0.00;HRun=0;HaplotypeScore=193.59;MQ=41.21;MQ0=2;QD=2.85;SB=-274.73	GT:AD:DP:GL:GQ	0/1:134,38:129:-95.85,-41.26,-324.12:99
+chr1	3408517	rs7368034	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=115;Dels=0.00;HRun=0;HaplotypeScore=120.54;MQ=42.22;MQ0=3;OQ=514.65;QD=4.48;SB=-116.36	GT:AD:DP:GL:GQ	0/1:73,33:82:-88.72,-33.97,-192.96:99
+chr1	3411446	rs6669870	C	T	607.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.14;MQ0=0;OQ=1485.27;QD=36.23;SB=-614.81	GT:AD:DP:GL:GQ	1/1:0,41:39:-152.13,-11.76,-0.02:99
+chr1	3411518	rs2821009	A	T	529.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.77;MQ0=0;OQ=1252.41;QD=34.79;SB=-623.61	GT:AD:DP:GL:GQ	1/1:0,36:35:-128.84,-10.55,-0.01:99
+chr1	3411757	rs2821008	A	G	31.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.15;MQ=59.41;MQ0=0;OQ=238.32;QD=6.11;SB=-110.60	GT:AD:DP:GL:GQ	0/1:25,14:37:-38.27,-11.15,-99.52:99
+chr1	3413327	rs947344	C	T	169.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=58.66;MQ0=0;OQ=1006.19;QD=19.35;SB=-478.56	GT:AD:DP:GL:GQ	0/1:21,31:45:-117.47,-13.57,-45.94:99
+chr1	3413493	rs2821006	A	G	514.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1416.92;QD=30.15;SB=-704.80	GT:AD:DP:GL:GQ	1/1:0,47:45:-145.32,-13.57,-0.04:99
+chr1	3413602	rs10797397	C	A	230.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.01;MQ=59.11;MQ0=0;OQ=969.58;QD=16.43;SB=-386.82	GT:AD:DP:GL:GQ	0/1:25,34:55:-116.81,-16.57,-75.73:99
+chr1	3414248	rs947345	G	A	253.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.28;MQ=59.23;MQ0=0;OQ=855.83;QD=14.26;SB=-381.90	GT:AD:DP:GL:GQ	0/1:31,29:53:-104.84,-15.98,-85.70:99
+chr1	3415290	rs2794358	A	G	117.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1082.49;QD=30.93;SB=-492.45	GT:AD:DP:GL:GQ	1/1:0,35:32:-111.85,-9.64,-0.02:96.25
+chr1	3416927	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=1;HaplotypeScore=20.42;MQ=57.31;MQ0=0;OQ=341.32;QD=7.11;SB=-84.89	GT:AD:DP:GL:GQ	0/1:26,19:38:-51.91,-14.49,-87.40:99
+chr1	3416981	rs56310990	G	C	2.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=51.26;MQ0=0;OQ=93.69;QD=3.02;SB=-14.81	GT:AD:DP:GL:GQ	0/1:25,6:25:-20.20,-7.54,-81.40:99
+chr1	3416998	.	C	T	35.62	PASS	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=49.93;MQ0=0;OQ=473.15;QD=15.77;SB=-230.75	GT:AD:DP:GL:GQ	0/1:10,20:24:-57.83,-7.23,-29.03:99
+chr1	3418020	rs2820999	T	G	23.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=1.35;MQ=59.30;MQ0=0;OQ=1099.49;QD=33.32;SB=-419.27	GT:AD:DP:GL:GQ	1/1:0,32:32:-113.54,-9.64,-0.01:96.28
+chr1	3418284	rs4648391	G	T	480.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=1326.40;QD=33.16;SB=-497.29	GT:AD:DP:GL:GQ	1/1:0,40:39:-136.24,-11.75,-0.02:99
+chr1	3418288	rs4648514	C	T	298.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=1504.64;QD=38.58;SB=-514.18	GT:AD:DP:GL:GQ	1/1:0,39:39:-154.07,-11.75,-0.02:99
+chr1	3418468	rs11585362	G	A	504.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1061.06;QD=36.59;SB=-446.58	GT:AD:DP:GL:GQ	1/1:0,29:29:-109.71,-8.74,-0.02:87.27
+chr1	3419555	rs11587354	C	A	388.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=2174.38;QD=35.07;SB=-358.82	GT:AD:DP:GL:GQ	1/1:0,62:58:-221.04,-17.47,-0.02:99
+chr1	3420506	.	T	A	214.92	PASS	AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1094.09;QD=36.47;SB=-408.28	GT:AD:DP:GL:GQ	1/1:0,30:30:-113.00,-9.04,-0.01:90.28
+chr1	3422067	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=4;HaplotypeScore=5.56;MQ=56.93;MQ0=0;OQ=142.54;QD=3.85;SB=26.11	GT:AD:DP:GL:GQ	0/1:17,20:22:-24.18,-6.64,-53.52:99
+chr1	3422138	rs12045137	C	G	147.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1703.92;QD=40.57;SB=-765.63	GT:AD:DP:GL:GQ	1/1:0,42:41:-174.00,-12.36,-0.02:99
+chr1	3422853	rs11587498	G	A	175.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=60.00;MQ0=0;OQ=415.52;QD=12.22;SB=-203.18	GT:AD:DP:GL:GQ	0/1:20,14:31:-54.19,-9.35,-54.52:99
+chr1	3424377	rs2820995	A	G	162.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=58.66;MQ0=0;OQ=1805.64;QD=27.36;SB=-525.83	GT:AD:DP:GL:GQ	1/1:0,66:60:-184.23,-18.11,-0.08:99
+chr1	3424844	rs2794362	G	C	500.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=1899.04;QD=42.20;SB=-801.86	GT:AD:DP:GL:GQ	1/1:0,45:44:-193.50,-13.26,-0.01:99
+chr1	3427795	rs2794365	T	C	272.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.56;MQ0=0;OQ=540.74;QD=12.87;SB=-223.28	GT:AD:DP:GL:GQ	0/1:22,20:39:-69.11,-11.75,-73.06:99
+chr1	3428053	rs11587384	G	A	58.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=58.59;MQ0=0;OQ=656.10;QD=19.88;SB=-350.39	GT:AD:DP:GL:GQ	0/1:13,20:30:-77.94,-9.05,-31.18:99
+chr1	3428530	rs10909958	C	T	169.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=60.00;MQ0=0;OQ=649.49;QD=10.31;SB=-164.81	GT:AD:DP:GL:GQ	0/1:40,23:61:-86.62,-18.39,-128.91:99
+chr1	3429888	rs10797398	G	C	1.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=0.26;MQ=58.87;MQ0=0;OQ=1501.66;QD=40.59;SB=-598.80	GT:AD:DP:GL:GQ	1/1:0,37:37:-153.77,-11.16,-0.02:99
+chr1	3430507	rs2794322	T	C	118.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=864.34;QD=26.19;SB=-416.15	GT:AD:DP:GL:GQ	1/1:0,33:29:-90.06,-8.75,-0.04:87.16
+chr1	3430803	rs12049449	A	C	10.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=1.13;MQ=59.39;MQ0=0;OQ=1279.24;QD=33.66;SB=-506.06	GT:AD:DP:GL:GQ	1/1:0,38:37:-131.52,-11.15,-0.02:99
+chr1	3431124	rs12093117	G	A	200.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.17;MQ=59.61;MQ0=0;OQ=828.18;QD=17.25;SB=-263.28	GT:AD:DP:GL:GQ	0/1:20,28:45:-99.67,-13.57,-58.69:99
+chr1	3432615	rs11589895	G	A	209.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.89;MQ0=0;OQ=771.91;QD=18.38;SB=-386.90	GT:AD:DP:GL:GQ	0/1:19,23:42:-93.13,-12.66,-62.18:99
+chr1	3433053	.	C	T	70.11	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=58.26;MQ0=0;OQ=707.05;QD=13.86;SB=-362.49	GT:AD:DP:GL:GQ	0/1:26,25:48:-88.45,-14.46,-91.49:99
+chr1	3435213	rs2821068	G	C	38.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=58.11;MQ0=0;OQ=1371.97;QD=37.08;SB=-540.03	GT:AD:DP:GL:GQ	1/1:0,36:33:-140.79,-9.95,-0.01:99
+chr1	3435771	rs883427	G	A	416.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.00;MQ0=0;OQ=1899.02;QD=38.76;SB=-741.50	GT:AD:DP:GL:GQ	1/1:0,49:48:-193.50,-14.46,-0.01:99
+chr1	3436171	rs11589175	G	A	118.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=494.22;QD=9.88;SB=-114.31	GT:AD:DP:GL:GQ	0/1:32,17:48:-69.83,-17.13,-113.83:99
+chr1	3436855	rs11811714	C	T	197.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=58.93;MQ0=0;OQ=2210.05;QD=36.23;SB=-988.23	GT:AD:DP:GL:GQ	1/1:0,61:58:-224.62,-17.49,-0.03:99
+chr1	3436977	rs56103034	G	C	151.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=60.00;MQ0=0;OQ=361.61;QD=12.91;SB=-169.18	GT:AD:DP:GL:GQ	0/1:15,13:27:-47.59,-8.14,-66.07:99
+chr1	3437069	.	A	C	13.05	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=2;HaplotypeScore=6.13;MQ=58.68;MQ0=0;QD=0.25;SB=74.24	GT:AD:DP:GL:GQ	0/1:37,15:37:-15.71,-11.15,-109.98:45.67
+chr1	3438669	rs61762171	G	A	197.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.08;MQ=59.50;MQ0=0;OQ=831.35;QD=18.07;SB=-356.42	GT:AD:DP:GL:GQ	0/1:21,25:43:-99.38,-12.97,-55.25:99
+chr1	3438727	rs55762450	C	A	163.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.54;MQ0=0;OQ=660.37;QD=13.21;SB=-236.28	GT:AD:DP:GL:GQ	0/1:20,30:45:-82.89,-13.57,-69.96:99
+chr1	3440115	rs2493313	T	C	297.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=56.74;MQ0=0;OQ=1008.77;QD=34.79;SB=-528.20	GT:AD:DP:GL:GQ	1/1:0,29:29:-104.47,-8.74,-0.01:87.25
+chr1	3444452	rs9970944	G	T	111.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.08;MQ=58.11;MQ0=0;OQ=1564.30;QD=32.59;SB=-784.47	GT:AD:DP:GL:GQ	1/1:1,47:45:-160.04,-13.56,-0.02:99
+chr1	3445102	rs12049456	G	A	432	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.32;MQ0=0;OQ=1256.64;QD=36.96;SB=-508.18	GT:AD:DP:GL:GQ	1/1:0,34:33:-129.26,-9.95,-0.01:99
+chr1	3445120	.	C	G	39.08	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=55.59;MQ0=2;QD=0.85;SB=59.22	GT:AD:DP:GL:GQ	0/1:40,6:41:-19.55,-12.36,-150.78:71.92
+chr1	3448511	rs2821064	A	T	100.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.44;MQ=58.81;MQ0=0;OQ=526.36;QD=13.50;SB=-238.77	GT:AD:DP:GL:GQ	0/1:20,19:39:-67.67,-11.75,-70.26:99
+chr1	3448541	rs2794331	G	C	111.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=58.71;MQ0=0;OQ=556.37;QD=15.45;SB=-245.10	GT:AD:DP:GL:GQ	0/1:19,17:32:-68.58,-9.65,-62.08:99
+chr1	3448992	rs12065874	C	T	177.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=59.46;MQ0=0;OQ=793.34;QD=18.45;SB=-374.15	GT:AD:DP:GL:GQ	0/1:19,24:39:-94.38,-11.76,-47.24:99
+chr1	3452764	rs10797401	T	C	166.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.03;MQ=59.52;MQ0=0;OQ=647.76;QD=16.61;SB=-319.33	GT:AD:DP:GL:GQ	0/1:16,23:38:-79.51,-11.45,-58.06:99
+chr1	3453088	rs28479691	G	A	97.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=55.43;MQ0=1;OQ=249.39;QD=11.34;SB=-131.56	GT:AD:DP:GL:GQ	0/1:11,11:18:-33.65,-5.43,-32.56:99
+chr1	3453209	rs13374309	C	G	5.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=2;HaplotypeScore=3.14;MQ=57.20;MQ0=0;OQ=292.98;QD=15.42;SB=-154.58	GT:AD:DP:GL:GQ	0/1:9,10:17:-37.71,-5.13,-33.06:99
+chr1	3455556	rs7539836	A	G	113.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=359.37;QD=13.82;SB=-189.55	GT:AD:DP:GL:GQ	0/1:12,14:25:-46.76,-7.53,-43.20:99
+chr1	3458010	rs7533321	G	A	155.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.46;MQ0=0;OQ=810.48;QD=18.85;SB=-428.48	GT:AD:DP:GL:GQ	0/1:17,25:39:-96.09,-11.75,-47.40:99
+chr1	3458818	rs6413780	A	C	146.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.53;MQ0=0;OQ=401.98;QD=8.20;SB=-115.74	GT:AD:DP:GL:GQ	0/1:29,20:47:-57.64,-14.16,-107.92:99
+chr1	3458949	rs7355038	G	A	151.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=59.19;MQ0=0;OQ=998.13;QD=19.19;SB=-471.50	GT:AD:DP:GL:GQ	0/1:22,30:52:-118.77,-15.67,-71.64:99
+chr1	3460223	rs10909965	T	G	23.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=2.59;MQ=58.78;MQ0=0;OQ=201.44;QD=10.60;SB=-54.94	GT:AD:DP:GL:GQ	0/1:10,9:17:-28.55,-5.12,-30.64:99
+chr1	3460241	rs12078542	T	C	57.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=58.39;MQ0=0;OQ=207.08;QD=7.14;SB=-117.62	GT:AD:DP:GL:GQ	0/1:17,12:22:-30.63,-6.64,-46.05:99
+chr1	3460729	rs1557089	T	G	340.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.05;MQ0=0;OQ=311.87;QD=12.99;SB=-162.75	GT:AD:DP:GL:GQ	0/1:12,12:20:-40.49,-6.02,-30.26:99
+chr1	3462253	rs7516641	A	G	481.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=514.29;QD=11.96;SB=-180.52	GT:AD:DP:GL:GQ	0/1:23,20:43:-67.67,-12.96,-92.19:99
+chr1	3466443	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=45;Dels=0.02;HRun=17;HaplotypeScore=21.57;MQ=53.85;MQ0=0;OQ=205.19;QD=4.56;SB=-78.83	GT:AD:DP:GL:GQ	0/1:24,20:32:-33.15,-9.34,-78.96:99
+chr1	3466697	.	C	G	64.69	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=58.96;MQ0=0;OQ=671.74;QD=12.44;SB=-259.12	GT:AD:DP:GL:GQ	0/1:31,23:50:-85.55,-15.09,-116.59:99
+chr1	3474782	rs56410789	G	A	184.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=59.61;MQ0=0;OQ=703.19;QD=14.65;SB=-349.63	GT:AD:DP:GL:GQ	0/1:25,22:45:-89.80,-16.20,-75.19:99
+chr1	3480873	.	T	C	0.25	PASS	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=3;HaplotypeScore=1.82;MQ=59.06;MQ0=0;OQ=234.33;QD=11.72;SB=-33.65	GT:AD:DP:GL:GQ	0/1:10,10:19:-32.44,-5.72,-41.44:99
+chr1	3480967	rs4431782	T	C	9.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=2.79;MQ=59.14;MQ0=0;OQ=141.27;QD=5.23;SB=-37.66	GT:AD:DP:GL:GQ	0/1:16,11:24:-24.65,-7.24,-64.66:99
+chr1	3482056	rs2821057	A	G	50.28	Indel	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.04;HRun=0;HaplotypeScore=40.06;MQ=43.76;MQ0=3;QD=0.93;SB=-23.61	GT:AD:DP:GL:GQ	0/1:44,8:48:-22.18,-13.87,-154.71:83.12
+chr1	3483124	rs2821056	A	T	583.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.89;MQ0=0;OQ=1839.69;QD=37.54;SB=-868.96	GT:AD:DP:GL:GQ	1/1:0,49:49:-187.56,-14.76,-0.01:99
+chr1	3483560	rs2821055	T	C	111.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=57.13;MQ0=0;OQ=1375.27;QD=31.98;SB=-687.18	GT:AD:DP:GL:GQ	1/1:0,43:41:-141.13,-12.35,-0.02:99
+chr1	3483710	rs2821054	G	T	266.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.07;MQ0=0;OQ=1733.58;QD=34.67;SB=-747.08	GT:AD:DP:GL:GQ	1/1:0,50:50:-176.97,-15.07,-0.02:99
+chr1	3484389	rs2794348	A	G	1.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=6.39;MQ=58.05;MQ0=0;OQ=1127.20;QD=31.31;SB=-545.88	GT:AD:DP:GL:GQ	1/1:0,36:34:-116.33,-10.25,-0.02:99
+chr1	3484478	rs2794347	G	C	132.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.47;MQ0=0;OQ=1529.91;QD=34.77;SB=-715.91	GT:AD:DP:GL:GQ	1/1:0,44:40:-156.62,-12.09,-0.05:99
+chr1	3484580	rs2794346	G	A	64.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=980.89;QD=28.85;SB=-342.41	GT:AD:DP:GL:GQ	1/1:1,32:27:-101.70,-8.14,-0.02:81.23
+chr1	3485237	rs2794344	G	A	227.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=58.20;MQ0=0;OQ=1135.92;QD=18.03;SB=-434.44	GT:AD:DP:GL:GQ	0/1:26,37:58:-134.36,-17.49,-77.46:99
+chr1	3485276	rs2794343	G	T	262.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=58.14;MQ0=0;OQ=635.86;QD=12.00;SB=-319.27	GT:AD:DP:GL:GQ	0/1:28,25:50:-81.94,-15.07,-81.25:99
+chr1	3485297	rs2794342	T	C	164.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.19;MQ=55.76;MQ0=0;OQ=873.19;QD=16.17;SB=-382.03	GT:AD:DP:GL:GQ	0/1:20,34:51:-105.98,-15.38,-70.34:99
+chr1	3485317	.	C	T	0.61	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=55.51;MQ0=0;OQ=217.69;QD=4.03;SB=-62.86	GT:AD:DP:GL:GQ	0/1:42,11:46:-38.92,-13.87,-116.02:99
+chr1	3485320	.	C	T	0.57	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=55.81;MQ0=0;OQ=186.10;QD=3.58;SB=-62.80	GT:AD:DP:GL:GQ	0/1:41,10:44:-35.15,-13.26,-125.21:99
+chr1	3485329	rs56044258	C	G	8.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=4.19;MQ=55.35;MQ0=0;OQ=1813.27;QD=38.58;SB=-922.42	GT:AD:DP:GL:GQ	1/1:0,47:43:-184.93,-12.96,-0.02:99
+chr1	3485401	rs2821053	T	C	608.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.09;MQ0=0;OQ=2115.06;QD=34.11;SB=-1060.08	GT:AD:DP:GL:GQ	1/1:0,62:60:-215.11,-18.07,-0.02:99
+chr1	3485841	rs2794341	T	C	133.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.28;MQ=59.57;MQ0=0;OQ=1280.08;QD=29.77;SB=-579.98	GT:AD:DP:GL:GQ	1/1:0,43:41:-131.63,-12.37,-0.04:99
+chr1	3485914	rs2821052	G	C	139.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=59.60;MQ0=0;OQ=1918.65;QD=40.82;SB=-901.42	GT:AD:DP:GL:GQ	1/1:0,47:46:-195.47,-13.86,-0.02:99
+chr1	3486188	rs2821051	T	C	180.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.51;MQ0=0;OQ=1502.08;QD=31.96;SB=-651.24	GT:AD:DP:GL:GQ	1/1:0,47:44:-153.81,-13.26,-0.02:99
+chr1	3486339	rs2794340	T	C	195.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=747.54;QD=27.69;SB=-185.41	GT:AD:DP:GL:GQ	1/1:0,27:25:-78.37,-7.54,-0.03:75.17
+chr1	3486805	rs2794339	G	A	3.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=790.02;QD=34.35;SB=-39.54	GT:AD:DP:GL:GQ	1/1:0,23:21:-82.60,-6.33,-0.01:63.20
+chr1	3486898	.	C	G	23.94	LowQual	AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=3.33;MQ=60.00;MQ0=0;QD=2.18;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,7:5:-7.19,-1.52,-10.35:56.76
+chr1	3486969	rs2821050	A	G	170.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.66;MQ0=0;OQ=230.85;QD=23.09;SB=-101.03	GT:AD:DP:GL:GQ	1/1:0,10:9:-26.68,-2.72,-0.01:27.04
+chr1	3487085	rs2821049	G	A	44.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.41;MQ0=1;OQ=1103.43;QD=35.59;SB=-441.32	GT:AD:DP:GL:GQ	1/1:0,31:29:-113.94,-8.74,-0.01:87.28
+chr1	3487785	rs2821048	T	C	3.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=3;HaplotypeScore=0.79;MQ=59.07;MQ0=0;OQ=795.96;QD=29.48;SB=-323.61	GT:AD:DP:GL:GQ	1/1:0,26:24:-83.19,-7.23,-0.01:72.20
+chr1	3488346	rs2821047	A	C	41.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=59.50;MQ0=0;OQ=1833.45;QD=33.34;SB=-923.21	GT:AD:DP:GL:GQ	1/1:0,55:53:-186.95,-15.96,-0.02:99
+chr1	3488543	rs2794338	G	A	5.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=2.25;MQ=59.38;MQ0=0;OQ=1108.21;QD=36.94;SB=-425.07	GT:AD:DP:GL:GQ	1/1:0,30:29:-114.42,-8.74,-0.01:87.27
+chr1	3488600	rs2821046	T	C	153.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=59.16;MQ0=0;OQ=1640.68;QD=29.83;SB=-825.95	GT:AD:DP:GL:GQ	1/1:0,55:53:-167.70,-15.99,-0.05:99
+chr1	3488885	rs2794337	T	G	92.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.67;MQ0=0;OQ=1036.65;QD=29.62;SB=-469.86	GT:AD:DP:GL:GQ	1/1:0,35:34:-107.28,-10.25,-0.03:99
+chr1	3488911	rs2794336	C	A	491.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1159.72;QD=31.34;SB=-543.79	GT:AD:DP:GL:GQ	1/1:0,37:35:-119.58,-10.55,-0.02:99
+chr1	3489106	rs2821045	A	G	0.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=15.70;MQ=58.09;MQ0=0;OQ=1342.02;QD=27.39;SB=-607.24	GT:AD:DP:GL:GQ	1/1:1,48:44:-137.83,-13.27,-0.05:99
+chr1	3489389	rs2794335	C	G	104.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=56.91;MQ0=0;OQ=2044.98;QD=41.73;SB=-1038.63	GT:AD:DP:GL:GQ	1/1:0,49:48:-208.10,-14.46,-0.02:99
+chr1	3489541	rs2821044	A	G	154.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=51.93;MQ0=0;OQ=1856.46;QD=32.01;SB=-939.38	GT:AD:DP:GL:GQ	1/1:0,58:53:-189.25,-15.96,-0.02:99
+chr1	3489730	.	G	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=5.70;MQ=38.46;MQ0=13;OQ=219.88;QD=2.71;SB=-20.96	GT:AD:DP:GL:GQ	0/1:65,15:58:-42.77,-17.50,-145.53:99
+chr1	3489856	rs61762194	A	G	22.79	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=13.90;MQ=6.46;MQ0=57;QD=0.35;SB=-34.94	GT:AD:DP:GL:GQ	0/1:19,46:3:-6.46,-0.90,-4.17:32.64
+chr1	3490108	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=0;HaplotypeScore=22.57;MQ=11.21;MQ0=79;OQ=52.09;QD=0.43;SB=2.03	GT:AD:DP:GL:GQ	0/1:64,55:12:-12.11,-3.62,-27.46:84.92
+chr1	3490124	.	G	C	37.51	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=28.89;MQ=9.24;MQ0=69;QD=0.40;SB=-36.43	GT:AD:DP:GL:GQ	0/1:52,37:3:-7.94,-0.91,-4.59:36.89
+chr1	3490204	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=9.07;MQ=18.33;MQ0=40;OQ=221.10;QD=2.91;SB=-48.02	GT:AD:DP:GL:GQ	0/1:38,34:16:-30.22,-4.83,-23.80:99
+chr1	3490220	.	G	C	14.47	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=1;HaplotypeScore=18.26;MQ=21.29;MQ0=44;QD=0.14;SB=5.04	GT:AD:DP:GL:GQ	0/1:89,13:27:-12.87,-8.16,-91.89:47.15
+chr1	3490238	.	G	C	29.48	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=1;HaplotypeScore=19.99;MQ=24.83;MQ0=54;QD=0.24;SB=65.23	GT:AD:DP:GL:GQ	0/1:92,32:39:-18.02,-11.79,-132.68:62.32
+chr1	3490274	rs61762197	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=195;Dels=0.00;HRun=0;HaplotypeScore=31.55;MQ=26.52;MQ0=97;OQ=140.78;QD=0.72;SB=53.20	GT:AD:DP:GL:GQ	0/1:172,21:60:-35.47,-18.11,-209.36:99
+chr1	3490294	rs61762198	G	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=144;Dels=0.00;HRun=0;HaplotypeScore=18.88;MQ=30.38;MQ0=61;OQ=410.69;QD=2.85;SB=-6.44	GT:AD:DP:GL:GQ	0/1:110,32:48:-58.84,-14.49,-102.11:99
+chr1	3490309	rs61762199	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=43.37;MQ=33.08;MQ0=48;OQ=683.06;QD=5.42;SB=-30.63	GT:AD:DP:GL:GQ	0/1:101,25:47:-85.76,-14.17,-79.46:99
+chr1	3490312	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=46.24;MQ=34.26;MQ0=40;OQ=200.77;QD=1.72;SB=-32.50	GT:AD:DP:GL:GQ	0/1:85,31:40:-35.43,-12.07,-95.25:99
+chr1	3490435	rs2995009	G	A	597.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.35;MQ0=0;OQ=1467.09;QD=38.61;SB=-711.36	GT:AD:DP:GL:GQ	1/1:0,38:38:-150.31,-11.45,-0.01:99
+chr1	3491040	rs2995008	T	C	284.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1828.19;QD=32.07;SB=-897.29	GT:AD:DP:GL:GQ	1/1:0,57:55:-186.44,-16.58,-0.04:99
+chr1	3492147	.	G	A	23.72	PASS	AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=55.26;MQ0=1;OQ=1679.66;QD=32.93;SB=-585.96	GT:AD:DP:GL:GQ	1/1:1,50:45:-171.57,-13.56,-0.02:99
+chr1	3492404	rs2487682	G	A	109.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=55.97;MQ0=0;OQ=1664.54;QD=34.68;SB=-566.34	GT:AD:DP:GL:GQ	1/1:2,46:43:-170.05,-12.95,-0.01:99
+chr1	3493214	rs10909977	C	T	290.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.46;MQ0=0;OQ=982.44;QD=37.79;SB=-341.35	GT:AD:DP:GL:GQ	1/1:0,26:26:-101.84,-7.83,-0.01:78.25
+chr1	3493427	rs12133810	G	A	0.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=6.10;MQ=60.00;MQ0=0;OQ=1731.58;QD=36.07;SB=-586.35	GT:AD:DP:GL:GQ	1/1:0,47:45:-176.76,-13.56,-0.02:99
+chr1	3493933	rs12139206	T	C	718.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.76;MQ0=0;OQ=2133.52;QD=33.87;SB=-1000.69	GT:AD:DP:GL:GQ	1/1:0,63:61:-216.96,-18.38,-0.03:99
+chr1	3494278	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=29.95;MQ=39.18;MQ0=0;OQ=57.06;QD=1.00;SB=32.12	GT:AD:DP:GL:GQ	0/1:51,6:50:-24.05,-15.06,-154.00:89.90
+chr1	3494280	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=31.95;MQ=39.34;MQ0=0;OQ=98.32;QD=1.76;SB=29.10	GT:AD:DP:GL:GQ	0/1:46,10:49:-27.88,-14.76,-138.47:99
+chr1	3494307	.	T	G	201.76	SnpCluster	AC=1;AF=0.50;AN=2;DP=58;Dels=0.10;HRun=2;HaplotypeScore=112.88;MQ=32.38;MQ0=0;QD=3.48;SB=-117.62	GT:AD:DP:GL:GQ	0/1:34,18:28:-31.59,-8.13,-64.60:99
+chr1	3494310	rs61762200	C	A	192.29	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=121.85;MQ=30.79;MQ0=0;QD=3.43;SB=-60.75	GT:AD:DP:GL:GQ	0/1:36,18:28:-30.95,-8.43,-66.22:99
+chr1	3494317	.	G	T	32.47	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=81.33;MQ=29.05;MQ0=0;QD=0.60;SB=-10.00	GT:AD:DP:GL:GQ	0/1:41,11:25:-14.06,-7.53,-79.10:65.31
+chr1	3494320	.	G	A	676.99	SnpCluster	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=53.82;MQ=29.06;MQ0=0;QD=13.02;SB=-10.00	GT:AD:DP:GL:GQ	0/1:6,41:24:-78.21,-7.23,-14.28:70.50
+chr1	3494331	.	C	T	224.74	SnpCluster	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=74.35;MQ=28.87;MQ0=0;QD=4.68;SB=-10.00	GT:AD:DP:GL:GQ	0/1:29,19:11:-29.07,-3.31,-14.19:99
+chr1	3494338	.	G	A	223.95	SnpCluster	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=78.36;MQ=28.88;MQ0=0;QD=4.76;SB=-10.00	GT:AD:DP:GL:GQ	0/1:25,22:10:-28.69,-3.01,-9.91:68.95
+chr1	3494340	.	G	A	250.50	SnpCluster	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=74.35;MQ=28.88;MQ0=0;QD=5.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:9,38:10:-31.35,-3.01,-6.64:36.27
+chr1	3494344	.	G	A	85.25	SnpCluster	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=68.88;MQ=28.67;MQ0=0;QD=1.85;SB=-10.00	GT:AD:DP:GL:GQ	0/1:41,5:14:-16.03,-4.22,-34.38:99
+chr1	3494347	.	A	T	143.02	SnpCluster	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=69.92;MQ=28.59;MQ0=0;QD=3.87;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,19:7:-19.69,-2.11,-6.98:48.71
+chr1	3494357	.	G	T	24.90	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=73.10;MQ=28.56;MQ0=0;QD=0.73;SB=-10.00	GT:AD:DP:GL:GQ	0/1:18,15:5:-7.28,-1.51,-10.87:57.73
+chr1	3494360	.	G	A	23.23	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=81.86;MQ=28.53;MQ0=0;QD=0.73;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,11:6:-7.41,-1.81,-14.17:56.05
+chr1	3494364	.	G	A	65.76	SnpCluster	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=1;HaplotypeScore=67.04;MQ=28.12;MQ0=1;QD=1.93;SB=-10.00	GT:AD:DP:GL:GQ	0/1:29,5:7:-11.97,-2.11,-13.57:98.60
+chr1	3494367	.	G	T	116.01	SnpCluster	AC=1;AF=0.50;AN=2;DP=34;Dels=0.03;HRun=0;HaplotypeScore=76.86;MQ=28.12;MQ0=1;QD=3.41;SB=-10.00	GT:AD:DP:GL:GQ	0/1:14,19:9:-17.59,-2.71,-15.13:99
+chr1	3494370	.	G	C	77.61	SnpCluster	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=62.98;MQ=28.25;MQ0=1;QD=2.87;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,7:9:-20.69,-9.65,-24.68:99
+chr1	3494377	.	G	T	26.91	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=64.80;MQ=28.23;MQ0=1;QD=1.03;SB=-10.00	GT:AD:DP:GL:GQ	0/1:20,4:4:-7.18,-1.20,-7.71:59.73
+chr1	3494378	.	G	A	98.30	SnpCluster	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=59.24;MQ=28.44;MQ0=1;QD=3.78;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,11:7:-15.22,-2.11,-10.61:84.98
+chr1	3494380	.	G	A	43.51	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=65.22;MQ=28.44;MQ0=1;QD=1.67;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,15:4:-12.40,-4.77,-6.87:20.98
+chr1	3494384	.	G	A	26.23	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=51.99;MQ=28.44;MQ0=1;QD=1.01;SB=-10.00	GT:AD:DP:GL:GQ	0/1:20,6:7:-8.02,-2.11,-15.94:59.06
+chr1	3494390	.	G	A	130.87	SnpCluster	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=39.84;MQ=28.27;MQ0=1;QD=6.54;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,12:6:-18.18,-1.81,-3.67:18.63
+chr1	3494414	.	G	A	19.25	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=1;HaplotypeScore=22.06;MQ=28.20;MQ0=1;QD=1.13;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,2:8:-7.61,-2.41,-20.11:52.04
+chr1	3494416	.	G	C	113.75	SnpCluster	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=18.24;MQ=27.40;MQ0=1;QD=6.32;SB=-10.00	GT:AD:DP:GL:GQ	0/1:14,4:8:-17.07,-2.41,-16.09:99
+chr1	3494417	.	A	T	24.41	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=25.18;MQ=27.40;MQ0=1;QD=1.36;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,5:8:-14.34,-8.61,-21.17:57.23
+chr1	3494420	.	C	A	17.09	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=28.79;MQ=27.40;MQ0=1;QD=0.95;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,11:6:-6.79,-1.81,-13.20:49.84
+chr1	3494428	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=21.58;MQ=27.57;MQ0=1;OQ=101.33;QD=5.07;SB=-10.00	GT:AD:DP:GL:GQ	0/1:14,6:9:-16.13,-2.71,-15.44:99
+chr1	3494440	.	A	G	20.51	LowQual	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=4;HaplotypeScore=16.99;MQ=27.20;MQ0=1;QD=1.28;SB=-10.00	GT:AD:DP:GL:GQ	0/1:14,2:6:-7.14,-1.81,-14.72:53.31
+chr1	3494450	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=19.98;MQ=27.07;MQ0=1;OQ=136.86;QD=9.12;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,11:7:-19.08,-2.11,-6.94:48.30
+chr1	3494456	.	G	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=17;Dels=0.12;HRun=1;HaplotypeScore=13.10;MQ=27.31;MQ0=1;OQ=95.30;QD=5.61;SB=-10.00	GT:AD:DP:GL:GQ	0/1:10,5:11:-16.13,-3.31,-22.08:99
+chr1	3494463	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=15.99;MQ=27.75;MQ0=0;OQ=76.78;QD=6.98;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,3:5:-12.47,-1.51,-7.14:56.32
+chr1	3494470	.	G	A	37.25	LowQual	AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=29.00;MQ0=0;QD=4.66;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,6:3:-7.91,-0.90,-3.57:26.65
+chr1	3494476	.	C	G	10.99	LowQual	AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=6.99;MQ=29.00;MQ0=0;QD=1.83;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,3:1:-4.35,-0.30,-0.00:1.76
+chr1	3494500	.	C	A	20.04	LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=24.21;MQ=29.00;MQ0=0;QD=1.43;SB=-10.00	GT:AD:DP:GL:GQ	0/1:6,8:6:-7.09,-1.81,-14.10:52.83
+chr1	3494506	.	G	A	17.29	LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.05;HRun=1;HaplotypeScore=32.64;MQ=29.00;MQ0=0;QD=0.91;SB=-10.00	GT:AD:DP:GL:GQ	0/1:14,4:10:-8.02,-3.01,-25.65:50.04
+chr1	3494513	.	G	A	25.23	LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=41.45;MQ=31.40;MQ0=0;QD=1.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,4:6:-7.61,-1.81,-13.27:58.06
+chr1	3494520	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=37.55;MQ=33.42;MQ0=0;OQ=64.77;QD=3.24;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,13:7:-11.87,-2.11,-12.97:97.60
+chr1	3494524	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=27.25;MQ=33.22;MQ0=0;OQ=65.77;QD=3.13;SB=-10.00	GT:AD:DP:GL:GQ	0/1:18,3:5:-11.37,-1.51,-6.04:45.31
+chr1	3494544	.	G	A	102.31	SnpCluster	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=60.62;MQ=32.58;MQ0=0;QD=4.09;SB=-10.00	GT:AD:DP:GL:GQ	0/1:21,4:9:-16.23,-2.71,-16.04:99
+chr1	3494547	.	G	T	87.64	SnpCluster	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=65.61;MQ=32.58;MQ0=0;QD=3.51;SB=-10.00	GT:AD:DP:GL:GQ	0/1:19,5:8:-14.46,-2.41,-14.43:99
+chr1	3494550	.	A	C	79.94	SnpCluster	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=1;HaplotypeScore=55.04;MQ=32.72;MQ0=0;QD=3.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:14,6:8:-16.58,-5.30,-13.73:84.35
+chr1	3494557	.	G	T	60.29	SnpCluster	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=39.81;MQ=31.18;MQ0=0;QD=2.87;SB=-10.00	GT:AD:DP:GL:GQ	0/1:11,8:4:-10.52,-1.20,-3.86:26.53
+chr1	3494560	.	G	A	91.28	SnpCluster	AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=38.65;MQ=31.18;MQ0=0;QD=4.35;SB=-10.00	GT:AD:DP:GL:GQ	1/1:7,11:4:-16.06,-4.57,-3.40:11.70
+chr1	3494564	.	G	A	29.24	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=32.50;MQ=31.29;MQ0=0;QD=1.46;SB=-10.00	GT:AD:DP:GL:GQ	0/1:18,2:6:-8.02,-1.81,-12.47:62.07
+chr1	3494574	.	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=26.98;MQ=29.00;MQ0=0;OQ=69.17;QD=4.94;SB=-10.00	GT:AD:DP:GL:GQ	1/1:6,8:3:-10.41,-0.90,-0.00:9.03
+chr1	3494590	.	G	A	142.91	SnpCluster	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=22.40;MQ=29.00;MQ0=0;QD=9.53;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,8:6:-19.38,-1.81,-3.57:17.63
+chr1	3494597	.	G	T	106.99	SnpCluster	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=25.38;MQ=29.00;MQ0=0;QD=7.64;SB=-10.00	GT:AD:DP:GL:GQ	0/1:9,5:11:-17.30,-3.31,-21.74:99
+chr1	3494600	.	G	A	30.23	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=11.39;MQ=29.00;MQ0=0;QD=3.02;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,6:5:-7.81,-1.51,-10.71:63.06
+chr1	3494624	.	A	G	3.02	PASS	AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=1;HaplotypeScore=2.14;MQ=23.68;MQ0=1;OQ=61.17;QD=10.20;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,5:4:-10.61,-1.20,-4.06:28.52
+chr1	3494941	rs3122612	T	C	27.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.13;MQ0=0;OQ=190.96;QD=21.22;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,9:7:-22.68,-2.11,-0.00:21.05
+chr1	3496357	rs2794320	A	G	629.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.59;MQ0=0;OQ=2197.16;QD=34.88;SB=-1063.87	GT:AD:DP:GL:GQ	1/1:0,63:62:-223.32,-18.67,-0.02:99
+chr1	3497672	rs12138013	G	A	514.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1894.53;QD=36.43;SB=-916.70	GT:AD:DP:GL:GQ	1/1:0,52:50:-193.07,-15.07,-0.03:99
+chr1	3497721	rs4648527	G	A	5.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=5.91;MQ=58.60;MQ0=0;OQ=1808.59;QD=36.17;SB=-904.68	GT:AD:DP:GL:GQ	1/1:0,50:47:-184.46,-14.16,-0.02:99
+chr1	3497811	rs4233026	A	G	453.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=985.33;QD=29.86;SB=-500.18	GT:AD:DP:GL:GQ	1/1:0,33:33:-102.16,-9.96,-0.04:99
+chr1	3499530	rs10909980	C	T	12.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.36;MQ0=0;OQ=831.01;QD=36.13;SB=-270.86	GT:AD:DP:GL:GQ	1/1:0,23:22:-86.69,-6.63,-0.01:66.21
+chr1	3501794	rs7513275	A	G	98.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=60.00;MQ0=0;OQ=215.59;QD=10.78;SB=-81.80	GT:AD:DP:GL:GQ	0/1:7,13:17:-29.97,-5.13,-27.54:99
+chr1	3502201	rs2794327	C	T	251.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=1770.81;QD=37.68;SB=-842.63	GT:AD:DP:GL:GQ	1/1:0,47:45:-180.68,-13.55,-0.01:99
+chr1	3502376	rs2821025	T	C	189.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.06;MQ0=0;OQ=1399.30;QD=34.13;SB=-531.22	GT:AD:DP:GL:GQ	1/1:1,40:40:-143.53,-12.05,-0.02:99
+chr1	3502406	rs2821024	G	A	10.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.84;MQ=59.12;MQ0=0;OQ=1381.75;QD=37.34;SB=-602.98	GT:AD:DP:GL:GQ	1/1:0,37:36:-141.77,-10.85,-0.01:99
+chr1	3502660	rs2821023	T	C	164.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.31;MQ0=0;OQ=631.91;QD=27.47;SB=-134.71	GT:AD:DP:GL:GQ	1/1:0,23:22:-66.81,-6.64,-0.03:66.13
+chr1	3503040	rs3001104	T	C	11.75	LowQual	AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=53.43;MQ0=0;QD=0.90;SB=-7.00	GT:AD:DP:GL:GQ	0/1:11,2:9:-7.15,-2.72,-25.40:44.29
+chr1	3503107	rs6697282	T	C	2.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.92;MQ0=0;OQ=303.24;QD=27.57;SB=-40.95	GT:AD:DP:GL:GQ	1/1:0,11:10:-33.91,-3.01,-0.00:30.08
+chr1	3503479	rs55936822	G	A	66.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=385.29;QD=13.76;SB=-81.58	GT:AD:DP:GL:GQ	0/1:14,14:27:-49.96,-8.15,-41.31:99
+chr1	3504130	rs3001107	A	T	92.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=60.00;MQ0=0;OQ=1158.27;QD=35.10;SB=-515.45	GT:AD:DP:GL:GQ	1/1:0,33:32:-119.42,-9.64,-0.01:96.30
+chr1	3504221	rs2995006	A	G	438.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=1363.50;QD=34.96;SB=-648.28	GT:AD:DP:GL:GQ	1/1:0,39:39:-139.95,-11.75,-0.02:99
+chr1	3504611	rs6701230	T	C	61.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=1071.54;QD=26.79;SB=-482.12	GT:AD:DP:GL:GQ	1/1:0,40:34:-110.77,-10.26,-0.03:99
+chr1	3505152	.	C	G	6.95	PASS	AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=54.64;MQ0=0;OQ=215.54;QD=15.40;SB=-56.93	GT:AD:DP:GL:GQ	1/1:2,12:6:-25.13,-1.81,-0.00:18.06
+chr1	3505256	rs2794328	C	A	31.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.33;MQ0=0;OQ=824.44;QD=29.44;SB=-191.27	GT:AD:DP:GL:GQ	1/1:1,27:24:-86.04,-7.23,-0.01:72.19
+chr1	3505590	rs2821011	T	C	3.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=58.95;MQ0=0;OQ=1307.30;QD=29.71;SB=-329.39	GT:AD:DP:GL:GQ	1/1:0,44:40:-134.34,-12.06,-0.03:99
+chr1	3506096	rs4648395	G	A	428.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.73;MQ0=0;OQ=1105.43;QD=35.66;SB=-453.34	GT:AD:DP:GL:GQ	1/1:0,31:29:-114.14,-8.74,-0.01:87.28
+chr1	3506280	rs7552280	C	T	597.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1498.57;QD=38.42;SB=-699.42	GT:AD:DP:GL:GQ	1/1:0,39:38:-153.45,-11.45,-0.01:99
+chr1	3506640	rs4018202	C	T	591.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=1796.97;QD=36.67;SB=-852.00	GT:AD:DP:GL:GQ	1/1:0,49:46:-183.30,-13.86,-0.02:99
+chr1	3507139	rs4648528	C	T	150.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.89;MQ0=0;OQ=1470.55;QD=35.01;SB=-673.24	GT:AD:DP:GL:GQ	1/1:0,42:39:-150.66,-11.76,-0.02:99
+chr1	3507337	rs61373700	C	G	106.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.76;MQ=57.26;MQ0=0;OQ=1716.27;QD=39.91;SB=-832.44	GT:AD:DP:GL:GQ	1/1:1,42:42:-175.24,-12.66,-0.02:99
+chr1	3507396	rs6693958	G	A	63.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=58.29;MQ0=0;OQ=1559.78;QD=38.04;SB=-721.97	GT:AD:DP:GL:GQ	1/1:0,41:40:-159.58,-12.05,-0.01:99
+chr1	3507433	rs59013990	G	C	40.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=59.41;MQ0=0;OQ=1114.70;QD=28.58;SB=-265.33	GT:AD:DP:GL:GQ	1/1:0,38:29:-115.08,-8.75,-0.02:87.28
+chr1	3508244	rs2821012	T	C	433.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=981.44;QD=28.87;SB=-510.19	GT:AD:DP:GL:GQ	1/1:0,34:32:-101.76,-9.65,-0.03:96.21
+chr1	3508275	rs12410528	G	A	77.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.32;MQ0=0;OQ=639.66;QD=18.81;SB=-281.31	GT:AD:DP:GL:GQ	0/1:14,20:31:-76.59,-9.34,-39.32:99
+chr1	3508279	rs12401505	C	T	12.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=2.61;MQ=59.32;MQ0=0;OQ=621.28;QD=18.27;SB=-279.19	GT:AD:DP:GL:GQ	0/1:14,19:31:-74.75,-9.34,-43.77:99
+chr1	3508347	rs56770023	C	T	305.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.60;MQ0=0;OQ=1098.04;QD=36.60;SB=-308.27	GT:AD:DP:GL:GQ	1/1:0,30:29:-113.40,-8.74,-0.01:87.27
+chr1	3508348	rs60957843	A	G	332.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=996.70;QD=34.37;SB=-270.42	GT:AD:DP:GL:GQ	1/1:0,29:29:-103.27,-8.74,-0.01:87.25
+chr1	3508499	rs2821013	C	A	29.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=4.32;MQ=59.05;MQ0=0;OQ=1719.86;QD=35.10;SB=-757.10	GT:AD:DP:GL:GQ	1/1:0,49:47:-175.58,-14.15,-0.01:99
+chr1	3508603	rs7514061	C	T	105.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.33;MQ0=0;OQ=1426.84;QD=33.97;SB=-607.00	GT:AD:DP:GL:GQ	1/1:0,42:38:-146.28,-11.45,-0.02:99
+chr1	3508717	rs2821014	A	C	0.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=3;HaplotypeScore=1.13;MQ=59.42;MQ0=0;OQ=907.74;QD=22.69;SB=-295.54	GT:AD:DP:GL:GQ	1/1:0,37:28:-94.37,-8.43,-0.01:84.22
+chr1	3508804	rs7521546	T	C	5.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=1.42;MQ=57.17;MQ0=0;OQ=713.23;QD=28.53;SB=-330.78	GT:AD:DP:GL:GQ	1/1:0,25:24:-74.93,-7.24,-0.02:72.16
+chr1	3509294	rs12024499	A	G	18.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=58.37;MQ0=0;OQ=1073.16;QD=24.96;SB=-338.38	GT:AD:DP:GL:GQ	1/1:0,43:37:-110.95,-11.17,-0.05:99
+chr1	3509463	rs12025426	T	C	57.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=59.00;MQ0=0;OQ=1068.56;QD=25.44;SB=-559.52	GT:AD:DP:GL:GQ	1/1:0,42:36:-110.49,-10.87,-0.05:99
+chr1	3509651	rs56328010	C	G	123.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.54;MQ=58.84;MQ0=0;OQ=608.86;QD=15.22;SB=-231.35	GT:AD:DP:GL:GQ	0/1:21,19:38:-75.63,-11.46,-87.10:99
+chr1	3509894	rs10752738	A	G	106.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=57.39;MQ0=0;OQ=1124.20;QD=31.23;SB=-480.45	GT:AD:DP:GL:GQ	1/1:0,36:33:-116.02,-9.94,-0.01:99
+chr1	3509987	rs2821015	T	C	88.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.95;MQ0=0;OQ=1023.67;QD=31.99;SB=-513.41	GT:AD:DP:GL:GQ	1/1:0,31:32:-108.71,-12.22,-2.76:94.68
+chr1	3510191	rs2794356	C	A	66.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=58.63;MQ0=0;OQ=1082.36;QD=31.83;SB=-352.40	GT:AD:DP:GL:GQ	1/1:0,34:33:-111.84,-9.95,-0.02:99
+chr1	3510399	rs2794355	C	T	148.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.22;MQ0=0;OQ=1723.81;QD=37.47;SB=-800.07	GT:AD:DP:GL:GQ	1/1:0,46:45:-175.99,-13.56,-0.02:99
+chr1	3510532	rs2821016	A	C	65.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.42;MQ0=0;OQ=868.96;QD=27.16;SB=-409.86	GT:AD:DP:GL:GQ	1/1:0,32:29:-90.51,-8.74,-0.03:87.13
+chr1	3511971	rs56140438	T	C	2680.91	Indel	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.68;MQ0=0;QD=34.82;SB=-1364.21	GT:AD:DP:GL:GQ	1/1:0,77:76:-271.70,-22.89,-0.02:99
+chr1	3513689	rs2794354	T	C	23.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=60.00;MQ0=0;OQ=1332.54;QD=30.29;SB=-459.40	GT:AD:DP:GL:GQ	1/1:0,44:41:-136.87,-12.36,-0.03:99
+chr1	3513757	rs2821018	T	C	1.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=4;HaplotypeScore=0.16;MQ=52.28;MQ0=0;OQ=1127.31;QD=32.21;SB=-555.88	GT:AD:DP:GL:GQ	1/1:0,35:33:-116.33,-9.94,-0.01:99
+chr1	3513776	rs2821019	A	C	16.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=3.24;MQ=52.84;MQ0=0;OQ=1256.82;QD=30.65;SB=-634.67	GT:AD:DP:GL:GQ	1/1:0,41:37:-129.29,-11.15,-0.02:99
+chr1	3513778	rs2821020	G	A	39.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=4.08;MQ=53.03;MQ0=0;OQ=1497.87;QD=35.66;SB=-772.68	GT:AD:DP:GL:GQ	1/1:0,42:39:-153.39,-11.75,-0.01:99
+chr1	3515181	rs2794353	G	C	0.02	FDRtranche1.00to2.00	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=5;HaplotypeScore=0.32;MQ=58.30;MQ0=0;OQ=1440.93;QD=40.03;SB=-600.98	GT:AD:DP:GL:GQ	1/1:0,36:34:-147.69,-10.24,-0.01:99
+chr1	3515467	rs36031771	G	A	114.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1598.59;QD=36.33;SB=-811.32	GT:AD:DP:GL:GQ	1/1:0,44:42:-163.46,-12.66,-0.02:99
+chr1	3515500	rs34852522	G	A	546.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1591.31;QD=37.01;SB=-737.47	GT:AD:DP:GL:GQ	1/1:1,42:41:-162.73,-12.35,-0.01:99
+chr1	3515696	rs10909986	G	A	566.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=1907.24;QD=38.92;SB=-905.69	GT:AD:DP:GL:GQ	1/1:0,49:48:-194.32,-14.46,-0.01:99
+chr1	3516250	rs12121341	A	G	86.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1093.76;QD=29.56;SB=-543.02	GT:AD:DP:GL:GQ	1/1:0,37:35:-112.99,-10.56,-0.03:99
+chr1	3518397	rs57902798	C	A	88.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.13;MQ0=0;OQ=809.40;QD=32.38;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,25:24:-84.53,-7.23,-0.01:72.21
+chr1	3518534	rs1539126	G	A	66.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=60.00;MQ0=0;OQ=1266.77;QD=36.19;SB=-476.64	GT:AD:DP:GL:GQ	1/1:0,34:33:-130.27,-9.94,-0.01:99
+chr1	3518701	rs2794326	T	C	149.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.07;MQ0=0;OQ=1658.37;QD=33.17;SB=-790.25	GT:AD:DP:GL:GQ	1/1:0,50:49:-169.45,-14.76,-0.03:99
+chr1	3519249	rs10909987	G	C	637.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1866.21;QD=40.57;SB=-960.72	GT:AD:DP:GL:GQ	1/1:0,45:44:-190.22,-13.26,-0.01:99
+chr1	3521082	rs4648396	C	T	0.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=5;HaplotypeScore=1.32;MQ=59.36;MQ0=0;OQ=2285.23;QD=39.40;SB=-1043.37	GT:AD:DP:GL:GQ	1/1:0,58:57:-232.12,-17.17,-0.02:99
+chr1	3521301	rs4648397	T	C	39.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=59.20;MQ0=0;OQ=1821.49;QD=31.41;SB=-869.61	GT:AD:DP:GL:GQ	1/1:0,58:57:-185.78,-17.19,-0.04:99
+chr1	3521455	rs4648398	C	T	121.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.69;MQ=58.90;MQ0=0;OQ=2021.45;QD=34.26;SB=-686.93	GT:AD:DP:GL:GQ	1/1:0,59:53:-205.75,-15.97,-0.02:99
+chr1	3522563	rs6693192	A	G	270.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=513.63;QD=9.88;SB=-275.26	GT:AD:DP:GL:GQ	0/1:30,22:52:-70.32,-15.67,-121.33:99
+chr1	3522569	rs6678958	G	A	350.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=670.10;QD=13.14;SB=-343.79	GT:AD:DP:GL:GQ	0/1:29,22:51:-85.67,-15.38,-96.37:99
+chr1	3523424	rs55728961	C	A	42.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=240.49;QD=10.46;SB=-10.00	GT:AD:DP:GL:GQ	0/1:14,9:23:-34.26,-6.93,-47.21:99
+chr1	3523484	rs56385042	T	C	1.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=3;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=309.24;QD=11.89;SB=-6.99	GT:AD:DP:GL:GQ	0/1:12,14:26:-42.05,-7.84,-46.91:99
+chr1	3523847	rs10797404	T	C	200.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=602.56;QD=14.01;SB=-77.79	GT:AD:DP:GL:GQ	0/1:21,22:42:-76.19,-12.65,-81.56:99
+chr1	3524383	rs4648532	A	G	19.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=2.34;MQ=56.80;MQ0=0;OQ=354.98;QD=11.45;SB=-152.32	GT:AD:DP:GL:GQ	0/1:16,15:28:-47.22,-8.44,-59.85:99
+chr1	3524566	rs10909988	A	G	146.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=60.00;MQ0=0;OQ=306.09;QD=9.28;SB=-127.66	GT:AD:DP:GL:GQ	0/1:17,15:30:-42.93,-9.04,-69.22:99
+chr1	3524652	rs7522500	G	C	8.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=6.16;MQ=57.13;MQ0=0;OQ=583.92;QD=14.24;SB=-274.31	GT:AD:DP:GL:GQ	0/1:21,20:34:-71.93,-10.26,-66.25:99
+chr1	3524668	rs7522507	G	A	205.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.19;MQ=57.92;MQ0=0;OQ=639.63;QD=14.21;SB=-315.32	GT:AD:DP:GL:GQ	0/1:22,23:42:-79.91,-12.67,-66.98:99
+chr1	3525324	rs7538707	A	G	23.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=845.73;QD=19.67;SB=-223.67	GT:AD:DP:GL:GQ	0/1:16,27:42:-100.51,-12.65,-58.85:99
+chr1	3526188	rs4648533	G	A	210.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=59.62;MQ0=0;OQ=1070.40;QD=17.55;SB=-483.49	GT:AD:DP:GL:GQ	0/1:29,32:60:-128.41,-18.08,-91.39:99
+chr1	3526260	rs4648534	T	C	399.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.82;MQ0=0;OQ=652.36;QD=10.19;SB=-312.36	GT:AD:DP:GL:GQ	0/1:38,26:63:-87.50,-18.98,-151.40:99
+chr1	3526320	rs4648535	C	A	306.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=54.45;MQ0=1;OQ=780.07;QD=10.99;SB=-371.06	GT:AD:DP:GL:GQ	0/1:40,31:67:-101.47,-20.18,-141.37:99
+chr1	3526422	rs4648399	A	G	309.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.19;MQ0=0;OQ=1278.95;QD=17.52;SB=-632.97	GT:AD:DP:GL:GQ	0/1:30,43:71:-152.57,-21.39,-116.57:99
+chr1	3527222	rs4648400	A	G	9.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=7.73;MQ=57.63;MQ0=0;OQ=603.16;QD=10.40;SB=-310.07	GT:AD:DP:GL:GQ	0/1:32,26:56:-80.48,-16.88,-126.15:99
+chr1	3527718	rs4648401	A	G	74.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=1.41;MQ=56.19;MQ0=0;OQ=587.94;QD=13.67;SB=-299.61	GT:AD:DP:GL:GQ	0/1:18,25:41:-74.44,-12.36,-73.19:99
+chr1	3528340	rs4400556	A	T	87.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=59.12;MQ0=0;OQ=994.97;QD=12.59;SB=-457.52	GT:AD:DP:GL:GQ	0/1:45,34:78:-126.28,-23.49,-166.80:99
+chr1	3528361	rs4364818	C	T	460.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.38;MQ0=0;OQ=945.91;QD=13.14;SB=-450.44	GT:AD:DP:GL:GQ	0/1:42,30:72:-119.57,-21.70,-148.80:99
+chr1	3528695	rs6424087	G	C	115.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=3.80;MQ=59.24;MQ0=0;OQ=909.93;QD=16.54;SB=-215.65	GT:AD:DP:GL:GQ	0/1:28,26:51:-109.65,-15.37,-108.54:99
+chr1	3528942	rs10909989	A	G	309.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.12;MQ=59.00;MQ0=0;OQ=981.47;QD=13.82;SB=-369.60	GT:AD:DP:GL:GQ	0/1:36,35:70:-122.52,-21.09,-148.98:99
+chr1	3529341	rs10909990	A	G	374.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=58.19;MQ0=0;OQ=916.10;QD=14.78;SB=-423.95	GT:AD:DP:GL:GQ	0/1:29,33:61:-113.27,-18.38,-114.82:99
+chr1	3529884	rs12757620	T	G	87.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=2.04;MQ=59.45;MQ0=0;OQ=798.71;QD=11.75;SB=-349.72	GT:AD:DP:GL:GQ	0/1:29,39:61:-101.54,-18.38,-103.90:99
+chr1	3532172	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=4.52;MQ=58.17;MQ0=0;OQ=111.86;QD=2.19;SB=68.21	GT:AD:DP:GL:GQ	0/1:30,21:37:-25.62,-11.15,-96.21:99
+chr1	3535452	rs41315304	G	A	150.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=58.25;MQ0=0;OQ=1069.05;QD=16.70;SB=-525.75	GT:AD:DP:GL:GQ	0/1:32,32:63:-129.18,-18.99,-99.29:99
+chr1	3536795	rs2821007	G	A	330.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.23;MQ0=0;OQ=1047.23;QD=17.45;SB=-508.04	GT:AD:DP:GL:GQ	0/1:27,33:59:-125.78,-17.78,-94.59:99
+chr1	3537996	rs2760321	T	C	53.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=58.11;MQ0=0;OQ=916.84;QD=24.78;SB=-335.79	GT:AD:DP:GL:GQ	1/1:0,37:31:-95.30,-9.36,-0.04:93.19
+chr1	3538692	rs2760320	G	C	208.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=58.15;MQ0=0;OQ=946.49;QD=15.02;SB=-485.84	GT:AD:DP:GL:GQ	0/1:35,28:62:-116.63,-18.70,-140.41:99
+chr1	3540707	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=4;HaplotypeScore=6.24;MQ=58.05;MQ0=0;OQ=310.07;QD=8.61;SB=35.15	GT:AD:DP:GL:GQ	0/1:20,16:27:-42.43,-8.14,-74.49:99
+chr1	3542640	rs2821061	A	G	174.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.68;MQ=60.00;MQ0=0;OQ=519.03;QD=10.38;SB=-253.57	GT:AD:DP:GL:GQ	0/1:27,23:48:-69.65,-14.47,-105.26:99
+chr1	3543649	rs2821058	T	C	578.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.21;MQ0=0;OQ=1559.49;QD=29.42;SB=-616.98	GT:AD:DP:GL:GQ	1/1:0,53:50:-159.58,-15.08,-0.04:99
+chr1	3545730	rs2760318	T	G	276.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=500.47;QD=13.53;SB=-245.40	GT:AD:DP:GL:GQ	0/1:16,21:34:-63.58,-10.25,-53.36:99
+chr1	3546316	rs2760317	T	C	74.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=59.23;MQ0=0;OQ=365.54;QD=12.18;SB=-82.96	GT:AD:DP:GL:GQ	0/1:16,13:27:-47.97,-8.14,-53.97:99
+chr1	3546766	rs2821032	A	G	15.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=5.71;MQ=58.45;MQ0=0;OQ=501.73;QD=10.45;SB=-117.63	GT:AD:DP:GL:GQ	0/1:27,21:44:-66.72,-13.26,-92.65:99
+chr1	3546958	.	G	C	33.36	PASS	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=52.99;MQ0=1;OQ=414.27;QD=15.34;SB=-224.70	GT:AD:DP:GL:GQ	0/1:11,16:20:-50.74,-6.03,-33.52:99
+chr1	3550868	rs12408890	C	T	50.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=714.51;QD=21.65;SB=-10.00	GT:AD:DP:GL:GQ	0/1:11,22:31:-84.07,-9.34,-33.99:99
+chr1	3556431	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=2;HaplotypeScore=3.37;MQ=56.43;MQ0=0;OQ=64.63;QD=2.69;SB=26.11	GT:AD:DP:GL:GQ	0/1:20,4:17:-14.89,-5.14,-48.86:97.47
+chr1	3556566	rs2251098	G	A	89.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=58.00;MQ0=0;OQ=575.61;QD=16.45;SB=-81.09	GT:AD:DP:GL:GQ	0/1:16,19:34:-71.09,-10.24,-59.62:99
+chr1	3560743	rs6697769	C	T	108.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=2.77;MQ=59.11;MQ0=0;OQ=591.49;QD=14.08;SB=-304.84	GT:AD:DP:GL:GQ	0/1:21,21:39:-74.19,-11.76,-62.78:99
+chr1	3562592	rs10752739	A	G	278.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=56.42;MQ0=0;OQ=804.83;QD=14.63;SB=-300.66	GT:AD:DP:GL:GQ	0/1:25,30:50:-98.83,-15.07,-88.55:99
+chr1	3562634	rs2181484	A	G	237.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=59.09;MQ0=0;OQ=421.19;QD=9.16;SB=-138.88	GT:AD:DP:GL:GQ	0/1:25,21:41:-57.77,-12.36,-88.24:99
+chr1	3564279	rs9662739	T	A	199.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=58.99;MQ0=0;OQ=516.88;QD=11.24;SB=-252.67	GT:AD:DP:GL:GQ	0/1:26,19:44:-68.23,-13.26,-93.50:99
+chr1	3564280	rs9662052	C	A	196.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=58.99;MQ0=0;OQ=511.23;QD=11.11;SB=-234.91	GT:AD:DP:GL:GQ	0/1:27,19:44:-67.66,-13.26,-88.90:99
+chr1	3565050	rs2368543	T	C	86.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.56;MQ=57.97;MQ0=0;OQ=928.11;QD=12.89;SB=-445.02	GT:AD:DP:GL:GQ	0/1:38,33:71:-117.49,-21.39,-151.96:99
+chr1	3565471	rs4648544	C	T	133.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=1.75;MQ=59.57;MQ0=0;OQ=791.33;QD=14.65;SB=-418.72	GT:AD:DP:GL:GQ	0/1:30,24:54:-98.68,-16.27,-109.24:99
+chr1	3565693	rs2208993	C	G	156.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.21;MQ0=0;OQ=372.36;QD=11.28;SB=-74.78	GT:AD:DP:GL:GQ	0/1:21,12:29:-49.27,-8.75,-66.40:99
+chr1	3565739	rs2208992	C	T	135.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=555.57;QD=16.34;SB=-208.21	GT:AD:DP:GL:GQ	0/1:17,17:34:-69.09,-10.25,-52.42:99
+chr1	3565920	rs2224718	T	C	463.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.60;MQ0=0;OQ=705.17;QD=14.10;SB=-316.42	GT:AD:DP:GL:GQ	0/1:24,26:48:-88.27,-14.47,-84.73:99
+chr1	3567181	rs4648545	A	G	559.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=1256.11;QD=14.78;SB=-595.27	GT:AD:DP:GL:GQ	0/1:42,43:84:-154.20,-25.30,-171.31:99
+chr1	3568175	rs1885863	C	T	33.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.95;MQ0=0;OQ=503.58;QD=17.98;SB=-117.62	GT:AD:DP:GL:GQ	0/1:13,15:28:-62.07,-8.43,-48.10:99
+chr1	3569688	rs1885861	A	T	263.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=805.05;QD=14.38;SB=-228.60	GT:AD:DP:GL:GQ	0/1:30,26:55:-100.35,-16.57,-108.86:99
+chr1	3572104	rs6679556	T	A	168.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.18;MQ0=0;OQ=534.82;QD=14.07;SB=-147.78	GT:AD:DP:GL:GQ	0/1:19,19:35:-67.31,-10.54,-60.93:99
+chr1	3572105	rs6679560	T	G	310.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.18;MQ0=0;OQ=483.25;QD=12.72;SB=-122.88	GT:AD:DP:GL:GQ	0/1:19,19:35:-62.15,-10.55,-61.28:99
+chr1	3572847	rs1885860	T	C	202.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=55.65;MQ0=0;OQ=1537.12;QD=28.47;SB=-796.29	GT:AD:DP:GL:GQ	1/1:0,54:50:-157.34,-15.08,-0.05:99
+chr1	3573552	rs1885859	G	C	126.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=931.27;QD=19.81;SB=-452.38	GT:AD:DP:GL:GQ	0/1:21,26:45:-109.97,-13.56,-87.15:99
+chr1	3575442	rs3765694	G	A	29.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=58.20;MQ0=0;OQ=1425.18;QD=36.54;SB=-559.30	GT:AD:DP:GL:GQ	1/1:0,39:37:-146.12,-11.15,-0.01:99
+chr1	3575611	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=3;HaplotypeScore=1.74;MQ=57.17;MQ0=0;OQ=76.89;QD=3.08;SB=14.07	GT:AD:DP:GL:GQ	0/1:14,11:13:-14.90,-3.93,-34.07:99
+chr1	3576288	rs1009345	G	A	91.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=59.80;MQ0=0;OQ=1800.40;QD=39.14;SB=-661.66	GT:AD:DP:GL:GQ	1/1:0,46:46:-183.64,-13.86,-0.02:99
+chr1	3576560	rs6657895	G	A	60.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=4.17;MQ=59.27;MQ0=0;OQ=1276.11;QD=33.58;SB=-586.96	GT:AD:DP:GL:GQ	1/1:1,37:35:-131.22,-10.55,-0.02:99
+chr1	3577406	rs3765697	C	T	0.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=5.64;MQ=56.35;MQ0=0;OQ=1305.04;QD=33.46;SB=-441.58	GT:AD:DP:GL:GQ	1/1:0,39:35:-134.11,-10.55,-0.02:99
+chr1	3578761	rs3765700	G	C	611.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=1985.98;QD=38.19;SB=-981.19	GT:AD:DP:GL:GQ	1/1:0,52:47:-202.21,-14.17,-0.02:99
+chr1	3578861	rs3765701	T	A	287.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.60;MQ0=0;OQ=1646.63;QD=35.03;SB=-839.93	GT:AD:DP:GL:GQ	1/1:0,47:46:-168.27,-13.86,-0.02:99
+chr1	3579831	rs56255778	C	A	326.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=59.60;MQ0=0;OQ=723.70;QD=12.70;SB=-343.37	GT:AD:DP:GL:GQ	0/1:30,27:51:-91.02,-15.37,-85.23:99
+chr1	3580285	rs6671482	G	A	126.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=1575.76;QD=35.81;SB=-662.31	GT:AD:DP:GL:GQ	1/1:1,43:41:-161.17,-12.35,-0.01:99
+chr1	3587189	.	C	T	94.68	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.81;MQ0=0;OQ=415.33;QD=10.65;SB=-200.88	GT:AD:DP:GL:GQ	0/1:25,14:37:-55.97,-11.16,-70.24:99
+chr1	3594672	rs12562573	G	A	160.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.53;MQ0=0;OQ=1829.37;QD=37.33;SB=-900.21	GT:AD:DP:GL:GQ	1/1:0,49:48:-186.54,-14.47,-0.02:99
+chr1	3594957	rs1885872	G	A	83.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.18;MQ=59.07;MQ0=0;OQ=1704.97;QD=37.89;SB=-859.63	GT:AD:DP:GL:GQ	1/1:0,45:44:-174.10,-13.26,-0.02:99
+chr1	3595447	rs1885870	G	C	563.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.58;MQ0=0;OQ=1514.49;QD=32.92;SB=-721.32	GT:AD:DP:GL:GQ	1/1:1,45:40:-155.08,-12.08,-0.04:99
+chr1	3596410	rs3765725	C	T	84.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.54;MQ0=0;OQ=1239.60;QD=30.23;SB=-472.10	GT:AD:DP:GL:GQ	1/1:0,41:33:-127.56,-9.95,-0.02:99
+chr1	3596486	rs3765727	G	A	208.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.62;MQ0=0;OQ=883.29;QD=18.03;SB=-364.54	GT:AD:DP:GL:GQ	0/1:22,27:47:-105.77,-14.16,-69.54:99
+chr1	3596710	rs3765728	G	A	119.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.63;MQ0=0;OQ=1974.23;QD=38.71;SB=-814.08	GT:AD:DP:GL:GQ	1/1:0,51:50:-201.02,-15.06,-0.01:99
+chr1	3597380	rs3765730	G	A	180.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.40;MQ0=0;OQ=530.99;QD=17.13;SB=-202.91	GT:AD:DP:GL:GQ	0/1:13,18:30:-65.42,-9.04,-41.88:99
+chr1	3597871	rs10732965	C	T	75.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=57.81;MQ0=0;OQ=940.44;QD=33.59;SB=-454.61	GT:AD:DP:GL:GQ	1/1:0,27:25:-97.64,-7.53,-0.01:75.24
+chr1	3598087	rs34868661	A	G	136.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=59.05;MQ0=0;OQ=432.49;QD=9.83;SB=-227.39	GT:AD:DP:GL:GQ	0/1:23,20:41:-58.89,-12.36,-89.12:99
+chr1	3598141	rs12126706	C	T	141.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.13;MQ0=0;OQ=455.42;QD=13.01;SB=-109.06	GT:AD:DP:GL:GQ	0/1:19,16:32:-58.47,-9.65,-57.68:99
+chr1	3598905	rs1078687	G	A	163.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.42;MQ0=0;OQ=1623.93;QD=33.83;SB=-687.95	GT:AD:DP:GL:GQ	1/1:0,47:43:-166.00,-12.96,-0.02:99
+chr1	3599033	rs879622	G	A	151.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.44;MQ0=0;OQ=684.79;QD=16.70;SB=-307.82	GT:AD:DP:GL:GQ	0/1:19,22:37:-82.91,-11.15,-57.20:99
+chr1	3599257	rs879621	C	A	346.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.17;MQ0=0;OQ=766.56;QD=13.69;SB=-343.33	GT:AD:DP:GL:GQ	0/1:29,27:55:-96.51,-16.57,-104.71:99
+chr1	3599783	rs2146660	A	G	32.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=3.25;MQ=57.85;MQ0=0;OQ=1704.59;QD=34.79;SB=-814.09	GT:AD:DP:GL:GQ	1/1:0,49:49:-174.06,-14.76,-0.02:99
+chr1	3600146	.	T	C	37.22	LowQual	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=2;HaplotypeScore=1.56;MQ=40.64;MQ0=2;QD=1.16;SB=-35.23	GT:AD:DP:GL:GQ	0/1:25,6:25:-14.54,-7.54,-78.76:70.05
+chr1	3600159	rs34095686	C	A	8.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=38.58;MQ0=3;OQ=139.88;QD=4.37;SB=-64.01	GT:AD:DP:GL:GQ	0/1:23,9:27:-25.41,-8.14,-69.86:99
+chr1	3600191	.	C	G	0.30	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=5.79;MQ=36.62;MQ0=7;OQ=200.47;QD=5.90;SB=-62.84	GT:AD:DP:GL:GQ	0/1:21,13:22:-29.96,-6.63,-63.33:99
+chr1	3600194	rs34612797	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=3;HaplotypeScore=5.12;MQ=34.72;MQ0=8;OQ=74.27;QD=2.12;SB=-16.93	GT:AD:DP:GL:GQ	0/1:24,11:20:-16.74,-6.03,-51.18:99
+chr1	3600242	.	C	T	27.02	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=31.01;MQ0=9;QD=0.82;SB=14.05	GT:AD:DP:GL:GQ	0/1:28,5:16:-10.81,-4.82,-45.03:59.85
+chr1	3600252	.	G	A	0.25	PASS	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=5.21;MQ=33.15;MQ0=7;OQ=119.84;QD=4.99;SB=-7.00	GT:AD:DP:GL:GQ	0/1:19,5:10:-18.28,-3.02,-16.17:99
+chr1	3600264	rs61762234	A	C	2.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=2;HaplotypeScore=2.09;MQ=34.74;MQ0=5;OQ=244.22;QD=13.57;SB=-10.00	GT:AD:DP:GL:GQ	1/1:4,14:8:-28.01,-2.41,-0.00:24.07
+chr1	3600309	.	C	A	44.81	LowQual	AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.74;MQ0=1;QD=8.96;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,5:2:-7.89,-0.60,-0.00:6.02
+chr1	3600350	.	C	T	27.34	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=4.81;MQ=17.75;MQ0=4;QD=2.28;SB=-31.62	GT:AD:DP:GL:GQ	0/1:8,4:3:-6.92,-0.91,-3.40:24.94
+chr1	3600367	rs35012159	G	C	33.49	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=10.16;MQ=14.95;MQ0=16;QD=0.93;SB=-40.88	GT:AD:DP:GL:GQ	0/1:29,7:6:-8.44,-1.81,-16.03:66.33
+chr1	3600427	.	C	T	85.30	DPFilter;HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=22.31;MQ=14.22;MQ0=48;QD=0.87;SB=11.05	GT:AD:DP:GL:GQ	0/1:88,10:24:-19.05,-7.24,-63.74:99
+chr1	3600428	.	G	A	105.38	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=22.15;MQ=14.50;MQ0=46;QD=1.12;SB=-26.63	GT:AD:DP:GL:GQ	0/1:84,9:25:-21.36,-7.54,-60.74:99
+chr1	3600437	.	G	C	161.98	HARD_TO_VALIDATE;SnpCluster	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=2;HaplotypeScore=28.11;MQ=14.54;MQ0=44;QD=1.78;SB=-27.40	GT:AD:DP:GL:GQ	0/1:81,9:25:-27.02,-7.53,-80.42:99
+chr1	3600440	.	A	C	23.09	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=2;HaplotypeScore=12.59;MQ=14.51;MQ0=44;QD=0.25;SB=-17.83	GT:AD:DP:GL:GQ	0/1:72,19:25:-13.12,-7.53,-77.67:55.91
+chr1	3600470	.	C	T	26.44	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=13.21;MQ=11.80;MQ0=28;QD=0.61;SB=2.03	GT:AD:DP:GL:GQ	0/1:41,2:8:-8.34,-2.41,-20.77:59.27
+chr1	3600475	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=2;HaplotypeScore=2.58;MQ=10.93;MQ0=23;OQ=89.38;QD=2.48;SB=-3.98	GT:AD:DP:GL:GQ	0/1:21,15:6:-14.03,-1.81,-7.79:59.84
+chr1	3600532	.	C	T	45.13	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=11.72;MQ0=9;QD=2.65;SB=-47.67	GT:AD:DP:GL:GQ	1/1:12,5:2:-7.92,-0.60,-0.00:6.02
+chr1	3600545	.	A	C	20.73	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=18.85;MQ0=10;QD=0.80;SB=-32.99	GT:AD:DP:GL:GQ	0/1:14,12:4:-6.56,-1.20,-7.53:53.53
+chr1	3600575	.	C	T	0.06	PASS	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=7.34;MQ=23.21;MQ0=9;OQ=164.83;QD=5.49;SB=-77.08	GT:AD:DP:GL:GQ	0/1:24,6:9:-22.48,-2.71,-11.26:85.52
+chr1	3600578	.	C	T	0.49	PASS	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=5.98;MQ=23.98;MQ0=9;OQ=197.36;QD=6.81;SB=-112.62	GT:AD:DP:GL:GQ	0/1:22,7:11:-26.34,-3.32,-14.46:99
+chr1	3600596	.	C	T	0.28	PASS	AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=33.58;MQ0=0;OQ=353.36;QD=25.24;SB=-175.22	GT:AD:DP:GL:GQ	1/1:0,14:10:-38.92,-3.01,-0.01:30.09
+chr1	3600667	.	C	T	19.38	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=1;HaplotypeScore=14.09;MQ=16.96;MQ0=7;QD=1.08;SB=-29.64	GT:AD:DP:GL:GQ	0/1:14,4:7:-7.33,-2.11,-16.23:52.17
+chr1	3600709	.	C	T	32.48	PASS	AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=3.31;MQ=14.75;MQ0=16;OQ=271.94;QD=8.77;SB=-129.00	GT:AD:DP:GL:GQ	1/1:10,20:8:-30.78,-2.41,-0.00:24.07
+chr1	3600734	.	C	A	11.22	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=17.16;MQ0=10;QD=0.59;SB=-7.00	GT:AD:DP:GL:GQ	0/1:17,2:6:-6.18,-1.81,-13.77:43.72
+chr1	3600738	.	C	T	23.24	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=5.72;MQ=17.16;MQ0=10;QD=1.22;SB=-6.99	GT:AD:DP:GL:GQ	0/1:14,5:6:-7.41,-1.81,-13.10:56.06
+chr1	3600746	.	G	A	0.90	PASS	AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=5.14;MQ=19.46;MQ0=10;OQ=147.44;QD=6.70;SB=-47.55	GT:AD:DP:GL:GQ	0/1:6,16:6:-19.82,-1.81,-3.10:12.90
+chr1	3600943	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=10.81;MQ0=18;OQ=79.37;QD=2.27;SB=-10.00	GT:AD:DP:GL:GQ	0/1:27,8:5:-12.73,-1.51,-3.55:20.36
+chr1	3600944	.	G	A	31.47	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=10.97;MQ0=17;QD=0.93;SB=-10.00	GT:AD:DP:GL:GQ	0/1:32,2:5:-7.94,-1.51,-9.29:64.30
+chr1	3600955	.	C	T	29.25	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=3.80;MQ=11.72;MQ0=17;QD=0.91;SB=-10.00	GT:AD:DP:GL:GQ	0/1:25,7:6:-8.02,-1.81,-11.97:62.08
+chr1	3600968	.	A	C	27.28	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=2;HaplotypeScore=4.96;MQ=11.75;MQ0=20;QD=0.80;SB=-10.00	GT:AD:DP:GL:GQ	0/1:18,16:5:-7.52,-1.51,-9.32:60.10
+chr1	3601000	.	G	C	23.03	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=2;HaplotypeScore=12.60;MQ=11.01;MQ0=30;QD=0.46;SB=-6.99	GT:AD:DP:GL:GQ	0/1:44,6:9:-8.30,-2.71,-30.70:55.84
+chr1	3601003	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=15.11;MQ=12.05;MQ0=28;OQ=191.04;QD=3.75;SB=-6.99	GT:AD:DP:GL:GQ	0/1:28,23:11:-25.70,-3.31,-14.21:99
+chr1	3601025	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=13.71;MQ=14.27;MQ0=33;OQ=53.75;QD=0.96;SB=-3.99	GT:AD:DP:GL:GQ	0/1:46,9:10:-11.67,-3.01,-22.44:86.59
+chr1	3601070	rs36156048	C	G	0.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=10.95;MQ=20.17;MQ0=10;OQ=79.41;QD=3.18;SB=-46.45	GT:AD:DP:GL:GQ	0/1:14,11:6:-13.03,-1.81,-11.69:98.78
+chr1	3601096	.	G	A	20.37	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=8.03;MQ=17.90;MQ0=5;QD=1.20;SB=-27.52	GT:AD:DP:GL:GQ	0/1:13,3:5:-6.83,-1.51,-8.44:53.16
+chr1	3601143	.	A	C	0.18	PASS	AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=20.37;MQ0=7;OQ=150.35;QD=6.54;SB=-72.98	GT:AD:DP:GL:GQ	0/1:14,9:10:-21.33,-3.01,-13.91:99
+chr1	3601165	.	C	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=11.69;MQ=24.21;MQ0=10;OQ=173.39;QD=5.78;SB=-3.99	GT:AD:DP:GL:GQ	0/1:22,8:11:-23.94,-3.31,-15.90:99
+chr1	3601175	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=2;HaplotypeScore=35.74;MQ=29.63;MQ0=10;OQ=194.57;QD=4.75;SB=-123.70	GT:AD:DP:GL:GQ	0/1:27,14:21:-29.07,-6.33,-61.55:99
+chr1	3601178	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=2;HaplotypeScore=14.60;MQ=30.57;MQ0=8;OQ=427.34;QD=9.94;SB=-58.96	GT:AD:DP:GL:GQ	0/1:21,22:25:-53.55,-7.53,-34.82:99
+chr1	3601218	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=2;HaplotypeScore=16.31;MQ=41.71;MQ0=5;OQ=182.10;QD=2.43;SB=-33.64	GT:AD:DP:GL:GQ	0/1:61,14:63:-40.49,-19.00,-224.09:99
+chr1	3601225	rs12722819	A	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=3;HaplotypeScore=15.63;MQ=42.30;MQ0=5;OQ=524.29;QD=6.32;SB=-141.88	GT:AD:DP:GL:GQ	0/1:52,30:59:-73.50,-17.79,-124.07:99
+chr1	3601229	rs12727450	T	C	0.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=3;HaplotypeScore=5.92;MQ=43.45;MQ0=6;OQ=762.30;QD=9.07;SB=-332.31	GT:AD:DP:GL:GQ	0/1:49,35:67:-99.71,-20.19,-147.26:99
+chr1	3601341	rs12239528	C	T	0.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.01;HRun=0;HaplotypeScore=14.56;MQ=44.93;MQ0=17;OQ=62.54;QD=0.70;SB=44.13	GT:AD:DP:GL:GQ	0/1:79,8:62:-27.92,-18.38,-184.40:95.37
+chr1	3601342	rs11581562	G	A	0.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.01;HRun=0;HaplotypeScore=14.40;MQ=44.68;MQ0=18;OQ=819.35;QD=9.10;SB=-177.16	GT:AD:DP:GL:GQ	0/1:53,33:59:-102.70,-17.49,-103.40:99
+chr1	3601389	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=2;HaplotypeScore=7.82;MQ=44.29;MQ0=18;OQ=186.02;QD=2.30;SB=-61.02	GT:AD:DP:GL:GQ	0/1:62,19:52:-37.55,-15.67,-142.29:99
+chr1	3601457	rs10910012	A	G	122.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=54.59;MQ0=0;OQ=1506.74;QD=29.54;SB=-756.93	GT:AD:DP:GL:GQ	1/1:0,51:48:-154.31,-14.48,-0.05:99
+chr1	3601752	rs3765731	G	A	361.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=59.28;MQ0=0;OQ=1001.62;QD=15.65;SB=-488.04	GT:AD:DP:GL:GQ	0/1:31,33:59:-121.23,-17.79,-88.90:99
+chr1	3601820	rs3765732	G	A	2.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=59.03;MQ0=0;OQ=1613.11;QD=33.61;SB=-476.00	GT:AD:DP:GL:GQ	1/1:0,46:44:-167.13,-15.44,-2.23:99
+chr1	3602293	rs1885869	T	C	376.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1214.50;QD=32.82;SB=-519.18	GT:AD:DP:GL:GQ	1/1:0,37:35:-125.05,-10.54,-0.02:99
+chr1	3603630	rs10910013	C	T	111.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.47;MQ0=0;OQ=534.95;QD=15.28;SB=-205.85	GT:AD:DP:GL:GQ	0/1:18,17:34:-67.02,-10.25,-59.55:99
+chr1	3603781	rs35837097	A	G	62.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.60;MQ=59.60;MQ0=0;OQ=546.71;QD=11.63;SB=-279.27	GT:AD:DP:GL:GQ	0/1:23,24:43:-70.92,-12.96,-83.70:99
+chr1	3605288	rs11580811	G	A	73.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.02;MQ=59.17;MQ0=0;OQ=263.75;QD=9.42;SB=-51.00	GT:AD:DP:GL:GQ	0/1:17,11:22:-36.29,-6.63,-43.95:99
+chr1	3606461	rs3765736	C	T	194.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=57.38;MQ0=0;OQ=406.81;QD=15.07;SB=-214.90	GT:AD:DP:GL:GQ	0/1:13,14:23:-50.90,-6.93,-35.03:99
+chr1	3606652	rs3765737	A	G	468.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=799.22;QD=12.89;SB=-323.13	GT:AD:DP:GL:GQ	0/1:30,32:60:-101.29,-18.08,-117.49:99
+chr1	3606658	rs3765738	G	A	253.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=58.79;MQ0=0;OQ=935.05;QD=15.08;SB=-404.78	GT:AD:DP:GL:GQ	0/1:33,29:61:-115.17,-18.38,-103.51:99
+chr1	3606835	rs4610947	C	A	292.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.39;MQ0=0;OQ=957.03;QD=17.09;SB=-493.95	GT:AD:DP:GL:GQ	0/1:24,31:55:-115.55,-16.56,-86.20:99
+chr1	3606979	rs4378145	G	A	258.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=57.58;MQ0=5;OQ=1287.24;QD=16.29;SB=-484.49	GT:AD:DP:GL:GQ	0/1:40,39:72:-153.70,-21.69,-124.59:99
+chr1	3607481	rs3765739	A	G	35.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=56.52;MQ0=0;OQ=316.46;QD=9.31;SB=-99.71	GT:AD:DP:GL:GQ	0/1:16,18:27:-43.07,-8.14,-49.38:99
+chr1	3608425	rs3819959	T	C	21.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=2.02;MQ=53.67;MQ0=0;OQ=372.33;QD=9.08;SB=-195.61	GT:AD:DP:GL:GQ	0/1:23,18:34:-50.76,-10.24,-80.92:99
+chr1	3608574	rs3765740	T	G	43.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=2;HaplotypeScore=1.03;MQ=59.11;MQ0=0;OQ=373.92;QD=14.38;SB=-208.83	GT:AD:DP:GL:GQ	0/1:12,14:26:-48.51,-7.83,-42.30:99
+chr1	3608643	rs3765741	A	G	139.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.25;MQ0=0;OQ=277.44;QD=11.10;SB=-3.99	GT:AD:DP:GL:GQ	0/1:13,12:23:-37.96,-6.93,-45.69:99
+chr1	3608686	rs3765742	G	A	11.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=299.52;QD=14.98;SB=-7.00	GT:AD:DP:GL:GQ	0/1:9,11:19:-38.96,-5.72,-31.25:99
+chr1	3608969	rs3765743	C	T	17.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=315.53;QD=15.78;SB=-3.99	GT:AD:DP:GL:GQ	0/1:10,10:19:-40.56,-5.72,-31.07:99
+chr1	3609567	rs4648550	T	A	206.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.98;MQ0=0;OQ=1535.78;QD=37.46;SB=-673.01	GT:AD:DP:GL:GQ	1/1:0,41:41:-157.17,-12.35,-0.01:99
+chr1	3609807	rs34881405	T	C	7.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.49;MQ=57.54;MQ0=0;OQ=345.64;QD=7.86;SB=-128.25	GT:AD:DP:GL:GQ	0/1:24,20:40:-49.91,-12.06,-96.00:99
+chr1	3610040	rs17379833	A	T	163.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.52;MQ0=0;OQ=999.11;QD=20.81;SB=-480.53	GT:AD:DP:GL:GQ	0/1:16,32:47:-117.35,-14.16,-58.41:99
+chr1	3610295	rs12742969	A	G	136.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=514.16;QD=10.49;SB=-277.41	GT:AD:DP:GL:GQ	0/1:28,21:47:-68.86,-14.16,-115.22:99
+chr1	3610320	rs12735439	C	A	230.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=60.00;MQ0=0;OQ=801.03;QD=16.35;SB=-378.77	GT:AD:DP:GL:GQ	0/1:22,27:48:-97.85,-14.46,-70.21:99
+chr1	3611339	rs3765749	A	T	129.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=60.00;MQ0=0;OQ=640.71;QD=17.32;SB=-252.96	GT:AD:DP:GL:GQ	0/1:16,21:36:-78.20,-10.84,-56.57:99
+chr1	3612044	rs3765751	A	G	0.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=6.05;MQ=58.84;MQ0=0;OQ=1141.41;QD=28.54;SB=-361.32	GT:AD:DP:GL:GQ	1/1:0,39:37:-117.76,-11.16,-0.04:99
+chr1	3612141	rs3765752	G	A	98.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.42;MQ0=0;OQ=790.33;QD=19.76;SB=-403.21	GT:AD:DP:GL:GQ	0/1:16,24:40:-94.37,-12.05,-52.81:99
+chr1	3612166	rs3765753	T	G	307.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=1135.84;QD=31.55;SB=-218.90	GT:AD:DP:GL:GQ	1/1:0,36:34:-117.19,-10.25,-0.02:99
+chr1	3612496	rs12086279	A	T	144.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=53.76;MQ0=0;OQ=264.24;QD=12.01;SB=-145.87	GT:AD:DP:GL:GQ	0/1:12,10:20:-35.73,-6.03,-37.15:99
+chr1	3612742	rs56124535	A	G	117.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=57.14;MQ0=0;OQ=143.16;QD=7.53;SB=-61.32	GT:AD:DP:GL:GQ	0/1:9,9:16:-22.43,-4.83,-33.66:99
+chr1	3612752	rs55976062	T	C	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=2;HaplotypeScore=16.88;MQ=55.46;MQ0=1;OQ=130.66;QD=6.88;SB=-60.86	GT:AD:DP:GL:GQ	0/1:11,8:16:-21.17,-4.82,-37.90:99
+chr1	3612857	rs10910014	T	C	4.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.85;MQ=45.10;MQ0=1;OQ=122.28;QD=3.82;SB=-65.87	GT:AD:DP:GL:GQ	0/1:18,14:19:-21.24,-5.73,-45.71:99
+chr1	3612894	rs58140697	A	G	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=4;HaplotypeScore=5.46;MQ=58.05;MQ0=0;OQ=210.19;QD=8.76;SB=-118.71	GT:AD:DP:GL:GQ	0/1:15,9:22:-30.93,-6.63,-52.73:99
+chr1	3612902	rs60071664	T	C	130.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=57.06;MQ0=0;OQ=194.42;QD=7.48;SB=-106.60	GT:AD:DP:GL:GQ	0/1:16,10:25:-30.26,-7.53,-62.36:99
+chr1	3613185	rs12564843	G	C	7.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=1.11;MQ=53.89;MQ0=0;OQ=1382.10;QD=38.39;SB=-571.48	GT:AD:DP:GL:GQ	1/1:0,36:33:-141.81,-9.95,-0.02:99
+chr1	3613274	rs9786966	A	G	67.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.62;MQ=57.45;MQ0=0;OQ=414.03;QD=10.62;SB=-167.59	GT:AD:DP:GL:GQ	0/1:21,18:36:-55.53,-10.85,-77.07:99
+chr1	3613481	rs55657548	C	T	77.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=58.92;MQ0=0;OQ=252.32;QD=6.47;SB=-105.49	GT:AD:DP:GL:GQ	0/1:27,11:38:-39.97,-11.45,-93.41:99
+chr1	3614769	rs10910016	G	A	258.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=59.57;MQ0=0;OQ=815.07;QD=15.09;SB=-428.45	GT:AD:DP:GL:GQ	0/1:27,26:50:-99.87,-15.07,-79.93:99
+chr1	3615542	rs3765755	G	C	6.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=2;HaplotypeScore=3.76;MQ=57.56;MQ0=0;OQ=289.35;QD=10.72;SB=-124.51	GT:AD:DP:GL:GQ	0/1:17,10:20:-38.26,-6.05,-38.86:99
+chr1	3615628	rs2368540	G	A	45.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=57.64;MQ0=0;OQ=1334.80;QD=39.26;SB=-676.69	GT:AD:DP:GL:GQ	1/1:0,34:34:-137.07,-10.24,-0.01:99
+chr1	3615736	rs2368539	G	A	82.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.19;MQ=58.99;MQ0=0;OQ=1720.73;QD=37.41;SB=-824.61	GT:AD:DP:GL:GQ	1/1:0,46:45:-175.68,-13.56,-0.02:99
+chr1	3616028	rs12130809	G	A	272.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=838.34;QD=17.11;SB=-389.14	GT:AD:DP:GL:GQ	0/1:23,26:48:-101.58,-14.46,-75.57:99
+chr1	3616588	rs3753208	C	T	1.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=2.44;MQ=57.64;MQ0=0;OQ=539.82;QD=20.76;SB=-254.78	GT:AD:DP:GL:GQ	0/1:9,17:24:-64.50,-7.23,-25.72:99
+chr1	3616624	rs3753209	G	A	11.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=58.89;MQ0=0;OQ=522.74;QD=24.89;SB=-281.33	GT:AD:DP:GL:GQ	0/1:4,17:19:-61.28,-5.73,-9.34:36.13
+chr1	3618071	rs3819961	T	C	130.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=2.02;MQ=59.30;MQ0=0;OQ=302.64;QD=9.17;SB=-168.93	GT:AD:DP:GL:GQ	0/1:19,14:29:-42.29,-8.74,-60.25:99
+chr1	3618163	rs3819962	C	T	161.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.36;MQ0=0;OQ=457.21;QD=12.70;SB=-166.18	GT:AD:DP:GL:GQ	0/1:20,16:35:-59.55,-10.55,-68.25:99
+chr1	3618201	rs3819963	C	T	122.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=60.00;MQ0=0;OQ=469.25;QD=9.98;SB=-160.23	GT:AD:DP:GL:GQ	0/1:28,19:40:-62.27,-12.06,-77.68:99
+chr1	3618523	rs6424089	A	G	234.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.55;MQ0=0;OQ=515.26;QD=10.10;SB=-135.54	GT:AD:DP:GL:GQ	0/1:28,23:50:-69.88,-15.07,-112.69:99
+chr1	3618537	rs6424090	A	G	547.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.83;MQ0=0;OQ=1664.50;QD=30.82;SB=-446.16	GT:AD:DP:GL:GQ	1/1:0,54:52:-170.07,-15.68,-0.04:99
+chr1	3619132	rs61568045	A	T	75.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=1.40;MQ=60.00;MQ0=0;OQ=702.41;QD=14.05;SB=-308.70	GT:AD:DP:GL:GQ	0/1:27,23:49:-88.29,-14.76,-94.54:99
+chr1	3619452	rs3765758	A	G	47.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.30;MQ0=0;OQ=878.57;QD=26.62;SB=-355.42	GT:AD:DP:GL:GQ	1/1:0,33:30:-91.48,-9.06,-0.04:90.16
+chr1	3620336	rs3765761	C	T	430.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.64;MQ0=0;OQ=893.13;QD=17.18;SB=-472.49	GT:AD:DP:GL:GQ	0/1:25,27:51:-107.96,-15.36,-81.84:99
+chr1	3620975	rs3765763	C	A	252.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.39;MQ0=0;OQ=502.24;QD=13.22;SB=-232.36	GT:AD:DP:GL:GQ	0/1:20,18:37:-64.65,-11.14,-68.16:99
+chr1	3621759	rs61759267	C	T	206.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=58.40;MQ0=0;OQ=667.68;QD=16.28;SB=-326.34	GT:AD:DP:GL:GQ	0/1:19,22:40:-82.11,-12.06,-61.46:99
+chr1	3622468	rs3753211	T	C	35.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=6.67;MQ=58.45;MQ0=0;OQ=511.74;QD=11.37;SB=-197.62	GT:AD:DP:GL:GQ	0/1:23,22:42:-67.14,-12.68,-73.45:99
+chr1	3622590	rs4648551	G	A	13.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=8.04;MQ=59.11;MQ0=0;OQ=881.37;QD=14.94;SB=-385.40	GT:AD:DP:GL:GQ	0/1:30,29:55:-108.00,-16.58,-90.70:99
+chr1	3623397	rs3765764	G	A	5.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.59;MQ0=0;OQ=1699.76;QD=37.77;SB=-349.25	GT:AD:DP:GL:GQ	1/1:0,44:44:-176.03,-15.59,-2.47:99
+chr1	3624319	rs3765765	C	A	38.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=752.18;QD=20.33;SB=-184.22	GT:AD:DP:GL:GQ	0/1:13,24:36:-89.34,-10.84,-42.24:99
+chr1	3624520	rs3765766	T	C	10.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=2;HaplotypeScore=2.32;MQ=58.08;MQ0=0;OQ=679.70;QD=30.90;SB=-324.14	GT:AD:DP:GL:GQ	1/1:0,22:21:-71.57,-6.33,-0.02:63.16
+chr1	3625325	rs3765767	G	C	128.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.30;MQ0=0;OQ=648.42;QD=19.65;SB=-303.36	GT:AD:DP:GL:GQ	0/1:15,18:33:-78.07,-9.95,-65.85:99
+chr1	3625451	rs3765768	C	T	99.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=57.87;MQ0=0;OQ=372.64;QD=16.94;SB=-111.62	GT:AD:DP:GL:GQ	0/1:9,13:20:-46.58,-6.03,-24.55:99
+chr1	3625480	rs3819968	G	T	164.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.32;MQ0=0;OQ=519.45;QD=15.28;SB=-228.94	GT:AD:DP:GL:GQ	0/1:15,19:32:-64.87,-9.64,-47.62:99
+chr1	3627107	rs3765771	G	C	208.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.53;MQ0=0;OQ=1861.37;QD=37.99;SB=-769.21	GT:AD:DP:GL:GQ	1/1:0,49:48:-189.76,-14.49,-0.04:99
+chr1	3627319	rs12731705	C	T	198.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.16;MQ0=0;OQ=1887.80;QD=37.76;SB=-826.61	GT:AD:DP:GL:GQ	1/1:0,50:48:-192.38,-14.46,-0.01:99
+chr1	3627473	rs2146658	T	G	374.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.91;MQ0=0;OQ=603.03;QD=10.05;SB=-295.81	GT:AD:DP:GL:GQ	0/1:35,25:58:-81.06,-17.47,-122.08:99
+chr1	3627672	rs2181487	C	A	40.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=4.14;MQ=58.10;MQ0=0;OQ=433.83;QD=7.35;SB=-156.52	GT:AD:DP:GL:GQ	0/1:34,22:49:-61.43,-14.77,-105.52:99
+chr1	3628534	rs1801174	C	T	158.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=59.66;MQ0=0;OQ=2550.78;QD=38.07;SB=-965.29	GT:AD:DP:GL:GQ	1/1:0,67:65:-258.68,-19.58,-0.02:99
+chr1	3628694	rs12737840	C	T	176.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.52;MQ=58.05;MQ0=0;OQ=694.01;QD=14.46;SB=-295.84	GT:AD:DP:GL:GQ	0/1:22,26:42:-85.35,-12.67,-62.54:99
+chr1	3629503	rs4648552	T	C	338.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=1294.39;QD=30.10;SB=-605.94	GT:AD:DP:GL:GQ	1/1:0,43:41:-133.06,-12.37,-0.04:99
+chr1	3629584	rs7537335	G	A	0.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=58.30;MQ0=0;OQ=677.32;QD=21.85;SB=-284.30	GT:AD:DP:GL:GQ	0/1:10,21:29:-79.75,-8.74,-30.01:99
+chr1	3629945	rs6424091	C	G	0.03	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=5;HaplotypeScore=2.31;MQ=58.54;MQ0=0;OQ=1470.54;QD=38.70;SB=-622.99	GT:AD:DP:GL:GQ	1/1:0,38:35:-150.65,-10.55,-0.01:99
+chr1	3630886	rs6687491	G	A	255.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.48;MQ0=0;OQ=516.42;QD=12.91;SB=-227.77	GT:AD:DP:GL:GQ	0/1:22,18:36:-65.79,-10.86,-57.81:99
+chr1	3630983	rs6701784	A	C	437.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=1276.86;QD=28.37;SB=-579.85	GT:AD:DP:GL:GQ	1/1:0,45:42:-131.31,-12.66,-0.04:99
+chr1	3632013	rs34178965	G	C	41.74	LowQual	AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;QD=13.91;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:2:-7.58,-0.60,-0.00:6.02
+chr1	3632108	.	A	G	92.54	PASS	AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.46;MQ0=0;OQ=246.19;QD=30.77;SB=-85.92	GT:AD:DP:GL:GQ	1/1:0,8:8:-28.20,-2.41,-0.00:24.07
+chr1	3633787	rs2296031	A	G	6.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=452.89;QD=19.69;SB=-150.34	GT:AD:DP:GL:GQ	0/1:6,16:22:-55.20,-6.63,-22.30:99
+chr1	3634209	rs2181486	A	G	1.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=4;HaplotypeScore=1.69;MQ=58.39;MQ0=0;OQ=887.40;QD=30.60;SB=-422.16	GT:AD:DP:GL:GQ	1/1:0,29:29:-92.36,-8.75,-0.03:87.19
+chr1	3634234	rs2146657	A	G	3.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=2.86;MQ=58.55;MQ0=0;OQ=912.28;QD=28.51;SB=-446.82	GT:AD:DP:GL:GQ	1/1:0,32:28:-94.83,-8.44,-0.02:84.21
+chr1	3634529	rs2236367	C	T	14.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=-0.18;MQ=58.05;MQ0=0;OQ=381.45;QD=15.89;SB=-87.90	GT:AD:DP:GL:GQ	0/1:11,13:23:-48.37,-6.94,-31.96:99
+chr1	3634665	rs2236366	A	G	76.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.83;MQ=58.92;MQ0=0;OQ=536.64;QD=13.76;SB=-250.32	GT:AD:DP:GL:GQ	0/1:16,23:35:-67.50,-10.56,-54.78:99
+chr1	3634718	rs2236365	G	C	250.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=58.69;MQ0=0;OQ=951.80;QD=19.04;SB=-496.24	GT:AD:DP:GL:GQ	0/1:20,30:47:-112.65,-14.19,-78.43:99
+chr1	3634912	rs12095248	A	G	50.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=529.65;QD=10.81;SB=-225.29	GT:AD:DP:GL:GQ	0/1:29,20:49:-71.01,-14.76,-117.85:99
+chr1	3635695	rs2254530	C	A	234.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=56.85;MQ0=0;OQ=701.30;QD=15.58;SB=-270.34	GT:AD:DP:GL:GQ	0/1:17,28:43:-86.38,-12.96,-55.17:99
+chr1	3635704	rs2096224	G	A	61.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.39;MQ0=0;OQ=843.06;QD=18.33;SB=-255.19	GT:AD:DP:GL:GQ	0/1:18,27:42:-100.25,-12.66,-49.65:99
+chr1	3635997	rs11589885	C	T	153.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.19;MQ=58.55;MQ0=0;OQ=582.90;QD=18.22;SB=-289.86	GT:AD:DP:GL:GQ	0/1:14,18:32:-71.22,-9.65,-43.73:99
+chr1	3636052	rs1885867	G	A	143.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.44;MQ0=0;OQ=1392.32;QD=33.96;SB=-648.62	GT:AD:DP:GL:GQ	1/1:1,40:37:-142.84,-11.16,-0.02:99
+chr1	3636074	rs1885866	T	C	394.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=1194.73;QD=27.15;SB=-580.01	GT:AD:DP:GL:GQ	1/1:0,44:39:-123.10,-11.76,-0.04:99
+chr1	3636151	rs1885865	G	A	33.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.52;MQ=59.03;MQ0=0;OQ=1851.65;QD=38.58;SB=-906.66	GT:AD:DP:GL:GQ	1/1:0,48:47:-188.76,-14.16,-0.01:99
+chr1	3637822	rs1745813	T	C	55.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=5.13;MQ=58.97;MQ0=0;OQ=680.74;QD=15.13;SB=-289.66	GT:AD:DP:GL:GQ	0/1:18,27:43:-84.33,-12.97,-62.63:99
+chr1	3638114	rs34661835	G	A	68.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=3.56;MQ=59.01;MQ0=0;OQ=1063.39;QD=15.19;SB=-366.89	GT:AD:DP:GL:GQ	0/1:37,33:66:-129.52,-19.90,-102.17:99
+chr1	3638739	rs4648553	G	A	223.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.68;MQ=58.64;MQ0=0;OQ=511.89;QD=10.66;SB=-215.18	GT:AD:DP:GL:GQ	0/1:26,22:40:-66.54,-12.07,-70.14:99
+chr1	3640958	rs1181869	C	T	138.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=782.45;QD=20.06;SB=-285.16	GT:AD:DP:GL:GQ	0/1:16,23:38:-92.98,-11.45,-54.47:99
+chr1	3640986	rs1181868	G	T	357.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=59.51;MQ0=0;OQ=742.19;QD=14.55;SB=-306.02	GT:AD:DP:GL:GQ	0/1:23,27:47:-91.66,-14.16,-72.26:99
+chr1	3641178	rs1181867	A	G	3.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=11.13;MQ=59.11;MQ0=0;OQ=463.08;QD=9.85;SB=-239.29	GT:AD:DP:GL:GQ	0/1:24,23:43:-62.56,-12.97,-88.46:99
+chr1	3642477	rs1047928	G	C	24.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.25;MQ0=0;OQ=1110.64;QD=19.83;SB=-354.44	GT:AD:DP:GL:GQ	0/1:25,31:54:-130.64,-16.30,-94.09:99
+chr1	3642678	rs61759293	G	A	143.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=59.59;MQ0=0;OQ=746.17;QD=16.22;SB=-262.29	GT:AD:DP:GL:GQ	0/1:23,23:46:-91.76,-13.86,-82.87:99
+chr1	3642682	rs9800	C	G	193.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=59.59;MQ0=0;OQ=608.81;QD=13.23;SB=-238.07	GT:AD:DP:GL:GQ	0/1:25,21:45:-77.74,-13.57,-107.75:99
+chr1	3643272	rs1181866	A	C	242.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1714.13;QD=34.28;SB=-732.08	GT:AD:DP:GL:GQ	1/1:0,50:49:-175.01,-14.76,-0.02:99
+chr1	3643286	rs1181865	T	C	423.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1563.43;QD=32.57;SB=-664.24	GT:AD:DP:GL:GQ	1/1:0,48:46:-159.95,-13.86,-0.02:99
+chr1	3644050	rs1181864	A	G	156.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=57.94;MQ0=0;OQ=704.72;QD=10.36;SB=-357.09	GT:AD:DP:GL:GQ	0/1:38,30:68:-94.25,-20.50,-152.69:99
+chr1	3644355	rs41315308	C	T	206.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.64;MQ=57.86;MQ0=0;OQ=957.61;QD=14.96;SB=-405.80	GT:AD:DP:GL:GQ	0/1:34,30:63:-118.03,-18.99,-105.73:99
+chr1	3646184	rs1181863	T	C	89.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=57.04;MQ0=1;OQ=1725.96;QD=27.84;SB=-738.77	GT:AD:DP:GL:GQ	1/1:0,62:55:-176.23,-16.59,-0.05:99
+chr1	3647330	rs61339658	C	T	216.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.48;MQ0=0;OQ=622.56;QD=14.15;SB=-204.90	GT:AD:DP:GL:GQ	0/1:24,20:43:-78.50,-12.96,-75.30:99
+chr1	3647619	rs12117836	G	A	258.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.76;MQ0=0;OQ=3087.35;QD=39.58;SB=-1142.52	GT:AD:DP:GL:GQ	1/1:0,78:77:-312.34,-23.20,-0.02:99
+chr1	3647643	rs55704710	C	T	372.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1117.31;QD=14.14;SB=-441.41	GT:AD:DP:GL:GQ	0/1:44,35:79:-138.82,-23.81,-145.27:99
+chr1	3648097	rs10797409	G	A	267.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.27;MQ0=0;OQ=783.87;QD=15.37;SB=-396.73	GT:AD:DP:GL:GQ	0/1:26,25:51:-97.04,-15.37,-93.66:99
+chr1	3648630	rs12068191	T	C	36.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=59.42;MQ0=0;OQ=210.22;QD=6.57;SB=-113.63	GT:AD:DP:GL:GQ	0/1:20,12:30:-33.36,-9.05,-73.41:99
+chr1	3649517	rs2298222	G	A	272.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.08;MQ=58.64;MQ0=0;OQ=639.47;QD=13.32;SB=-210.21	GT:AD:DP:GL:GQ	0/1:28,20:45:-80.80,-13.57,-77.92:99
+chr1	3650201	rs10910020	A	G	239.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=60.00;MQ0=0;OQ=830.62;QD=14.32;SB=-256.96	GT:AD:DP:GL:GQ	0/1:22,36:55:-102.93,-16.58,-89.31:99
+chr1	3650655	rs61759295	C	T	319.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=56.32;MQ0=0;OQ=1049.42;QD=17.20;SB=-513.15	GT:AD:DP:GL:GQ	0/1:29,32:58:-125.70,-17.48,-89.86:99
+chr1	3650715	.	C	T	1.43	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=1;HaplotypeScore=2.94;MQ=58.05;MQ0=0;OQ=1053.29;QD=21.50;SB=-546.76	GT:AD:DP:GL:GQ	0/1:18,30:49:-126.44,-17.83,-68.95:99
+chr1	3650833	rs61759296	C	T	365.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=780.11;QD=18.14;SB=-365.90	GT:AD:DP:GL:GQ	0/1:18,25:43:-94.25,-12.96,-66.61:99
+chr1	3650834	rs61759297	A	G	444.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=732.78;QD=16.65;SB=-378.33	GT:AD:DP:GL:GQ	0/1:18,26:44:-89.82,-13.26,-70.47:99
+chr1	3651042	.	A	G	50.56	PASS	AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.01;MQ0=0;OQ=2317.73;QD=30.50;SB=-942.03	GT:AD:DP:GL:GQ	1/1:0,76:75:-235.44,-22.63,-0.08:99
+chr1	3651109	.	A	G	1.79	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=5.08;MQ=56.71;MQ0=0;OQ=273.27;QD=7.01;SB=-125.50	GT:AD:DP:GL:GQ	0/1:24,15:37:-41.77,-11.16,-93.00:99
+chr1	3651611	rs61759298	C	T	14.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=6.20;MQ=59.36;MQ0=0;OQ=487.25;QD=13.53;SB=-201.22	GT:AD:DP:GL:GQ	0/1:19,17:31:-61.35,-9.34,-53.39:99
+chr1	3651666	rs61759299	G	A	290.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=58.58;MQ0=0;OQ=537.51;QD=11.69;SB=-229.48	GT:AD:DP:GL:GQ	0/1:28,18:45:-70.60,-13.56,-93.90:99
+chr1	3652705	rs3737589	A	G	232.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=1820.89;QD=33.11;SB=-644.31	GT:AD:DP:GL:GQ	1/1:0,55:53:-185.70,-15.97,-0.02:99
+chr1	3652806	.	C	A	30.45	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=18.21;MQ=58.71;MQ0=0;QD=0.56;SB=77.26	GT:AD:DP:GL:GQ	0/1:38,16:41:-18.69,-12.36,-124.87:63.28
+chr1	3652917	rs3737590	A	T	248.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.59;MQ0=0;OQ=534.27;QD=11.87;SB=-180.50	GT:AD:DP:GL:GQ	0/1:25,20:43:-69.67,-12.96,-88.74:99
+chr1	3652988	rs3737591	G	A	355.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=743.37;QD=18.13;SB=-354.36	GT:AD:DP:GL:GQ	0/1:19,22:40:-89.67,-12.05,-59.56:99
+chr1	3653501	.	C	T	1.63	PASS	AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=1;HaplotypeScore=4.19;MQ=56.43;MQ0=0;OQ=295.19;QD=12.30;SB=-147.16	GT:AD:DP:GL:GQ	0/1:12,11:20:-38.83,-6.03,-35.51:99
+chr1	3654278	rs61759300	C	T	319.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=59.50;MQ0=0;OQ=838.34;QD=14.71;SB=-382.16	GT:AD:DP:GL:GQ	0/1:29,28:55:-103.70,-16.58,-94.60:99
+chr1	3654412	.	G	A	1.87	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=3.14;MQ=59.58;MQ0=0;OQ=1116.86;QD=20.31;SB=-482.46	GT:AD:DP:GL:GQ	0/1:23,32:54:-131.23,-16.26,-80.42:99
+chr1	3655727	rs12120656	G	T	277.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.16;MQ0=0;OQ=2493.88;QD=34.64;SB=-1022.51	GT:AD:DP:GL:GQ	1/1:0,71:69:-252.99,-20.78,-0.02:99
+chr1	3657359	rs61759301	C	A	268.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=59.56;MQ0=0;OQ=858.70;QD=16.20;SB=-443.00	GT:AD:DP:GL:GQ	0/1:24,29:52:-104.82,-15.66,-81.51:99
+chr1	3657864	rs4648554	T	C	343.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.67;MQ0=0;OQ=2306.57;QD=35.49;SB=-875.99	GT:AD:DP:GL:GQ	1/1:0,65:64:-234.26,-19.28,-0.02:99
+chr1	3658613	rs12128253	A	C	493.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=800.32;QD=17.40;SB=-351.83	GT:AD:DP:GL:GQ	0/1:19,27:46:-97.17,-13.85,-71.32:99
+chr1	3658641	rs12123850	G	T	445.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1182.07;QD=31.95;SB=-471.02	GT:AD:DP:GL:GQ	1/1:0,37:33:-121.80,-9.94,-0.01:99
+chr1	3659032	rs41315312	C	T	393.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=747.09;QD=16.24;SB=-297.79	GT:AD:DP:GL:GQ	0/1:23,23:45:-91.55,-13.56,-71.39:99
+chr1	3659061	rs10797410	A	G	617.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1286.97;QD=30.64;SB=-659.94	GT:AD:DP:GL:GQ	1/1:0,42:41:-132.32,-12.36,-0.04:99
+chr1	3659065	rs10910021	C	G	483.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=1547.05;QD=38.68;SB=-689.48	GT:AD:DP:GL:GQ	1/1:0,40:36:-158.30,-10.85,-0.01:99
+chr1	3659480	rs10797411	T	C	0.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=7.27;MQ=57.71;MQ0=0;OQ=1720.61;QD=33.09;SB=-601.34	GT:AD:DP:GL:GQ	1/1:0,51:50:-175.67,-15.06,-0.02:99
+chr1	3659744	.	C	T	75.39	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=20;HaplotypeScore=21.91;MQ=50.61;MQ0=1;QD=1.13;SB=59.16	GT:AD:DP:GL:GQ	0/1:57,10:52:-26.50,-15.68,-150.70:99
+chr1	3659750	.	T	C	207.45	SnpCluster	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=50.10;MQ=49.95;MQ0=1;QD=3.05;SB=-120.43	GT:AD:DP:GL:GQ	0/1:53,15:58:-41.51,-17.48,-178.17:99
+chr1	3659751	.	T	C	331.47	SnpCluster	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=48.26;MQ=49.78;MQ0=1;QD=4.95;SB=-162.44	GT:AD:DP:GL:GQ	0/1:46,21:55:-53.00,-16.57,-149.72:99
+chr1	3660887	rs1181889	T	C	275.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.83;MQ=59.11;MQ0=0;OQ=722.62;QD=13.90;SB=-328.30	GT:AD:DP:GL:GQ	0/1:24,28:49:-90.30,-14.76,-97.70:99
+chr1	3661651	rs1181888	A	G	399.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=490.27;QD=11.14;SB=-251.93	GT:AD:DP:GL:GQ	0/1:22,22:42:-64.98,-12.67,-82.79:99
+chr1	3662016	rs4648555	C	A	364.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=510.62;QD=9.46;SB=-259.25	GT:AD:DP:GL:GQ	0/1:34,20:53:-70.31,-15.96,-121.67:99
+chr1	3662783	rs12128087	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=13;HaplotypeScore=8.43;MQ=60.15;MQ0=0;OQ=558.18;QD=10.94;SB=-253.17	GT:AD:DP:GL:GQ	0/1:30,21:47:-73.27,-14.17,-94.61:99
+chr1	3663356	rs4648405	T	G	117.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.45;MQ0=0;OQ=421.62;QD=10.04;SB=-89.84	GT:AD:DP:GL:GQ	0/1:24,18:40:-57.50,-12.05,-84.73:99
+chr1	3663862	rs1181887	T	G	544.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1620.49;QD=34.48;SB=-656.23	GT:AD:DP:GL:GQ	1/1:0,47:47:-165.65,-14.16,-0.01:99
+chr1	3664012	rs7542464	C	T	327.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.16;MQ0=0;OQ=1410.26;QD=37.11;SB=-358.47	GT:AD:DP:GL:GQ	1/1:0,38:38:-144.63,-11.46,-0.02:99
+chr1	3664166	.	G	A	2.11	PASS	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=3;HaplotypeScore=2.17;MQ=59.59;MQ0=0;OQ=801.46;QD=17.81;SB=-414.44	GT:AD:DP:GL:GQ	0/1:20,25:43:-96.39,-12.96,-61.16:99
+chr1	3664614	rs1181886	A	T	88.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=59.65;MQ0=0;OQ=779.71;QD=14.44;SB=-332.65	GT:AD:DP:GL:GQ	0/1:28,26:52:-96.92,-15.66,-100.50:99
+chr1	3664618	rs9424312	T	A	76.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=946.40;QD=17.53;SB=-254.96	GT:AD:DP:GL:GQ	0/1:24,30:54:-114.19,-16.27,-85.78:99
+chr1	3664638	rs59291549	A	G	339.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.66;MQ0=0;OQ=754.74;QD=11.44;SB=-151.30	GT:AD:DP:GL:GQ	0/1:31,35:62:-97.45,-18.69,-125.83:99
+chr1	3664862	rs6682863	G	A	201.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=59.78;MQ0=0;OQ=631.54;QD=12.63;SB=-190.86	GT:AD:DP:GL:GQ	0/1:30,20:45:-80.00,-13.57,-81.03:99
+chr1	3665697	rs12128570	C	G	270.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=50.42;MQ0=0;OQ=767.84;QD=13.01;SB=-344.88	GT:AD:DP:GL:GQ	0/1:34,25:56:-96.94,-16.88,-141.00:99
+chr1	3665819	rs12131045	T	G	461.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.52;MQ0=0;OQ=642.50;QD=12.12;SB=-333.74	GT:AD:DP:GL:GQ	0/1:24,29:50:-82.60,-15.07,-87.60:99
+chr1	3665937	rs12128669	C	T	521.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.12;MQ0=0;OQ=862.45;QD=14.37;SB=-269.15	GT:AD:DP:GL:GQ	0/1:32,28:59:-107.30,-17.77,-116.90:99
+chr1	3666427	rs1181885	C	T	33.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.66;MQ0=0;OQ=1204.99;QD=21.91;SB=-603.11	GT:AD:DP:GL:GQ	0/1:19,36:52:-139.46,-15.68,-54.65:99
+chr1	3666458	rs1181884	T	C	438.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1123.89;QD=17.56;SB=-533.09	GT:AD:DP:GL:GQ	0/1:26,38:63:-134.65,-18.98,-101.24:99
+chr1	3666632	rs12406474	T	C	126.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=1.53;MQ=58.86;MQ0=0;OQ=740.89;QD=13.00;SB=-344.59	GT:AD:DP:GL:GQ	0/1:29,28:56:-94.24,-16.87,-116.11:99
+chr1	3667793	rs1181883	T	C	251.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=59.64;MQ0=0;OQ=2030.56;QD=31.73;SB=-682.90	GT:AD:DP:GL:GQ	1/1:0,64:64:-206.69,-19.29,-0.05:99
+chr1	3668081	rs1181882	G	C	162.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=60.00;MQ0=0;OQ=1618.57;QD=31.13;SB=-715.93	GT:AD:DP:GL:GQ	1/1:0,52:43:-165.50,-13.00,-0.06:99
+chr1	3668091	rs7516756	A	G	107.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=613.13;QD=11.57;SB=-116.72	GT:AD:DP:GL:GQ	0/1:27,26:49:-79.36,-14.77,-98.00:99
+chr1	3668371	rs7516968	A	G	62.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=209.36;QD=9.10;SB=-37.93	GT:AD:DP:GL:GQ	0/1:13,10:22:-30.85,-6.63,-52.05:99
+chr1	3668596	.	G	A	15.65	PASS	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=57.44;MQ0=0;OQ=384.28;QD=10.98;SB=-65.05	GT:AD:DP:GL:GQ	0/1:22,13:35:-52.26,-10.55,-81.04:99
+chr1	3668758	rs1181881	A	G	16.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.26;MQ=57.96;MQ0=0;OQ=916.82;QD=30.56;SB=-341.43	GT:AD:DP:GL:GQ	1/1:0,30:29:-95.29,-8.74,-0.02:87.21
+chr1	3668764	rs1181880	C	T	45.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.66;MQ0=0;OQ=531.41;QD=18.98;SB=-213.73	GT:AD:DP:GL:GQ	0/1:11,17:28:-64.87,-8.45,-34.91:99
+chr1	3668999	rs1181879	T	C	13.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.38;MQ=59.44;MQ0=0;OQ=1208.95;QD=29.49;SB=-449.15	GT:AD:DP:GL:GQ	1/1:0,41:38:-124.52,-11.46,-0.04:99
+chr1	3669006	rs4648556	G	A	196.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=59.44;MQ0=0;OQ=524.36;QD=12.79;SB=-228.74	GT:AD:DP:GL:GQ	0/1:24,17:40:-67.77,-12.05,-80.81:99
+chr1	3669167	rs4648557	T	C	163.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=60.00;MQ0=0;OQ=314.58;QD=10.15;SB=-171.98	GT:AD:DP:GL:GQ	0/1:15,16:28:-43.19,-8.45,-53.69:99
+chr1	3669321	rs4648558	A	T	213.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=59.30;MQ0=0;OQ=430.63;QD=13.05;SB=-151.85	GT:AD:DP:GL:GQ	0/1:18,15:33:-56.29,-9.94,-66.61:99
+chr1	3669635	rs10910024	C	T	223.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=60.00;MQ0=0;OQ=261.53;QD=10.46;SB=-131.12	GT:AD:DP:GL:GQ	0/1:15,10:24:-36.67,-7.23,-47.59:99
+chr1	3669916	rs56079032	G	A	49.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.11;MQ0=0;OQ=457.75;QD=17.61;SB=-143.18	GT:AD:DP:GL:GQ	0/1:10,16:25:-56.59,-7.54,-35.59:99
+chr1	3670503	rs1181878	G	A	204.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.96;MQ=58.92;MQ0=0;OQ=593.13;QD=15.21;SB=-209.18	GT:AD:DP:GL:GQ	0/1:21,18:39:-74.34,-11.75,-76.92:99
+chr1	3670589	rs1181877	C	T	442.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=59.71;MQ0=0;OQ=1051.46;QD=16.43;SB=-536.72	GT:AD:DP:GL:GQ	0/1:31,33:61:-126.81,-18.38,-107.46:99
+chr1	3670923	rs6669358	A	G	271.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.35;MQ=59.49;MQ0=0;OQ=863.52;QD=11.83;SB=-442.10	GT:AD:DP:GL:GQ	0/1:40,33:71:-111.03,-21.40,-156.37:99
+chr1	3671541	rs1181876	A	G	312.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.35;MQ0=0;OQ=557.92;QD=8.72;SB=-268.23	GT:AD:DP:GL:GQ	0/1:36,28:60:-77.16,-18.08,-144.69:99
+chr1	3671691	rs1181875	T	C	354.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.69;MQ0=0;OQ=768.78;QD=12.60;SB=-310.35	GT:AD:DP:GL:GQ	0/1:32,29:59:-97.93,-17.77,-128.86:99
+chr1	3671930	rs1181874	C	A	548.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=1553.48;QD=14.00;SB=-588.81	GT:AD:DP:GL:GQ	0/1:58,53:110:-191.77,-33.14,-192.67:99
+chr1	3673550	rs1181873	A	C	65.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.41;MQ0=0;OQ=502.42;QD=12.88;SB=-249.39	GT:AD:DP:GL:GQ	0/1:20,19:38:-64.97,-11.45,-71.58:99
+chr1	3673967	rs1181872	T	A	314.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=59.13;MQ0=0;OQ=665.69;QD=15.48;SB=-321.70	GT:AD:DP:GL:GQ	0/1:19,24:41:-82.21,-12.35,-69.45:99
+chr1	3674181	rs1181871	A	G	201.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=52.16;MQ0=0;OQ=271.85;QD=7.55;SB=-59.74	GT:AD:DP:GL:GQ	0/1:21,15:32:-40.11,-9.65,-77.03:99
+chr1	3674814	rs1181870	C	A	305.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=57.69;MQ0=0;OQ=866.35;QD=12.93;SB=-280.62	GT:AD:DP:GL:GQ	0/1:36,31:65:-109.50,-19.58,-123.19:99
+chr1	3677599	rs1175552	C	A	135.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=60.00;MQ0=0;OQ=585.48;QD=10.09;SB=-188.53	GT:AD:DP:GL:GQ	0/1:34,24:53:-77.81,-15.97,-102.27:99
+chr1	3678505	rs1175551	T	C	166.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=58.20;MQ0=0;OQ=103.01;QD=7.92;SB=-65.87	GT:AD:DP:GL:GQ	0/1:7,6:12:-17.20,-3.62,-26.14:99
+chr1	3679407	.	C	G	26.93	LowQual	AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=2.22;MQ=48.93;MQ0=0;QD=2.45;SB=-6.99	GT:AD:DP:GL:GQ	0/1:3,8:4:-7.19,-1.21,-8.24:59.76
+chr1	3681100	rs1184341	C	T	108.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=3.04;MQ=59.23;MQ0=0;OQ=426.67;QD=14.22;SB=-164.69	GT:AD:DP:GL:GQ	0/1:15,15:28:-54.39,-8.44,-49.07:99
+chr1	3681124	rs2797432	A	G	199.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=396.40;QD=12.39;SB=-160.61	GT:AD:DP:GL:GQ	0/1:13,19:29:-51.67,-8.74,-51.47:99
+chr1	3681330	rs1181893	A	C	235.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.61;MQ0=0;OQ=409.25;QD=27.28;SB=-143.01	GT:AD:DP:GL:GQ	1/1:0,15:13:-44.52,-3.92,-0.01:39.10
+chr1	3681388	rs1175550	A	G	206.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=59.14;MQ0=0;OQ=268.33;QD=9.94;SB=-118.66	GT:AD:DP:GL:GQ	0/1:16,11:27:-38.26,-8.14,-61.45:99
+chr1	3681587	rs1175549	A	C	56.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=1.73;MQ=59.28;MQ0=0;OQ=317.74;QD=9.93;SB=-135.67	GT:AD:DP:GL:GQ	0/1:18,14:31:-44.40,-9.34,-64.53:99
+chr1	3682892	rs1175548	A	G	294.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.99;MQ0=0;OQ=521.21;QD=11.33;SB=-266.55	GT:AD:DP:GL:GQ	0/1:25,21:43:-68.36,-12.95,-93.71:99
+chr1	3683615	rs1175547	G	T	106.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=58.25;MQ0=0;OQ=658.75;QD=16.47;SB=-219.58	GT:AD:DP:GL:GQ	0/1:18,22:39:-80.91,-11.75,-53.72:99
+chr1	3683769	rs1175546	C	T	14.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=58.95;MQ0=0;OQ=845.89;QD=19.22;SB=-175.68	GT:AD:DP:GL:GQ	0/1:18,26:42:-100.52,-12.65,-61.88:99
+chr1	3684656	rs1891934	G	A	75.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=59.58;MQ0=0;OQ=574.95;QD=13.07;SB=-268.25	GT:AD:DP:GL:GQ	0/1:26,18:41:-73.14,-12.36,-73.56:99
+chr1	3684836	.	T	G	29.95	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=2;HaplotypeScore=5.28;MQ=57.94;MQ0=0;QD=0.88;SB=50.17	GT:AD:DP:GL:GQ	0/1:20,14:25:-13.81,-7.53,-70.58:62.78
+chr1	3685860	rs2799182	T	C	179.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.18;MQ=58.63;MQ0=0;OQ=681.56;QD=13.36;SB=-324.12	GT:AD:DP:GL:GQ	0/1:23,28:50:-86.51,-15.07,-94.22:99
+chr1	3686231	rs61759305	C	T	280.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=512.50;QD=17.08;SB=-238.52	GT:AD:DP:GL:GQ	0/1:14,16:29:-63.27,-8.74,-47.74:99
+chr1	3686750	rs8379	A	C	132.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.70;MQ0=0;OQ=512.51;QD=8.27;SB=-204.80	GT:AD:DP:GL:GQ	0/1:39,23:59:-72.31,-17.77,-139.60:99
+chr1	3687151	rs2996428	C	T	323.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=59.68;MQ0=0;OQ=1332.10;QD=18.25;SB=-588.63	GT:AD:DP:GL:GQ	0/1:30,43:68:-156.98,-20.49,-102.01:99
+chr1	3688388	rs2799186	C	G	198.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=60.00;MQ0=0;OQ=1120.38;QD=14.55;SB=-296.13	GT:AD:DP:GL:GQ	0/1:44,32:77:-141.06,-25.73,-190.14:99
+chr1	3688807	rs12122058	C	T	132.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=1.81;MQ=60.00;MQ0=0;OQ=788.10;QD=15.16;SB=-353.46	GT:AD:DP:GL:GQ	0/1:27,25:50:-97.16,-15.07,-93.28:99
+chr1	3689428	rs2799185	G	C	86.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.23;MQ0=0;OQ=644.64;QD=17.42;SB=-205.64	GT:AD:DP:GL:GQ	0/1:18,19:35:-78.30,-10.56,-70.47:99
+chr1	3689489	rs2799184	T	G	198.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.30;MQ=56.35;MQ0=0;OQ=514.42;QD=13.19;SB=-238.40	GT:AD:DP:GL:GQ	0/1:19,20:37:-65.87,-11.14,-65.31:99
+chr1	3689844	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=16;HaplotypeScore=12.40;MQ=56.82;MQ0=0;OQ=207.53;QD=3.10;SB=47.88	GT:AD:DP:GL:GQ	0/1:50,16:53:-40.01,-15.97,-140.82:99
+chr1	3691351	rs2996426	A	G	107.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=2.66;MQ=59.77;MQ0=0;OQ=576.97;QD=11.10;SB=-273.25	GT:AD:DP:GL:GQ	0/1:26,26:49:-75.76,-14.78,-98.82:99
+chr1	3693197	rs2368537	G	C	138.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.55;MQ0=0;OQ=1805.49;QD=35.40;SB=-781.23	GT:AD:DP:GL:GQ	1/1:0,51:46:-184.17,-13.88,-0.03:99
+chr1	3693570	rs2253143	G	A	60.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.58;MQ=58.41;MQ0=0;OQ=495.55;QD=11.26;SB=-141.61	GT:AD:DP:GL:GQ	0/1:26,18:41:-65.20,-12.37,-77.20:99
+chr1	3694312	rs12142183	T	G	312.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=59.65;MQ0=0;OQ=615.52;QD=11.61;SB=-311.76	GT:AD:DP:GL:GQ	0/1:22,31:47:-79.00,-14.16,-79.12:99
+chr1	3694564	.	G	C	39.33	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=6.24;MQ=58.81;MQ0=0;QD=0.72;SB=44.18	GT:AD:DP:GL:GQ	0/1:42,12:37:-18.38,-11.17,-134.23:72.16
+chr1	3701498	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=71;Dels=0.03;HRun=20;HaplotypeScore=51.30;MQ=52.45;MQ0=0;OQ=259.27;QD=3.65;SB=80.25	GT:AD:DP:GL:GQ	0/1:46,23:54:-44.89,-15.68,-134.64:99
+chr1	3708347	rs6681383	G	A	128.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.34;MQ0=0;OQ=1078.39;QD=18.92;SB=-322.85	GT:AD:DP:GL:GQ	0/1:24,33:53:-127.10,-15.97,-69.66:99
+chr1	3712148	rs2996425	A	T	193.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=59.02;MQ0=0;OQ=2222.50;QD=35.85;SB=-1018.88	GT:AD:DP:GL:GQ	1/1:0,62:60:-225.85,-18.07,-0.02:99
+chr1	3714307	rs61759320	G	A	326.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=53.55;MQ0=0;OQ=770.50;QD=14.01;SB=-354.84	GT:AD:DP:GL:GQ	0/1:29,25:53:-96.31,-15.97,-95.14:99
+chr1	3714663	.	A	C	15.04	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=2;HaplotypeScore=8.17;MQ=57.66;MQ0=0;QD=0.38;SB=56.19	GT:AD:DP:GL:GQ	0/1:24,16:28:-13.21,-8.44,-81.36:47.74
+chr1	3727878	.	C	T	38.08	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=59.48;MQ0=0;OQ=1399.61;QD=17.28;SB=-662.18	GT:AD:DP:GL:GQ	0/1:40,41:81:-167.65,-24.40,-140.98:99
+chr1	3731503	.	A	G	18.90	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=3;HaplotypeScore=1.79;MQ=54.69;MQ0=0;QD=0.73;SB=5.04	GT:AD:DP:GL:GQ	0/1:21,5:21:-11.50,-6.33,-70.25:51.68
+chr1	3735976	rs1836	A	G	124.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.74;MQ0=0;OQ=2210.40;QD=31.13;SB=-963.45	GT:AD:DP:GL:GQ	1/1:0,70:69:-227.21,-23.18,-2.59:99
+chr1	3736114	rs2275830	T	C	634.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=2088.07;QD=30.71;SB=-734.31	GT:AD:DP:GL:GQ	1/1:0,68:67:-212.46,-20.22,-0.07:99
+chr1	3736443	rs2275828	G	T	17.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=3.28;MQ=59.05;MQ0=0;OQ=2655.56;QD=36.38;SB=-1342.28	GT:AD:DP:GL:GQ	1/1:0,73:72:-269.16,-21.68,-0.02:99
+chr1	3736449	rs2275826	C	G	89.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.10;MQ0=0;OQ=3375.97;QD=43.84;SB=-1685.64	GT:AD:DP:GL:GQ	1/1:0,77:77:-336.60,-23.20,-0.02:99
+chr1	3737179	rs4648417	C	T	55.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=58.05;MQ0=0;OQ=1230.92;QD=34.19;SB=-377.48	GT:AD:DP:GL:GQ	1/1:0,35:33:-126.70,-9.95,-0.02:99
+chr1	3737440	rs6424058	C	T	106.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=3.83;MQ=56.84;MQ0=0;OQ=1463.09;QD=34.84;SB=-699.35	GT:AD:DP:GL:GQ	1/1:0,42:38:-149.91,-11.45,-0.01:99
+chr1	3737463	rs6413779	T	C	36.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=57.40;MQ0=0;OQ=1023.14;QD=33.00;SB=-220.63	GT:AD:DP:GL:GQ	1/1:0,31:31:-105.92,-9.34,-0.02:93.25
+chr1	3737945	rs7522227	A	G	230.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.22;MQ0=0;OQ=2674.63;QD=34.29;SB=-1340.60	GT:AD:DP:GL:GQ	1/1:0,77:76:-271.07,-22.89,-0.02:99
+chr1	3738031	rs7524765	T	C	717.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2886.44;QD=35.20;SB=-1305.64	GT:AD:DP:GL:GQ	1/1:0,82:82:-292.25,-24.70,-0.03:99
+chr1	3738548	rs17403836	A	C	593.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.20;MQ0=0;OQ=3340.65;QD=35.92;SB=-1448.19	GT:AD:DP:GL:GQ	1/1:0,93:93:-333.07,-28.01,-0.02:99
+chr1	3738842	rs61768911	C	G	310.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.39;MQ0=2;OQ=606.83;QD=30.34;SB=-199.55	GT:AD:DP:GL:GQ	1/1:0,19:16:-64.28,-4.83,-0.01:48.16
+chr1	3738927	.	T	C	23.45	LowQual	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=5.48;MQ=47.67;MQ0=1;QD=0.60;SB=-5.57	GT:AD:DP:GL:GQ	0/1:32,7:31:-14.97,-9.34,-106.27:56.26
+chr1	3738930	.	T	C	7.68	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.51;MQ=48.29;MQ0=0;OQ=738.60;QD=19.44;SB=-353.38	GT:AD:DP:GL:GQ	0/1:6,32:31:-86.49,-9.35,-16.38:70.33
+chr1	3738954	rs61768912	T	C	1249.83	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.18;MQ0=0;QD=28.41;SB=-561.89	GT:AD:DP:GL:GQ	1/1:0,43:40:-128.60,-12.06,-0.04:99
+chr1	3738962	rs61768913	A	G	1521.07	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=53.09;MQ0=0;QD=28.17;SB=-501.21	GT:AD:DP:GL:GQ	1/1:0,54:48:-155.73,-14.47,-0.04:99
+chr1	3738964	rs61768914	A	G	1823.57	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=53.35;MQ0=0;QD=32.56;SB=-678.27	GT:AD:DP:GL:GQ	1/1:0,56:52:-185.96,-15.66,-0.02:99
+chr1	3738975	rs61768915	T	C	185.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=53.83;MQ0=0;OQ=2377.40;QD=34.96;SB=-853.97	GT:AD:DP:GL:GQ	1/1:0,68:67:-241.35,-20.18,-0.03:99
+chr1	3739217	rs6684560	G	A	167.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=55.03;MQ0=0;OQ=2027.81;QD=36.87;SB=-859.02	GT:AD:DP:GL:GQ	1/1:1,54:53:-206.39,-15.97,-0.02:99
+chr1	3739448	rs6676260	T	C	481.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=1276.86;QD=30.40;SB=-555.08	GT:AD:DP:GL:GQ	1/1:0,42:41:-131.31,-12.36,-0.03:99
+chr1	3739507	rs10797344	C	G	65.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.02;MQ=59.28;MQ0=0;OQ=2404.57;QD=37.57;SB=-1028.99	GT:AD:DP:GL:GQ	1/1:0,64:58:-244.08,-17.49,-0.04:99
+chr1	3739508	rs10797345	G	A	56.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.68;MQ=59.28;MQ0=0;OQ=2416.64;QD=37.76;SB=-1154.54	GT:AD:DP:GL:GQ	1/1:0,64:63:-245.28,-18.99,-0.03:99
+chr1	3739554	rs6673716	A	G	130.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.53;MQ0=0;OQ=1461.81;QD=29.83;SB=-615.96	GT:AD:DP:GL:GQ	1/1:0,49:46:-149.80,-13.87,-0.04:99
+chr1	3739633	rs6673807	A	G	581.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=2050.62;QD=35.36;SB=-778.99	GT:AD:DP:GL:GQ	1/1:0,58:58:-208.67,-17.47,-0.02:99
+chr1	3740027	rs2368533	G	A	618.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=2881.32;QD=38.94;SB=-1374.05	GT:AD:DP:GL:GQ	1/1:0,74:73:-291.74,-21.99,-0.02:99
+chr1	3740589	rs6677381	A	G	634.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=2780.11;QD=35.64;SB=-1088.76	GT:AD:DP:GL:GQ	1/1:0,78:77:-281.62,-23.19,-0.02:99
+chr1	3740591	rs6680017	T	G	509.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=2637.83;QD=34.26;SB=-1082.49	GT:AD:DP:GL:GQ	1/1:0,77:75:-267.39,-22.59,-0.02:99
+chr1	3740758	.	T	A	7.56	PASS	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.28;MQ0=1;OQ=174.11;QD=4.71;SB=-20.31	GT:AD:DP:GL:GQ	0/1:28,9:34:-30.93,-10.24,-98.40:99
+chr1	3741138	rs2887273	C	G	484.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2855.33;QD=43.26;SB=-1170.05	GT:AD:DP:GL:GQ	1/1:0,66:66:-289.13,-19.88,-0.02:99
+chr1	3741826	rs4648419	C	G	552.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.30;MQ0=0;OQ=3843.78;QD=42.24;SB=-1290.87	GT:AD:DP:GL:GQ	1/1:0,91:88:-383.38,-26.52,-0.03:99
+chr1	3742892	.	G	T	16.29	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=20;HaplotypeScore=18.89;MQ=55.03;MQ0=1;QD=0.28;SB=44.02	GT:AD:DP:GL:GQ	0/1:50,6:41:-19.70,-14.80,-98.51:49.02
+chr1	3742917	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=52;Dels=0.02;HRun=20;HaplotypeScore=34.21;MQ=57.45;MQ0=0;OQ=170.67;QD=3.28;SB=56.18	GT:AD:DP:GL:GQ	0/1:37,14:43:-33.01,-12.65,-114.45:99
+chr1	3742996	rs2275824	A	T	710.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.86;MQ0=0;OQ=2009.53;QD=35.25;SB=-882.57	GT:AD:DP:GL:GQ	1/1:0,57:56:-204.56,-16.87,-0.02:99
+chr1	3744349	rs12409082	G	C	531.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3059.06;QD=43.09;SB=-1422.83	GT:AD:DP:GL:GQ	1/1:0,71:71:-309.52,-21.40,-0.02:99
+chr1	3744456	rs6683827	G	T	2.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=4.28;MQ=58.86;MQ0=0;OQ=2501.40;QD=35.73;SB=-1071.46	GT:AD:DP:GL:GQ	1/1:0,70:69:-253.75,-20.78,-0.02:99
+chr1	3745535	rs1891941	T	C	731.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2479.06;QD=35.42;SB=-1217.69	GT:AD:DP:GL:GQ	1/1:0,70:69:-251.51,-20.78,-0.02:99
+chr1	3745729	rs1891940	T	C	456.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=1634.49;QD=34.78;SB=-697.28	GT:AD:DP:GL:GQ	1/1:0,47:46:-167.05,-13.85,-0.01:99
+chr1	3745735	rs1891939	T	G	249.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=1553.73;QD=33.78;SB=-800.51	GT:AD:DP:GL:GQ	1/1:0,46:45:-158.97,-13.55,-0.02:99
+chr1	3745980	rs1539649	A	G	625.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=2553.81;QD=30.77;SB=-1180.11	GT:AD:DP:GL:GQ	1/1:0,83:80:-259.03,-24.12,-0.06:99
+chr1	3746353	rs7535887	T	C	654.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1854.47;QD=30.91;SB=-854.01	GT:AD:DP:GL:GQ	1/1:0,60:59:-189.08,-17.79,-0.05:99
+chr1	3746392	rs10797346	T	C	305.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2579.74;QD=35.83;SB=-1200.15	GT:AD:DP:GL:GQ	1/1:0,72:72:-261.58,-21.69,-0.02:99
+chr1	3747160	rs10909800	C	T	207.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2281.73;QD=39.34;SB=-904.67	GT:AD:DP:GL:GQ	1/1:0,58:58:-231.78,-17.47,-0.02:99
+chr1	3748578	rs4381131	T	C	118.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=57.58;MQ0=0;OQ=1302.81;QD=35.21;SB=-612.36	GT:AD:DP:GL:GQ	1/1:0,37:37:-133.88,-11.14,-0.01:99
+chr1	3748616	rs4411084	A	G	124.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=57.27;MQ0=0;OQ=1453.01;QD=29.06;SB=-634.87	GT:AD:DP:GL:GQ	1/1:0,50:46:-148.93,-13.88,-0.04:99
+chr1	3749212	rs3765774	T	A	197.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=2826.29;QD=36.71;SB=-1358.75	GT:AD:DP:GL:GQ	1/1:0,77:76:-286.23,-22.89,-0.02:99
+chr1	3749644	rs10797347	A	G	265.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=59.07;MQ0=0;OQ=1626.88;QD=34.61;SB=-812.67	GT:AD:DP:GL:GQ	1/1:0,47:46:-166.29,-13.86,-0.01:99
+chr1	3749797	rs10909801	A	G	1.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=13.74;MQ=53.38;MQ0=0;OQ=1309.63;QD=23.81;SB=-631.48	GT:AD:DP:GL:GQ	1/1:0,53:41:-134.59,-12.37,-0.04:99
+chr1	3749921	rs6701360	G	A	575.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.91;MQ0=0;OQ=2426.40;QD=38.51;SB=-904.68	GT:AD:DP:GL:GQ	1/1:0,63:63:-246.25,-18.99,-0.03:99
+chr1	3749974	rs6690371	A	G	48.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.93;MQ=58.34;MQ0=0;OQ=1681.22;QD=35.03;SB=-728.27	GT:AD:DP:GL:GQ	1/1:0,48:48:-171.73,-14.47,-0.03:99
+chr1	3749989	rs6678020	C	T	441.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.59;MQ0=0;OQ=1518.29;QD=37.96;SB=-571.34	GT:AD:DP:GL:GQ	1/1:0,40:39:-155.43,-11.75,-0.01:99
+chr1	3750090	rs6680552	C	T	728	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.60;MQ0=1;OQ=1998.34;QD=35.06;SB=-998.84	GT:AD:DP:GL:GQ	1/1:0,57:51:-203.43,-15.36,-0.01:99
+chr1	3750216	rs6695657	T	C	130.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.67;MQ0=0;OQ=1753.47;QD=29.72;SB=-613.96	GT:AD:DP:GL:GQ	1/1:0,59:56:-178.99,-16.89,-0.06:99
+chr1	3750378	rs10752723	A	G	15.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=1.50;MQ=56.80;MQ0=0;OQ=1482.59;QD=32.95;SB=-488.54	GT:AD:DP:GL:GQ	1/1:1,43:41:-151.86,-12.35,-0.01:99
+chr1	3751141	rs6698930	T	A	637.91	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=7;HaplotypeScore=46.26;MQ=41.75;MQ0=0;QD=7.78;SB=8.51	GT:AD:DP:GL:GQ	0/1:49,33:69:-87.87,-20.79,-167.40:99
+chr1	3751339	rs2275822	C	T	226.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.23;MQ0=0;OQ=2373.96;QD=39.57;SB=-964.37	GT:AD:DP:GL:GQ	1/1:0,60:60:-241.00,-18.08,-0.02:99
+chr1	3751510	rs2275821	A	G	573.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.31;MQ0=0;OQ=3500.46;QD=35.36;SB=-1716.03	GT:AD:DP:GL:GQ	1/1:0,99:96:-349.05,-28.91,-0.03:99
+chr1	3751936	rs6699784	T	C	22.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1634.61;QD=34.05;SB=-680.60	GT:AD:DP:GL:GQ	1/1:0,48:47:-167.07,-14.16,-0.02:99
+chr1	3751940	rs6699785	T	C	457.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1716.61;QD=35.76;SB=-707.61	GT:AD:DP:GL:GQ	1/1:0,48:48:-175.26,-14.46,-0.02:99
+chr1	3752276	rs6687498	C	A	0.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=7.86;MQ=58.29;MQ0=1;OQ=1565.75;QD=34.79;SB=-714.95	GT:AD:DP:GL:GQ	1/1:1,44:44:-160.17,-13.25,-0.01:99
+chr1	3752464	rs4494088	C	T	130.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.01;MQ0=0;OQ=2585.87;QD=39.18;SB=-1275.71	GT:AD:DP:GL:GQ	1/1:0,66:65:-262.19,-19.58,-0.02:99
+chr1	3752510	.	C	A	11.64	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=20;HaplotypeScore=16.03;MQ=54.71;MQ0=1;QD=0.16;SB=98.34	GT:AD:DP:GL:GQ	0/1:63,8:53:-20.38,-15.96,-171.47:44.17
+chr1	3752581	rs4534323	A	T	713.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2157.31;QD=36.56;SB=-930.57	GT:AD:DP:GL:GQ	1/1:0,59:59:-219.34,-17.77,-0.02:99
+chr1	3753724	rs12047360	G	A	108.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=59.36;MQ0=0;OQ=1255.98;QD=34.89;SB=-564.33	GT:AD:DP:GL:GQ	1/1:0,36:33:-129.19,-9.94,-0.01:99
+chr1	3754321	rs34401151	C	T	220.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.55;MQ0=0;OQ=2357.19;QD=36.83;SB=-1184.12	GT:AD:DP:GL:GQ	1/1:0,63:62:-242.18,-21.42,-2.88:99
+chr1	3754471	rs55873991	T	C	460.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=2216.85;QD=34.64;SB=-478.52	GT:AD:DP:GL:GQ	1/1:0,64:60:-225.28,-18.07,-0.01:99
+chr1	3755409	rs4648346	G	A	377.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=56.94;MQ0=0;OQ=2718.34;QD=38.83;SB=-1289.71	GT:AD:DP:GL:GQ	1/1:0,70:68:-275.43,-20.48,-0.02:99
+chr1	3755538	rs4648423	C	T	3.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=5.11;MQ=59.49;MQ0=0;OQ=1662.33;QD=36.94;SB=-681.30	GT:AD:DP:GL:GQ	1/1:0,44:44:-169.84,-13.26,-0.02:99
+chr1	3755615	rs4648347	T	C	415.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=60.19;MQ0=0;OQ=2002.26;QD=34.52;SB=-940.97	GT:AD:DP:GL:GQ	1/1:0,58:56:-203.83,-16.87,-0.02:99
+chr1	3755919	rs12097923	G	T	175.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=59.51;MQ0=0;OQ=2007.64;QD=34.03;SB=-971.58	GT:AD:DP:GL:GQ	1/1:0,58:57:-204.37,-17.17,-0.02:99
+chr1	3756146	rs17404435	G	T	642.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.27;MQ0=0;OQ=1775.93;QD=34.82;SB=-654.09	GT:AD:DP:GL:GQ	1/1:0,51:50:-181.19,-15.06,-0.02:99
+chr1	3756301	rs6683156	C	T	153.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=59.62;MQ0=0;OQ=3593.95;QD=38.64;SB=-1767.70	GT:AD:DP:GL:GQ	1/1:0,92:90:-358.39,-27.12,-0.03:99
+chr1	3757458	rs3765779	A	G	312.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1547.17;QD=29.19;SB=-677.55	GT:AD:DP:GL:GQ	1/1:0,53:50:-158.35,-15.08,-0.05:99
+chr1	3757556	rs3765780	C	T	73.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=1220.87;QD=37.00;SB=-540.71	GT:AD:DP:GL:GQ	1/1:0,33:32:-125.68,-9.64,-0.01:96.30
+chr1	3758579	rs1539647	T	C	5.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=3.94;MQ=58.65;MQ0=1;OQ=2215.43;QD=29.94;SB=-922.78	GT:AD:DP:GL:GQ	1/1:1,73:71:-228.15,-21.41,-3.03:99
+chr1	3758589	rs1539648	T	C	162.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=59.09;MQ0=0;OQ=2319.86;QD=30.52;SB=-925.48	GT:AD:DP:GL:GQ	1/1:0,76:73:-235.63,-22.01,-0.06:99
+chr1	3759091	rs6657021	A	G	451.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.04;MQ0=0;OQ=2173.33;QD=30.19;SB=-1093.08	GT:AD:DP:GL:GQ	1/1:0,72:68:-220.98,-20.51,-0.06:99
+chr1	3759136	rs6668213	G	C	44.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.72;MQ0=0;OQ=2874.30;QD=41.66;SB=-1253.95	GT:AD:DP:GL:GQ	1/1:0,69:66:-291.04,-19.89,-0.02:99
+chr1	3759146	rs6693152	C	T	203.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.07;MQ0=0;OQ=2711.10;QD=38.73;SB=-1194.58	GT:AD:DP:GL:GQ	1/1:0,70:68:-274.71,-20.49,-0.02:99
+chr1	3759189	rs6657132	A	G	408.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=1707.03;QD=31.04;SB=-847.00	GT:AD:DP:GL:GQ	1/1:0,55:50:-174.32,-15.07,-0.03:99
+chr1	3759225	rs6668306	G	C	258.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.53;MQ0=0;OQ=1917.17;QD=39.13;SB=-849.44	GT:AD:DP:GL:GQ	1/1:0,49:46:-195.32,-13.87,-0.02:99
+chr1	3759237	rs6693259	C	T	255.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1813.57;QD=38.59;SB=-875.61	GT:AD:DP:GL:GQ	1/1:0,47:47:-184.96,-14.17,-0.02:99
+chr1	3759339	.	T	C	4.24	PASS	AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=37.66;MQ0=0;OQ=1291.89;QD=29.36;SB=-665.80	GT:AD:DP:GL:GQ	1/1:0,44:41:-132.82,-12.37,-0.04:99
+chr1	3759424	rs11576718	T	C	18.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.78;MQ0=0;OQ=1915.98;QD=34.84;SB=-646.27	GT:AD:DP:GL:GQ	1/1:0,55:53:-195.20,-15.96,-0.02:99
+chr1	3759450	rs11578021	G	C	393.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=2482.73;QD=42.08;SB=-1009.18	GT:AD:DP:GL:GQ	1/1:0,59:57:-251.88,-17.18,-0.02:99
+chr1	3760255	rs4130539	C	A	200.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.57;MQ=59.43;MQ0=0;OQ=2921.40;QD=36.07;SB=-1317.55	GT:AD:DP:GL:GQ	1/1:0,81:81:-295.75,-24.40,-0.03:99
+chr1	3760285	rs4233023	G	A	128.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.42;MQ0=0;OQ=2979.99;QD=37.25;SB=-1007.64	GT:AD:DP:GL:GQ	1/1:0,80:76:-301.61,-22.90,-0.03:99
+chr1	3760596	rs4582731	T	C	194.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1740.97;QD=31.65;SB=-868.36	GT:AD:DP:GL:GQ	1/1:0,55:54:-177.73,-16.29,-0.05:99
+chr1	3760968	rs12023761	T	C	207.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=57.12;MQ0=0;OQ=2651.31;QD=33.99;SB=-1110.83	GT:AD:DP:GL:GQ	1/1:0,78:75:-268.74,-22.59,-0.02:99
+chr1	3760980	rs12023762	T	C	71.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=2.08;MQ=56.93;MQ0=0;OQ=2310.56;QD=34.49;SB=-1074.87	GT:AD:DP:GL:GQ	1/1:0,66:64:-234.66,-19.27,-0.02:99
+chr1	3761023	rs12026284	G	A	45.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=57.92;MQ0=0;OQ=1613.24;QD=38.41;SB=-773.05	GT:AD:DP:GL:GQ	1/1:0,42:41:-164.92,-12.35,-0.01:99
+chr1	3761229	rs12024538	T	C	108.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=57.43;MQ0=0;OQ=2622.46;QD=34.06;SB=-1093.09	GT:AD:DP:GL:GQ	1/1:0,77:74:-265.86,-22.29,-0.03:99
+chr1	3761407	rs7552678	C	T	182.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=55.63;MQ0=0;OQ=2322.80;QD=37.46;SB=-1101.95	GT:AD:DP:GL:GQ	1/1:0,61:58:-235.88,-17.47,-0.01:99
+chr1	3761583	rs10909805	A	T	36.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=57.39;MQ0=0;OQ=1183.25;QD=32.87;SB=-378.79	GT:AD:DP:GL:GQ	1/1:0,36:34:-121.93,-10.24,-0.02:99
+chr1	3762135	rs4648348	G	T	313.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.61;MQ0=0;OQ=2805.56;QD=36.44;SB=-1091.90	GT:AD:DP:GL:GQ	1/1:0,77:77:-284.17,-23.19,-0.03:99
+chr1	3762966	rs6424059	C	T	50.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1794.59;QD=39.88;SB=-207.77	GT:AD:DP:GL:GQ	1/1:0,45:45:-183.06,-13.56,-0.01:99
+chr1	3763112	rs6424060	C	A	1.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=57.94;MQ0=0;OQ=1225.37;QD=36.04;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,34:33:-126.13,-9.94,-0.01:99
+chr1	3763448	rs7542369	C	G	0.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=407.00;QD=27.13;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,15:12:-44.31,-3.64,-0.03:36.11
+chr1	3763578	rs4648428	A	G	5.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=286.53;QD=20.47;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,13:11:-32.26,-3.33,-0.02:33.05
+chr1	3764486	rs10909806	C	A	23.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=2.13;MQ=58.37;MQ0=0;OQ=1559.40;QD=35.44;SB=-546.78	GT:AD:DP:GL:GQ	1/1:0,44:43:-159.54,-12.95,-0.01:99
+chr1	3765314	rs4376673	C	G	417.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1404.99;QD=36.03;SB=-615.54	GT:AD:DP:GL:GQ	1/1:0,39:36:-144.12,-10.87,-0.03:99
+chr1	3765882	rs9786959	A	G	29.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=1920.48;QD=30.48;SB=-862.57	GT:AD:DP:GL:GQ	1/1:0,63:60:-195.68,-18.09,-0.05:99
+chr1	3767471	rs11800725	A	G	13.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=58.98;MQ0=0;OQ=1927.36;QD=30.11;SB=-765.33	GT:AD:DP:GL:GQ	1/1:0,64:61:-196.39,-18.41,-0.06:99
+chr1	3767577	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=17;HaplotypeScore=9.33;MQ=55.19;MQ0=0;OQ=73.00;QD=1.66;SB=10.79	GT:AD:DP:GL:GQ	0/1:33,10:33:-20.53,-9.94,-95.54:99
+chr1	3767595	.	G	A	13.29	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=17;HaplotypeScore=14.08;MQ=55.46;MQ0=0;QD=0.23;SB=74.24	GT:AD:DP:GL:GQ	0/1:47,10:46:-18.45,-13.86,-142.27:45.92
+chr1	3769011	rs4400555	C	T	258.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.08;MQ0=0;OQ=2381.95;QD=39.05;SB=-1005.83	GT:AD:DP:GL:GQ	1/1:0,61:61:-241.80,-18.38,-0.02:99
+chr1	3769497	rs4573474	G	C	208.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.06;MQ0=0;OQ=1909.70;QD=37.45;SB=-679.47	GT:AD:DP:GL:GQ	1/1:0,51:49:-194.60,-14.79,-0.05:99
+chr1	3769504	rs4475689	T	C	437.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.81;MQ0=0;OQ=1544.26;QD=28.60;SB=-549.88	GT:AD:DP:GL:GQ	1/1:0,54:50:-158.07,-15.09,-0.05:99
+chr1	3769540	rs4393098	C	T	134.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.73;MQ0=0;OQ=2714.04;QD=39.33;SB=-879.18	GT:AD:DP:GL:GQ	1/1:0,69:68:-275.01,-20.48,-0.02:99
+chr1	3770416	rs10909807	A	G	70.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=59.66;MQ0=0;OQ=2327.40;QD=34.23;SB=-632.25	GT:AD:DP:GL:GQ	1/1:0,68:65:-236.35,-19.58,-0.03:99
+chr1	3770956	rs10797348	C	A	725.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2194.69;QD=35.40;SB=-970.66	GT:AD:DP:GL:GQ	1/1:0,62:61:-223.07,-18.37,-0.02:99
+chr1	3770996	rs10752724	C	G	36.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.68;MQ0=0;OQ=3059.04;QD=41.90;SB=-884.77	GT:AD:DP:GL:GQ	1/1:0,73:70:-309.51,-21.10,-0.03:99
+chr1	3772468	rs10909809	C	T	66.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.41;MQ=58.92;MQ0=0;OQ=1387.22;QD=35.57;SB=-471.11	GT:AD:DP:GL:GQ	1/1:0,38:37:-142.33,-11.16,-0.02:99
+chr1	3773138	rs10909810	A	C	280.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.04;MQ0=0;OQ=955.91;QD=32.96;SB=-323.98	GT:AD:DP:GL:GQ	1/1:0,29:29:-99.19,-8.74,-0.02:87.21
+chr1	3773433	rs10797349	C	T	164.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=58.68;MQ0=0;OQ=1490.84;QD=33.88;SB=-752.63	GT:AD:DP:GL:GQ	1/1:0,44:39:-152.69,-11.75,-0.02:99
+chr1	3773480	rs10797350	T	C	13.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.15;MQ=58.30;MQ0=0;OQ=1471.72;QD=30.66;SB=-684.88	GT:AD:DP:GL:GQ	1/1:0,48:45:-150.79,-13.57,-0.03:99
+chr1	3773523	rs10752726	T	G	347.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=1497.10;QD=33.27;SB=-446.81	GT:AD:DP:GL:GQ	1/1:0,45:43:-153.31,-12.95,-0.01:99
+chr1	3773611	rs12035912	C	T	197.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=58.30;MQ0=0;OQ=2493.51;QD=37.78;SB=-1130.03	GT:AD:DP:GL:GQ	1/1:0,66:64:-252.96,-19.28,-0.02:99
+chr1	3775032	.	T	C	552.80	SnpCluster	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=33.42;MQ=46.78;MQ0=0;QD=6.28;SB=-111.60	GT:AD:DP:GL:GQ	0/1:60,28:83:-83.58,-25.02,-222.80:99
+chr1	3775037	.	G	T	197.57	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=30.55;MQ=47.65;MQ0=0;QD=2.00;SB=65.19	GT:AD:DP:GL:GQ	0/1:82,15:90:-57.60,-34.56,-265.76:99
+chr1	3775038	rs11801559	A	G	304.07	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=1;HaplotypeScore=31.22;MQ=47.58;MQ0=0;QD=3.07;SB=-149.93	GT:AD:DP:GL:GQ	0/1:75,24:82:-58.40,-24.71,-264.98:99
+chr1	3775067	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=55.99;MQ=43.63;MQ0=2;OQ=741.54;QD=4.41;SB=-115.85	GT:AD:DP:GL:GQ	0/1:87,38:131:-206.86,-129.42,-352.70:99
+chr1	3775068	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=171;Dels=0.00;HRun=2;HaplotypeScore=57.14;MQ=43.69;MQ0=2;OQ=621.12;QD=3.63;SB=-22.34	GT:AD:DP:GL:GQ	0/1:130,41:133:-105.49,-40.09,-359.21:99
+chr1	3775097	.	C	T	202.73	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=156;Dels=0.02;HRun=0;HaplotypeScore=180.15;MQ=42.01;MQ0=2;QD=1.30;SB=-48.46	GT:AD:DP:GL:GQ	0/1:127,21:125:-62.81,-39.25,-356.59:99
+chr1	3775132	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=0;HaplotypeScore=17.94;MQ=41.24;MQ0=3;OQ=65.49;QD=0.68;SB=-47.12	GT:AD:DP:GL:GQ	0/1:77,9:78:-49.90,-40.06,-295.84:98.32
+chr1	3779522	rs11581471	A	G	100.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.41;MQ0=0;OQ=1287.54;QD=29.26;SB=-667.82	GT:AD:DP:GL:GQ	1/1:0,44:42:-132.38,-12.67,-0.05:99
+chr1	3779990	rs12130391	G	A	164	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.47;MQ0=0;OQ=2160.23;QD=35.41;SB=-916.74	GT:AD:DP:GL:GQ	1/1:0,60:57:-219.63,-17.18,-0.03:99
+chr1	3780767	.	T	C	4.63	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=30.96;MQ0=11;OQ=368.82;QD=6.36;SB=-104.61	GT:AD:DP:GL:GQ	0/1:34,24:38:-51.63,-11.46,-83.55:99
+chr1	3781074	rs10752727	C	T	2.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=7.70;MQ=37.12;MQ0=12;OQ=1286.15;QD=21.08;SB=-457.95	GT:AD:DP:GL:GQ	1/1:3,58:36:-135.18,-10.85,-2.98:78.66
+chr1	3783772	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=19;HaplotypeScore=32.14;MQ=55.75;MQ0=0;OQ=200.26;QD=4.01;SB=53.19	GT:AD:DP:GL:GQ	0/1:32,18:38:-34.76,-11.45,-99.41:99
+chr1	3784133	rs12132240	C	T	668.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.52;MQ0=0;OQ=2396.10;QD=39.93;SB=-998.03	GT:AD:DP:GL:GQ	1/1:0,60:60:-243.21,-18.07,-0.02:99
+chr1	3785251	rs10737189	T	C	42.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=4.18;MQ=59.45;MQ0=0;OQ=2617.88;QD=31.17;SB=-945.37	GT:AD:DP:GL:GQ	1/1:0,84:80:-265.43,-24.12,-0.06:99
+chr1	3786402	rs12071660	G	A	151.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2743.00;QD=38.63;SB=-1108.49	GT:AD:DP:GL:GQ	1/1:0,71:69:-277.90,-20.79,-0.02:99
+chr1	3787079	rs4074710	T	C	1.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=9.84;MQ=58.78;MQ0=0;OQ=1684.95;QD=27.18;SB=-797.66	GT:AD:DP:GL:GQ	1/1:2,60:56:-176.09,-16.89,-4.01:99
+chr1	3787169	rs61768959	C	T	435.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1824.58;QD=38.82;SB=-789.07	GT:AD:DP:GL:GQ	1/1:0,47:46:-186.05,-13.86,-0.01:99
+chr1	3787855	rs4073324	C	T	458.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1383.49;QD=37.39;SB=-414.06	GT:AD:DP:GL:GQ	1/1:0,37:37:-141.95,-11.15,-0.02:99
+chr1	3787909	rs4073323	A	G	2.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=3.99;MQ=59.35;MQ0=0;OQ=1345.64;QD=32.04;SB=-424.45	GT:AD:DP:GL:GQ	1/1:0,42:40:-138.17,-12.05,-0.02:99
+chr1	3788260	rs12084944	C	T	298.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=888.25;QD=37.01;SB=-436.08	GT:AD:DP:GL:GQ	1/1:0,24:23:-92.42,-6.93,-0.01:69.22
+chr1	3788534	rs12030906	T	C	0.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.02;HRun=0;HaplotypeScore=9.00;MQ=56.58;MQ0=0;OQ=1607.45;QD=29.23;SB=-436.47	GT:AD:DP:GL:GQ	1/1:0,54:48:-164.35,-14.16,-0.02:99
+chr1	3789424	rs4382652	G	A	2153.41	Indel	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=4.66;MQ=56.10;MQ0=0;QD=35.30;SB=-1010.66	GT:AD:DP:GL:GQ	1/1:0,61:57:-218.95,-17.18,-0.03:99
+chr1	3790102	rs3205087	A	G	382.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.28;MQ0=0;OQ=1027.83;QD=26.35;SB=-300.09	GT:AD:DP:GL:GQ	1/1:0,39:35:-106.42,-10.57,-0.05:99
+chr1	3790340	rs7555538	G	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=8;HaplotypeScore=0.92;MQ=59.43;MQ0=0;OQ=2444.86;QD=33.49;SB=-1058.90	GT:AD:DP:GL:GQ	1/1:0,73:70:-248.10,-21.09,-0.03:99
+chr1	3791107	rs10909817	T	G	151.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=57.75;MQ0=0;OQ=1681.31;QD=32.33;SB=-830.07	GT:AD:DP:GL:GQ	1/1:0,51:49:-171.73,-14.76,-0.02:99
+chr1	3792631	rs11584721	G	C	5.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=5.57;MQ=57.48;MQ0=0;OQ=2243.27;QD=40.06;SB=-1057.19	GT:AD:DP:GL:GQ	1/1:1,55:53:-227.93,-15.97,-0.02:99
+chr1	3793561	rs12136187	C	A	227.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.95;MQ0=0;OQ=1328.46;QD=34.06;SB=-683.01	GT:AD:DP:GL:GQ	1/1:0,39:37:-136.44,-11.15,-0.01:99
+chr1	3793615	rs7367066	T	C	611.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.19;MQ0=0;OQ=1618.23;QD=29.97;SB=-707.63	GT:AD:DP:GL:GQ	1/1:0,53:51:-165.45,-15.38,-0.04:99
+chr1	3795300	rs6678851	C	T	1.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=5.47;MQ=59.65;MQ0=0;OQ=2468.27;QD=37.97;SB=-809.33	GT:AD:DP:GL:GQ	1/1:0,65:63:-250.43,-18.98,-0.02:99
+chr1	3795934	rs4075974	G	A	558.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.49;MQ0=0;OQ=2140.67;QD=39.64;SB=-940.34	GT:AD:DP:GL:GQ	1/1:0,54:54:-217.66,-16.27,-0.01:99
+chr1	3796218	rs10909819	T	C	98.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=58.14;MQ0=0;OQ=2198.60;QD=32.33;SB=-948.97	GT:AD:DP:GL:GQ	1/1:0,68:64:-223.47,-19.28,-0.03:99
+chr1	3796503	rs4520357	T	A	245.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.09;MQ0=0;OQ=3186.37;QD=35.40;SB=-1505.31	GT:AD:DP:GL:GQ	1/1:0,90:85:-322.25,-25.60,-0.02:99
+chr1	3797453	rs4274008	G	C	114.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=59.65;MQ0=0;OQ=2739.80;QD=42.15;SB=-1186.93	GT:AD:DP:GL:GQ	1/1:0,65:64:-277.59,-19.29,-0.02:99
+chr1	3798031	rs6701422	T	C	38.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=51.74;MQ0=0;OQ=1832.37;QD=30.04;SB=-733.76	GT:AD:DP:GL:GQ	1/1:0,60:57:-186.87,-17.19,-0.05:99
+chr1	3798222	rs4446914	G	A	207.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.90;MQ=50.14;MQ0=0;OQ=2015.61;QD=38.03;SB=-988.99	GT:AD:DP:GL:GQ	1/1:0,53:52:-205.17,-15.67,-0.02:99
+chr1	3798375	.	A	G	51.46	PASS	AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=16.12;MQ0=4;OQ=176.38;QD=13.57;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,13:6:-21.21,-1.81,-0.00:18.05
+chr1	3798911	rs12757258	A	C	37.05	LowQual	AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.57;MQ0=1;QD=7.41;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,3:2:-7.11,-0.60,-0.00:6.02
+chr1	3798957	rs12757292	A	C	18.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.60;MQ0=1;OQ=75.37;QD=3.14;SB=-10.00	GT:AD:DP:GL:GQ	0/1:11,13:13:-14.74,-3.92,-26.95:99
+chr1	3799283	rs11807227	G	A	605.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.57;MQ0=0;OQ=2371.97;QD=38.88;SB=-744.48	GT:AD:DP:GL:GQ	1/1:0,61:60:-240.80,-18.08,-0.02:99
+chr1	3800246	rs4568776	A	G	199.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=2257.59;QD=31.80;SB=-934.52	GT:AD:DP:GL:GQ	1/1:0,71:68:-229.39,-20.50,-0.04:99
+chr1	3801063	rs7515869	A	T	278.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=61.08;MQ0=0;OQ=1948.49;QD=33.03;SB=-981.77	GT:AD:DP:GL:GQ	1/1:0,57:54:-198.46,-16.27,-0.03:99
+chr1	3801228	rs6674160	G	A	506.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.72;MQ0=0;OQ=1203.93;QD=37.62;SB=-496.15	GT:AD:DP:GL:GQ	1/1:0,32:32:-124.00,-9.65,-0.02:96.29
+chr1	3801965	rs10909822	A	C	705.90	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=42.43;MQ0=0;QD=30.69;SB=-332.99	GT:AD:DP:GL:GQ	1/1:1,22:22:-74.19,-6.63,-0.02:66.14
+chr1	3801968	.	T	A	440.70	SnpCluster	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=38.89;MQ0=0;QD=11.60;SB=-170.81	GT:AD:DP:GL:GQ	0/1:21,17:32:-56.99,-9.64,-61.90:99
+chr1	3801971	.	G	T	508.15	SnpCluster	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=35.42;MQ0=0;QD=14.52;SB=-198.56	GT:AD:DP:GL:GQ	0/1:17,18:35:-64.64,-10.54,-61.42:99
+chr1	3801978	.	G	C	1059.09	Indel;SnpCluster	AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=45.04;MQ0=0;QD=40.73;SB=-392.21	GT:AD:DP:GL:GQ	1/1:0,26:25:-109.50,-7.53,-0.01:75.25
+chr1	3802009	rs12133786	A	C	321.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=52.45;MQ0=0;OQ=1401.55;QD=33.37;SB=-709.03	GT:AD:DP:GL:GQ	1/1:0,42:41:-143.76,-12.35,-0.02:99
+chr1	3802570	rs10797352	T	C	148.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.68;MQ0=0;OQ=1740.38;QD=32.84;SB=-623.49	GT:AD:DP:GL:GQ	1/1:0,53:51:-177.65,-15.37,-0.03:99
+chr1	3802708	rs10797353	C	G	720.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2712.05;QD=38.74;SB=-1379.38	GT:AD:DP:GL:GQ	1/1:0,69:70:-279.01,-24.65,-4.23:99
+chr1	3804150	rs10797354	T	C	170.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=59.56;MQ0=0;OQ=1825.12;QD=32.59;SB=-712.23	GT:AD:DP:GL:GQ	1/1:0,56:54:-186.12,-16.27,-0.03:99
+chr1	3804602	rs6658198	T	C	302.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.62;MQ0=0;OQ=2079.20;QD=34.65;SB=-977.94	GT:AD:DP:GL:GQ	1/1:0,60:60:-211.53,-18.07,-0.02:99
+chr1	3806368	rs35131135	T	C	13.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=58.87;MQ0=0;OQ=1257.30;QD=30.67;SB=-415.16	GT:AD:DP:GL:GQ	1/1:0,40:36:-129.33,-10.85,-0.01:99
+chr1	3806714	rs61770363	G	A	10.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.71;MQ0=0;OQ=641.87;QD=35.66;SB=-278.65	GT:AD:DP:GL:GQ	1/1:0,18:18:-67.78,-5.43,-0.01:54.17
+chr1	3806753	rs4072725	C	T	77.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.52;MQ0=0;OQ=544.23;QD=34.01;SB=-280.66	GT:AD:DP:GL:GQ	1/1:0,16:15:-58.01,-4.52,-0.01:45.14
+chr1	3808604	rs10797355	T	C	125.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=53.60;MQ0=1;OQ=2350.13;QD=34.56;SB=-914.68	GT:AD:DP:GL:GQ	1/1:0,68:66:-238.63,-19.89,-0.03:99
+chr1	3808731	rs10797356	G	A	43.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=2.07;MQ=58.71;MQ0=0;OQ=2012.52;QD=37.27;SB=-776.06	GT:AD:DP:GL:GQ	1/1:0,54:52:-204.86,-15.67,-0.02:99
+chr1	3809184	rs6672335	A	G	119.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.56;MQ0=0;OQ=1683.69;QD=31.77;SB=-530.84	GT:AD:DP:GL:GQ	1/1:0,53:48:-171.97,-14.46,-0.02:99
+chr1	3809865	rs10909828	G	A	654.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=2184.41;QD=38.32;SB=-826.35	GT:AD:DP:GL:GQ	1/1:0,57:56:-222.04,-16.87,-0.02:99
+chr1	3809876	rs12139857	G	C	137.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.22;MQ0=0;OQ=2518.12;QD=42.68;SB=-984.74	GT:AD:DP:GL:GQ	1/1:0,59:58:-255.41,-17.48,-0.02:99
+chr1	3811076	rs6687869	G	A	107.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.45;MQ0=0;OQ=1628.97;QD=38.79;SB=-568.34	GT:AD:DP:GL:GQ	1/1:0,42:42:-166.50,-12.65,-0.01:99
+chr1	3811194	rs10797357	G	A	521.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.15;MQ0=0;OQ=1858.19;QD=37.92;SB=-535.68	GT:AD:DP:GL:GQ	1/1:0,49:48:-189.42,-14.46,-0.01:99
+chr1	3812563	rs10909830	C	T	206.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=58.81;MQ0=0;OQ=2305.91;QD=36.60;SB=-919.31	GT:AD:DP:GL:GQ	1/1:0,63:60:-234.20,-18.08,-0.02:99
+chr1	3812792	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=14.74;MQ=58.39;MQ0=0;OQ=154.04;QD=2.80;SB=80.30	GT:AD:DP:GL:GQ	0/1:43,12:42:-31.36,-12.67,-148.77:99
+chr1	3816486	rs35332894	A	G	12.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.52;MQ=58.25;MQ0=1;OQ=1726.98;QD=27.41;SB=-682.71	GT:AD:DP:GL:GQ	1/1:0,63:54:-176.33,-16.29,-0.05:99
+chr1	3817341	rs61770379	C	T	109.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.38;MQ0=0;OQ=1418.14;QD=38.33;SB=-728.97	GT:AD:DP:GL:GQ	1/1:0,37:36:-145.41,-10.84,-0.01:99
+chr1	3819020	rs34825671	C	T	409.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1564.33;QD=39.11;SB=-750.02	GT:AD:DP:GL:GQ	1/1:0,40:40:-160.03,-12.05,-0.01:99
+chr1	3819278	rs35368826	T	C	12.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.26;MQ=60.00;MQ0=0;OQ=1199.67;QD=27.90;SB=-424.22	GT:AD:DP:GL:GQ	1/1:0,43:38:-123.59,-11.46,-0.04:99
+chr1	3819474	rs35583447	A	G	89.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.69;MQ0=0;OQ=1939.06;QD=31.79;SB=-974.91	GT:AD:DP:GL:GQ	1/1:0,61:57:-197.52,-17.18,-0.03:99
+chr1	3819901	rs34284135	A	G	55.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.81;MQ0=0;OQ=1296.25;QD=30.15;SB=-641.91	GT:AD:DP:GL:GQ	1/1:0,43:38:-133.23,-11.45,-0.02:99
+chr1	3820479	rs4073647	C	A	185.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=59.55;MQ0=0;OQ=1638.97;QD=32.14;SB=-804.86	GT:AD:DP:GL:GQ	1/1:0,51:47:-167.50,-14.16,-0.02:99
+chr1	3820963	rs35355307	G	A	127.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.69;MQ0=0;OQ=2262.75;QD=37.09;SB=-711.99	GT:AD:DP:GL:GQ	1/1:0,61:59:-229.89,-17.78,-0.03:99
+chr1	3821092	rs35241263	A	G	89.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=58.63;MQ0=0;OQ=1378.97;QD=27.04;SB=-599.21	GT:AD:DP:GL:GQ	1/1:0,51:45:-141.53,-13.58,-0.05:99
+chr1	3821416	rs34803434	G	A	80.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=58.07;MQ0=0;OQ=1633.32;QD=35.51;SB=-688.34	GT:AD:DP:GL:GQ	1/1:1,45:44:-166.94,-13.26,-0.02:99
+chr1	3823053	rs61770387	C	T	609.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2714.99;QD=39.35;SB=-1139.68	GT:AD:DP:GL:GQ	1/1:0,69:68:-275.10,-20.48,-0.02:99
+chr1	3823181	rs61770388	T	C	199.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.19;MQ0=0;OQ=1728.56;QD=33.24;SB=-864.04	GT:AD:DP:GL:GQ	1/1:0,52:50:-176.46,-15.06,-0.02:99
+chr1	3824979	rs61770390	T	C	82.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=55.31;MQ0=0;OQ=486.55;QD=7.85;SB=-261.22	GT:AD:DP:GL:GQ	0/1:37,25:59:-69.72,-17.78,-147.85:99
+chr1	3824990	.	C	T	3.46	PASS	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.66;MQ=55.46;MQ0=0;OQ=1251.91;QD=19.56;SB=-545.38	GT:AD:DP:GL:GQ	0/1:27,37:61:-146.86,-18.39,-82.02:99
+chr1	3825051	.	C	A	3.22	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=2;HaplotypeScore=3.18;MQ=58.29;MQ0=0;OQ=820.60;QD=11.56;SB=-414.89	GT:AD:DP:GL:GQ	0/1:42,29:71:-106.73,-21.38,-145.16:99
+chr1	3825054	.	T	C	10.09	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=3.18;MQ=58.08;MQ0=0;OQ=722.16;QD=10.47;SB=-351.97	GT:AD:DP:GL:GQ	0/1:40,28:65:-95.08,-19.58,-155.89:99
+chr1	3825324	rs61770392	A	T	88.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=57.20;MQ0=0;OQ=1894.97;QD=35.09;SB=-920.36	GT:AD:DP:GL:GQ	1/1:0,54:51:-193.10,-15.37,-0.02:99
+chr1	3827005	.	C	T	22.22	LowQual	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=43.17;MQ0=3;QD=1.48;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,3:9:-8.21,-2.71,-24.78:55.03
+chr1	3827011	.	C	T	25.21	LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=2.11;MQ=38.99;MQ0=3;QD=1.80;SB=-10.00	GT:AD:DP:GL:GQ	0/1:12,2:8:-8.21,-2.41,-21.31:58.03
+chr1	3830505	rs35265992	A	G	0.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=4;HaplotypeScore=5.22;MQ=58.50;MQ0=0;OQ=970.90;QD=17.34;SB=-315.39	GT:AD:DP:GL:GQ	0/1:20,36:52:-116.04,-15.67,-75.68:99
+chr1	3830738	rs35974482	G	A	171.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.40;MQ=57.87;MQ0=0;OQ=551.40;QD=12.53;SB=-198.84	GT:AD:DP:GL:GQ	0/1:25,19:40:-70.48,-12.05,-78.52:99
+chr1	3830888	rs35314156	G	C	209.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.07;MQ0=0;OQ=668.40;QD=13.37;SB=-257.46	GT:AD:DP:GL:GQ	0/1:30,20:50:-85.20,-15.08,-125.99:99
+chr1	3831972	rs34835780	T	C	632.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.64;MQ0=0;OQ=2285.64;QD=35.16;SB=-1132.81	GT:AD:DP:GL:GQ	1/1:0,65:64:-232.17,-19.28,-0.02:99
+chr1	3833915	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=17.15;MQ=47.19;MQ0=1;OQ=288.77;QD=3.66;SB=-113.05	GT:AD:DP:GL:GQ	0/1:64,15:78:-55.66,-23.49,-226.25:99
+chr1	3895148	.	C	A	18	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=35.10;MQ0=1;OQ=333.31;QD=9.80;SB=-100.81	GT:AD:DP:GL:GQ	0/1:15,18:23:-43.54,-6.93,-34.49:99
+chr1	3895632	.	G	A	3.06	PASS	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=4;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=959.16;QD=14.11;SB=-372.32	GT:AD:DP:GL:GQ	0/1:38,30:68:-119.69,-20.49,-137.83:99
+chr1	3895766	rs61770398	T	C	202.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=59.18;MQ0=0;OQ=960.24;QD=12.98;SB=-389.21	GT:AD:DP:GL:GQ	0/1:40,34:73:-121.30,-21.99,-162.55:99
+chr1	3899769	.	C	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=8.09;MQ=59.49;MQ0=0;OQ=340.78;QD=7.57;SB=47.18	GT:AD:DP:GL:GQ	0/1:26,19:34:-47.63,-10.27,-85.91:99
+chr1	3902626	rs12073174	A	G	196.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.14;MQ0=0;OQ=542.74;QD=11.31;SB=-148.64	GT:AD:DP:GL:GQ	0/1:27,21:46:-71.41,-13.85,-105.98:99
+chr1	3902680	rs61770400	C	T	70.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.09;MQ=59.24;MQ0=0;OQ=954.92;QD=15.65;SB=-346.04	GT:AD:DP:GL:GQ	0/1:29,32:59:-116.56,-17.78,-99.06:99
+chr1	3903888	.	C	T	983.33	SnpCluster	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.15;MQ0=0;QD=17.88;SB=-501.10	GT:AD:DP:GL:GQ	0/1:24,31:52:-117.28,-15.67,-81.69:99
+chr1	3903897	rs12076404	C	T	1044.63	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.20;MQ0=0;QD=18.01;SB=-538.06	GT:AD:DP:GL:GQ	0/1:25,33:54:-124.01,-16.27,-82.66:99
+chr1	3903898	.	G	A	621.65	SnpCluster	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.17;MQ0=0;QD=11.10;SB=-272.76	GT:AD:DP:GL:GQ	0/1:33,23:52:-81.12,-15.67,-110.15:99
+chr1	3904122	.	C	T	64.01	PASS	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=58.92;MQ0=0;OQ=1312.00;QD=16.00;SB=-449.98	GT:AD:DP:GL:GQ	0/1:43,39:81:-158.89,-24.40,-148.69:99
+chr1	3904123	rs7518198	G	A	275.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=58.92;MQ0=0;OQ=1318.95;QD=16.08;SB=-404.76	GT:AD:DP:GL:GQ	0/1:38,44:78:-158.67,-23.50,-132.87:99
+chr1	3904259	rs55651676	C	G	11.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=0.67;MQ=58.80;MQ0=0;OQ=719.49;QD=18.45;SB=-354.47	GT:AD:DP:GL:GQ	0/1:17,22:35:-85.79,-10.56,-59.36:99
+chr1	3904673	rs56300127	T	C	189.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.07;MQ0=0;OQ=384.21;QD=11.30;SB=-194.60	GT:AD:DP:GL:GQ	0/1:17,17:31:-51.05,-9.34,-58.99:99
+chr1	3905021	rs10915614	A	G	3.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=4;HaplotypeScore=1.21;MQ=59.48;MQ0=0;OQ=428.89;QD=9.75;SB=-152.44	GT:AD:DP:GL:GQ	0/1:24,19:41:-58.53,-12.36,-93.35:99
+chr1	3905038	.	G	A	50.50	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.41;MQ0=0;OQ=477.39;QD=12.24;SB=-188.87	GT:AD:DP:GL:GQ	0/1:22,17:37:-62.18,-11.16,-67.50:99
+chr1	3905246	.	C	T	93.17	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=58.57;MQ0=0;OQ=1011.86;QD=16.32;SB=-440.98	GT:AD:DP:GL:GQ	0/1:30,32:58:-121.96,-17.49,-85.78:99
+chr1	3905920	rs7548668	T	C	26.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=6.64;MQ=59.57;MQ0=0;OQ=666.76;QD=12.35;SB=-179.62	GT:AD:DP:GL:GQ	0/1:27,27:46:-83.82,-13.86,-87.80:99
+chr1	3906227	rs9793287	T	C	337.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.61;MQ0=0;OQ=444.12;QD=9.25;SB=-215.36	GT:AD:DP:GL:GQ	0/1:27,21:46:-61.57,-13.87,-101.57:99
+chr1	3906248	rs12562706	C	A	152.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=59.59;MQ0=0;OQ=415.45;QD=9.23;SB=-231.91	GT:AD:DP:GL:GQ	0/1:25,20:41:-57.18,-12.35,-86.80:99
+chr1	3906531	rs7526903	G	A	280.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=909.30;QD=17.83;SB=-442.97	GT:AD:DP:GL:GQ	0/1:23,27:47:-108.38,-14.16,-65.40:99
+chr1	3906648	rs7551771	C	T	37.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=2.80;MQ=60.06;MQ0=0;OQ=776.93;QD=15.54;SB=-354.36	GT:AD:DP:GL:GQ	0/1:26,24:48:-95.43,-14.46,-92.96:99
+chr1	3906868	rs7519349	A	G	578.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=764.11;QD=13.64;SB=-362.95	GT:AD:DP:GL:GQ	0/1:26,30:56:-96.58,-16.88,-105.57:99
+chr1	3906970	rs7519458	A	G	232.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.80;MQ=60.00;MQ0=0;OQ=762.22;QD=13.14;SB=-199.60	GT:AD:DP:GL:GQ	0/1:26,31:57:-96.69,-17.19,-106.25:99
+chr1	3907888	rs10799162	T	C	190.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=58.79;MQ0=0;OQ=719.58;QD=13.33;SB=-230.44	GT:AD:DP:GL:GQ	0/1:27,27:53:-91.22,-15.97,-102.46:99
+chr1	3907889	rs10799163	G	T	86.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.13;MQ=58.79;MQ0=0;OQ=758.50;QD=14.05;SB=-193.54	GT:AD:DP:GL:GQ	0/1:27,26:51:-94.50,-15.37,-86.70:99
+chr1	3907912	rs10915345	G	A	203.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=59.62;MQ0=0;OQ=1037.45;QD=17.01;SB=-258.26	GT:AD:DP:GL:GQ	0/1:29,32:57:-124.21,-17.18,-83.11:99
+chr1	3909896	rs6683165	G	A	201.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=59.62;MQ0=0;OQ=837.44;QD=12.88;SB=-252.13	GT:AD:DP:GL:GQ	0/1:38,27:62:-105.71,-18.68,-120.77:99
+chr1	3910104	rs10799194	C	T	90.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=1.69;MQ=60.00;MQ0=0;OQ=794.06;QD=13.23;SB=-418.44	GT:AD:DP:GL:GQ	0/1:34,26:57:-99.88,-17.19,-98.75:99
+chr1	3919557	rs9426474	A	G	111.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=1753.83;QD=29.73;SB=-828.62	GT:AD:DP:GL:GQ	1/1:0,59:55:-179.01,-16.59,-0.05:99
+chr1	3922104	rs9426475	T	C	209.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=54.82;MQ0=0;OQ=1570.14;QD=28.55;SB=-720.64	GT:AD:DP:GL:GQ	1/1:0,55:50:-160.65,-15.09,-0.06:99
+chr1	3922325	rs10915469	T	C	562.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1863.57;QD=28.24;SB=-798.65	GT:AD:DP:GL:GQ	1/1:0,66:58:-189.99,-17.49,-0.05:99
+chr1	3922572	rs7540846	C	T	41.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=2;HaplotypeScore=0.57;MQ=53.34;MQ0=0;OQ=2905.34;QD=34.59;SB=-1359.03	GT:AD:DP:GL:GQ	1/1:0,81:75:-294.15,-22.60,-0.03:99
+chr1	3922839	rs7516192	G	C	540.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.04;MQ0=0;OQ=2588.44;QD=42.43;SB=-1244.89	GT:AD:DP:GL:GQ	1/1:0,61:60:-262.44,-18.08,-0.02:99
+chr1	3922855	rs9426476	A	G	185.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.74;MQ=58.63;MQ0=0;OQ=2064.09;QD=34.40;SB=-842.35	GT:AD:DP:GL:GQ	1/1:0,60:58:-210.01,-17.47,-0.02:99
+chr1	3922974	rs7541241	C	A	552.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.64;MQ0=0;OQ=1520.98;QD=33.80;SB=-673.30	GT:AD:DP:GL:GQ	1/1:0,45:44:-155.71,-13.26,-0.03:99
+chr1	3923246	rs9426498	T	C	9.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=52.33;MQ0=0;OQ=1450.84;QD=25.91;SB=-720.70	GT:AD:DP:GL:GQ	1/1:0,56:46:-148.71,-13.88,-0.05:99
+chr1	3923458	rs9426499	A	C	507.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1349.47;QD=30.67;SB=-364.89	GT:AD:DP:GL:GQ	1/1:0,44:42:-138.57,-12.66,-0.04:99
+chr1	3923596	rs9426477	A	G	619.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=2188.14;QD=34.73;SB=-945.36	GT:AD:DP:GL:GQ	1/1:0,63:61:-222.42,-18.37,-0.02:99
+chr1	3923941	rs6698811	T	C	664.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=2773.83;QD=33.83;SB=-1404.50	GT:AD:DP:GL:GQ	1/1:0,82:80:-281.00,-24.10,-0.03:99
+chr1	3936055	rs10753378	T	C	376.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.51;MQ0=0;OQ=543.43;QD=11.56;SB=-218.27	GT:AD:DP:GL:GQ	0/1:23,24:45:-71.19,-13.57,-90.09:99
+chr1	3938219	.	C	T	61.19	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.45;MQ=59.60;MQ0=0;OQ=740.10;QD=12.76;SB=-319.83	GT:AD:DP:GL:GQ	0/1:30,28:53:-93.28,-15.99,-88.25:99
+chr1	3940015	rs4654525	C	T	311.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.10;MQ0=0;OQ=1004.75;QD=15.00;SB=-479.00	GT:AD:DP:GL:GQ	0/1:36,31:66:-123.64,-19.88,-133.78:99
+chr1	3942839	rs60972376	A	C	11.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=4.30;MQ=58.67;MQ0=0;OQ=585.81;QD=11.96;SB=-197.90	GT:AD:DP:GL:GQ	0/1:20,28:43:-74.82,-12.96,-73.58:99
+chr1	3942909	rs55887893	C	T	197.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.21;MQ=60.00;MQ0=0;OQ=588.30;QD=11.77;SB=-314.85	GT:AD:DP:GL:GQ	0/1:29,21:47:-76.28,-14.17,-92.23:99
+chr1	3944651	rs59118111	G	C	246.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=60.00;MQ0=0;OQ=1068.67;QD=16.44;SB=-449.44	GT:AD:DP:GL:GQ	0/1:32,33:64:-129.45,-19.30,-140.55:99
+chr1	3945187	rs4654538	G	A	29.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.53;MQ=58.81;MQ0=0;OQ=1094.72;QD=19.90;SB=-430.80	GT:AD:DP:GL:GQ	0/1:23,32:55:-129.32,-16.57,-83.23:99
+chr1	3947137	rs4654543	T	C	110.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=60.00;MQ0=0;OQ=382.96;QD=9.82;SB=-135.53	GT:AD:DP:GL:GQ	0/1:21,18:38:-53.04,-11.46,-84.39:99
+chr1	3947479	rs10449244	C	A	197.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=60.00;MQ0=0;OQ=744.81;QD=13.07;SB=-230.89	GT:AD:DP:GL:GQ	0/1:29,28:53:-93.73,-15.97,-94.52:99
+chr1	3948534	rs4654544	A	G	534.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=551.19;QD=12.53;SB=-251.96	GT:AD:DP:GL:GQ	0/1:21,23:44:-71.67,-13.27,-84.12:99
+chr1	3949636	rs4654436	T	C	195.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=3.10;MQ=59.16;MQ0=0;OQ=834.97;QD=11.60;SB=-298.88	GT:AD:DP:GL:GQ	0/1:38,34:66:-106.67,-19.89,-140.32:99
+chr1	3949646	rs6426416	A	T	32.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=3;HaplotypeScore=2.47;MQ=59.20;MQ0=0;OQ=1168.58;QD=15.38;SB=-401.17	GT:AD:DP:GL:GQ	0/1:38,38:72:-141.84,-21.70,-126.75:99
+chr1	3950380	.	A	G	266.35	PASS	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=1356.42;QD=15.96;SB=-652.62	GT:AD:DP:GL:GQ	0/1:40,45:85:-164.53,-25.60,-164.89:99
+chr1	3950813	rs10737411	A	G	175.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=1;HaplotypeScore=2.09;MQ=59.83;MQ0=0;OQ=1386.28;QD=12.84;SB=-502.53	GT:AD:DP:GL:GQ	0/1:55,53:107:-174.15,-32.24,-226.13:99
+chr1	3951883	rs6657331	G	C	1.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.77;MQ=59.14;MQ0=0;OQ=976.24;QD=22.70;SB=-437.36	GT:AD:DP:GL:GQ	0/1:16,27:40:-112.97,-12.06,-59.28:99
+chr1	3951915	rs12145443	C	T	0.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=14.98;MQ=58.72;MQ0=0;OQ=829.82;QD=21.84;SB=-313.85	GT:AD:DP:GL:GQ	0/1:13,25:37:-97.41,-11.15,-45.43:99
+chr1	3952816	rs10799236	A	G	574.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=747.27;QD=14.10;SB=-330.89	GT:AD:DP:GL:GQ	0/1:27,26:52:-93.67,-15.66,-106.05:99
+chr1	3953295	rs12038964	T	C	361.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.86;MQ0=0;OQ=750.82;QD=12.31;SB=-348.04	GT:AD:DP:GL:GQ	0/1:30,31:60:-96.45,-18.08,-120.40:99
+chr1	3953370	rs12040628	A	G	147.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.81;MQ=59.55;MQ0=0;OQ=749.75;QD=14.70;SB=-277.27	GT:AD:DP:GL:GQ	0/1:21,30:49:-93.03,-14.77,-83.59:99
+chr1	3954832	rs9426500	A	C	437.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=970.97;QD=16.46;SB=-363.09	GT:AD:DP:GL:GQ	0/1:25,34:59:-118.15,-17.77,-92.14:99
+chr1	3955140	rs7413013	G	C	5.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.97;MQ=59.17;MQ0=0;OQ=1282.99;QD=22.91;SB=-362.10	GT:AD:DP:GL:GQ	0/1:21,35:56:-148.46,-16.87,-92.34:99
+chr1	3955487	rs9426501	T	C	61.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=4.29;MQ=58.95;MQ0=0;OQ=1025.38;QD=16.54;SB=-268.62	GT:AD:DP:GL:GQ	0/1:26,36:60:-123.90,-18.08,-97.56:99
+chr1	3956324	rs28609919	G	C	274.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=59.69;MQ0=0;OQ=890.13;QD=14.84;SB=-464.74	GT:AD:DP:GL:GQ	0/1:33,27:59:-110.08,-17.78,-139.21:99
+chr1	3957249	rs12756251	G	A	25.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=3.32;MQ=59.14;MQ0=0;OQ=1510.62;QD=18.65;SB=-581.41	GT:AD:DP:GL:GQ	0/1:36,45:78:-177.84,-23.50,-121.43:99
+chr1	3957262	rs12733769	T	A	184.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=3.12;MQ=59.13;MQ0=0;OQ=1410.63;QD=17.63;SB=-590.40	GT:AD:DP:GL:GQ	0/1:34,46:77:-167.55,-23.20,-118.80:99
+chr1	3957348	rs12135298	A	G	336.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=58.25;MQ0=0;OQ=781.36;QD=12.21;SB=-403.89	GT:AD:DP:GL:GQ	0/1:34,30:63:-100.41,-18.99,-132.61:99
+chr1	3959579	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=7.87;MQ=33.13;MQ0=5;OQ=83.58;QD=1.58;SB=-67.89	GT:AD:DP:GL:GQ	0/1:44,9:38:-23.11,-11.47,-97.21:99
+chr1	3959589	.	G	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=1;HaplotypeScore=8.30;MQ=33.13;MQ0=5;OQ=210.60;QD=3.76;SB=-42.01	GT:AD:DP:GL:GQ	0/1:42,14:42:-37.00,-12.66,-114.99:99
+chr1	3959610	rs4654559	T	C	0.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=19.50;MQ=38.33;MQ0=4;OQ=745.10;QD=13.55;SB=-325.28	GT:AD:DP:GL:GQ	0/1:20,35:43:-90.76,-12.97,-56.11:99
+chr1	3959618	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=35.45;MQ=40.78;MQ0=4;OQ=377.28;QD=6.50;SB=-163.72	GT:AD:DP:GL:GQ	0/1:35,17:42:-66.15,-25.14,-90.45:99
+chr1	3959638	rs12137425	A	G	6.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=49.20;MQ0=1;OQ=205.57;QD=4.28;SB=-109.83	GT:AD:DP:GL:GQ	0/1:33,15:40:-35.90,-12.06,-107.08:99
+chr1	3959766	.	G	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=11.71;MQ=40.06;MQ0=2;OQ=205.60;QD=3.54;SB=-53.76	GT:AD:DP:GL:GQ	0/1:44,14:49:-38.61,-14.76,-139.54:99
+chr1	3959787	rs11807610	T	C	0.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=13.45;MQ=43.41;MQ0=2;OQ=585.11;QD=10.45;SB=-259.35	GT:AD:DP:GL:GQ	0/1:22,34:43:-74.76,-12.96,-79.59:99
+chr1	3959815	rs10915563	A	G	47.44	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=13.21;MQ=50.51;MQ0=1;QD=0.72;SB=62.23	GT:AD:DP:GL:GQ	0/1:56,10:52:-23.70,-15.67,-173.58:80.28
+chr1	3959825	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=18.02;MQ=51.36;MQ0=1;OQ=581.75;QD=8.19;SB=-258.36	GT:AD:DP:GL:GQ	0/1:43,28:61:-79.84,-18.38,-149.14:99
+chr1	3959826	.	A	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=1;HaplotypeScore=9.14;MQ=50.86;MQ0=1;OQ=291.12;QD=3.93;SB=-139.48	GT:AD:DP:GL:GQ	0/1:51,23:56:-49.27,-16.88,-163.75:99
+chr1	3959854	rs10799245	C	A	521.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.17;MQ0=0;OQ=879.17;QD=14.65;SB=-268.32	GT:AD:DP:GL:GQ	0/1:29,31:55:-107.78,-16.58,-78.49:99
+chr1	3961215	rs6670453	G	C	331.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=59.13;MQ0=0;OQ=833.59;QD=15.73;SB=-292.89	GT:AD:DP:GL:GQ	0/1:29,24:53:-102.62,-15.98,-127.58:99
+chr1	3961230	rs6672877	G	T	118.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.94;MQ=59.07;MQ0=0;OQ=633.10;QD=12.66;SB=-213.34	GT:AD:DP:GL:GQ	0/1:27,23:49:-81.35,-14.76,-89.22:99
+chr1	3961237	rs12045715	G	A	510.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=793.63;QD=15.56;SB=-285.83	GT:AD:DP:GL:GQ	0/1:26,25:51:-98.03,-15.38,-79.59:99
+chr1	3961468	rs12045781	G	A	286.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=60.00;MQ0=0;OQ=606.20;QD=13.78;SB=-238.18	GT:AD:DP:GL:GQ	0/1:24,20:42:-76.57,-12.66,-72.65:99
+chr1	3961548	rs10799247	A	G	169.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.55;MQ=58.33;MQ0=0;OQ=674.03;QD=12.04;SB=-151.92	GT:AD:DP:GL:GQ	0/1:31,24:52:-86.36,-15.67,-108.75:99
+chr1	3962010	rs4654565	G	A	105.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=336.97;QD=12.96;SB=-103.61	GT:AD:DP:GL:GQ	0/1:14,12:25:-44.52,-7.54,-43.04:99
+chr1	3962589	rs4654447	A	G	258.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.65;MQ0=0;OQ=712.70;QD=13.45;SB=-356.22	GT:AD:DP:GL:GQ	0/1:26,27:50:-89.62,-15.07,-95.62:99
+chr1	3962703	rs4654448	A	C	265.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=756.85;QD=13.52;SB=-251.86	GT:AD:DP:GL:GQ	0/1:29,27:55:-95.53,-16.56,-103.20:99
+chr1	3962856	rs4654567	T	C	95.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=59.17;MQ0=0;OQ=415.90;QD=9.24;SB=-159.46	GT:AD:DP:GL:GQ	0/1:25,20:42:-57.53,-12.66,-94.60:99
+chr1	3962899	rs4654449	G	A	419.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=60.00;MQ0=0;OQ=648.86;QD=14.75;SB=-335.88	GT:AD:DP:GL:GQ	0/1:22,22:42:-80.82,-12.65,-78.42:99
+chr1	3963307	rs7520607	T	C	230.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.28;MQ=58.42;MQ0=0;OQ=845.59;QD=14.58;SB=-424.34	GT:AD:DP:GL:GQ	0/1:26,32:53:-103.81,-15.97,-95.34:99
+chr1	3963607	rs4654568	T	G	463.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.07;MQ0=0;OQ=931.94;QD=16.64;SB=-413.80	GT:AD:DP:GL:GQ	0/1:24,32:56:-113.34,-16.87,-88.78:99
+chr1	3963626	rs12027462	C	T	248.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=57.57;MQ0=0;OQ=963.52;QD=17.21;SB=-429.93	GT:AD:DP:GL:GQ	0/1:26,30:55:-116.20,-16.57,-93.29:99
+chr1	3963784	rs4654451	G	A	171.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=59.79;MQ0=0;OQ=912.02;QD=16.00;SB=-225.51	GT:AD:DP:GL:GQ	0/1:28,28:53:-110.46,-15.98,-78.09:99
+chr1	3964643	rs6426429	A	G	60.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=1.27;MQ=59.56;MQ0=0;OQ=582.81;QD=11.00;SB=-285.59	GT:AD:DP:GL:GQ	0/1:28,25:51:-76.94,-15.38,-106.26:99
+chr1	3965132	rs4074993	C	G	325.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.87;MQ=59.28;MQ0=0;OQ=814.87;QD=14.05;SB=-345.07	GT:AD:DP:GL:GQ	0/1:34,24:55:-101.37,-16.60,-121.74:99
+chr1	3965479	rs4074994	T	C	268.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=52.28;MQ0=0;OQ=617.78;QD=12.36;SB=-300.36	GT:AD:DP:GL:GQ	0/1:25,25:49:-79.83,-14.77,-98.86:99
+chr1	3965536	rs57323923	T	C	0.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=4;HaplotypeScore=2.11;MQ=50.55;MQ0=0;OQ=424.15;QD=8.48;SB=-173.38	GT:AD:DP:GL:GQ	0/1:29,21:47:-59.86,-14.17,-115.12:99
+chr1	3965975	.	C	G	7.70	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=58.67;MQ0=0;OQ=589.92;QD=12.04;SB=-25.38	GT:AD:DP:GL:GQ	0/1:32,17:46:-76.14,-13.87,-119.93:99
+chr1	3965977	.	T	C	0.69	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=2;HaplotypeScore=1.11;MQ=58.22;MQ0=0;OQ=427.57;QD=8.55;SB=-16.87	GT:AD:DP:GL:GQ	0/1:33,17:49:-60.80,-14.76,-127.29:99
+chr1	3966027	rs7414863	A	C	144.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.13;MQ0=0;OQ=452.26;QD=9.42;SB=-62.85	GT:AD:DP:GL:GQ	0/1:27,21:45:-62.07,-13.56,-92.65:99
+chr1	3966540	rs3935559	C	G	391.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=1031.71;QD=18.42;SB=-312.99	GT:AD:DP:GL:GQ	0/1:24,32:56:-123.36,-16.90,-103.47:99
+chr1	3966816	.	G	A	1.68	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=5.13;MQ=57.97;MQ0=0;OQ=1415.89;QD=20.52;SB=-484.12	GT:AD:DP:GL:GQ	0/1:24,45:61:-163.26,-18.38,-64.39:99
+chr1	3967294	rs12747294	C	T	4.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=8.87;MQ=56.15;MQ0=1;OQ=813.80;QD=16.95;SB=-391.14	GT:AD:DP:GL:GQ	0/1:22,26:45:-98.22,-13.56,-71.93:99
+chr1	3967372	rs6702213	C	T	194.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=34.49;MQ0=0;OQ=718.26;QD=12.17;SB=-239.54	GT:AD:DP:GL:GQ	0/1:33,26:54:-91.39,-16.28,-98.59:99
+chr1	3967404	rs6661264	T	C	167.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=40.81;MQ0=0;OQ=475.36;QD=8.80;SB=-244.91	GT:AD:DP:GL:GQ	0/1:34,20:52:-66.49,-15.67,-131.05:99
+chr1	3967405	rs6675434	G	A	377.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.63;MQ0=0;OQ=533.67;QD=9.70;SB=-290.77	GT:AD:DP:GL:GQ	0/1:34,21:52:-72.31,-15.66,-122.28:99
+chr1	3967434	rs12747604	C	T	38.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=46.12;MQ0=0;OQ=331.44;QD=7.71;SB=-108.07	GT:AD:DP:GL:GQ	0/1:29,14:41:-48.79,-12.36,-91.55:99
+chr1	3967444	rs56081307	C	A	64.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=45.65;MQ0=0;OQ=391.03;QD=8.32;SB=-188.48	GT:AD:DP:GL:GQ	0/1:31,16:44:-55.64,-13.25,-103.38:99
+chr1	3967458	rs6661363	T	C	158.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=46.22;MQ0=0;OQ=383.22;QD=7.82;SB=-172.51	GT:AD:DP:GL:GQ	0/1:29,19:44:-54.87,-13.26,-104.62:99
+chr1	3967912	rs6675979	G	A	278.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=58.64;MQ0=0;OQ=1206.49;QD=19.46;SB=-623.12	GT:AD:DP:GL:GQ	0/1:25,37:60:-142.02,-18.08,-76.63:99
+chr1	3968006	rs12731145	A	G	28.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=5.76;MQ=59.49;MQ0=0;OQ=439.53;QD=9.77;SB=-228.43	GT:AD:DP:GL:GQ	0/1:27,18:43:-60.19,-12.95,-105.51:99
+chr1	3968073	rs6426431	G	A	223.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=59.56;MQ0=0;OQ=482.88;QD=9.29;SB=-221.45	GT:AD:DP:GL:GQ	0/1:34,18:50:-66.64,-15.07,-119.13:99
+chr1	3968105	rs12744667	G	A	365.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=59.56;MQ0=0;OQ=827.90;QD=15.62;SB=-433.93	GT:AD:DP:GL:GQ	0/1:27,26:51:-101.44,-15.36,-92.63:99
+chr1	3968106	rs55866108	A	G	217.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=59.57;MQ0=0;OQ=738.88;QD=13.68;SB=-284.42	GT:AD:DP:GL:GQ	0/1:27,27:53:-93.14,-15.96,-108.96:99
+chr1	3968537	rs12753281	C	G	269.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.90;MQ0=0;OQ=1244.08;QD=14.99;SB=-559.96	GT:AD:DP:GL:GQ	0/1:45,38:83:-152.72,-25.03,-193.42:99
+chr1	3968581	rs12736036	A	G	78.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=3.15;MQ=57.56;MQ0=0;OQ=949.82;QD=11.58;SB=-430.05	GT:AD:DP:GL:GQ	0/1:44,38:77:-121.46,-23.19,-177.75:99
+chr1	3968726	rs34940664	G	T	190.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.33;MQ0=0;OQ=1575.63;QD=16.24;SB=-709.50	GT:AD:DP:GL:GQ	0/1:45,52:96:-189.76,-28.91,-164.22:99
+chr1	3968753	rs35749996	A	G	455.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1487.59;QD=17.92;SB=-656.99	GT:AD:DP:GL:GQ	0/1:35,48:83:-177.04,-25.00,-145.40:99
+chr1	3968768	rs12753644	C	G	340.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=1876.77;QD=20.85;SB=-779.42	GT:AD:DP:GL:GQ	0/1:40,50:90:-218.08,-27.12,-169.27:99
+chr1	3968858	rs12045134	A	C	23.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=5.51;MQ=58.42;MQ0=0;OQ=708.96;QD=8.54;SB=-321.59	GT:AD:DP:GL:GQ	0/1:52,31:81:-98.58,-24.40,-189.89:99
+chr1	3968949	rs12047590	G	T	243.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=59.74;MQ0=0;OQ=980.09;QD=13.61;SB=-395.21	GT:AD:DP:GL:GQ	0/1:39,33:71:-122.68,-21.39,-124.97:99
+chr1	3969008	rs12027284	C	T	226.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.68;MQ0=0;OQ=1351.13;QD=18.77;SB=-463.00	GT:AD:DP:GL:GQ	0/1:32,40:69:-159.19,-20.80,-95.94:99
+chr1	3969221	rs12045225	A	G	0.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=9.56;MQ=58.22;MQ0=0;OQ=654.37;QD=13.09;SB=-95.63	GT:AD:DP:GL:GQ	0/1:21,29:44:-81.99,-13.27,-67.60:99
+chr1	3969391	rs12046014	A	G	106.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.88;MQ=58.95;MQ0=0;OQ=580.96;QD=9.37;SB=-244.16	GT:AD:DP:GL:GQ	0/1:36,26:57:-78.56,-17.18,-134.21:99
+chr1	3969440	rs12044268	T	C	521.33	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=58.87;MQ0=0;QD=12.72;SB=-263.94	GT:AD:DP:GL:GQ	0/1:19,21:40:-67.48,-12.06,-76.36:99
+chr1	3969444	rs12048464	G	T	535.50	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.71;MQ0=0;QD=14.88;SB=-256.96	GT:AD:DP:GL:GQ	0/1:18,18:36:-67.68,-10.85,-54.15:99
+chr1	3969450	rs34283588	G	A	563.46	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.55;MQ0=0;QD=17.61;SB=-257.77	GT:AD:DP:GL:GQ	0/1:15,17:30:-68.67,-9.04,-41.92:99
+chr1	3969504	rs12028147	C	A	128.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.50;MQ0=0;OQ=1173.33;QD=18.92;SB=-401.82	GT:AD:DP:GL:GQ	0/1:25,37:62:-139.29,-18.67,-88.93:99
+chr1	3969731	rs35514116	C	A	193.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=2.36;MQ=59.11;MQ0=0;OQ=1169.40;QD=14.99;SB=-425.64	GT:AD:DP:GL:GQ	0/1:38,39:78:-146.50,-26.28,-138.29:99
+chr1	3969738	rs35902612	G	T	87.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=3.60;MQ=59.14;MQ0=0;OQ=1314.22;QD=16.22;SB=-492.89	GT:AD:DP:GL:GQ	0/1:38,43:80:-158.80,-24.09,-135.14:99
+chr1	3969835	rs34306433	G	C	322.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=60.00;MQ0=0;OQ=1225.99;QD=18.03;SB=-578.33	GT:AD:DP:GL:GQ	0/1:31,36:68:-148.71,-22.83,-138.52:99
+chr1	3970192	rs34458454	T	C	115.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=60.00;MQ0=0;OQ=393.81;QD=8.04;SB=-222.38	GT:AD:DP:GL:GQ	0/1:28,21:43:-55.63,-12.97,-98.60:99
+chr1	3970255	rs34994381	G	A	356.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1045.77;QD=16.09;SB=-475.47	GT:AD:DP:GL:GQ	0/1:34,31:61:-126.25,-18.39,-98.09:99
+chr1	3970431	rs35579324	A	T	318.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.56;MQ0=0;OQ=768.67;QD=14.78;SB=-345.07	GT:AD:DP:GL:GQ	0/1:26,26:52:-95.82,-15.67,-98.48:99
+chr1	3970448	rs35474759	C	T	457.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=955.78;QD=18.03;SB=-501.52	GT:AD:DP:GL:GQ	0/1:25,28:52:-114.52,-15.66,-86.38:99
+chr1	3970842	rs12049555	G	A	157.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=59.39;MQ0=0;OQ=384.99;QD=10.13;SB=-163.62	GT:AD:DP:GL:GQ	0/1:23,15:35:-52.33,-10.55,-71.59:99
+chr1	3970912	rs6664533	C	T	146.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=3.51;MQ=58.67;MQ0=0;OQ=505.76;QD=14.45;SB=-247.75	GT:AD:DP:GL:GQ	0/1:19,16:34:-64.11,-10.25,-57.21:99
+chr1	3971010	rs6664655	C	G	360.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=59.06;MQ0=0;OQ=1105.77;QD=14.94;SB=-455.72	GT:AD:DP:GL:GQ	0/1:42,32:74:-136.16,-22.30,-181.19:99
+chr1	3971024	rs6686502	G	A	241.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=59.09;MQ0=0;OQ=1058.60;QD=13.93;SB=-346.09	GT:AD:DP:GL:GQ	0/1:42,34:75:-131.76,-22.62,-128.76:99
+chr1	3971052	rs6672264	T	C	278.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.20;MQ0=0;OQ=887.02;QD=10.95;SB=-268.12	GT:AD:DP:GL:GQ	0/1:49,32:80:-116.09,-24.10,-192.61:99
+chr1	3971195	rs6686709	G	C	441.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=533.40;QD=11.85;SB=-281.29	GT:AD:DP:GL:GQ	0/1:29,16:42:-69.28,-12.66,-112.85:99
+chr1	3971259	rs6680847	A	G	343.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=805.68;QD=13.21;SB=-291.63	GT:AD:DP:GL:GQ	0/1:33,28:60:-101.92,-18.07,-129.04:99
+chr1	3971430	rs6675053	T	C	59.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=57.14;MQ0=0;OQ=478.62;QD=6.74;SB=-133.24	GT:AD:DP:GL:GQ	0/1:48,23:70:-72.24,-21.10,-194.61:99
+chr1	3971753	.	C	A	69.39	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=12;HaplotypeScore=26.59;MQ=52.60;MQ0=0;QD=1.16;SB=62.22	GT:AD:DP:GL:GQ	0/1:50,10:49:-24.98,-14.76,-146.09:99
+chr1	3971766	rs12030209	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=12;HaplotypeScore=17.56;MQ=52.68;MQ0=0;OQ=817.96;QD=12.39;SB=-315.05	GT:AD:DP:GL:GQ	0/1:32,34:60:-103.15,-18.07,-109.51:99
+chr1	3972069	rs55798869	G	T	4.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=3;HaplotypeScore=5.71;MQ=56.04;MQ0=0;OQ=802.09;QD=13.37;SB=-418.83	GT:AD:DP:GL:GQ	0/1:32,28:52:-99.17,-15.67,-74.15:99
+chr1	3972136	rs55745368	T	C	189.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=59.03;MQ0=0;OQ=1099.26;QD=12.08;SB=-445.57	GT:AD:DP:GL:GQ	0/1:52,39:91:-140.63,-27.42,-210.68:99
+chr1	3972189	rs7414301	T	C	60.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=5.42;MQ=59.51;MQ0=0;OQ=1011.76;QD=11.76;SB=-466.68	GT:AD:DP:GL:GQ	0/1:46,40:86:-130.38,-25.92,-186.30:99
+chr1	3972623	.	A	C	192.74	PASS	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.77;MQ0=0;OQ=1230.69;QD=15.38;SB=-527.79	GT:AD:DP:GL:GQ	0/1:36,44:79:-150.15,-23.80,-134.39:99
+chr1	3972753	rs10915589	G	A	130.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.30;MQ0=0;OQ=1165.16;QD=17.65;SB=-331.36	GT:AD:DP:GL:GQ	0/1:30,36:63:-138.78,-18.98,-103.29:99
+chr1	3972924	rs12023372	G	C	321.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.20;MQ0=0;OQ=1325.91;QD=18.94;SB=-613.61	GT:AD:DP:GL:GQ	0/1:33,37:69:-156.66,-20.79,-145.10:99
+chr1	3973210	rs12023479	G	A	281.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.70;MQ0=0;OQ=1046.55;QD=13.59;SB=-512.32	GT:AD:DP:GL:GQ	0/1:44,33:77:-131.15,-23.21,-144.02:99
+chr1	3973292	.	A	G	33.55	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=55.10;MQ0=0;OQ=633.05;QD=11.94;SB=-175.56	GT:AD:DP:GL:GQ	0/1:28,25:47:-80.75,-14.16,-95.41:99
+chr1	3973506	.	G	A	176.17	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.46;MQ0=0;OQ=876.83;QD=12.71;SB=-380.14	GT:AD:DP:GL:GQ	0/1:42,27:67:-111.16,-20.19,-131.21:99
+chr1	3973875	rs4654459	T	A	52.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=2.73;MQ=58.55;MQ0=0;OQ=1176.09;QD=14.70;SB=-563.67	GT:AD:DP:GL:GQ	0/1:41,39:78:-144.39,-23.49,-149.95:99
+chr1	3973955	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=17;HaplotypeScore=22.03;MQ=54.06;MQ0=0;OQ=55.47;QD=1.03;SB=65.23	GT:AD:DP:GL:GQ	0/1:43,10:44:-22.08,-13.25,-133.74:88.31
+chr1	3974003	.	A	G	105.47	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.51;MQ0=0;OQ=461.72;QD=11.26;SB=-234.29	GT:AD:DP:GL:GQ	0/1:22,19:40:-61.51,-12.06,-83.11:99
+chr1	3974203	.	T	G	66.57	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=57.62;MQ0=0;OQ=954.85;QD=13.84;SB=-428.75	GT:AD:DP:GL:GQ	0/1:35,34:68:-119.25,-20.48,-128.89:99
+chr1	3974239	rs35998568	G	A	463.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.48;MQ0=0;OQ=1184.56;QD=17.95;SB=-510.14	GT:AD:DP:GL:GQ	0/1:31,35:66:-141.63,-19.89,-102.39:99
+chr1	3974376	rs57696600	C	T	6.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=4;HaplotypeScore=1.87;MQ=59.16;MQ0=0;OQ=1418.07;QD=19.70;SB=-722.06	GT:AD:DP:GL:GQ	0/1:30,42:71:-166.49,-21.40,-92.47:99
+chr1	3974614	rs4457544	A	T	403.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1649.20;QD=19.18;SB=-732.91	GT:AD:DP:GL:GQ	0/1:34,52:86:-194.11,-25.90,-133.63:99
+chr1	3974846	rs12025374	G	A	466.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.31;MQ0=0;OQ=1051.59;QD=16.43;SB=-403.40	GT:AD:DP:GL:GQ	0/1:31,33:63:-127.44,-18.99,-100.16:99
+chr1	3975091	rs12049502	T	C	199.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.55;MQ0=0;OQ=805.28;QD=16.78;SB=-288.47	GT:AD:DP:GL:GQ	0/1:19,29:47:-97.97,-14.16,-75.75:99
+chr1	3975721	rs34928897	A	G	109.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=2.98;MQ=59.19;MQ0=1;OQ=1038.58;QD=10.93;SB=-532.63	GT:AD:DP:GL:GQ	0/1:53,42:94:-135.47,-28.33,-210.33:99
+chr1	3975829	rs12060834	A	C	406.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1062.88;QD=14.56;SB=-251.81	GT:AD:DP:GL:GQ	0/1:37,36:73:-131.56,-21.98,-139.84:99
+chr1	3975904	rs12026411	G	T	347.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=57.00;MQ0=0;OQ=1228.86;QD=14.99;SB=-454.51	GT:AD:DP:GL:GQ	0/1:42,40:82:-150.86,-24.69,-151.44:99
+chr1	3976117	rs12034312	C	T	244.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=60.00;MQ0=0;OQ=1562.01;QD=18.38;SB=-442.95	GT:AD:DP:GL:GQ	0/1:40,45:84:-184.80,-25.32,-123.96:99
+chr1	3976389	rs35297022	T	C	334.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=962.55;QD=13.95;SB=-357.60	GT:AD:DP:GL:GQ	0/1:35,34:68:-120.03,-20.49,-141.31:99
+chr1	3976394	rs35043594	A	T	325.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=916.45;QD=13.68;SB=-308.03	GT:AD:DP:GL:GQ	0/1:36,31:67:-115.11,-20.18,-137.00:99
+chr1	3976477	rs4641284	A	G	171.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=58.95;MQ0=0;OQ=487.70;QD=11.08;SB=-180.60	GT:AD:DP:GL:GQ	0/1:26,18:42:-64.71,-12.65,-94.45:99
+chr1	3976506	rs34448752	C	T	57.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=56.85;MQ0=0;OQ=445.94;QD=14.86;SB=-105.62	GT:AD:DP:GL:GQ	0/1:16,14:29:-56.62,-8.74,-46.04:99
+chr1	3976567	.	C	T	0.32	PASS	AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=1.54;MQ=51.77;MQ0=0;OQ=226.37;QD=18.86;SB=-10.00	GT:AD:DP:GL:GQ	0/1:3,9:11:-29.24,-3.32,-8.40:50.74
+chr1	3976658	rs35326871	G	T	11.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.52;MQ0=0;OQ=1096.88;QD=17.41;SB=-10.00	GT:AD:DP:GL:GQ	0/1:25,38:62:-131.64,-18.67,-93.14:99
+chr1	3977151	rs10915596	T	G	1.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=3.48;MQ=59.09;MQ0=0;OQ=756.41;QD=14.83;SB=-45.56	GT:AD:DP:GL:GQ	0/1:22,29:48:-93.38,-14.46,-82.79:99
+chr1	3977453	rs4654599	G	T	361.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.46;MQ0=0;OQ=1289.21;QD=16.74;SB=-567.82	GT:AD:DP:GL:GQ	0/1:35,42:77:-155.40,-23.19,-125.68:99
+chr1	3977541	rs4654600	T	C	61.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=3.43;MQ=59.43;MQ0=0;OQ=838.26;QD=17.11;SB=-388.65	GT:AD:DP:GL:GQ	0/1:18,30:47:-103.58,-16.47,-75.42:99
+chr1	3977567	rs4654601	G	A	272.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.55;MQ0=0;OQ=1148.82;QD=18.83;SB=-426.81	GT:AD:DP:GL:GQ	0/1:26,35:60:-136.24,-18.08,-87.47:99
+chr1	3977950	rs4654604	T	C	322.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=59.65;MQ0=0;OQ=975.26;QD=14.78;SB=-339.18	GT:AD:DP:GL:GQ	0/1:28,38:65:-120.40,-19.59,-110.65:99
+chr1	3978231	rs4129099	T	C	330.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=733.04;QD=11.64;SB=-345.90	GT:AD:DP:GL:GQ	0/1:32,31:62:-95.28,-18.69,-130.06:99
+chr1	3978308	rs4129100	G	A	317.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=1482.59;QD=16.85;SB=-689.02	GT:AD:DP:GL:GQ	0/1:42,46:86:-177.46,-25.92,-132.95:99
+chr1	3980624	rs4323679	C	T	566.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=703.77;QD=12.13;SB=-349.85	GT:AD:DP:GL:GQ	0/1:35,23:57:-90.85,-17.19,-108.01:99
+chr1	3980746	rs35182639	G	A	123.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=4.13;MQ=59.70;MQ0=0;OQ=1453.16;QD=18.63;SB=-621.68	GT:AD:DP:GL:GQ	0/1:35,43:76:-171.51,-22.91,-105.10:99
+chr1	3980982	rs12747944	G	A	386.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=60.00;MQ0=0;OQ=715.67;QD=12.56;SB=-369.37	GT:AD:DP:GL:GQ	0/1:32,24:53:-90.82,-15.97,-105.07:99
+chr1	3981385	rs17404600	C	T	307.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.06;MQ=59.56;MQ0=0;OQ=909.30;QD=17.16;SB=-459.01	GT:AD:DP:GL:GQ	0/1:26,27:49:-108.98,-14.77,-70.07:99
+chr1	3981945	.	G	C	7.35	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=2;HaplotypeScore=2.62;MQ=59.25;MQ0=0;OQ=783.42;QD=13.99;SB=-334.02	GT:AD:DP:GL:GQ	0/1:33,23:54:-97.92,-16.29,-122.30:99
+chr1	3981947	rs10799260	C	T	127.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=2.62;MQ=59.25;MQ0=0;OQ=721.41;QD=12.88;SB=-288.75	GT:AD:DP:GL:GQ	0/1:33,23:55:-91.99,-16.57,-116.30:99
+chr1	3982051	rs10753384	A	G	287.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.81;MQ=59.62;MQ0=0;OQ=891.61;QD=14.62;SB=-286.59	GT:AD:DP:GL:GQ	0/1:30,31:60:-110.52,-18.08,-117.65:99
+chr1	3982227	rs10799261	T	C	592.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=920.95;QD=13.35;SB=-433.27	GT:AD:DP:GL:GQ	0/1:35,34:67:-115.56,-20.18,-140.96:99
+chr1	3982891	rs12023925	T	C	257.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=59.13;MQ0=0;OQ=486.42;QD=9.18;SB=-229.40	GT:AD:DP:GL:GQ	0/1:30,23:50:-67.00,-15.07,-113.54:99
+chr1	3984164	rs7418256	T	G	46.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=4;HaplotypeScore=1.00;MQ=59.72;MQ0=0;OQ=1495.13;QD=18.23;SB=-531.78	GT:AD:DP:GL:GQ	0/1:33,49:80:-176.89,-24.10,-113.02:99
+chr1	3984958	rs6426436	A	G	575.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=842.05;QD=12.95;SB=-332.89	GT:AD:DP:GL:GQ	0/1:35,30:64:-106.77,-19.28,-141.35:99
+chr1	3985143	rs5015188	T	C	159.92	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=12.99;MQ=58.62;MQ0=0;QD=2.25;SB=-60.43	GT:AD:DP:GL:GQ	0/1:60,11:70:-40.36,-21.09,-240.05:99
+chr1	3985147	rs5015187	T	C	314.93	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=67.96;MQ=58.31;MQ0=0;QD=4.37;SB=-165.46	GT:AD:DP:GL:GQ	0/1:57,15:70:-55.86,-21.08,-223.89:99
+chr1	3985151	rs5015186	T	C	601.51	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.01;HRun=1;HaplotypeScore=11.99;MQ=58.34;MQ0=0;QD=8.24;SB=-304.19	GT:AD:DP:GL:GQ	0/1:49,23:71:-84.52,-21.09,-190.22:99
+chr1	3985364	rs4233266	A	G	350.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=58.47;MQ0=0;OQ=817.82;QD=10.76;SB=-299.84	GT:AD:DP:GL:GQ	0/1:41,35:71:-106.46,-21.39,-162.85:99
+chr1	3985761	rs4654611	G	C	378.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=59.78;MQ0=0;OQ=1274.73;QD=15.36;SB=-534.37	GT:AD:DP:GL:GQ	0/1:45,38:78:-154.27,-23.51,-187.35:99
+chr1	3985811	rs4654612	C	T	99.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=4.68;MQ=59.17;MQ0=0;OQ=618.20;QD=11.04;SB=-273.28	GT:AD:DP:GL:GQ	0/1:30,25:47:-79.28,-14.18,-83.87:99
+chr1	3988267	rs3829818	C	G	50.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.32;MQ0=0;OQ=1075.32;QD=19.55;SB=-391.87	GT:AD:DP:GL:GQ	0/1:26,29:54:-127.10,-16.29,-99.01:99
+chr1	3988626	rs34649702	A	C	437.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=920.32;QD=18.41;SB=-485.28	GT:AD:DP:GL:GQ	0/1:20,30:49:-110.07,-14.76,-69.08:99
+chr1	3988704	rs55889146	T	A	313.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.71;MQ0=0;OQ=1088.43;QD=16.75;SB=-492.44	GT:AD:DP:GL:GQ	0/1:29,36:65:-131.71,-19.58,-109.61:99
+chr1	3989745	rs35412083	G	A	332.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.92;MQ0=0;OQ=1097.15;QD=11.93;SB=-405.76	GT:AD:DP:GL:GQ	0/1:55,36:89:-139.82,-26.82,-176.39:99
+chr1	3990405	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=94;Dels=0.03;HRun=18;HaplotypeScore=33.42;MQ=54.32;MQ0=1;OQ=80.49;QD=0.86;SB=90.81	GT:AD:DP:GL:GQ	0/1:76,15:73:-32.44,-21.10,-200.50:99
+chr1	3990446	rs34385055	G	A	276.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=58.88;MQ0=0;OQ=865.10;QD=15.73;SB=-440.45	GT:AD:DP:GL:GQ	0/1:26,29:49:-104.56,-14.77,-74.37:99
+chr1	3990572	rs10915650	T	C	322.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=53.91;MQ0=0;OQ=802.60;QD=15.43;SB=-363.11	GT:AD:DP:GL:GQ	0/1:19,33:50:-98.61,-15.07,-76.41:99
+chr1	3990932	rs4654614	C	T	267.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=1697.75;QD=19.97;SB=-727.98	GT:AD:DP:GL:GQ	0/1:36,49:85:-198.66,-25.60,-134.20:99
+chr1	3991939	.	G	T	133.26	Indel	AC=1;AF=0.50;AN=2;DP=31;Dels=0.03;HRun=0;HaplotypeScore=37.12;MQ=55.25;MQ0=0;QD=4.30;SB=-33.93	GT:AD:DP:GL:GQ	0/1:22,8:23:-23.24,-6.63,-47.74:99
+chr1	3992866	rs34160796	A	G	334.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.66;MQ0=0;OQ=483.28;QD=9.29;SB=-177.56	GT:AD:DP:GL:GQ	0/1:33,19:51:-66.97,-15.36,-129.46:99
+chr1	3993123	rs10915661	A	G	223.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.93;MQ=58.90;MQ0=0;OQ=752.89;QD=12.76;SB=-356.58	GT:AD:DP:GL:GQ	0/1:32,27:57:-95.74,-17.17,-122.04:99
+chr1	3993398	rs10799273	A	G	39.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=58.69;MQ0=0;OQ=432.60;QD=13.52;SB=-183.96	GT:AD:DP:GL:GQ	0/1:16,16:30:-55.58,-9.04,-60.72:99
+chr1	3993415	rs55877711	T	C	152.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=59.43;MQ0=0;OQ=474.94;QD=14.39;SB=-232.31	GT:AD:DP:GL:GQ	0/1:16,17:31:-60.12,-9.34,-57.39:99
+chr1	3993656	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=16;HaplotypeScore=11.17;MQ=56.96;MQ0=0;OQ=77.46;QD=1.25;SB=65.19	GT:AD:DP:GL:GQ	0/1:50,11:45:-24.60,-13.57,-123.37:99
+chr1	3994923	rs4654469	G	A	168.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.96;MQ=59.68;MQ0=0;OQ=1491.96;QD=20.44;SB=-717.78	GT:AD:DP:GL:GQ	0/1:30,43:72:-174.18,-21.70,-94.37:99
+chr1	3995705	rs34085171	T	G	1347.57	Indel	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.38;MQ0=0;QD=15.85;SB=-684.75	GT:AD:DP:GL:GQ	0/1:40,45:84:-163.34,-25.30,-143.02:99
+chr1	3997814	.	A	G	166.71	PASS	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.77;MQ0=0;OQ=1047.22;QD=13.09;SB=-493.22	GT:AD:DP:GL:GQ	0/1:44,36:80:-132.11,-24.10,-175.80:99
+chr1	3999521	rs7533488	A	C	424.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=59.32;MQ0=0;OQ=1161.71;QD=14.17;SB=-423.73	GT:AD:DP:GL:GQ	0/1:41,40:80:-143.55,-24.09,-150.24:99
+chr1	4000164	rs10753345	T	C	207.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=54.60;MQ0=3;OQ=972.02;QD=12.62;SB=-388.88	GT:AD:DP:GL:GQ	0/1:39,38:72:-122.18,-21.70,-141.20:99
+chr1	4000350	rs10915304	A	G	90.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=49.42;MQ0=0;OQ=302.07;QD=8.39;SB=-112.62	GT:AD:DP:GL:GQ	0/1:20,15:32:-43.14,-9.65,-72.05:99
+chr1	4001557	rs35079847	T	C	179.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=42.74;MQ0=4;OQ=737.26;QD=10.24;SB=-356.16	GT:AD:DP:GL:GQ	0/1:43,29:67:-97.19,-20.18,-162.42:99
+chr1	4002410	rs9792845	T	A	39.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=2;HaplotypeScore=2.16;MQ=49.63;MQ0=6;OQ=1137.13;QD=12.92;SB=-561.60	GT:AD:DP:GL:GQ	0/1:48,40:80:-141.09,-24.09,-168.17:99
+chr1	4002600	.	C	T	9.93	PASS	AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=34.65;MQ0=18;OQ=1297.58;QD=10.30;SB=-536.53	GT:AD:DP:GL:GQ	0/1:72,54:87:-159.25,-26.21,-171.14:99
+chr1	4003027	rs7539155	C	T	270.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=49.52;MQ0=2;OQ=1241.45;QD=15.71;SB=-511.02	GT:AD:DP:GL:GQ	0/1:40,39:77:-150.62,-23.19,-144.23:99
+chr1	4003660	rs34911143	C	G	406.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1137.88;QD=19.96;SB=-593.22	GT:AD:DP:GL:GQ	0/1:26,31:56:-133.94,-16.87,-107.70:99
+chr1	4003790	.	T	C	0.57	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=5.22;MQ=56.08;MQ0=0;OQ=469.98;QD=8.55;SB=-182.54	GT:AD:DP:GL:GQ	0/1:35,20:52:-65.94,-15.66,-138.69:99
+chr1	4003932	rs60522686	C	T	104.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=60.00;MQ0=0;OQ=1130.00;QD=21.32;SB=-533.08	GT:AD:DP:GL:GQ	0/1:20,33:53:-132.25,-15.97,-67.95:99
+chr1	4004106	rs12036981	T	A	126.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=56.22;MQ0=2;OQ=519.83;QD=10.19;SB=-138.13	GT:AD:DP:GL:GQ	0/1:29,21:47:-69.43,-14.17,-100.44:99
+chr1	4004617	rs12036953	A	G	190.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.43;MQ0=0;OQ=561.78;QD=8.64;SB=-245.46	GT:AD:DP:GL:GQ	0/1:41,24:63:-78.44,-18.98,-164.76:99
+chr1	4005149	rs5018354	G	T	769.64	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=5;HaplotypeScore=8.12;MQ=53.93;MQ0=0;QD=10.84;SB=-410.03	GT:AD:DP:GL:GQ	0/1:41,30:69:-101.03,-20.78,-142.34:99
+chr1	4005155	.	A	T	709.63	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=5;HaplotypeScore=11.69;MQ=54.09;MQ0=0;QD=10.28;SB=-304.00	GT:AD:DP:GL:GQ	0/1:43,26:65:-93.83,-19.58,-142.00:99
+chr1	4005156	.	A	T	576.66	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=13.11;MQ=54.00;MQ0=0;QD=8.48;SB=-291.97	GT:AD:DP:GL:GQ	0/1:44,24:63:-79.93,-18.98,-151.00:99
+chr1	4005449	rs34905442	A	G	30.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=5.92;MQ=57.79;MQ0=0;OQ=842.19;QD=15.89;SB=-428.92	GT:AD:DP:GL:GQ	0/1:23,30:52:-103.18,-15.68,-83.89:99
+chr1	4010416	rs55645535	A	G	3.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=3;HaplotypeScore=0.83;MQ=58.64;MQ0=0;OQ=504.55;QD=16.28;SB=-163.34	GT:AD:DP:GL:GQ	0/1:10,21:29:-62.49,-8.75,-36.79:99
+chr1	4012539	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=20;HaplotypeScore=3.78;MQ=46.27;MQ0=3;OQ=496.42;QD=5.23;SB=131.33	GT:AD:DP:GL:GQ	0/1:70,25:77:-76.14,-23.22,-185.60:99
+chr1	4012545	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=7;HaplotypeScore=6.81;MQ=48.30;MQ0=1;OQ=296.48;QD=3.12;SB=125.35	GT:AD:DP:GL:GQ	0/1:68,26:74:-55.23,-22.30,-199.64:99
+chr1	4015436	rs10799171	T	C	582.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=1395.24;QD=29.69;SB=-603.59	GT:AD:DP:GL:GQ	1/1:0,47:45:-143.16,-13.58,-0.05:99
+chr1	4015788	rs6426377	G	C	79.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=58.24;MQ0=0;OQ=2118.03;QD=39.96;SB=-1018.28	GT:AD:DP:GL:GQ	1/1:0,53:49:-215.40,-14.76,-0.01:99
+chr1	4016464	rs3856168	T	C	206.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=58.60;MQ0=0;OQ=1420.67;QD=28.41;SB=-682.89	GT:AD:DP:GL:GQ	1/1:0,50:45:-145.69,-13.57,-0.04:99
+chr1	4017003	rs4654403	T	C	46.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=59.61;MQ0=0;OQ=1716.77;QD=29.10;SB=-823.60	GT:AD:DP:GL:GQ	1/1:0,59:55:-175.31,-16.59,-0.05:99
+chr1	4017098	rs4654404	C	T	8.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=4.56;MQ=58.64;MQ0=0;OQ=1853.34;QD=38.61;SB=-777.68	GT:AD:DP:GL:GQ	1/1:0,48:47:-188.93,-14.16,-0.01:99
+chr1	4018431	rs4654475	T	C	39.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=59.54;MQ0=0;OQ=1443.50;QD=28.87;SB=-682.71	GT:AD:DP:GL:GQ	1/1:0,50:46:-147.99,-13.88,-0.05:99
+chr1	4018760	rs7419106	C	G	402.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1082.64;QD=34.92;SB=-389.10	GT:AD:DP:GL:GQ	1/1:0,31:28:-111.87,-8.45,-0.02:84.27
+chr1	4018847	rs10799175	T	C	20.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=4.16;MQ=58.50;MQ0=0;OQ=814.89;QD=26.29;SB=-376.57	GT:AD:DP:GL:GQ	1/1:1,29:28:-88.39,-10.61,-3.32:72.94
+chr1	4019483	rs10799177	G	A	473.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.36;MQ0=0;OQ=1615.08;QD=33.65;SB=-313.91	GT:AD:DP:GL:GQ	1/1:0,48:42:-165.11,-12.66,-0.02:99
+chr1	4019522	rs9792946	G	A	281.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=54.50;MQ0=0;OQ=2603.69;QD=38.29;SB=-1110.00	GT:AD:DP:GL:GQ	1/1:0,68:66:-263.98,-19.89,-0.02:99
+chr1	4019590	rs7418034	G	A	135.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=43.49;MQ0=0;OQ=1841.94;QD=30.70;SB=-845.46	GT:AD:DP:GL:GQ	1/1:0,59:50:-190.21,-17.45,-2.43:99
+chr1	4019593	rs7412152	A	C	123.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=42.41;MQ0=0;OQ=1763.32;QD=29.89;SB=-853.08	GT:AD:DP:GL:GQ	1/1:0,59:51:-179.93,-15.36,-0.02:99
+chr1	4019614	rs7411249	C	G	15.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.88;MQ=36.55;MQ0=1;OQ=1713.38;QD=32.33;SB=-801.51	GT:AD:DP:GL:GQ	1/1:0,53:41:-174.94,-12.36,-0.02:99
+chr1	4019841	rs7412217	A	G	301.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=36.34;MQ0=0;OQ=1308.64;QD=29.08;SB=-633.25	GT:AD:DP:GL:GQ	1/1:0,45:37:-134.46,-11.14,-0.01:99
+chr1	4019863	rs4310408	A	G	15.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=44.42;MQ0=0;OQ=1396.45;QD=30.36;SB=-620.23	GT:AD:DP:GL:GQ	1/1:0,46:40:-143.25,-12.05,-0.02:99
+chr1	4019987	rs10737398	C	T	456.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.86;MQ0=6;OQ=1422.85;QD=30.93;SB=-467.35	GT:AD:DP:GL:GQ	1/1:0,46:37:-145.88,-11.15,-0.01:99
+chr1	4020055	rs7411353	C	A	1052.58	Indel;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=9;HaplotypeScore=6.69;MQ=42.23;MQ0=1;QD=22.40;SB=-302.56	GT:AD:DP:GL:GQ	1/1:0,47:31:-108.85,-9.34,-0.01:93.27
+chr1	4020059	.	T	A	16.07	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=4;HaplotypeScore=6.64;MQ=40.62;MQ0=1;QD=0.41;SB=14.07	GT:AD:DP:GL:GQ	0/1:27,12:17:-10.01,-5.13,-48.93:48.79
+chr1	4020065	rs6426379	G	C	834.47	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=40.47;MQ0=0;QD=30.91;SB=-369.17	GT:AD:DP:GL:GQ	1/1:1,26:20:-87.04,-6.03,-0.01:60.20
+chr1	4020216	rs6426380	C	T	178.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=56.52;MQ0=0;OQ=2286.70;QD=38.76;SB=-938.24	GT:AD:DP:GL:GQ	1/1:0,59:59:-232.28,-17.78,-0.03:99
+chr1	4020359	rs4233255	T	A	506.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.30;MQ0=1;OQ=1405.72;QD=30.56;SB=-629.64	GT:AD:DP:GL:GQ	1/1:0,46:40:-144.18,-12.05,-0.02:99
+chr1	4020451	rs4654476	A	G	27.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.11;MQ0=0;OQ=1489.65;QD=28.65;SB=-689.96	GT:AD:DP:GL:GQ	1/1:0,52:47:-152.59,-14.18,-0.04:99
+chr1	4020454	rs4654477	T	C	48.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.13;MQ=59.54;MQ0=0;OQ=1536.11;QD=30.72;SB=-613.94	GT:AD:DP:GL:GQ	1/1:0,50:48:-157.24,-14.48,-0.04:99
+chr1	4020656	rs4233256	A	C	90.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=59.09;MQ0=0;OQ=1344.37;QD=29.23;SB=-633.78	GT:AD:DP:GL:GQ	1/1:0,46:45:-138.07,-13.57,-0.05:99
+chr1	4020738	rs4233257	G	A	285.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=56.81;MQ0=0;OQ=1954.21;QD=35.53;SB=-857.02	GT:AD:DP:GL:GQ	1/1:0,55:50:-199.02,-15.06,-0.01:99
+chr1	4020758	rs4233258	T	C	590.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.92;MQ0=0;OQ=1509.42;QD=29.03;SB=-773.63	GT:AD:DP:GL:GQ	1/1:0,52:49:-154.57,-14.78,-0.05:99
+chr1	4020965	rs10915373	A	G	41.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=3.05;MQ=59.15;MQ0=0;OQ=2124.75;QD=32.19;SB=-981.05	GT:AD:DP:GL:GQ	1/1:0,66:61:-216.09,-18.38,-0.03:99
+chr1	4021209	rs12087801	A	G	66.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=59.44;MQ0=0;OQ=1399.12;QD=34.12;SB=-653.32	GT:AD:DP:GL:GQ	1/1:0,41:40:-143.51,-12.05,-0.01:99
+chr1	4021244	rs7524590	A	G	21.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.56;MQ0=0;OQ=1518.93;QD=29.21;SB=-554.05	GT:AD:DP:GL:GQ	1/1:0,52:47:-155.52,-14.17,-0.04:99
+chr1	4021467	rs6426381	T	C	70.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.82;MQ0=0;OQ=1271.75;QD=29.58;SB=-623.00	GT:AD:DP:GL:GQ	1/1:0,43:40:-130.79,-12.06,-0.03:99
+chr1	4021470	rs6665286	C	T	565.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.82;MQ0=0;OQ=1632.61;QD=37.97;SB=-837.35	GT:AD:DP:GL:GQ	1/1:0,43:42:-166.86,-12.66,-0.02:99
+chr1	4021576	rs10799179	C	T	140.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.60;MQ0=0;OQ=2105.87;QD=36.95;SB=-1023.68	GT:AD:DP:GL:GQ	1/1:0,57:54:-214.19,-16.27,-0.02:99
+chr1	4022324	rs10799180	T	C	96.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1478.38;QD=30.80;SB=-697.61	GT:AD:DP:GL:GQ	1/1:0,48:47:-151.47,-14.18,-0.04:99
+chr1	4023064	rs12044274	A	T	27.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.00;MQ0=0;OQ=1175.00;QD=33.57;SB=-370.25	GT:AD:DP:GL:GQ	1/1:0,34:33:-121.10,-9.94,-0.02:99
+chr1	4023346	rs12728781	C	T	64.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=58.67;MQ0=0;OQ=1081.51;QD=30.90;SB=-492.01	GT:AD:DP:GL:GQ	1/1:1,34:29:-111.75,-8.74,-0.01:87.27
+chr1	4023709	rs10915381	G	C	0.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=3.44;MQ=58.92;MQ0=0;OQ=2348.10;QD=41.93;SB=-727.93	GT:AD:DP:GL:GQ	1/1:0,56:54:-238.42,-16.28,-0.02:99
+chr1	4024015	rs6672626	C	T	663.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=46.30;MQ0=0;OQ=1764.84;QD=37.55;SB=-805.32	GT:AD:DP:GL:GQ	1/1:0,47:46:-180.09,-13.86,-0.02:99
+chr1	4024120	rs6672716	C	T	182.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=36.16;MQ0=0;OQ=1966.97;QD=37.83;SB=-833.61	GT:AD:DP:GL:GQ	1/1:0,51:51:-203.16,-18.10,-2.88:99
+chr1	4024270	.	T	A	112.05	Indel	AC=1;AF=0.50;AN=2;DP=33;Dels=0.03;HRun=0;HaplotypeScore=2.93;MQ=35.48;MQ0=0;QD=3.40;SB=-51.99	GT:AD:DP:GL:GQ	0/1:21,11:28:-22.63,-8.14,-76.45:99
+chr1	4024272	.	A	T	86.10	Indel	AC=1;AF=0.50;AN=2;DP=34;Dels=0.03;HRun=0;HaplotypeScore=5.09;MQ=34.14;MQ0=0;QD=2.53;SB=-27.82	GT:AD:DP:GL:GQ	0/1:23,10:27:-19.73,-7.83,-71.54:99
+chr1	4024295	rs6683289	T	C	432.26	Indel;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=27.02;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,16:16:-46.84,-4.84,-0.03:48.07
+chr1	4024297	rs6665849	G	C	696.90	Indel;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=43.56;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,16:16:-73.28,-4.82,-0.00:48.16
+chr1	4024305	.	T	C	154.38	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=7.02;SB=-40.68	GT:AD:DP:GL:GQ	0/1:15,7:22:-25.35,-6.63,-60.61:99
+chr1	4024357	.	T	G	116.82	Indel	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=28.57;MQ0=0;QD=4.67;SB=-30.96	GT:AD:DP:GL:GQ	0/1:17,8:23:-21.89,-6.93,-59.79:99
+chr1	4024403	.	G	T	1246.60	Indel	AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=28.45;MQ0=0;QD=33.69;SB=-622.14	GT:AD:DP:GL:GQ	1/1:0,37:35:-128.26,-10.54,-0.01:99
+chr1	4024413	.	C	T	38.79	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=14.98;MQ=32.72;MQ0=0;QD=0.90;SB=-26.14	GT:AD:DP:GL:GQ	0/1:37,6:40:-19.21,-12.05,-127.12:71.63
+chr1	4024463	.	G	C	836.03	Indel	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=5.63;MQ=36.44;MQ0=0;QD=16.39;SB=-259.21	GT:AD:DP:GL:GQ	0/1:27,24:51:-102.25,-15.37,-114.08:99
+chr1	4024467	.	C	T	697.56	Indel	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=4.47;MQ=36.57;MQ0=0;QD=13.95;SB=-194.79	GT:AD:DP:GL:GQ	0/1:28,22:49:-87.80,-14.76,-98.23:99
+chr1	4024517	rs28542205	C	G	1129.16	Indel	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=18.36;MQ=32.35;MQ0=0;QD=26.26;SB=-522.33	GT:AD:DP:GL:GQ	0/1:8,31:35:-126.75,-10.55,-27.16:99
+chr1	4024521	.	G	C	975.12	Indel	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=18.89;MQ=30.36;MQ0=0;QD=23.78;SB=-491.19	GT:AD:DP:GL:GQ	0/1:9,27:35:-115.01,-14.21,-36.24:99
+chr1	4024603	.	G	C	2.26	PASS	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=24.41;MQ0=0;OQ=50.98;QD=5.66;SB=-6.99	GT:AD:DP:GL:GQ	0/1:1,8:3:-9.29,-0.90,-4.69:37.89
+chr1	4024673	.	T	C	8.19	PASS	AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=30.71;MQ0=0;OQ=656.07;QD=31.24;SB=-288.45	GT:AD:DP:GL:GQ	1/1:0,21:20:-69.20,-6.03,-0.01:60.17
+chr1	4024788	.	T	C	850.29	Indel	AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.58;MQ0=0;QD=34.01;SB=-338.76	GT:AD:DP:GL:GQ	1/1:0,25:25:-88.63,-7.53,-0.01:75.20
+chr1	4024845	.	T	G	1.74	PASS	AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=68.85;QD=17.21;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,3:4:-11.37,-1.20,-3.44:22.35
+chr1	4024894	.	T	C	62.45	Indel	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=29.00;MQ0=0;QD=12.49;SB=-41.94	GT:AD:DP:GL:GQ	0/1:2,3:4:-10.73,-1.20,-4.27:30.63
+chr1	4024923	.	G	A	22.24	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=8;Dels=0.25;HRun=0;HaplotypeScore=23.92;MQ=29.00;MQ0=0;QD=2.78;SB=-0.97	GT:AD:DP:GL:GQ	0/1:4,2:6:-7.31,-1.81,-14.76:55.05
+chr1	4024936	.	T	G	14.90	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=16;Dels=0.06;HRun=0;HaplotypeScore=31.98;MQ=29.00;MQ0=0;QD=0.93;SB=4.38	GT:AD:DP:GL:GQ	0/1:12,2:8:-11.00,-6.24,-20.74:47.59
+chr1	4024944	.	C	T	21.22	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=58.95;MQ=29.00;MQ0=0;QD=1.25;SB=8.05	GT:AD:DP:GL:GQ	0/1:15,2:9:-8.11,-2.71,-25.25:54.02
+chr1	4024945	.	A	T	15.01	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=58.95;MQ=29.00;MQ0=0;QD=0.88;SB=8.04	GT:AD:DP:GL:GQ	0/1:13,4:9:-7.48,-2.71,-24.43:47.70
+chr1	4024946	.	C	T	97.28	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=64.95;MQ=29.00;MQ0=0;QD=5.72;SB=8.05	GT:AD:DP:GL:GQ	0/1:13,4:11:-16.32,-3.31,-25.25:99
+chr1	4024979	.	C	T	611.81	Indel;SnpCluster	AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=6.71;MQ=29.00;MQ0=0;QD=33.99;SB=-293.67	GT:AD:DP:GL:GQ	1/1:0,16:16:-64.77,-4.82,-0.00:48.16
+chr1	4024982	.	T	G	173	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=11.86;MQ=29.00;MQ0=0;QD=9.11;SB=14.07	GT:AD:DP:GL:GQ	0/1:10,7:16:-25.40,-4.82,-33.30:99
+chr1	4024983	.	C	T	250.37	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=11.86;MQ=29.00;MQ0=0;QD=13.18;SB=14.06	GT:AD:DP:GL:GQ	0/1:11,8:16:-33.14,-4.82,-27.15:99
+chr1	4025014	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=2;HaplotypeScore=18.19;MQ=29.00;MQ0=0;OQ=197.67;QD=9.88;SB=17.08	GT:AD:DP:GL:GQ	0/1:13,7:18:-28.47,-5.42,-39.21:99
+chr1	4025033	.	G	A	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=9.30;MQ=27.51;MQ0=1;OQ=89.74;QD=8.97;SB=2.03	GT:AD:DP:GL:GQ	0/1:5,5:9:-14.97,-2.71,-16.97:99
+chr1	4025048	.	C	T	21.22	DPFilter;Indel;LowQual	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=1;HaplotypeScore=32.62;MQ=27.51;MQ0=1;QD=2.12;SB=2.04	GT:AD:DP:GL:GQ	0/1:8,2:9:-8.11,-2.71,-25.19:54.03
+chr1	4025070	.	G	A	35.48	LowQual	AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=1;HaplotypeScore=6.00;MQ=29.00;MQ0=0;QD=8.87;SB=-6.99	GT:AD:DP:GL:GQ	0/1:2,2:3:-7.73,-0.90,-3.47:25.65
+chr1	4025144	.	C	T	71.12	Indel	AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=8.89;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,6:5:-11.90,-1.51,-7.69:61.87
+chr1	4025168	.	G	C	48.97	LowQual	AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=29.00;MQ0=0;QD=7.00;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,5:4:-9.39,-1.21,-8.09:68.89
+chr1	4025186	.	C	T	0.12	PASS	AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=78.13;QD=19.53;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,3:4:-12.30,-1.20,-3.90:26.92
+chr1	4025245	.	C	T	49.25	LowQual;SnpCluster	AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=16.42;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,2:2:-8.33,-0.60,-0.00:6.02
+chr1	4025247	.	G	C	137.89	SnpCluster	AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.94;MQ0=1;QD=27.58;SB=-52.47	GT:AD:DP:GL:GQ	1/1:1,4:4:-17.32,-1.21,-0.00:12.04
+chr1	4025253	.	T	C	341.02	SnpCluster	AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.68;MQ0=2;QD=26.23;SB=-182.78	GT:AD:DP:GL:GQ	1/1:1,12:11:-37.69,-3.31,-0.01:33.09
+chr1	4025355	.	C	T	528.21	SnpCluster	AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=33.01;SB=-144.72	GT:AD:DP:GL:GQ	1/1:1,15:16:-59.68,-4.82,-3.30:15.20
+chr1	4025359	.	T	C	305.09	SnpCluster	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=29.00;MQ0=0;QD=23.47;SB=-70.88	GT:AD:DP:GL:GQ	0/1:2,11:13:-37.71,-3.92,-7.64:37.23
+chr1	4025364	.	T	A	90.08	SnpCluster	AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=29.00;MQ0=0;QD=18.02;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,3:3:-12.50,-0.90,-0.00:9.03
+chr1	4025431	.	G	C	10.49	LowQual	AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=10.49;SB=-10.00	GT:AD:DP:GL:GQ	0/1:0,1:1:-4.29,-0.30,-0.00:1.76
+chr1	4025466	.	T	C	25.23	LowQual	AC=1;AF=0.50;AN=2;DP=3;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=29.00;MQ0=0;QD=8.41;SB=-10.00	GT:AD:DP:GL:GQ	0/1:0,2:3:-9.75,-4.24,-3.95:1.79
+chr1	4025523	.	A	C	21.19	LowQual	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=1;HaplotypeScore=4.30;MQ=29.00;MQ0=0;QD=4.24;SB=-10.00	GT:AD:DP:GL:GQ	0/1:3,2:3:-6.30,-0.90,-3.10:21.92
+chr1	4025542	.	T	C	37.83	LowQual	AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=12.61;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,2:2:-7.19,-0.60,-0.00:6.02
+chr1	4025586	.	G	C	7.40	PASS	AC=1;AF=0.50;AN=2;DP=5;Dels=0.20;HRun=0;HaplotypeScore=2.25;MQ=29.00;MQ0=0;OQ=51.98;QD=10.40;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,3:3:-9.39,-0.90,-3.95:30.43
+chr1	4025618	.	C	T	7.86	PASS	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=29.00;MQ0=0;OQ=87.13;QD=12.45;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,5:3:-12.20,-0.90,-0.00:9.03
+chr1	4025642	.	T	C	158.22	Indel	AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=31.64;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,5:5:-19.38,-1.51,-0.00:15.05
+chr1	4025697	.	A	T	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=29.00;MQ0=0;OQ=113.07;QD=22.61;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,4:5:-16.09,-1.51,-3.64:21.34
+chr1	4025746	.	T	G	32.28	LowQual	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=3.93;MQ=23.71;MQ0=1;QD=6.46;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,2:3:-7.41,-0.90,-3.74:28.36
+chr1	4025760	.	T	C	33.23	LowQual	AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=26.51;MQ0=0;QD=8.31;SB=-10.00	GT:AD:DP:GL:GQ	0/1:1,2:3:-10.45,-4.14,-3.85:1.79
+chr1	4026171	.	A	T	209.87	Indel	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=25.28;MQ0=0;QD=14.99;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,9:8:-26.67,-2.41,-4.00:15.91
+chr1	4026180	.	C	G	33.92	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.28;MQ0=0;QD=2.42;SB=-10.00	GT:AD:DP:GL:GQ	0/1:9,5:9:-9.39,-2.71,-29.13:66.75
+chr1	4026184	.	C	T	21.22	LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.28;MQ0=0;QD=1.52;SB=-10.00	GT:AD:DP:GL:GQ	0/1:9,5:9:-8.11,-2.71,-25.08:54.02
+chr1	4026206	.	C	G	51.98	Indel	AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.01;MQ0=1;QD=7.43;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,5:3:-9.39,-0.90,-4.15:32.44
+chr1	4026210	.	G	C	48.85	LowQual	AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.61;MQ0=1;QD=8.14;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,5:2:-8.29,-0.60,-0.00:6.02
+chr1	4026326	.	G	C	28.47	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=22.92;MQ=30.24;MQ0=0;QD=1.90;SB=-27.39	GT:AD:DP:GL:GQ	0/1:8,6:9:-8.84,-2.71,-32.55:61.30
+chr1	4026330	.	C	T	15.30	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=20.94;MQ=33.42;MQ0=0;QD=0.96;SB=-6.99	GT:AD:DP:GL:GQ	0/1:14,2:11:-8.11,-3.31,-31.44:48.01
+chr1	4026341	.	A	T	151.96	Indel	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=32.82;MQ=37.84;MQ0=1;QD=7.24;SB=-45.98	GT:AD:DP:GL:GQ	0/1:14,7:14:-22.70,-4.22,-31.99:99
+chr1	4026383	.	A	G	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=27.11;MQ=37.86;MQ0=1;OQ=685.36;QD=14.58;SB=-116.05	GT:AD:DP:GL:GQ	1/1:7,40:26:-76.32,-7.85,-4.20:36.49
+chr1	4026434	.	C	G	29.02	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.33;MQ0=0;QD=0.81;SB=5.05	GT:AD:DP:GL:GQ	0/1:34,2:8:-8.60,-2.41,-25.63:61.85
+chr1	4026435	.	A	T	728.54	SnpCluster	AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.33;MQ0=0;QD=20.24;SB=-50.99	GT:AD:DP:GL:GQ	1/1:2,34:20:-76.44,-6.02,-0.00:60.19
+chr1	4026437	.	T	A	762.24	SnpCluster	AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.33;MQ0=0;QD=21.17;SB=-46.39	GT:AD:DP:GL:GQ	1/1:2,34:20:-79.81,-6.02,-0.00:60.20
+chr1	4026440	.	T	G	564.23	SnpCluster	AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.87;MQ0=0;QD=17.10;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,31:17:-60.01,-5.12,-0.00:51.15
+chr1	4026444	.	C	G	41.07	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=34.30;MQ0=1;QD=1.28;SB=-6.99	GT:AD:DP:GL:GQ	0/1:30,2:3:-8.29,-0.90,-4.25:33.44
+chr1	4026449	.	A	T	483.60	SnpCluster	AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=34.81;MQ0=1;QD=16.68;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,29:14:-51.95,-4.22,-0.00:42.13
+chr1	4026483	.	G	A	173.76	Indel	AC=2;AF=1.00;AN=2;DP=7;Dels=0.14;HRun=0;HaplotypeScore=0.00;MQ=25.96;MQ0=0;QD=24.82;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,6:5:-20.94,-1.51,-0.00:15.05
+chr1	4026581	.	T	C	45.31	PASS	AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.51;MQ0=0;OQ=56.13;QD=14.03;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,4:3:-9.11,-0.91,-0.01:9
+chr1	4026636	.	T	A	64.25	PASS	AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.75;MQ0=0;OQ=1092.89;QD=35.25;SB=-113.17	GT:AD:DP:GL:GQ	1/1:0,31:29:-112.88,-8.73,-0.01:87.28
+chr1	4026761	.	T	A	283.60	PASS	AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=39.63;MQ0=0;OQ=910.42;QD=32.51;SB=-440.82	GT:AD:DP:GL:GQ	1/1:0,28:25:-94.63,-7.53,-0.01:75.24
+chr1	4026798	.	G	C	10.99	LowQual	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=12.99;MQ=22.58;MQ0=0;QD=2.20;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,3:1:-4.35,-0.30,-0.00:1.76
+chr1	4026914	.	T	C	49.44	PASS	AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.57;MQ0=0;OQ=246.59;QD=24.66;SB=-150.73	GT:AD:DP:GL:GQ	1/1:0,10:9:-28.25,-2.72,-0.01:27.05
+chr1	4026927	.	A	T	206.91	PASS	AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.61;MQ0=0;OQ=634.07;QD=30.19;SB=-308.12	GT:AD:DP:GL:GQ	1/1:0,21:18:-67.00,-5.42,-0.01:54.16
+chr1	4027026	.	C	T	64.95	Indel	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=32.20;MQ0=1;QD=1.71;SB=-49.74	GT:AD:DP:GL:GQ	0/1:32,6:37:-20.92,-11.15,-115.91:97.79
+chr1	4027042	.	T	C	614.97	Indel	AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=29.00;MQ0=0;QD=27.95;SB=-154.73	GT:AD:DP:GL:GQ	1/1:0,22:21:-65.11,-6.34,-0.03:63.13
+chr1	4027052	.	T	C	696.49	Indel	AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=34.82;SB=-114.05	GT:AD:DP:GL:GQ	1/1:0,20:20:-73.24,-6.03,-0.01:60.18
+chr1	4027210	.	G	C	19.50	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=26.88;MQ0=0;QD=1.39;SB=-27.39	GT:AD:DP:GL:GQ	0/1:12,2:10:-8.24,-3.01,-36.19:52.28
+chr1	4027332	.	C	G	36.70	PASS	AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.49;MQ0=0;OQ=1976.71;QD=43.93;SB=-544.06	GT:AD:DP:GL:GQ	1/1:0,45:45:-201.27,-13.56,-0.01:99
+chr1	4027338	.	T	C	290.59	PASS	AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.34;MQ0=0;OQ=1625.12;QD=35.33;SB=-497.48	GT:AD:DP:GL:GQ	1/1:0,46:46:-166.11,-13.85,-0.01:99
+chr1	4027382	rs4654478	T	C	529.46	Indel	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=33.88;MQ0=0;QD=11.77;SB=-150.80	GT:AD:DP:GL:GQ	0/1:25,20:45:-69.78,-13.55,-102.60:99
+chr1	4027391	.	A	T	124.12	Indel	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=29.00;MQ0=0;QD=3.18;SB=-45.98	GT:AD:DP:GL:GQ	0/1:32,7:37:-26.84,-11.14,-119.06:99
+chr1	4027395	.	T	A	21.79	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=29.00;MQ0=0;QD=0.61;SB=-10.00	GT:AD:DP:GL:GQ	0/1:32,4:36:-16.30,-10.84,-120.25:54.60
+chr1	4027428	rs4654405	C	A	54.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=1067.75;QD=35.59;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,30:30:-110.36,-9.03,-0.00:90.28
+chr1	4027512	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=38;Dels=0.03;HRun=0;HaplotypeScore=41.12;MQ=30.70;MQ0=0;OQ=583.71;QD=15.36;SB=-96.83	GT:AD:DP:GL:GQ	0/1:11,26:29:-70.09,-8.44,-49.32:99
+chr1	4027516	.	C	G	4.55	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=30.66;MQ0=0;OQ=294.17;QD=7.54;SB=2.04	GT:AD:DP:GL:GQ	0/1:30,9:29:-41.44,-8.74,-84.22:99
+chr1	4027660	rs4654407	G	A	193.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=42.76;MQ0=0;OQ=2435.59;QD=39.28;SB=-760.64	GT:AD:DP:GL:GQ	1/1:0,62:62:-247.16,-18.68,-0.02:99
+chr1	4027721	rs4654408	C	T	529.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.67;MQ0=0;OQ=1726.14;QD=39.23;SB=-623.32	GT:AD:DP:GL:GQ	1/1:0,44:43:-176.21,-12.95,-0.01:99
+chr1	4027907	rs4654409	G	A	268.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.85;MQ0=0;OQ=2188.75;QD=36.48;SB=-1120.98	GT:AD:DP:GL:GQ	1/1:0,60:57:-222.49,-17.18,-0.03:99
+chr1	4028014	rs10915398	T	C	85.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.65;MQ0=0;OQ=1826.56;QD=33.83;SB=-678.24	GT:AD:DP:GL:GQ	1/1:0,54:52:-186.26,-15.66,-0.02:99
+chr1	4028230	rs10753357	A	C	280.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.61;MQ0=0;OQ=1933.90;QD=32.78;SB=-901.67	GT:AD:DP:GL:GQ	1/1:0,59:56:-196.99,-16.87,-0.02:99
+chr1	4028383	rs10753358	C	A	101.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=2;HaplotypeScore=0.96;MQ=59.50;MQ0=0;OQ=3292.23;QD=35.40;SB=-1450.96	GT:AD:DP:GL:GQ	1/1:0,93:90:-328.22,-27.11,-0.03:99
+chr1	4028555	rs10915400	C	T	609.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2231.72;QD=39.15;SB=-1113.00	GT:AD:DP:GL:GQ	1/1:0,57:57:-226.78,-17.18,-0.02:99
+chr1	4028627	rs11586513	G	A	570.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2205.25;QD=39.38;SB=-957.37	GT:AD:DP:GL:GQ	1/1:0,56:55:-224.12,-16.57,-0.01:99
+chr1	4029107	rs17404781	C	A	590.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=2642.82;QD=36.71;SB=-848.25	GT:AD:DP:GL:GQ	1/1:0,72:72:-267.88,-21.68,-0.02:99
+chr1	4029794	rs4603097	A	G	153.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=2799.69;QD=36.36;SB=-819.68	GT:AD:DP:GL:GQ	1/1:1,76:76:-283.57,-22.89,-0.02:99
+chr1	4030208	rs4130940	A	G	693.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3003.68;QD=34.53;SB=-1360.53	GT:AD:DP:GL:GQ	1/1:0,87:86:-303.98,-25.91,-0.03:99
+chr1	4030429	rs4130941	T	C	169.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=60.00;MQ0=0;OQ=3432.78;QD=35.76;SB=-1689.36	GT:AD:DP:GL:GQ	1/1:0,96:95:-342.28,-28.61,-0.03:99
+chr1	4030544	rs4391636	T	C	184.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2626.35;QD=31.27;SB=-1250.03	GT:AD:DP:GL:GQ	1/1:0,84:83:-266.29,-25.03,-0.07:99
+chr1	4030874	rs4262509	T	C	686.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=2253.22;QD=36.34;SB=-816.67	GT:AD:DP:GL:GQ	1/1:0,62:62:-228.93,-18.68,-0.02:99
+chr1	4031041	rs4400586	C	T	220	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=2740.70;QD=40.30;SB=-1397.85	GT:AD:DP:GL:GQ	1/1:0,68:68:-277.67,-20.48,-0.01:99
+chr1	4031109	rs7537141	A	G	223.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.17;MQ=58.69;MQ0=0;OQ=2389.72;QD=33.66;SB=-1060.09	GT:AD:DP:GL:GQ	1/1:0,70:68:-242.58,-20.48,-0.02:99
+chr1	4031170	rs7537236	A	G	284.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.42;MQ0=0;OQ=1865.29;QD=33.31;SB=-585.57	GT:AD:DP:GL:GQ	1/1:0,56:52:-190.13,-15.66,-0.02:99
+chr1	4031176	rs7537237	A	G	151.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=58.47;MQ0=0;OQ=1912.22;QD=32.97;SB=-672.55	GT:AD:DP:GL:GQ	1/1:0,58:55:-194.84,-16.57,-0.03:99
+chr1	4031220	rs7532788	C	T	294.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.01;MQ0=0;OQ=2323.83;QD=38.10;SB=-1060.94	GT:AD:DP:GL:GQ	1/1:0,60:59:-235.99,-17.78,-0.02:99
+chr1	4031586	rs3936238	A	G	138.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=58.69;MQ0=0;OQ=2519.09;QD=35.48;SB=-1162.71	GT:AD:DP:GL:GQ	1/1:0,71:71:-255.52,-21.39,-0.03:99
+chr1	4031878	rs9628649	C	T	644.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.66;MQ0=0;OQ=2284.52;QD=38.72;SB=-825.09	GT:AD:DP:GL:GQ	1/1:0,59:58:-232.06,-17.48,-0.02:99
+chr1	4031986	rs9628650	G	T	130.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=59.09;MQ0=0;OQ=2689.72;QD=35.39;SB=-1301.17	GT:AD:DP:GL:GQ	1/1:0,75:74:-272.58,-22.29,-0.02:99
+chr1	4032433	rs7529548	G	C	483.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=2621.92;QD=40.34;SB=-1086.06	GT:AD:DP:GL:GQ	1/1:0,65:62:-265.80,-18.69,-0.02:99
+chr1	4032637	rs7538658	C	T	720.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2747.15;QD=39.25;SB=-1233.63	GT:AD:DP:GL:GQ	1/1:0,70:70:-278.33,-21.09,-0.03:99
+chr1	4032742	rs7529853	G	C	195.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.01;HRun=0;HaplotypeScore=1.43;MQ=59.67;MQ0=0;OQ=2970.07;QD=42.43;SB=-1256.98	GT:AD:DP:GL:GQ	1/1:0,69:70:-300.61,-20.79,-0.02:99
+chr1	4032815	rs10157040	T	G	55.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.79;MQ=60.00;MQ0=0;OQ=2073.63;QD=33.99;SB=-743.38	GT:AD:DP:GL:GQ	1/1:0,61:60:-210.97,-18.07,-0.02:99
+chr1	4032895	rs60405213	A	G	332.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=1606.75;QD=29.75;SB=-645.91	GT:AD:DP:GL:GQ	1/1:0,54:50:-164.30,-15.08,-0.04:99
+chr1	4032956	rs10157057	T	C	590.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.21;MQ0=0;OQ=1852.28;QD=34.95;SB=-804.30	GT:AD:DP:GL:GQ	1/1:0,53:53:-188.83,-15.97,-0.02:99
+chr1	4033505	.	A	T	38.74	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=20;HaplotypeScore=16.08;MQ=50.01;MQ0=1;QD=0.73;SB=62.20	GT:AD:DP:GL:GQ	0/1:43,10:38:-18.61,-11.45,-119.32:71.58
+chr1	4035925	rs6686087	G	A	676.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.29;MQ0=0;OQ=1910.92;QD=36.06;SB=-777.68	GT:AD:DP:GL:GQ	1/1:0,53:52:-194.71,-15.68,-0.03:99
+chr1	4036210	rs7553013	A	G	89.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=1455.02;QD=35.49;SB=-567.89	GT:AD:DP:GL:GQ	1/1:0,41:41:-149.10,-12.35,-0.01:99
+chr1	4037078	rs6671404	G	A	595.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.26;MQ0=0;OQ=2338.43;QD=39.63;SB=-1084.95	GT:AD:DP:GL:GQ	1/1:0,59:59:-237.45,-17.77,-0.02:99
+chr1	4037233	.	C	T	0.09	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=10.47;MQ=23.53;MQ0=14;OQ=386.45;QD=7.43;SB=-174.70	GT:AD:DP:GL:GQ	0/1:24,28:16:-46.75,-4.82,-13.21:83.85
+chr1	4037300	rs12731949	G	A	33.47	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=10.93;MQ=13.10;MQ0=15;QD=0.96;SB=-6.99	GT:AD:DP:GL:GQ	0/1:26,6:3:-7.53,-0.90,-3.57:26.65
+chr1	4037316	.	A	G	19.58	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=4.32;MQ=10.60;MQ0=15;QD=0.68;SB=-10.00	GT:AD:DP:GL:GQ	0/1:25,4:3:-6.14,-0.91,-2.76:18.51
+chr1	4037317	rs12747176	C	T	33.48	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=4.32;MQ=10.78;MQ0=15;QD=1.20;SB=-10.00	GT:AD:DP:GL:GQ	0/1:25,3:3:-7.53,-0.90,-3.30:23.93
+chr1	4037349	rs55974954	C	T	4.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=15.25;MQ0=10;OQ=78.13;QD=3.91;SB=-10.00	GT:AD:DP:GL:GQ	0/1:11,9:5:-12.60,-1.51,-5.79:42.85
+chr1	4037373	.	C	T	49.25	HARD_TO_VALIDATE;LowQual;SnpCluster	AC=2;AF=1.00;AN=2;DP=23;Dels=0.09;HRun=0;HaplotypeScore=5.10;MQ=12.43;MQ0=14;QD=2.14;SB=-10.00	GT:AD:DP:GL:GQ	1/1:17,4:2:-8.33,-0.60,-0.00:6.02
+chr1	4037374	rs58910132	A	G	67.17	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.10;HRun=0;HaplotypeScore=2.46;MQ=12.64;MQ0=13;QD=3.20;SB=-10.00	GT:AD:DP:GL:GQ	1/1:14,5:3:-10.21,-0.90,-0.00:9.03
+chr1	4037375	.	C	T	89.13	HARD_TO_VALIDATE;SnpCluster	AC=2;AF=1.00;AN=2;DP=21;Dels=0.10;HRun=0;HaplotypeScore=2.62;MQ=12.64;MQ0=13;QD=4.24;SB=-10.00	GT:AD:DP:GL:GQ	1/1:14,5:3:-12.40,-0.90,-0.00:9.03
+chr1	4037523	.	C	T	36.25	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=8.14;MQ=8.07;MQ0=27;QD=0.91;SB=-10.00	GT:AD:DP:GL:GQ	0/1:35,5:3:-7.81,-0.90,-3.47:25.65
+chr1	4037532	.	G	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=7.98;MQ=8.93;MQ0=30;OQ=75.12;QD=1.67;SB=-10.00	GT:AD:DP:GL:GQ	0/1:32,13:5:-12.30,-1.51,-6.19:46.86
+chr1	4037589	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=30.55;MQ=12.67;MQ0=42;OQ=141.32;QD=1.74;SB=-10.00	GT:AD:DP:GL:GQ	0/1:62,18:18:-22.84,-5.42,-40.02:99
+chr1	4037590	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=31.66;MQ=13.12;MQ0=42;OQ=99.34;QD=1.18;SB=-10.00	GT:AD:DP:GL:GQ	0/1:65,14:18:-18.65,-5.43,-43.06:99
+chr1	4037755	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=10.80;MQ=28.57;MQ0=9;OQ=123.11;QD=4.25;SB=-10.00	GT:AD:DP:GL:GQ	0/1:16,13:15:-20.11,-4.52,-34.90:99
+chr1	4037764	.	G	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=11.39;MQ=27.02;MQ0=10;OQ=406.03;QD=10.68;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,21:18:-49.31,-5.43,-18.48:99
+chr1	4037797	.	G	A	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=1;HaplotypeScore=2.36;MQ=25.37;MQ0=16;OQ=242.41;QD=2.96;SB=-0.99	GT:AD:DP:GL:GQ	0/1:69,13:49:-42.29,-14.76,-143.27:99
+chr1	4037813	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=1;HaplotypeScore=30.43;MQ=23.50;MQ0=19;OQ=796.43;QD=8.38;SB=2.04	GT:AD:DP:GL:GQ	0/1:48,46:55:-99.50,-16.57,-97.10:99
+chr1	4037822	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=0;HaplotypeScore=35.10;MQ=23.24;MQ0=31;OQ=606.69;QD=4.81;SB=-57.33	GT:AD:DP:GL:GQ	0/1:70,54:63:-82.95,-19.00,-147.74:99
+chr1	4037843	rs61768802	C	A	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=180;Dels=0.00;HRun=1;HaplotypeScore=17.92;MQ=21.78;MQ0=58;OQ=417.65;QD=2.32;SB=-34.91	GT:AD:DP:GL:GQ	0/1:148,32:87:-71.25,-26.21,-246.67:99
+chr1	4037880	rs61768803	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=196;Dels=0.00;HRun=0;HaplotypeScore=29.31;MQ=22.28;MQ0=61;OQ=120.84;QD=0.62;SB=11.02	GT:AD:DP:GL:GQ	0/1:165,26:69:-36.22,-20.85,-175.88:99
+chr1	4037929	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=1;HaplotypeScore=2.77;MQ=21.90;MQ0=34;OQ=107.87;QD=1.14;SB=35.15	GT:AD:DP:GL:GQ	0/1:76,17:46:-27.95,-13.88,-137.64:99
+chr1	4037943	.	C	T	85.40	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=21.61;MQ0=16;OQ=809.30;QD=13.95;SB=-392.58	GT:AD:DP:GL:GQ	0/1:14,44:31:-93.56,-9.34,-20.82:99
+chr1	4037953	.	T	C	0.02	FDRtranche1.00to2.00	AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;HRun=3;HaplotypeScore=11.12;MQ=21.57;MQ0=12;OQ=534.72;QD=14.07;SB=-137.10	GT:AD:DP:GL:GQ	1/1:2,36:20:-60.44,-6.03,-3.38:26.46
+chr1	4037971	.	G	A	35.49	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=11.71;MQ0=7;QD=2.96;SB=-7.00	GT:AD:DP:GL:GQ	0/1:2,10:3:-7.73,-0.90,-2.97:20.65
+chr1	4038007	.	C	T	11.96	PASS	AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=24.37;MQ0=17;OQ=478.18;QD=12.58;SB=-0.67	GT:AD:DP:GL:GQ	1/1:9,29:15:-54.99,-4.52,-3.70:8.18
+chr1	4038085	.	G	A	6.73	PASS	AC=2;AF=1.00;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=25.54;MQ0=21;OQ=1434.12;QD=19.65;SB=-222.29	GT:AD:DP:GL:GQ	1/1:0,70:37:-147.01,-11.15,-0.01:99
+chr1	4038095	.	A	C	37.18	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=2;HaplotypeScore=5.05;MQ=31.28;MQ0=12;QD=0.48;SB=35.10	GT:AD:DP:GL:GQ	0/1:67,11:51:-22.37,-15.37,-153.89:70.01
+chr1	4038119	rs61768805	A	G	52.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=34.39;MQ0=8;OQ=2201.59;QD=25.60;SB=-880.89	GT:AD:DP:GL:GQ	1/1:0,86:64:-223.78,-19.28,-0.04:99
+chr1	4038137	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=1;HaplotypeScore=16.06;MQ=35.46;MQ0=14;OQ=344.80;QD=2.45;SB=-97.28	GT:AD:DP:GL:GQ	0/1:105,36:95:-66.41,-28.65,-282.14:99
+chr1	4038181	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=35.03;MQ0=15;OQ=1093.66;QD=4.11;SB=-524.11	GT:AD:DP:GL:GQ	0/1:186,80:195:-171.41,-58.76,-524.00:99
+chr1	4038248	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=280;Dels=0.00;HRun=0;HaplotypeScore=30.85;MQ=29.46;MQ0=44;OQ=1065.01;QD=3.80;SB=-230.16	GT:AD:DP:GL:GQ	0/1:155,104:139:-156.85,-47.07,-312.49:99
+chr1	4038269	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=221;Dels=0.00;HRun=2;HaplotypeScore=13.90;MQ=27.15;MQ0=44;OQ=427.47;QD=1.93;SB=-154.75	GT:AD:DP:GL:GQ	0/1:158,62:110:-79.18,-33.15,-296.78:99
+chr1	4038306	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=30.95;MQ=24.15;MQ0=24;OQ=80.75;QD=0.71;SB=17.44	GT:AD:DP:GL:GQ	0/1:88,21:54:-27.64,-16.28,-152.20:99
+chr1	4038311	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=30.17;MQ=23.18;MQ0=20;OQ=320.40;QD=3.56;SB=-113.10	GT:AD:DP:GL:GQ	0/1:60,30:46:-49.20,-13.87,-108.56:99
+chr1	4038321	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=3;HaplotypeScore=15.26;MQ=23.68;MQ0=14;OQ=766.53;QD=12.99;SB=-327.28	GT:AD:DP:GL:GQ	0/1:10,49:31:-89.28,-9.34,-16.69:73.43
+chr1	4038334	.	G	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.69;MQ=25.40;MQ0=9;OQ=78.94;QD=1.49;SB=-27.72	GT:AD:DP:GL:GQ	0/1:40,11:25:-21.55,-10.37,-63.16:99
+chr1	4038397	.	A	G	17.54	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.28;MQ=29.53;MQ0=4;OQ=326.31;QD=7.42;SB=-58.84	GT:AD:DP:GL:GQ	0/1:24,20:28:-44.35,-8.44,-57.72:99
+chr1	4038422	rs61768806	G	A	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=18.20;MQ=33.84;MQ0=4;OQ=183.71;QD=3.40;SB=-62.31	GT:AD:DP:GL:GQ	0/1:35,13:24:-31.46,-9.80,-50.09:99
+chr1	4038450	rs9426493	G	A	0.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=7.50;MQ=40.53;MQ0=7;OQ=257.95;QD=3.31;SB=38.10	GT:AD:DP:GL:GQ	0/1:50,27:46:-42.95,-13.87,-108.04:99
+chr1	4038485	.	T	C	49.84	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=1;HaplotypeScore=36.99;MQ=38.79;MQ0=13;QD=0.38;SB=-42.38	GT:AD:DP:GL:GQ	0/1:107,23:79:-32.08,-23.81,-273.26:82.67
+chr1	4038495	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=3;HaplotypeScore=26.37;MQ=38.36;MQ0=11;OQ=110.49;QD=0.81;SB=81.70	GT:AD:DP:GL:GQ	0/1:101,35:77:-37.55,-23.22,-250.69:99
+chr1	4038559	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=2;HaplotypeScore=4.40;MQ=37.40;MQ0=14;OQ=181.94;QD=1.28;SB=76.72	GT:AD:DP:GL:GQ	0/1:114,27:102:-52.21,-30.74,-302.69:99
+chr1	4038595	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=10.57;MQ=44.92;MQ0=10;OQ=118.91;QD=1.67;SB=44.58	GT:AD:DP:GL:GQ	0/1:49,22:52:-30.86,-15.68,-162.15:99
+chr1	4038920	rs12240075	G	A	506.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.13;MQ0=0;OQ=3029.69;QD=39.35;SB=-1486.40	GT:AD:DP:GL:GQ	1/1:0,77:75:-306.57,-22.59,-0.02:99
+chr1	4039098	rs4073835	G	A	496.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2305.48;QD=39.08;SB=-997.03	GT:AD:DP:GL:GQ	1/1:0,59:59:-234.15,-17.78,-0.02:99
+chr1	4039791	rs4639725	C	T	236.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=59.67;MQ0=0;OQ=2672.94;QD=38.18;SB=-1315.36	GT:AD:DP:GL:GQ	1/1:0,70:69:-270.90,-20.79,-0.02:99
+chr1	4039890	rs4436359	C	A	272.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.38;MQ=60.00;MQ0=0;OQ=1804.54;QD=34.70;SB=-797.85	GT:AD:DP:GL:GQ	1/1:1,51:51:-184.06,-15.36,-0.02:99
+chr1	4040736	rs6684922	G	A	149.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=2464.15;QD=39.74;SB=-984.31	GT:AD:DP:GL:GQ	1/1:0,62:61:-250.01,-18.37,-0.01:99
+chr1	4041212	rs7418376	A	G	9.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=4.36;MQ=59.69;MQ0=0;OQ=2587.00;QD=34.49;SB=-1318.64	GT:AD:DP:GL:GQ	1/1:0,75:71:-262.30,-21.38,-0.02:99
+chr1	4041774	rs6657076	T	C	524.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.94;MQ0=0;OQ=2268.81;QD=30.25;SB=-1070.20	GT:AD:DP:GL:GQ	1/1:0,75:71:-230.53,-21.41,-0.06:99
+chr1	4045735	rs10915422	A	C	14.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=4.42;MQ=59.68;MQ0=0;OQ=2455.12;QD=33.63;SB=-728.83	GT:AD:DP:GL:GQ	1/1:0,73:71:-249.12,-21.38,-0.02:99
+chr1	4045888	rs10915423	A	C	727.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2031.28;QD=35.02;SB=-998.12	GT:AD:DP:GL:GQ	1/1:0,58:58:-206.73,-17.47,-0.02:99
+chr1	4046948	rs10915425	T	G	80.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=53.47;MQ0=0;OQ=1869.59;QD=31.69;SB=-736.37	GT:AD:DP:GL:GQ	1/1:0,59:55:-190.57,-16.57,-0.02:99
+chr1	4046996	rs55774050	C	G	2240.61	Indel	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=9.46;MQ=51.11;MQ0=0;QD=43.09;SB=-978.74	GT:AD:DP:GL:GQ	1/1:0,52:52:-227.66,-15.67,-0.01:99
+chr1	4047821	rs11578552	T	C	402.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=2100.45;QD=30.89;SB=-846.51	GT:AD:DP:GL:GQ	1/1:0,68:66:-213.69,-19.91,-0.06:99
+chr1	4047883	rs11577344	C	T	490.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1935.40;QD=37.95;SB=-660.87	GT:AD:DP:GL:GQ	1/1:0,51:48:-197.13,-14.46,-0.01:99
+chr1	4049164	rs7411603	A	G	3.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=6.69;MQ=58.71;MQ0=0;OQ=1270.28;QD=27.03;SB=-493.17	GT:AD:DP:GL:GQ	1/1:0,47:41:-130.65,-12.36,-0.04:99
+chr1	4050387	rs10753365	G	A	99.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=58.61;MQ0=0;OQ=1534.51;QD=32.65;SB=-464.08	GT:AD:DP:GL:GQ	1/1:0,46:42:-157.07,-12.67,-0.03:99
+chr1	4051611	rs4548406	T	C	78.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.20;MQ0=0;OQ=1346.57;QD=28.65;SB=-544.85	GT:AD:DP:GL:GQ	1/1:0,47:44:-138.29,-13.28,-0.05:99
+chr1	4051999	rs12123119	C	T	624.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2169.89;QD=37.41;SB=-1044.39	GT:AD:DP:GL:GQ	1/1:0,58:55:-220.59,-16.57,-0.02:99
+chr1	4052066	rs4654410	C	T	678.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=2087.99;QD=37.96;SB=-873.17	GT:AD:DP:GL:GQ	1/1:0,55:53:-212.40,-15.97,-0.02:99
+chr1	4052788	rs4481820	C	A	313.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.81;MQ0=0;OQ=1188.08;QD=18.86;SB=-612.83	GT:AD:DP:GL:GQ	0/1:26,37:61:-140.47,-18.38,-73.47:99
+chr1	4052947	rs6676961	T	G	272.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=60.00;MQ0=0;OQ=1401.56;QD=15.75;SB=-713.67	GT:AD:DP:GL:GQ	0/1:39,50:87:-169.64,-26.20,-144.08:99
+chr1	4053067	rs12125719	A	G	101.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.17;MQ0=0;OQ=1483.09;QD=29.08;SB=-606.95	GT:AD:DP:GL:GQ	1/1:0,51:48:-151.94,-14.48,-0.05:99
+chr1	4053090	rs12125725	A	G	83.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.17;MQ0=0;OQ=1585.81;QD=31.09;SB=-493.18	GT:AD:DP:GL:GQ	1/1:0,51:49:-162.20,-14.77,-0.03:99
+chr1	4053122	rs12126649	T	C	176.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.71;MQ=59.24;MQ0=0;OQ=907.97;QD=14.88;SB=-331.31	GT:AD:DP:GL:GQ	0/1:25,36:59:-111.87,-17.79,-96.53:99
+chr1	4055170	rs12033210	T	C	0.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=1.74;MQ=28.53;MQ0=2;OQ=209.19;QD=4.65;SB=-102.57	GT:AD:DP:GL:GQ	0/1:32,13:39:-35.96,-11.75,-110.64:99
+chr1	4056038	rs10799198	G	A	260.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.90;MQ=58.67;MQ0=0;OQ=782.28;QD=15.96;SB=-386.17	GT:AD:DP:GL:GQ	0/1:25,24:47:-95.68,-14.17,-75.73:99
+chr1	4057058	rs4600014	A	G	442.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=917.69;QD=13.70;SB=-389.30	GT:AD:DP:GL:GQ	0/1:34,33:66:-114.93,-19.88,-136.81:99
+chr1	4057633	rs4361964	G	C	120.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=2.73;MQ=59.22;MQ0=0;OQ=837.80;QD=15.51;SB=-437.88	GT:AD:DP:GL:GQ	0/1:29,25:53:-103.04,-15.97,-126.00:99
+chr1	4057702	rs4351611	C	T	297.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=59.56;MQ0=0;OQ=594.05;QD=11.21;SB=-284.78	GT:AD:DP:GL:GQ	0/1:33,20:53:-78.67,-15.98,-105.42:99
+chr1	4057917	.	A	T	65.58	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.62;MQ0=0;OQ=752.30;QD=12.54;SB=-170.72	GT:AD:DP:GL:GQ	0/1:33,27:58:-95.98,-17.47,-122.23:99
+chr1	4058815	rs10915428	G	T	369.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.39;MQ0=0;OQ=1224.65;QD=16.11;SB=-630.74	GT:AD:DP:GL:GQ	0/1:35,41:75:-148.34,-22.59,-115.71:99
+chr1	4059239	rs10799199	C	T	251.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.66;MQ0=0;OQ=1243.57;QD=18.84;SB=-304.82	GT:AD:DP:GL:GQ	0/1:29,37:64:-146.92,-19.28,-100.42:99
+chr1	4059378	.	C	T	11.57	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=3;HaplotypeScore=0.47;MQ=59.47;MQ0=0;OQ=1236.26;QD=14.72;SB=-551.55	GT:AD:DP:GL:GQ	0/1:45,38:82:-151.61,-24.70,-168.36:99
+chr1	4060338	rs10799200	T	C	170.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=152.75;QD=7.64;SB=-10.00	GT:AD:DP:GL:GQ	0/1:13,7:19:-24.28,-5.72,-48.27:99
+chr1	4064782	rs61768818	G	A	481.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.07;MQ0=0;OQ=848.15;QD=13.90;SB=-350.47	GT:AD:DP:GL:GQ	0/1:34,27:59:-105.87,-17.77,-118.54:99
+chr1	4066674	rs12032257	C	T	294.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=59.36;MQ0=0;OQ=916.01;QD=14.09;SB=-410.80	GT:AD:DP:GL:GQ	0/1:35,30:64:-114.18,-19.29,-113.47:99
+chr1	4067283	.	T	C	0.61	PASS	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=2;HaplotypeScore=4.39;MQ=59.62;MQ0=0;OQ=557.04;QD=9.13;SB=-241.90	GT:AD:DP:GL:GQ	0/1:35,25:58:-76.48,-17.49,-133.72:99
+chr1	4067926	rs7542313	A	G	387.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=220.94;QD=10.52;SB=-100.82	GT:AD:DP:GL:GQ	0/1:11,10:19:-31.10,-5.72,-40.90:99
+chr1	4075727	.	C	T	158.87	PASS	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.34;MQ=59.67;MQ0=0;OQ=1143.65;QD=16.34;SB=-503.75	GT:AD:DP:GL:GQ	0/1:35,35:66:-137.54,-19.89,-102.02:99
+chr1	4075966	rs6670920	T	C	606.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=1104.32;QD=15.13;SB=-452.80	GT:AD:DP:GL:GQ	0/1:30,43:71:-135.11,-21.40,-121.92:99
+chr1	4077630	rs4654486	G	A	691.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2711.47;QD=39.87;SB=-1087.95	GT:AD:DP:GL:GQ	1/1:0,68:68:-274.75,-20.48,-0.02:99
+chr1	4078163	rs10737402	T	C	504.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=530.04;QD=10.82;SB=-231.26	GT:AD:DP:GL:GQ	0/1:26,23:49:-71.06,-14.78,-100.24:99
+chr1	4080498	rs12042946	T	C	249.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=60.30;MQ0=0;OQ=891.53;QD=12.56;SB=-237.45	GT:AD:DP:GL:GQ	0/1:37,34:69:-113.22,-20.78,-148.64:99
+chr1	4080702	rs12040805	C	T	139.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.60;MQ0=0;OQ=776.81;QD=15.54;SB=-108.61	GT:AD:DP:GL:GQ	0/1:26,24:46:-94.83,-13.87,-71.68:99
+chr1	4081256	rs10753367	T	C	35.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=3;HaplotypeScore=2.04;MQ=59.74;MQ0=0;OQ=1167.96;QD=12.98;SB=-513.88	GT:AD:DP:GL:GQ	0/1:48,42:88:-146.59,-26.51,-188.24:99
+chr1	4081433	rs10799203	T	G	17.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.74;MQ=59.59;MQ0=0;OQ=328.89;QD=7.15;SB=-123.86	GT:AD:DP:GL:GQ	0/1:29,17:43:-49.13,-12.95,-102.00:99
+chr1	4082645	rs4400585	G	T	491.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=492.73;QD=10.71;SB=-210.53	GT:AD:DP:GL:GQ	0/1:27,19:44:-65.81,-13.26,-82.00:99
+chr1	4082866	rs10915437	A	G	75.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=4.59;MQ=58.36;MQ0=0;OQ=891.90;QD=12.56;SB=-289.16	GT:AD:DP:GL:GQ	0/1:37,34:68:-112.97,-20.49,-138.67:99
+chr1	4083359	rs56090673	C	T	320.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1009.69;QD=17.11;SB=-451.46	GT:AD:DP:GL:GQ	0/1:27,32:58:-121.73,-17.48,-93.77:99
+chr1	4083978	rs7531421	A	G	116.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=57.42;MQ0=0;OQ=435.48;QD=7.02;SB=-215.25	GT:AD:DP:GL:GQ	0/1:41,21:60:-64.91,-18.08,-162.54:99
+chr1	4084862	rs6675734	C	T	47.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=5.09;MQ=59.20;MQ0=0;OQ=1105.86;QD=19.07;SB=-554.64	GT:AD:DP:GL:GQ	0/1:25,33:57:-131.05,-17.18,-82.44:99
+chr1	4084986	rs10753368	A	G	566.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=1198.41;QD=14.10;SB=-565.61	GT:AD:DP:GL:GQ	0/1:44,41:83:-148.13,-25.00,-168.94:99
+chr1	4085630	rs6679136	C	T	24.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=4.32;MQ=58.42;MQ0=0;OQ=804.43;QD=14.36;SB=-252.24	GT:AD:DP:GL:GQ	0/1:29,27:53:-99.70,-15.97,-99.87:99
+chr1	4085663	rs6669476	G	A	136.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=57.81;MQ0=0;OQ=833.61;QD=13.89;SB=-171.20	GT:AD:DP:GL:GQ	0/1:32,27:56:-103.51,-16.87,-106.04:99
+chr1	4086169	rs6426389	C	T	138.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=59.69;MQ0=0;OQ=1183.25;QD=19.72;SB=-609.44	GT:AD:DP:GL:GQ	0/1:26,34:60:-139.68,-18.07,-94.16:99
+chr1	4086333	rs6663976	C	G	599.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=3962.79;QD=44.03;SB=-1451.88	GT:AD:DP:GL:GQ	1/1:0,90:89:-395.28,-26.81,-0.02:99
+chr1	4087812	rs4654487	T	C	259.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.38;MQ=59.52;MQ0=0;OQ=1480.85;QD=30.85;SB=-766.73	GT:AD:DP:GL:GQ	1/1:0,48:47:-151.71,-14.17,-0.04:99
+chr1	4089403	.	G	C	16.75	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.80;MQ=58.74;MQ0=0;QD=0.45;SB=53.21	GT:AD:DP:GL:GQ	0/1:27,10:26:-12.79,-7.84,-102.04:49.49
+chr1	4089489	rs7536041	T	C	90.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=59.19;MQ0=0;OQ=812.10;QD=15.62;SB=-146.31	GT:AD:DP:GL:GQ	0/1:23,29:51:-99.86,-15.37,-93.49:99
+chr1	4090545	rs4282783	T	G	725.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2332.11;QD=35.34;SB=-970.80	GT:AD:DP:GL:GQ	1/1:0,66:66:-236.81,-19.88,-0.02:99
+chr1	4091584	rs4654488	A	T	219.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.30;MQ=60.00;MQ0=0;OQ=743.21;QD=16.52;SB=-370.44	GT:AD:DP:GL:GQ	0/1:20,25:44:-90.86,-13.25,-75.80:99
+chr1	4092168	rs10915441	C	G	2.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=4;HaplotypeScore=3.62;MQ=59.69;MQ0=0;OQ=1389.48;QD=18.78;SB=-645.48	GT:AD:DP:GL:GQ	0/1:35,39:69:-163.06,-20.83,-116.77:99
+chr1	4092567	rs10915442	A	G	394.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.42;MQ0=0;OQ=572.04;QD=14.30;SB=-311.22	GT:AD:DP:GL:GQ	0/1:18,22:39:-72.24,-11.76,-67.58:99
+chr1	4093270	rs10799206	C	G	674.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.42;MQ0=0;OQ=2045.47;QD=38.59;SB=-902.40	GT:AD:DP:GL:GQ	1/1:0,52:50:-208.16,-15.07,-0.02:99
+chr1	4093286	rs12409803	G	A	414.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=57.03;MQ0=0;OQ=773.71;QD=14.33;SB=-322.45	GT:AD:DP:GL:GQ	0/1:28,26:51:-96.03,-15.38,-79.04:99
+chr1	4093324	rs10915443	G	C	254.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=58.02;MQ0=0;OQ=1430.72;QD=20.15;SB=-674.45	GT:AD:DP:GL:GQ	0/1:30,40:69:-167.15,-20.79,-134.28:99
+chr1	4093733	rs6693173	A	G	464.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=1381.36;QD=28.78;SB=-644.93	GT:AD:DP:GL:GQ	1/1:0,48:45:-141.76,-13.57,-0.04:99
+chr1	4094457	rs4131506	A	C	340.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.60;MQ0=0;OQ=704.94;QD=12.15;SB=-316.99	GT:AD:DP:GL:GQ	0/1:32,26:58:-91.25,-17.47,-120.43:99
+chr1	4094660	rs4131508	A	G	571.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=1332.71;QD=17.31;SB=-634.89	GT:AD:DP:GL:GQ	0/1:33,44:77:-159.75,-23.19,-134.55:99
+chr1	4094683	rs4630099	A	G	443.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1288.63;QD=16.31;SB=-670.63	GT:AD:DP:GL:GQ	0/1:36,43:77:-155.34,-23.19,-143.15:99
+chr1	4095397	rs10915444	T	C	1.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=8.82;MQ=58.53;MQ0=0;OQ=789.45;QD=10.25;SB=-380.13	GT:AD:DP:GL:GQ	0/1:49,28:72:-103.91,-21.68,-179.32:99
+chr1	4095558	rs35986531	G	A	271.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=1.49;MQ=56.64;MQ0=0;OQ=1336.75;QD=16.71;SB=-522.69	GT:AD:DP:GL:GQ	0/1:36,44:75:-159.55,-22.59,-133.47:99
+chr1	4095815	rs12118815	A	T	0.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=1;HaplotypeScore=13.10;MQ=57.70;MQ0=3;OQ=1249.48;QD=13.88;SB=-570.06	GT:AD:DP:GL:GQ	0/1:44,46:80:-152.33,-24.10,-146.70:99
+chr1	4095919	.	A	T	39.64	LowQual	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=51.56;MQ0=5;QD=0.50;SB=-37.91	GT:AD:DP:GL:GQ	0/1:71,9:66:-27.13,-19.88,-223.94:72.48
+chr1	4096225	.	A	G	48.26	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.44;MQ=52.24;MQ0=7;QD=0.68;SB=74.28	GT:AD:DP:GL:GQ	0/1:64,7:63:-27.09,-18.98,-229.53:81.10
+chr1	4096236	.	T	G	0.06	PASS	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=54.07;MQ0=3;OQ=91.64;QD=1.31;SB=86.24	GT:AD:DP:GL:GQ	0/1:61,9:66:-32.33,-19.88,-208.22:99
+chr1	4096240	.	A	T	0.08	PASS	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=53.91;MQ0=2;OQ=161.77;QD=2.16;SB=86.29	GT:AD:DP:GL:GQ	0/1:64,11:72:-41.14,-21.68,-231.71:99
+chr1	4096257	.	A	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=53.32;MQ0=2;OQ=207.48;QD=2.56;SB=92.31	GT:AD:DP:GL:GQ	0/1:68,13:79:-47.82,-23.79,-251.49:99
+chr1	4096278	.	A	G	232.76	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=0;HaplotypeScore=27.32;MQ=52.46;MQ0=1;QD=2.68;SB=98.35	GT:AD:DP:GL:GQ	0/1:72,15:85:-52.16,-25.60,-288.15:99
+chr1	4096286	.	G	A	106.04	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=1;HaplotypeScore=48.93;MQ=51.56;MQ0=1;QD=1.18;SB=98.32	GT:AD:DP:GL:GQ	0/1:78,12:85:-39.49,-25.60,-276.62:99
+chr1	4096288	rs34088827	G	A	955.67	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=1;HaplotypeScore=48.46;MQ=51.26;MQ0=1;QD=10.62;SB=-379.33	GT:AD:DP:GL:GQ	0/1:57,33:88:-125.36,-26.51,-207.05:99
+chr1	4096294	.	A	T	86.31	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=1;HaplotypeScore=32.32;MQ=50.46;MQ0=1;QD=0.97;SB=89.30	GT:AD:DP:GL:GQ	0/1:73,16:80:-36.01,-24.10,-264.64:99
+chr1	4096606	rs28726337	A	G	0.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=2;HaplotypeScore=13.44;MQ=43.57;MQ0=1;OQ=262.51;QD=2.76;SB=-123.92	GT:AD:DP:GL:GQ	0/1:75,20:86:-55.44,-25.91,-287.10:99
+chr1	4096617	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=1;HaplotypeScore=34.91;MQ=42.33;MQ0=1;OQ=1160.59;QD=10.01;SB=-606.06	GT:AD:DP:GL:GQ	0/1:70,46:109:-152.17,-32.83,-258.54:99
+chr1	4096620	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=123;Dels=0.01;HRun=0;HaplotypeScore=30.11;MQ=42.25;MQ0=1;OQ=989.14;QD=8.04;SB=-388.23	GT:AD:DP:GL:GQ	0/1:72,50:106:-134.12,-31.93,-263.47:99
+chr1	4096638	rs28412783	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=181;Dels=0.02;HRun=0;HaplotypeScore=64.64;MQ=40.70;MQ0=1;OQ=1178.07;QD=6.51;SB=-446.63	GT:AD:DP:GL:GQ	0/1:123,47:169:-194.38,-73.29,-545.37:99
+chr1	4096655	rs61768832	A	G	321.42	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=228;Dels=0.00;HRun=1;HaplotypeScore=261.82;MQ=41.93;MQ0=0;QD=1.41;SB=-157.54	GT:AD:DP:GL:GQ	0/1:199,29:224:-102.90,-67.48,-791.83:99
+chr1	4096678	.	T	G	1342.80	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=236;Dels=0.00;HRun=0;HaplotypeScore=216.99;MQ=43.01;MQ0=0;QD=5.69;SB=-512.77	GT:AD:DP:GL:GQ	0/1:166,63:218:-227.86,-90.30,-587.53:99
+chr1	4096685	.	A	G	1626.24	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=239;Dels=0.00;HRun=1;HaplotypeScore=162.66;MQ=41.97;MQ0=0;QD=6.80;SB=-808.35	GT:AD:DP:GL:GQ	0/1:167,72:225:-233.68,-67.78,-652.24:99
+chr1	4096698	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=228;Dels=0.00;HRun=0;HaplotypeScore=76.98;MQ=42.62;MQ0=0;OQ=2269.48;QD=9.95;SB=-1066.45	GT:AD:DP:GL:GQ	0/1:129,90:219:-325.16,-94.93,-493.11:99
+chr1	4096706	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=230;Dels=0.00;HRun=1;HaplotypeScore=79.95;MQ=43.15;MQ0=0;OQ=1034.27;QD=4.50;SB=-170.01	GT:AD:DP:GL:GQ	0/1:185,45:223:-173.88,-67.17,-658.24:99
+chr1	4096718	rs61768834	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=216;Dels=0.00;HRun=0;HaplotypeScore=38.48;MQ=44.61;MQ0=0;OQ=645.34;QD=2.99;SB=-265.93	GT:AD:DP:GL:GQ	0/1:168,32:157:-165.70,-97.89,-554.00:99
+chr1	4096731	.	G	A	559.62	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=83.54;MQ=45.39;MQ0=0;QD=3.13;SB=44.95	GT:AD:DP:GL:GQ	0/1:150,29:155:-105.94,-46.69,-468.61:99
+chr1	4096732	rs61768835	A	G	2251.43	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.00;HRun=2;HaplotypeScore=115.12;MQ=45.31;MQ0=0;QD=13.17;SB=-1083.79	GT:AD:DP:GL:GQ	0/1:80,91:158:-276.04,-47.61,-312.72:99
+chr1	4096736	rs61768836	A	G	2066.81	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.02;HRun=0;HaplotypeScore=91.40;MQ=45.63;MQ0=0;QD=12.23;SB=-1029.89	GT:AD:DP:GL:GQ	0/1:85,81:160:-257.27,-47.30,-336.21:99
+chr1	4096755	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=1;HaplotypeScore=46.33;MQ=46.26;MQ0=0;OQ=201.55;QD=1.56;SB=65.52	GT:AD:DP:GL:GQ	0/1:112,17:113:-57.49,-34.05,-383.82:99
+chr1	4096759	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=42.17;MQ=46.84;MQ0=0;OQ=310.94;QD=2.51;SB=-151.81	GT:AD:DP:GL:GQ	0/1:106,18:122:-71.13,-36.75,-367.88:99
+chr1	4096775	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=30.95;MQ=47.51;MQ0=0;OQ=647.24;QD=5.73;SB=52.09	GT:AD:DP:GL:GQ	0/1:87,26:107:-100.24,-32.23,-298.38:99
+chr1	4096805	.	A	G	20.07	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=14.94;MQ=48.07;MQ0=0;QD=0.18;SB=107.37	GT:AD:DP:GL:GQ	0/1:94,15:99:-35.11,-29.83,-355.50:52.86
+chr1	4096811	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=1;HaplotypeScore=14.56;MQ=47.07;MQ0=0;OQ=301.49;QD=2.87;SB=92.31	GT:AD:DP:GL:GQ	0/1:85,20:99:-63.26,-29.83,-325.00:99
+chr1	4096845	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=1;HaplotypeScore=27.21;MQ=46.78;MQ0=0;OQ=135.08;QD=1.34;SB=107.37	GT:AD:DP:GL:GQ	0/1:86,15:98:-46.31,-29.52,-344.47:99
+chr1	4096895	rs6702633	G	A	282.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=48.03;MQ0=0;OQ=1209.14;QD=19.50;SB=-562.59	GT:AD:DP:GL:GQ	0/1:26,36:60:-142.27,-18.07,-91.55:99
+chr1	4097116	rs6663939	C	T	575.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=1353.52;QD=17.35;SB=-623.00	GT:AD:DP:GL:GQ	0/1:38,40:78:-162.13,-23.49,-140.27:99
+chr1	4097278	rs4408122	C	T	90.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=3.55;MQ=60.00;MQ0=0;OQ=1285.61;QD=19.78;SB=-663.71	GT:AD:DP:GL:GQ	0/1:26,39:64:-151.13,-19.28,-94.25:99
+chr1	4097502	rs10915445	G	A	15.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=4.76;MQ=58.14;MQ0=0;OQ=1551.73;QD=21.26;SB=-659.25	GT:AD:DP:GL:GQ	0/1:29,44:69:-179.24,-20.78,-91.34:99
+chr1	4097702	rs4233259	G	A	393.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.88;MQ0=0;OQ=488.96;QD=11.64;SB=-238.49	GT:AD:DP:GL:GQ	0/1:23,19:39:-63.93,-11.75,-79.38:99
+chr1	4097847	rs4233260	A	G	265.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.25;MQ0=0;OQ=841.80;QD=15.31;SB=-425.02	GT:AD:DP:GL:GQ	0/1:21,34:53:-103.45,-15.98,-81.47:99
+chr1	4098460	rs4654489	C	T	575.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1233.62;QD=17.37;SB=-483.09	GT:AD:DP:GL:GQ	0/1:34,37:71:-148.05,-21.40,-108.91:99
+chr1	4098462	rs4654412	C	G	408.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=1295.21;QD=18.24;SB=-423.31	GT:AD:DP:GL:GQ	0/1:36,35:70:-153.90,-21.10,-151.48:99
+chr1	4098561	rs4654490	T	C	109.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=5.61;MQ=59.35;MQ0=0;OQ=707.20;QD=11.05;SB=-320.12	GT:AD:DP:GL:GQ	0/1:35,29:62:-92.69,-18.69,-135.70:99
+chr1	4098636	rs4654491	A	T	298.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.55;MQ=58.32;MQ0=0;OQ=679.16;QD=12.81;SB=-348.54	GT:AD:DP:GL:GQ	0/1:28,25:51:-86.56,-15.36,-108.00:99
+chr1	4101675	rs4654492	C	T	166.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=985.64;QD=17.92;SB=-310.22	GT:AD:DP:GL:GQ	0/1:24,31:53:-117.81,-15.96,-85.09:99
+chr1	4102203	rs10799207	G	A	234.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=645.03;QD=15.36;SB=-340.37	GT:AD:DP:GL:GQ	0/1:22,20:41:-80.15,-12.36,-66.12:99
+chr1	4102678	rs7542208	A	G	473.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.58;MQ0=0;OQ=945.73;QD=14.78;SB=-439.91	GT:AD:DP:GL:GQ	0/1:26,38:62:-116.54,-18.69,-104.23:99
+chr1	4102853	rs12143662	C	T	77.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=3.06;MQ=59.31;MQ0=0;OQ=653.08;QD=14.51;SB=-306.78	GT:AD:DP:GL:GQ	0/1:23,22:43:-81.54,-12.95,-84.16:99
+chr1	4103423	rs12096127	C	T	146.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=3;HaplotypeScore=0.93;MQ=59.48;MQ0=0;OQ=1299.31;QD=16.24;SB=-452.94	GT:AD:DP:GL:GQ	0/1:42,38:79:-157.01,-23.79,-152.41:99
+chr1	4104350	.	G	A	39.75	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=50.14;MQ=43.88;MQ0=0;QD=0.41;SB=41.13	GT:AD:DP:GL:GQ	0/1:55,43:59:-25.05,-17.79,-166.63:72.58
+chr1	4104372	.	C	A	158.64	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=1;HaplotypeScore=261.20;MQ=40.26;MQ0=0;QD=1.18;SB=50.16	GT:AD:DP:GL:GQ	0/1:118,16:102:-49.87,-30.72,-316.01:99
+chr1	4104378	.	T	C	1045.41	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=132;Dels=0.09;HRun=0;HaplotypeScore=252.28;MQ=39.40;MQ0=0;QD=7.92;SB=47.18	GT:AD:DP:GL:GQ	0/1:70,50:112:-140.05,-32.23,-268.85:99
+chr1	4104379	.	G	A	1387.27	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=131;Dels=0.09;HRun=0;HaplotypeScore=164.33;MQ=39.20;MQ0=0;QD=10.59;SB=44.10	GT:AD:DP:GL:GQ	0/1:65,54:109:-173.34,-31.33,-223.67:99
+chr1	4104399	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=192;Dels=0.00;HRun=0;HaplotypeScore=398.28;MQ=38.87;MQ0=2;OQ=296.43;QD=1.54;SB=-98.03	GT:AD:DP:GL:GQ	0/1:164,28:154:-79.31,-46.39,-472.12:99
+chr1	4104401	rs61768839	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=194;Dels=0.00;HRun=0;HaplotypeScore=419.03;MQ=39.00;MQ0=2;OQ=166.93;QD=0.86;SB=-91.09	GT:AD:DP:GL:GQ	0/1:156,37:153:-66.06,-46.09,-471.26:99
+chr1	4104420	rs56397723	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=252;Dels=0.01;HRun=1;HaplotypeScore=92.55;MQ=41.09;MQ0=3;OQ=4650.56;QD=18.45;SB=-702.42	GT:AD:DP:GL:GQ	0/1:91,159:212:-464.06,-63.56,-317.29:99
+chr1	4104448	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=303;Dels=0.00;HRun=1;HaplotypeScore=67.42;MQ=41.21;MQ0=8;OQ=4147.70;QD=13.69;SB=-263.14	GT:AD:DP:GL:GQ	0/1:172,131:260:-413.77,-78.32,-559.37:99
+chr1	4104453	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=303;Dels=0.00;HRun=0;HaplotypeScore=122.24;MQ=41.63;MQ0=7;OQ=1110.55;QD=3.67;SB=-37.03	GT:AD:DP:GL:GQ	0/1:232,70:246:-188.46,-74.12,-759.14:99
+chr1	4104461	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=296;Dels=0.01;HRun=1;HaplotypeScore=119.61;MQ=41.59;MQ0=7;OQ=214.27;QD=0.72;SB=-23.14	GT:AD:DP:GL:GQ	0/1:251,42:244:-97.34,-72.63,-828.00:99
+chr1	4104464	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=293;Dels=0.00;HRun=0;HaplotypeScore=47.37;MQ=41.56;MQ0=7;OQ=330.17;QD=1.13;SB=-9.81	GT:AD:DP:GL:GQ	0/1:251,41:246:-110.42,-74.12,-748.00:99
+chr1	4104493	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=1;HaplotypeScore=30.82;MQ=42.50;MQ0=6;OQ=2710.70;QD=12.73;SB=-739.33	GT:AD:DP:GL:GQ	0/1:93,120:174:-326.79,-52.44,-298.85:99
+chr1	4104517	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=157;Dels=0.00;HRun=0;HaplotypeScore=91.08;MQ=42.89;MQ0=5;OQ=579.51;QD=3.69;SB=-277.61	GT:AD:DP:GL:GQ	0/1:123,34:134:-101.62,-40.38,-368.83:99
+chr1	4104540	rs62641248	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=101.41;MQ=39.74;MQ0=1;OQ=311.08;QD=3.34;SB=-25.45	GT:AD:DP:GL:GQ	0/1:75,18:80:-58.50,-24.10,-250.10:99
+chr1	4104551	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=87.22;MQ=37.20;MQ0=4;OQ=331.14;QD=4.87;SB=-44.20	GT:AD:DP:GL:GQ	0/1:51,17:54:-52.67,-16.27,-140.50:99
+chr1	4104561	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=32.90;MQ=39.14;MQ0=4;OQ=99.56;QD=1.56;SB=92.30	GT:AD:DP:GL:GQ	0/1:53,11:58:-30.72,-17.48,-172.38:99
+chr1	4104601	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=0;HaplotypeScore=38.41;MQ=39.91;MQ0=6;OQ=155.34;QD=0.76;SB=68.34	GT:AD:DP:GL:GQ	0/1:183,21:180:-73.04,-54.23,-586.07:99
+chr1	4104605	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=211;Dels=0.00;HRun=1;HaplotypeScore=39.02;MQ=40.58;MQ0=6;OQ=226.77;QD=1.07;SB=164.51	GT:AD:DP:GL:GQ	0/1:188,23:190:-83.19,-57.23,-627.45:99
+chr1	4104633	rs56023565	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=168;Dels=0.00;HRun=0;HaplotypeScore=43.28;MQ=41.56;MQ0=5;OQ=1077.06;QD=6.41;SB=128.56	GT:AD:DP:GL:GQ	0/1:117,50:150:-156.17,-45.18,-408.43:99
+chr1	4104638	rs62641251	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=155;Dels=0.00;HRun=1;HaplotypeScore=82.61;MQ=42.16;MQ0=4;OQ=1017.44;QD=6.56;SB=-202.97	GT:AD:DP:GL:GQ	0/1:99,56:128:-143.60,-38.57,-325.85:99
+chr1	4104646	rs56328141	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=133;Dels=0.05;HRun=0;HaplotypeScore=83.44;MQ=42.94;MQ0=3;OQ=598.93;QD=4.50;SB=-113.26	GT:AD:DP:GL:GQ	0/1:76,33:104:-104.27,-41.10,-292.97:99
+chr1	4104661	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=114;Dels=0.03;HRun=0;HaplotypeScore=168.88;MQ=43.79;MQ0=2;OQ=339.54;QD=2.98;SB=-7.31	GT:AD:DP:GL:GQ	0/1:92,17:99:-69.57,-32.33,-280.39:99
+chr1	4104695	rs58865682	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.00;HRun=0;HaplotypeScore=26.95;MQ=46.39;MQ0=1;OQ=148.27;QD=1.39;SB=113.35	GT:AD:DP:GL:GQ	0/1:90,17:100:-48.23,-30.12,-318.63:99
+chr1	4104698	rs59763636	A	C	13.51	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=104;Dels=0.00;HRun=0;HaplotypeScore=26.94;MQ=46.80;MQ0=1;QD=0.13;SB=110.36	GT:AD:DP:GL:GQ	0/1:87,17:97:-33.83,-29.22,-321.32:46.15
+chr1	4104799	rs56113813	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=1;HaplotypeScore=110.54;MQ=45.23;MQ0=4;OQ=195.94;QD=2.13;SB=86.31	GT:AD:DP:GL:GQ	0/1:78,14:77:-46.07,-23.20,-257.99:99
+chr1	4106070	rs9426471	T	C	595.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=1098.91;QD=16.16;SB=-453.97	GT:AD:DP:GL:GQ	0/1:32,36:68:-133.66,-20.48,-129.09:99
+chr1	4106148	rs9426494	C	T	344.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=60.00;MQ0=0;OQ=1566.25;QD=17.40;SB=-768.74	GT:AD:DP:GL:GQ	0/1:44,46:88:-186.42,-26.51,-142.07:99
+chr1	4107203	rs6680278	C	T	328.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.92;MQ0=0;OQ=777.87;QD=13.89;SB=-285.17	GT:AD:DP:GL:GQ	0/1:32,24:55:-97.64,-16.57,-110.93:99
+chr1	4107258	rs6672998	G	A	334.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=520.45;QD=13.01;SB=-193.18	GT:AD:DP:GL:GQ	0/1:23,17:40:-67.38,-12.05,-82.67:99
+chr1	4107272	rs17406305	C	T	361.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=435.04;QD=9.89;SB=-220.70	GT:AD:DP:GL:GQ	0/1:26,18:41:-59.15,-12.36,-84.72:99
+chr1	4108156	rs7528351	G	A	171.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=978.84;QD=16.88;SB=-340.32	GT:AD:DP:GL:GQ	0/1:29,29:58:-118.64,-17.47,-104.14:99
+chr1	4108402	rs7539733	C	T	327.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=58.92;MQ0=0;OQ=799.67;QD=15.38;SB=-336.43	GT:AD:DP:GL:GQ	0/1:24,28:47:-97.41,-14.16,-80.03:99
+chr1	4108778	rs9426495	G	A	284.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=3.59;MQ=59.34;MQ0=0;OQ=895.14;QD=14.21;SB=-321.33	GT:AD:DP:GL:GQ	0/1:34,29:62:-111.48,-18.68,-120.65:99
+chr1	4108797	rs9426472	G	C	415.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=59.27;MQ0=0;OQ=1011.60;QD=17.75;SB=-519.74	GT:AD:DP:GL:GQ	0/1:27,30:53:-120.42,-15.97,-106.06:99
+chr1	4109900	.	A	G	31.51	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=2;HaplotypeScore=6.53;MQ=57.95;MQ0=0;QD=0.55;SB=59.23	GT:AD:DP:GL:GQ	0/1:35,22:36:-17.29,-10.85,-119.86:64.34
+chr1	4110024	rs6690263	C	T	117.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=60.00;MQ0=0;OQ=1118.91;QD=21.11;SB=-400.94	GT:AD:DP:GL:GQ	0/1:20,32:53:-134.68,-19.51,-68.02:99
+chr1	4110064	rs6695126	A	G	708.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1770.58;QD=35.41;SB=-875.05	GT:AD:DP:GL:GQ	1/1:0,50:50:-180.66,-15.06,-0.02:99
+chr1	4110262	rs6683453	G	A	435.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.65;MQ0=0;OQ=1205.59;QD=18.27;SB=-574.05	GT:AD:DP:GL:GQ	0/1:29,37:64:-143.13,-19.28,-100.61:99
+chr1	4110315	rs9426473	G	A	464.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=896.46;QD=18.68;SB=-396.93	GT:AD:DP:GL:GQ	0/1:19,29:46:-106.79,-13.86,-67.55:99
+chr1	4110338	rs9426496	A	G	430.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=545.25;QD=11.36;SB=-275.98	GT:AD:DP:GL:GQ	0/1:25,23:47:-71.97,-14.16,-100.50:99
+chr1	4111600	rs12752733	G	A	194.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.12;MQ0=0;OQ=1088.74;QD=20.54;SB=-407.75	GT:AD:DP:GL:GQ	0/1:20,33:51:-127.52,-15.37,-66.14:99
+chr1	4111741	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=11;HaplotypeScore=4.85;MQ=55.91;MQ0=0;OQ=88.59;QD=2.16;SB=32.11	GT:AD:DP:GL:GQ	0/1:33,8:32:-21.79,-9.64,-86.81:99
+chr1	4112024	.	C	T	265.51	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.50;MQ0=0;OQ=941.42;QD=16.81;SB=-396.13	GT:AD:DP:GL:GQ	0/1:27,29:55:-113.99,-16.57,-97.04:99
+chr1	4112929	rs4654494	C	G	169.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=60.00;MQ0=0;OQ=822.69;QD=13.27;SB=-341.77	GT:AD:DP:GL:GQ	0/1:34,28:54:-101.84,-16.28,-127.78:99
+chr1	4113201	rs55759139	G	A	249.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.37;MQ=59.68;MQ0=0;OQ=761.01;QD=13.12;SB=-311.83	GT:AD:DP:GL:GQ	0/1:32,26:53:-95.35,-15.97,-100.34:99
+chr1	4113760	rs4498774	A	C	130.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.50;MQ=58.71;MQ0=0;OQ=628.38;QD=9.67;SB=-313.59	GT:AD:DP:GL:GQ	0/1:36,29:64:-85.41,-19.28,-138.00:99
+chr1	4114825	rs7339911	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=10;HaplotypeScore=3.32;MQ=58.55;MQ0=0;OQ=757.63;QD=12.42;SB=-183.20	GT:AD:DP:GL:GQ	0/1:36,25:59:-96.82,-17.77,-126.07:99
+chr1	4116025	rs9988443	G	A	336.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.45;MQ0=0;OQ=1567.78;QD=20.63;SB=-720.28	GT:AD:DP:GL:GQ	0/1:30,46:75:-182.67,-22.61,-94.32:99
+chr1	4116630	rs4336820	T	C	72.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.26;MQ=59.52;MQ0=0;OQ=1667.19;QD=34.73;SB=-687.27	GT:AD:DP:GL:GQ	1/1:0,48:47:-170.32,-14.16,-0.01:99
+chr1	4116791	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=2;HaplotypeScore=12.66;MQ=58.95;MQ0=0;OQ=57.38;QD=1.43;SB=71.25	GT:AD:DP:GL:GQ	0/1:31,9:34:-19.31,-10.29,-109.30:90.22
+chr1	4117150	rs12062237	T	C	0.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=3;HaplotypeScore=3.14;MQ=57.94;MQ0=0;OQ=1345.47;QD=32.82;SB=-624.25	GT:AD:DP:GL:GQ	1/1:0,41:39:-138.15,-11.75,-0.02:99
+chr1	4118916	rs3890798	A	G	534.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=2055.84;QD=30.23;SB=-868.59	GT:AD:DP:GL:GQ	1/1:0,68:65:-209.23,-19.60,-0.06:99
+chr1	4119595	rs6426391	A	T	243.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.73;MQ0=0;OQ=1272.79;QD=18.45;SB=-602.37	GT:AD:DP:GL:GQ	0/1:28,41:68:-151.04,-20.48,-104.90:99
+chr1	4119856	.	G	A	80.75	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=54.88;MQ0=1;OQ=952.98;QD=16.15;SB=-461.48	GT:AD:DP:GL:GQ	0/1:28,31:56:-115.46,-16.88,-95.51:99
+chr1	4120161	rs7549636	G	A	106.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=3.96;MQ=59.21;MQ0=1;OQ=708.05;QD=15.39;SB=-359.50	GT:AD:DP:GL:GQ	0/1:23,23:43:-87.04,-12.95,-74.47:99
+chr1	4120271	rs6426392	T	C	252.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.44;MQ0=0;OQ=208.98;QD=7.74;SB=-130.51	GT:AD:DP:GL:GQ	0/1:16,11:25:-31.72,-7.54,-55.62:99
+chr1	4121295	rs4414012	C	T	109.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=243.26;QD=16.22;SB=-32.52	GT:AD:DP:GL:GQ	0/1:7,8:15:-32.13,-4.52,-23.19:99
+chr1	4121459	rs4614226	C	T	3.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.33;MQ0=0;OQ=708.73;QD=25.31;SB=-192.72	GT:AD:DP:GL:GQ	0/1:8,20:25:-81.69,-7.53,-15.26:77.23
+chr1	4122266	rs4654495	C	T	267.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.05;MQ0=0;OQ=844.66;QD=17.24;SB=-383.42	GT:AD:DP:GL:GQ	0/1:22,27:48:-102.21,-14.46,-81.80:99
+chr1	4122640	.	C	T	27.21	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=1;HaplotypeScore=9.85;MQ=48.82;MQ0=0;QD=3.40;SB=2.03	GT:AD:DP:GL:GQ	0/1:6,2:7:-8.11,-2.11,-18.35:60.04
+chr1	4122866	rs4654413	A	G	16.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.58;MQ0=0;OQ=1224.52;QD=28.48;SB=-81.37	GT:AD:DP:GL:GQ	1/1:0,43:41:-126.09,-12.38,-0.05:99
+chr1	4122935	rs4654414	G	A	17.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=53.29;MQ0=0;OQ=1666.36;QD=36.23;SB=-267.85	GT:AD:DP:GL:GQ	1/1:1,45:42:-170.23,-12.65,-0.01:99
+chr1	4123288	rs4233261	T	C	17.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=4.16;MQ=58.63;MQ0=0;OQ=2395.13;QD=34.71;SB=-1054.42	GT:AD:DP:GL:GQ	1/1:0,69:66:-243.12,-19.88,-0.02:99
+chr1	4123748	rs6679293	T	C	176.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.14;MQ0=0;OQ=1906.56;QD=31.26;SB=-831.63	GT:AD:DP:GL:GQ	1/1:0,61:59:-194.29,-17.79,-0.05:99
+chr1	4123963	rs4654496	C	T	83.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=2067.60;QD=39.01;SB=-750.62	GT:AD:DP:GL:GQ	1/1:0,53:53:-210.36,-15.97,-0.02:99
+chr1	4124418	rs4654497	T	C	597.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=1506.19;QD=30.74;SB=-582.98	GT:AD:DP:GL:GQ	1/1:0,49:47:-154.24,-14.17,-0.04:99
+chr1	4126306	rs4367764	C	T	454.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2115.14;QD=39.17;SB=-864.64	GT:AD:DP:GL:GQ	1/1:0,54:53:-215.11,-15.97,-0.01:99
+chr1	4127324	rs12123330	C	T	249.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1048.68;QD=17.77;SB=-496.03	GT:AD:DP:GL:GQ	0/1:27,32:56:-125.03,-16.88,-80.71:99
+chr1	4127494	rs4468133	G	A	195.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=2.26;MQ=60.00;MQ0=0;OQ=1260.59;QD=18.01;SB=-425.95	GT:AD:DP:GL:GQ	0/1:31,38:68:-152.64,-23.30,-109.48:99
+chr1	4128172	rs4654498	A	G	107.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.33;MQ=59.19;MQ0=0;OQ=2014.82;QD=35.35;SB=-1032.76	GT:AD:DP:GL:GQ	1/1:0,57:56:-205.08,-16.87,-0.01:99
+chr1	4128310	rs4654499	G	T	305.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=983.44;QD=17.88;SB=-296.34	GT:AD:DP:GL:GQ	0/1:22,33:55:-118.19,-16.56,-78.95:99
+chr1	4130572	rs3890729	A	T	141.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=59.18;MQ0=0;OQ=905.47;QD=17.75;SB=-227.90	GT:AD:DP:GL:GQ	0/1:23,28:51:-109.19,-15.36,-88.04:99
+chr1	4131311	rs10915460	G	A	189.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=57.39;MQ0=0;OQ=480.50;QD=13.35;SB=-233.54	GT:AD:DP:GL:GQ	0/1:19,17:33:-61.28,-9.95,-54.49:99
+chr1	4131491	rs10915461	A	G	151.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.56;MQ=51.87;MQ0=0;OQ=492.21;QD=9.65;SB=-268.94	GT:AD:DP:GL:GQ	0/1:28,23:49:-67.28,-14.77,-113.16:99
+chr1	4131545	rs10915462	T	C	155.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=54.56;MQ0=0;OQ=299.94;QD=7.69;SB=-143.28	GT:AD:DP:GL:GQ	0/1:25,14:37:-44.43,-11.15,-99.76:99
+chr1	4131617	rs6688343	T	C	208.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=2.28;MQ=58.31;MQ0=0;OQ=662.26;QD=13.25;SB=-230.45	GT:AD:DP:GL:GQ	0/1:25,25:48:-83.97,-14.46,-97.39:99
+chr1	4131656	rs6688428	T	C	133.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.51;MQ=58.40;MQ0=0;OQ=444.13;QD=10.83;SB=-97.71	GT:AD:DP:GL:GQ	0/1:22,19:40:-59.75,-12.06,-84.80:99
+chr1	4131666	rs6688431	T	C	70.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=58.40;MQ0=0;OQ=339.10;QD=8.27;SB=-98.71	GT:AD:DP:GL:GQ	0/1:23,18:37:-48.34,-11.15,-87.20:99
+chr1	4131704	.	G	A	41.43	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=58.60;MQ0=0;OQ=706.66;QD=14.13;SB=-238.75	GT:AD:DP:GL:GQ	0/1:28,22:49:-88.72,-14.77,-84.55:99
+chr1	4131824	rs12032295	C	T	752.83	Indel	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.96;MQ0=0;QD=14.20;SB=-367.84	GT:AD:DP:GL:GQ	0/1:30,23:51:-93.93,-15.37,-94.00:99
+chr1	4132377	rs12405392	C	T	226.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=4.69;MQ=59.66;MQ0=0;OQ=1021.86;QD=15.03;SB=-451.99	GT:AD:DP:GL:GQ	0/1:34,34:62:-124.15,-18.68,-109.47:99
+chr1	4132399	rs56827341	A	G	272.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=59.66;MQ0=0;OQ=903.58;QD=13.29;SB=-319.89	GT:AD:DP:GL:GQ	0/1:32,36:65:-113.24,-19.60,-113.27:99
+chr1	4132555	rs11580927	G	A	598.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=853.00;QD=13.76;SB=-450.44	GT:AD:DP:GL:GQ	0/1:34,28:61:-106.96,-18.38,-120.31:99
+chr1	4132654	rs11583685	T	C	237.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.58;MQ=60.00;MQ0=0;OQ=809.75;QD=12.46;SB=-338.53	GT:AD:DP:GL:GQ	0/1:35,30:64:-103.54,-19.28,-136.81:99
+chr1	4134373	rs6690519	C	T	596.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2577.92;QD=39.66;SB=-1051.40	GT:AD:DP:GL:GQ	1/1:0,65:64:-261.39,-19.28,-0.02:99
+chr1	4134652	rs12743431	G	A	916.73	Indel	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.05;MQ0=0;QD=16.08;SB=-472.04	GT:AD:DP:GL:GQ	0/1:25,32:53:-110.92,-15.97,-91.04:99
+chr1	4134672	rs61037363	C	T	207.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=58.34;MQ0=0;OQ=1244.96;QD=19.15;SB=-619.07	GT:AD:DP:GL:GQ	0/1:27,38:61:-146.16,-18.38,-83.21:99
+chr1	4135628	rs4654501	G	A	449.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.45;MQ0=0;OQ=800.03;QD=17.78;SB=-327.85	GT:AD:DP:GL:GQ	0/1:21,24:44:-96.54,-13.26,-71.19:99
+chr1	4136297	rs4531262	C	T	292.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.55;MQ0=0;OQ=900.23;QD=17.65;SB=-443.97	GT:AD:DP:GL:GQ	0/1:23,28:50:-108.37,-15.06,-81.34:99
+chr1	4136842	rs4233262	C	T	514.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1175.57;QD=19.27;SB=-513.00	GT:AD:DP:GL:GQ	0/1:27,34:61:-139.22,-18.38,-97.14:99
+chr1	4137022	rs12726068	G	A	202.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1078.50;QD=19.97;SB=-346.48	GT:AD:DP:GL:GQ	0/1:22,32:54:-127.40,-16.27,-78.49:99
+chr1	4137146	rs12741551	C	T	188.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.60;MQ=60.00;MQ0=0;OQ=744.97;QD=14.06;SB=-275.26	GT:AD:DP:GL:GQ	0/1:28,23:51:-95.75,-17.97,-99.94:99
+chr1	4137455	rs34927664	C	T	374.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.87;MQ0=0;OQ=672.79;QD=16.41;SB=-286.16	GT:AD:DP:GL:GQ	0/1:20,21:40:-82.61,-12.05,-71.71:99
+chr1	4137533	rs6687719	A	G	359.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.55;MQ0=0;OQ=693.89;QD=13.61;SB=-371.11	GT:AD:DP:GL:GQ	0/1:24,27:51:-88.05,-15.37,-93.98:99
+chr1	4137942	rs4654415	A	G	54.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=3;HaplotypeScore=0.52;MQ=59.28;MQ0=0;OQ=812.82;QD=15.63;SB=-375.38	GT:AD:DP:GL:GQ	0/1:23,29:51:-99.93,-15.36,-91.58:99
+chr1	4137964	rs4654416	T	C	201.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=58.39;MQ0=0;OQ=863.33;QD=15.70;SB=-318.29	GT:AD:DP:GL:GQ	0/1:25,30:54:-105.89,-16.27,-96.91:99
+chr1	4138124	rs4654417	A	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.04;HRun=0;HaplotypeScore=22.45;MQ=53.05;MQ0=0;OQ=979.60;QD=14.62;SB=-425.14	GT:AD:DP:GL:GQ	0/1:30,34:67:-120.52,-19.28,-120.75:99
+chr1	4138539	rs10915465	C	T	116.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=932.04;QD=16.95;SB=-231.54	GT:AD:DP:GL:GQ	0/1:26,28:51:-111.86,-15.37,-73.76:99
+chr1	4138848	rs4233263	T	C	563.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.57;MQ0=0;OQ=1932.95;QD=31.18;SB=-950.38	GT:AD:DP:GL:GQ	1/1:0,61:61:-196.93,-18.40,-0.06:99
+chr1	4140038	rs4233264	T	C	391.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.43;MQ0=0;OQ=1125.34;QD=13.89;SB=-437.57	GT:AD:DP:GL:GQ	0/1:41,40:80:-139.92,-24.10,-167.96:99
+chr1	4140287	rs4654502	A	G	258.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=716.89;QD=12.36;SB=-328.15	GT:AD:DP:GL:GQ	0/1:28,30:57:-92.15,-17.18,-113.12:99
+chr1	4140357	rs4654503	A	G	175.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.08;MQ=60.00;MQ0=0;OQ=528.96;QD=9.98;SB=-287.63	GT:AD:DP:GL:GQ	0/1:26,24:47:-70.35,-14.17,-96.77:99
+chr1	4140721	rs12074230	G	C	441.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=1211.59;QD=19.54;SB=-432.34	GT:AD:DP:GL:GQ	0/1:29,33:61:-142.82,-18.38,-122.06:99
+chr1	4141214	rs61770887	T	A	176.81	Indel	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=41.85;MQ0=5;QD=2.39;SB=-58.97	GT:AD:DP:GL:GQ	0/1:35,39:44:-34.22,-13.25,-135.84:99
+chr1	4141739	.	C	G	151.90	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.44;MQ0=0;OQ=861.28;QD=11.64;SB=-403.50	GT:AD:DP:GL:GQ	0/1:45,29:72:-111.12,-21.71,-193.89:99
+chr1	4143108	rs7544125	G	A	98.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=44.58;MQ0=4;OQ=463.56;QD=6.62;SB=-223.67	GT:AD:DP:GL:GQ	0/1:38,32:54:-65.91,-16.27,-136.81:99
+chr1	4143110	rs7515133	T	G	11.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=44.83;MQ0=4;OQ=280.65;QD=3.95;SB=-136.72	GT:AD:DP:GL:GQ	0/1:40,31:55:-47.92,-16.57,-148.31:99
+chr1	4143183	rs4408123	T	C	60.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.41;MQ=54.71;MQ0=0;OQ=2012.85;QD=31.45;SB=-855.54	GT:AD:DP:GL:GQ	1/1:0,63:62:-204.92,-18.70,-0.05:99
+chr1	4143665	rs4654505	C	T	14.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=7.02;MQ=58.52;MQ0=0;OQ=1278.62;QD=17.05;SB=-644.75	GT:AD:DP:GL:GQ	0/1:36,39:72:-152.84,-21.70,-110.95:99
+chr1	4143971	rs56322069	G	A	219.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=58.68;MQ0=0;OQ=1179.12;QD=14.38;SB=-509.98	GT:AD:DP:GL:GQ	0/1:47,35:78:-144.69,-23.49,-153.28:99
+chr1	4144717	rs4654419	G	T	409.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.48;MQ0=0;OQ=576.97;QD=11.10;SB=-278.60	GT:AD:DP:GL:GQ	0/1:31,21:52:-76.65,-15.66,-108.30:99
+chr1	4144899	rs4654506	A	G	59.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=1.57;MQ=57.19;MQ0=0;OQ=798.47;QD=12.67;SB=-355.09	GT:AD:DP:GL:GQ	0/1:32,31:63:-102.12,-18.99,-128.03:99
+chr1	4145034	rs4654420	T	C	208.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=57.63;MQ0=0;OQ=567.20;QD=9.30;SB=-299.19	GT:AD:DP:GL:GQ	0/1:35,26:59:-77.79,-17.78,-138.00:99
+chr1	4145265	rs10799210	A	G	75.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=52.55;MQ0=0;OQ=2612.65;QD=35.79;SB=-1182.09	GT:AD:DP:GL:GQ	1/1:0,72:73:-267.51,-24.47,-2.66:99
+chr1	4146179	rs4354511	G	A	19.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=3;HaplotypeScore=1.79;MQ=39.00;MQ0=1;OQ=2945.76;QD=39.28;SB=-1473.93	GT:AD:DP:GL:GQ	1/1:0,75:73:-298.18,-21.99,-0.02:99
+chr1	4146185	rs61770891	T	G	349.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=40.44;MQ0=1;OQ=1123.38;QD=15.18;SB=-586.47	GT:AD:DP:GL:GQ	0/1:35,39:73:-137.61,-21.99,-124.99:99
+chr1	4146278	rs35969529	A	C	46.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=2.80;MQ=52.18;MQ0=0;OQ=652.54;QD=12.55;SB=-341.77	GT:AD:DP:GL:GQ	0/1:27,25:52:-84.21,-15.67,-95.88:99
+chr1	4146315	rs34096100	G	A	254.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.76;MQ0=0;OQ=657.20;QD=13.41;SB=-218.51	GT:AD:DP:GL:GQ	0/1:28,21:47:-83.18,-14.17,-82.42:99
+chr1	4146537	.	C	T	111.88	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=53.66;MQ0=1;OQ=1107.86;QD=16.06;SB=-448.39	GT:AD:DP:GL:GQ	0/1:34,35:67:-134.26,-20.19,-114.24:99
+chr1	4146953	rs4654421	T	C	433.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.82;MQ0=0;OQ=2189.94;QD=31.74;SB=-1040.77	GT:AD:DP:GL:GQ	1/1:0,69:68:-222.64,-20.51,-0.06:99
+chr1	4147013	rs4654422	T	A	163.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.20;MQ0=1;OQ=3024.40;QD=36.88;SB=-1331.44	GT:AD:DP:GL:GQ	1/1:1,80:81:-309.61,-27.75,-3.59:99
+chr1	4148323	rs35837871	C	T	12.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=2.85;MQ=58.88;MQ0=0;OQ=689.43;QD=12.77;SB=-158.63	GT:AD:DP:GL:GQ	0/1:29,24:49:-86.99,-14.77,-93.34:99
+chr1	4148556	rs10753370	A	G	191.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=57.40;MQ0=0;OQ=2083.85;QD=34.73;SB=-1040.92	GT:AD:DP:GL:GQ	1/1:0,60:59:-211.99,-17.77,-0.02:99
+chr1	4149011	rs12084286	A	G	120.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=57.86;MQ0=0;OQ=472.12;QD=10.26;SB=-116.70	GT:AD:DP:GL:GQ	0/1:26,20:42:-63.15,-12.65,-98.66:99
+chr1	4149320	rs10733015	T	C	59.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=3.72;MQ=56.65;MQ0=0;OQ=2004.37;QD=30.37;SB=-729.73	GT:AD:DP:GL:GQ	1/1:0,65:63:-204.08,-19.00,-0.06:99
+chr1	4149923	rs4654507	T	C	369.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.77;MQ0=0;OQ=1162.12;QD=14.53;SB=-509.31	GT:AD:DP:GL:GQ	0/1:40,40:79:-143.29,-23.80,-162.73:99
+chr1	4150793	rs11808641	A	G	288.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=1163.51;QD=16.62;SB=-493.62	GT:AD:DP:GL:GQ	0/1:32,38:70:-140.72,-21.09,-129.98:99
+chr1	4151258	rs35392680	C	A	277.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=1.25;MQ=59.48;MQ0=0;OQ=1358.51;QD=16.77;SB=-581.67	GT:AD:DP:GL:GQ	0/1:37,44:80:-163.23,-24.09,-127.72:99
+chr1	4151486	rs35452955	A	T	64.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=0.98;MQ=60.00;MQ0=0;OQ=1469.46;QD=19.34;SB=-729.32	GT:AD:DP:GL:GQ	0/1:30,45:74:-172.52,-22.29,-110.18:99
+chr1	4151668	rs6703301	G	T	631.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3028.09;QD=37.38;SB=-1101.60	GT:AD:DP:GL:GQ	1/1:0,81:80:-306.41,-24.09,-0.01:99
+chr1	4151981	rs34414875	C	T	365.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1305.64;QD=16.32;SB=-537.52	GT:AD:DP:GL:GQ	0/1:41,39:80:-157.95,-24.10,-144.69:99
+chr1	4152854	rs10915467	A	T	474.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1268.93;QD=17.38;SB=-610.43	GT:AD:DP:GL:GQ	0/1:33,40:72:-151.86,-21.68,-124.21:99
+chr1	4153158	rs12722935	C	T	465.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1317.34;QD=16.26;SB=-636.13	GT:AD:DP:GL:GQ	0/1:41,40:80:-159.12,-24.10,-137.48:99
+chr1	4153203	rs55974255	T	G	492.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1277.21;QD=15.39;SB=-533.71	GT:AD:DP:GL:GQ	0/1:38,45:83:-156.01,-25.00,-142.96:99
+chr1	4153672	rs6679104	T	C	519.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=1796.89;QD=30.98;SB=-648.94	GT:AD:DP:GL:GQ	1/1:0,58:56:-183.31,-16.88,-0.04:99
+chr1	4153751	rs12750830	G	A	339.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=841.06;QD=12.19;SB=-424.91	GT:AD:DP:GL:GQ	0/1:41,27:67:-107.58,-20.19,-146.61:99
+chr1	4153835	rs12740143	T	G	222.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=59.66;MQ0=0;OQ=767.69;QD=11.29;SB=-346.80	GT:AD:DP:GL:GQ	0/1:40,28:68:-100.53,-20.48,-145.06:99
+chr1	4154543	rs12143082	T	C	171.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=1.73;MQ=59.61;MQ0=1;OQ=1104.97;QD=14.17;SB=-407.20	GT:AD:DP:GL:GQ	0/1:39,39:74:-136.07,-22.29,-143.19:99
+chr1	4154828	rs4578184	A	T	236.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.74;MQ0=0;OQ=3286.63;QD=37.35;SB=-1618.09	GT:AD:DP:GL:GQ	1/1:0,87:86:-327.66,-25.90,-0.02:99
+chr1	4156046	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=80;Dels=0.01;HRun=20;HaplotypeScore=22.75;MQ=49.75;MQ0=0;OQ=501.86;QD=6.27;SB=92.27	GT:AD:DP:GL:GQ	0/1:48,31:64:-72.46,-18.99,-149.51:99
+chr1	4157196	rs4276878	C	G	356.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1452.13;QD=15.78;SB=-539.06	GT:AD:DP:GL:GQ	0/1:47,45:92:-176.24,-27.75,-207.05:99
+chr1	4159822	rs34626829	T	C	256.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=60.00;MQ0=0;OQ=966.32;QD=13.24;SB=-369.17	GT:AD:DP:GL:GQ	0/1:40,33:72:-121.60,-21.69,-157.15:99
+chr1	4159905	rs4654509	T	C	45.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=1.31;MQ=59.48;MQ0=0;OQ=2796.88;QD=34.96;SB=-1388.49	GT:AD:DP:GL:GQ	1/1:0,80:80:-283.30,-24.10,-0.03:99
+chr1	4160278	rs6667065	G	A	347.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=1508.83;QD=20.12;SB=-751.28	GT:AD:DP:GL:GQ	0/1:32,43:74:-176.46,-22.30,-103.02:99
+chr1	4160487	rs6426401	C	G	585.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2415.89;QD=43.14;SB=-1118.15	GT:AD:DP:GL:GQ	1/1:0,56:56:-245.19,-16.88,-0.02:99
+chr1	4163843	rs4654511	A	G	129.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=2;HaplotypeScore=0.90;MQ=59.46;MQ0=0;OQ=1014.81;QD=11.80;SB=-473.86	GT:AD:DP:GL:GQ	0/1:46,40:85:-130.38,-25.61,-186.22:99
+chr1	4163857	rs4654512	A	G	307.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=59.44;MQ0=0;OQ=1070.59;QD=12.90;SB=-521.48	GT:AD:DP:GL:GQ	0/1:46,37:83:-135.34,-25.00,-185.85:99
+chr1	4164344	rs4529679	G	C	272.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.61;MQ=59.36;MQ0=0;OQ=772.49;QD=10.73;SB=-392.69	GT:AD:DP:GL:GQ	0/1:46,26:70:-101.64,-21.10,-199.05:99
+chr1	4166949	rs16840901	T	C	388.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.68;MQ0=0;OQ=1039.54;QD=14.24;SB=-434.53	GT:AD:DP:GL:GQ	0/1:37,36:73:-129.23,-21.99,-150.63:99
+chr1	4167749	rs10915471	T	G	58.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=3.59;MQ=59.58;MQ0=0;OQ=744.43;QD=13.54;SB=-264.89	GT:AD:DP:GL:GQ	0/1:27,27:49:-92.49,-14.76,-80.31:99
+chr1	4168111	rs35122589	C	T	228.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=59.26;MQ0=0;OQ=1364.57;QD=16.64;SB=-443.34	GT:AD:DP:GL:GQ	0/1:40,41:80:-163.84,-24.10,-142.82:99
+chr1	4168454	rs12095632	C	G	92.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=2.95;MQ=59.32;MQ0=0;OQ=1054.00;QD=19.16;SB=-475.80	GT:AD:DP:GL:GQ	0/1:24,31:54:-124.96,-16.28,-104.73:99
+chr1	4168730	rs4130091	T	C	180.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.33;MQ0=0;OQ=1367.19;QD=28.48;SB=-696.78	GT:AD:DP:GL:GQ	1/1:0,48:44:-140.35,-13.27,-0.05:99
+chr1	4169351	rs6426402	G	T	131.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=3.41;MQ=58.55;MQ0=0;OQ=809.13;QD=11.40;SB=-425.17	GT:AD:DP:GL:GQ	0/1:41,30:69:-104.98,-20.78,-138.71:99
+chr1	4169394	rs6426403	C	G	338.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=57.89;MQ0=0;OQ=727.35;QD=12.99;SB=-274.92	GT:AD:DP:GL:GQ	0/1:33,23:54:-92.30,-16.28,-134.02:99
+chr1	4169498	rs6426404	G	A	414.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.75;MQ0=0;OQ=1380.19;QD=18.40;SB=-605.61	GT:AD:DP:GL:GQ	0/1:34,41:72:-163.00,-21.69,-105.58:99
+chr1	4169658	rs60017975	A	G	318.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.77;MQ0=0;OQ=1450.14;QD=18.13;SB=-530.63	GT:AD:DP:GL:GQ	0/1:31,49:79:-172.10,-23.80,-127.67:99
+chr1	4170881	rs7550659	A	G	248.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=51.70;MQ0=0;OQ=2075.07;QD=30.97;SB=-804.69	GT:AD:DP:GL:GQ	1/1:0,66:63:-211.13,-18.99,-0.04:99
+chr1	4171135	rs10799212	A	G	40.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=3.91;MQ=40.70;MQ0=1;OQ=2175.11;QD=31.07;SB=-612.96	GT:AD:DP:GL:GQ	1/1:1,69:67:-221.14,-20.20,-0.04:99
+chr1	4171182	rs12410442	G	A	385.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=27.19;MQ0=4;OQ=361.27;QD=10.95;SB=-197.20	GT:AD:DP:GL:GQ	0/1:20,13:27:-47.55,-8.14,-48.20:99
+chr1	4171315	.	C	A	41.63	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=20;HaplotypeScore=7.30;MQ=33.40;MQ0=5;QD=0.97;SB=41.16	GT:AD:DP:GL:GQ	0/1:37,6:31:-16.79,-9.34,-90.98:74.46
+chr1	4171344	rs10799213	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.01;HRun=20;HaplotypeScore=28.32;MQ=47.02;MQ0=1;OQ=768.09;QD=11.30;SB=-343.49	GT:AD:DP:GL:GQ	0/1:35,32:53:-95.75,-15.66,-101.72:99
+chr1	4171386	rs12022636	C	A	71.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=6.39;MQ=55.43;MQ0=0;OQ=1032.82;QD=16.66;SB=-507.94	GT:AD:DP:GL:GQ	0/1:28,34:59:-124.34,-17.77,-88.85:99
+chr1	4171443	rs10799214	T	A	380.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.02;MQ=52.31;MQ0=0;OQ=893.79;QD=14.65;SB=-401.19	GT:AD:DP:GL:GQ	0/1:30,31:58:-110.14,-17.48,-102.42:99
+chr1	4171775	rs7553814	A	G	404.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.01;MQ0=0;OQ=970.08;QD=12.93;SB=-503.90	GT:AD:DP:GL:GQ	0/1:40,35:74:-122.58,-22.29,-161.95:99
+chr1	4171833	rs7553919	A	G	37.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=3;HaplotypeScore=0.95;MQ=59.60;MQ0=0;OQ=2384.19;QD=34.55;SB=-1112.82	GT:AD:DP:GL:GQ	1/1:0,69:66:-242.02,-19.88,-0.02:99
+chr1	4171990	rs7554028	A	G	628.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=1;OQ=2341.28;QD=30.02;SB=-854.63	GT:AD:DP:GL:GQ	1/1:0,78:76:-237.79,-22.93,-0.08:99
+chr1	4173512	rs7517572	T	A	699.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=2653.94;QD=34.47;SB=-1331.37	GT:AD:DP:GL:GQ	1/1:0,77:72:-269.00,-21.69,-0.02:99
+chr1	4173702	rs10753372	T	C	483.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.88;MQ0=0;OQ=510.62;QD=9.82;SB=-265.21	GT:AD:DP:GL:GQ	0/1:30,22:52:-70.02,-15.68,-118.09:99
+chr1	4173822	rs10737404	T	C	229.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1647.35;QD=29.95;SB=-655.93	GT:AD:DP:GL:GQ	1/1:0,55:53:-168.37,-15.99,-0.05:99
+chr1	4174045	rs10915473	C	T	65.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=45.21;MQ0=0;OQ=1332.73;QD=36.02;SB=-585.26	GT:AD:DP:GL:GQ	1/1:0,37:35:-136.87,-10.55,-0.02:99
+chr1	4174057	.	C	T	1039.01	SnpCluster	AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=42.84;MQ0=0;QD=33.52;SB=-399.52	GT:AD:DP:GL:GQ	1/1:2,29:27:-107.50,-8.14,-0.01:81.26
+chr1	4174060	.	A	C	853.72	SnpCluster	AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=1.07;MQ=43.67;MQ0=0;QD=27.54;SB=-294.55	GT:AD:DP:GL:GQ	1/1:0,31:26:-88.97,-7.83,-0.01:78.20
+chr1	4174064	.	A	C	949.90	SnpCluster	AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=44.60;MQ0=0;QD=28.78;SB=-378.69	GT:AD:DP:GL:GQ	1/1:0,33:28:-98.58,-8.43,-0.01:84.24
+chr1	4174382	rs1908491	C	T	0.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=6.22;MQ=54.65;MQ0=0;OQ=1883.08;QD=36.21;SB=-503.01	GT:AD:DP:GL:GQ	1/1:0,52:48:-191.91,-14.46,-0.01:99
+chr1	4174484	rs10915474	T	A	225.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=55.68;MQ0=0;OQ=801.30;QD=15.41;SB=-299.67	GT:AD:DP:GL:GQ	0/1:26,26:51:-98.78,-15.36,-93.02:99
+chr1	4174489	rs1908492	C	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=7;HaplotypeScore=1.12;MQ=55.99;MQ0=0;OQ=1860.19;QD=37.20;SB=-932.70	GT:AD:DP:GL:GQ	1/1:0,50:48:-189.62,-14.46,-0.02:99
+chr1	4174597	rs1908493	C	T	268.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=59.04;MQ0=0;OQ=2611.89;QD=38.41;SB=-1140.03	GT:AD:DP:GL:GQ	1/1:0,68:66:-264.79,-19.88,-0.02:99
+chr1	4174874	rs1495245	T	A	732.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=2554.22;QD=37.56;SB=-1304.61	GT:AD:DP:GL:GQ	1/1:0,68:68:-259.02,-20.48,-0.02:99
+chr1	4174974	rs11578399	C	A	12.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=3.61;MQ=59.22;MQ0=0;OQ=421.58;QD=7.81;SB=-139.06	GT:AD:DP:GL:GQ	0/1:37,17:52:-61.11,-15.67,-117.17:99
+chr1	4175032	rs1495246	C	G	204.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=56.85;MQ0=0;OQ=2607.23;QD=39.50;SB=-1308.71	GT:AD:DP:GL:GQ	1/1:0,66:62:-264.33,-18.68,-0.02:99
+chr1	4175046	.	T	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=2;HaplotypeScore=9.95;MQ=56.80;MQ0=0;OQ=180.72;QD=2.78;SB=92.29	GT:AD:DP:GL:GQ	0/1:40,25:50:-36.42,-15.06,-130.62:99
+chr1	4175151	rs10915476	G	A	237.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.01;MQ0=0;OQ=567.09;QD=12.07;SB=-92.91	GT:AD:DP:GL:GQ	0/1:29,18:45:-73.55,-13.56,-90.83:99
+chr1	4175279	rs1495247	C	T	209.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=2597.96;QD=37.11;SB=-1279.76	GT:AD:DP:GL:GQ	1/1:0,70:67:-263.40,-20.19,-0.02:99
+chr1	4175302	rs7411802	C	A	438.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=58.93;MQ0=0;OQ=2181.45;QD=35.76;SB=-1110.34	GT:AD:DP:GL:GQ	1/1:0,61:61:-221.75,-18.37,-0.02:99
+chr1	4175576	rs4326593	G	A	325.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=55.58;MQ0=0;OQ=888.28;QD=16.76;SB=-433.95	GT:AD:DP:GL:GQ	0/1:25,28:48:-106.58,-14.47,-68.77:99
+chr1	4175736	rs4615813	G	C	667.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.55;MQ0=0;OQ=2403.10;QD=41.43;SB=-1195.96	GT:AD:DP:GL:GQ	1/1:0,58:56:-243.91,-16.87,-0.02:99
+chr1	4175807	rs28600106	C	T	6.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=7.59;MQ=48.39;MQ0=0;OQ=365.75;QD=9.89;SB=-206.69	GT:AD:DP:GL:GQ	0/1:22,15:31:-49.20,-9.35,-60.01:99
+chr1	4175944	rs2898790	T	C	0.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=5.41;MQ=54.62;MQ0=0;OQ=1686.61;QD=30.67;SB=-329.61	GT:AD:DP:GL:GQ	1/1:0,55:50:-172.27,-15.06,-0.02:99
+chr1	4176053	rs2411737	G	C	0.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=4.08;MQ=49.96;MQ0=0;OQ=907.29;QD=30.24;SB=-45.91	GT:AD:DP:GL:GQ	1/1:0,30:23:-94.32,-6.93,-0.01:69.23
+chr1	4176083	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=2;HaplotypeScore=5.12;MQ=50.79;MQ0=0;OQ=53.84;QD=1.17;SB=68.23	GT:AD:DP:GL:GQ	0/1:30,16:35:-19.21,-10.54,-99.51:86.68
+chr1	4176698	rs10915477	G	A	75.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=1.92;MQ=55.80;MQ0=0;OQ=3415.18;QD=40.18;SB=-1433.92	GT:AD:DP:GL:GQ	1/1:0,85:84:-340.52,-25.30,-0.02:99
+chr1	4176748	rs12060660	A	C	70.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=3.65;MQ=58.23;MQ0=0;OQ=2781.95;QD=35.21;SB=-941.32	GT:AD:DP:GL:GQ	1/1:0,78:78:-285.04,-25.98,-3.27:99
+chr1	4176763	rs10915478	T	C	721.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.18;MQ0=0;OQ=2617.35;QD=33.99;SB=-1088.89	GT:AD:DP:GL:GQ	1/1:0,77:74:-265.34,-22.29,-0.02:99
+chr1	4176794	rs12060664	A	G	585.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2362.72;QD=33.28;SB=-1094.09	GT:AD:DP:GL:GQ	1/1:0,71:67:-239.88,-20.19,-0.03:99
+chr1	4177795	rs4654423	T	C	596.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1639.97;QD=29.29;SB=-739.78	GT:AD:DP:GL:GQ	1/1:0,56:52:-167.62,-15.68,-0.04:99
+chr1	4177808	rs10915479	T	C	281.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.62;MQ0=0;OQ=507.44;QD=10.36;SB=-255.93	GT:AD:DP:GL:GQ	0/1:30,19:46:-67.89,-13.86,-108.27:99
+chr1	4179046	rs12116719	G	A	182.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=2853.60;QD=39.09;SB=-1453.00	GT:AD:DP:GL:GQ	1/1:0,73:73:-288.97,-22.00,-0.02:99
+chr1	4179422	rs59176411	C	T	132.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=56.41;MQ0=0;OQ=2598.61;QD=37.12;SB=-1098.00	GT:AD:DP:GL:GQ	1/1:1,69:68:-267.13,-20.49,-3.69:99
+chr1	4179485	rs10737405	A	G	230.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.59;MQ0=0;OQ=1795.14;QD=34.52;SB=-680.95	GT:AD:DP:GL:GQ	1/1:1,51:52:-187.08,-15.66,-3.98:99
+chr1	4180030	rs6657617	C	T	6.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=2.45;MQ=59.28;MQ0=0;OQ=2474.15;QD=38.66;SB=-836.62	GT:AD:DP:GL:GQ	1/1:0,64:62:-251.01,-18.68,-0.02:99
+chr1	4180081	rs6426405	G	A	604.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2617.17;QD=39.06;SB=-1069.36	GT:AD:DP:GL:GQ	1/1:0,67:67:-265.32,-20.19,-0.02:99
+chr1	4180490	rs4592237	G	A	306.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.29;MQ0=0;OQ=1850.80;QD=34.92;SB=-947.36	GT:AD:DP:GL:GQ	1/1:0,53:49:-188.69,-14.77,-0.02:99
+chr1	4181020	rs10799216	G	A	235.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.51;MQ=59.57;MQ0=0;OQ=3471.51;QD=40.37;SB=-1574.60	GT:AD:DP:GL:GQ	1/1:0,86:85:-346.15,-25.60,-0.02:99
+chr1	4181670	rs4233265	T	C	517.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.29;MQ0=0;OQ=2065.74;QD=31.30;SB=-824.68	GT:AD:DP:GL:GQ	1/1:0,66:65:-210.21,-19.60,-0.06:99
+chr1	4182159	rs4654425	A	G	260.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=1828.94;QD=35.17;SB=-776.99	GT:AD:DP:GL:GQ	1/1:0,52:51:-186.50,-15.36,-0.02:99
+chr1	4182646	rs11579829	C	T	305.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.69;MQ0=0;OQ=2773.62;QD=37.48;SB=-1347.81	GT:AD:DP:GL:GQ	1/1:0,74:71:-280.97,-21.39,-0.02:99
+chr1	4183175	rs2132177	C	A	639.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2919.91;QD=36.50;SB=-1144.30	GT:AD:DP:GL:GQ	1/1:0,80:79:-295.60,-23.79,-0.02:99
+chr1	4184348	rs55978003	G	A	105.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.52;MQ=59.27;MQ0=0;OQ=776.05;QD=15.22;SB=-305.78	GT:AD:DP:GL:GQ	0/1:27,23:48:-95.35,-14.46,-90.95:99
+chr1	4184779	rs7528938	C	T	220.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=59.11;MQ0=0;OQ=1623.71;QD=34.55;SB=-657.89	GT:AD:DP:GL:GQ	1/1:1,44:43:-165.98,-12.96,-0.02:99
+chr1	4185286	rs17415519	A	G	242.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.28;MQ=60.00;MQ0=0;OQ=1345.26;QD=33.63;SB=-658.93	GT:AD:DP:GL:GQ	1/1:0,40:39:-138.12,-11.75,-0.01:99
+chr1	4185339	.	G	T	41.06	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=12;HaplotypeScore=2.80;MQ=54.83;MQ0=0;QD=0.98;SB=22.81	GT:AD:DP:GL:GQ	0/1:35,7:35:-17.93,-10.54,-103.81:73.90
+chr1	4185557	rs4654516	G	C	54.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.67;MQ=58.74;MQ0=0;OQ=2607.62;QD=37.25;SB=-842.00	GT:AD:DP:GL:GQ	1/1:1,69:66:-264.40,-19.92,-0.05:99
+chr1	4187570	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=2;HaplotypeScore=8.14;MQ=58.89;MQ0=0;OQ=68.10;QD=0.81;SB=131.41	GT:AD:DP:GL:GQ	0/1:59,24:60:-28.18,-18.09,-178.30:99
+chr1	4188372	rs1874267	T	G	455.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=59.37;MQ0=0;OQ=1048.28;QD=15.88;SB=-524.40	GT:AD:DP:GL:GQ	0/1:29,37:66:-127.99,-19.88,-107.31:99
+chr1	4188412	rs1874266	A	G	468.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.24;MQ0=0;OQ=798.75;QD=14.52;SB=-409.67	GT:AD:DP:GL:GQ	0/1:23,32:52:-98.84,-15.68,-83.89:99
+chr1	4188663	rs10915480	A	G	337.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.23;MQ0=0;OQ=1153.25;QD=13.73;SB=-560.60	GT:AD:DP:GL:GQ	0/1:38,45:83:-146.27,-27.66,-153.88:99
+chr1	4188905	rs10753374	A	G	386.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1195.33;QD=15.73;SB=-552.85	GT:AD:DP:GL:GQ	0/1:35,41:76:-145.71,-22.90,-141.29:99
+chr1	4189544	rs10753375	T	G	601.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1995.47;QD=35.01;SB=-845.10	GT:AD:DP:GL:GQ	1/1:0,57:56:-203.15,-16.86,-0.01:99
+chr1	4189582	rs10799217	A	G	68.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=59.39;MQ0=0;OQ=909.16;QD=14.90;SB=-461.96	GT:AD:DP:GL:GQ	0/1:30,31:61:-112.58,-18.38,-119.06:99
+chr1	4189759	rs10799218	T	C	84.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=3;HaplotypeScore=1.76;MQ=58.80;MQ0=0;OQ=827.52;QD=11.18;SB=-285.14	GT:AD:DP:GL:GQ	0/1:41,32:73:-108.03,-22.00,-167.09:99
+chr1	4191122	rs6426406	T	C	3.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=7.31;MQ=59.57;MQ0=0;OQ=717.35;QD=10.71;SB=-224.24	GT:AD:DP:GL:GQ	0/1:37,30:64:-94.30,-19.28,-145.85:99
+chr1	4191702	rs7541544	T	C	425.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=59.70;MQ0=0;OQ=729.14;QD=11.76;SB=-343.04	GT:AD:DP:GL:GQ	0/1:32,30:60:-94.28,-18.09,-122.33:99
+chr1	4191813	rs7534461	C	G	457.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.78;MQ0=0;OQ=1324.41;QD=15.96;SB=-593.50	GT:AD:DP:GL:GQ	0/1:46,37:83:-160.73,-25.00,-206.24:99
+chr1	4191898	rs7534558	C	T	290.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=2.06;MQ=60.00;MQ0=0;OQ=1246.57;QD=14.17;SB=-621.73	GT:AD:DP:GL:GQ	0/1:50,38:86:-153.86,-25.92,-153.30:99
+chr1	4191985	rs10799219	G	C	69.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=2.07;MQ=59.38;MQ0=0;OQ=1617.32;QD=21.86;SB=-548.71	GT:AD:DP:GL:GQ	0/1:32,42:72:-186.71,-21.70,-128.86:99
+chr1	4192218	rs10159168	A	T	343.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1388.76;QD=16.94;SB=-472.56	GT:AD:DP:GL:GQ	0/1:39,43:82:-166.86,-24.70,-146.13:99
+chr1	4195817	rs1390135	T	G	143.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=58.67;MQ0=0;OQ=705.86;QD=11.20;SB=-334.03	GT:AD:DP:GL:GQ	0/1:33,30:61:-92.25,-18.38,-113.54:99
+chr1	4197896	.	G	A	10.32	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.52;MQ0=0;OQ=1035.41;QD=21.57;SB=-410.45	GT:AD:DP:GL:GQ	0/1:18,30:48:-121.29,-14.46,-58.46:99
+chr1	4198535	rs1495242	A	G	438.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1076.27;QD=12.97;SB=-544.21	GT:AD:DP:GL:GQ	0/1:44,39:81:-135.31,-24.40,-175.25:99
+chr1	4199191	rs12124378	C	T	379.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=1302.45;QD=20.35;SB=-581.61	GT:AD:DP:GL:GQ	0/1:26,38:63:-152.50,-18.97,-95.47:99
+chr1	4199881	.	G	T	32.56	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=2;HaplotypeScore=5.28;MQ=57.83;MQ0=0;QD=0.74;SB=74.26	GT:AD:DP:GL:GQ	0/1:31,13:34:-16.78,-10.24,-105.31:65.40
+chr1	4200007	.	G	A	96.98	PASS	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.35;MQ0=0;OQ=1236.21;QD=18.45;SB=-537.73	GT:AD:DP:GL:GQ	0/1:28,39:63:-145.88,-18.98,-96.95:99
+chr1	4200165	rs6426407	A	G	72.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=58.49;MQ0=0;OQ=1344.67;QD=18.17;SB=-519.96	GT:AD:DP:GL:GQ	0/1:29,44:72:-159.44,-21.69,-113.24:99
+chr1	4200817	rs4654518	G	A	711.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=2818.25;QD=39.69;SB=-1209.38	GT:AD:DP:GL:GQ	1/1:0,71:70:-285.42,-21.08,-0.01:99
+chr1	4202021	rs12124548	G	A	209.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.70;MQ0=0;OQ=1241.05;QD=20.02;SB=-465.47	GT:AD:DP:GL:GQ	0/1:26,36:61:-145.77,-18.38,-85.04:99
+chr1	4202445	rs12405770	A	G	576.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1249.87;QD=15.62;SB=-595.92	GT:AD:DP:GL:GQ	0/1:37,43:79:-152.07,-23.80,-148.48:99
+chr1	4202474	rs6426409	T	G	405.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.78;MQ0=0;OQ=1102.86;QD=13.13;SB=-556.72	GT:AD:DP:GL:GQ	0/1:44,40:82:-138.27,-24.70,-157.66:99
+chr1	4204888	rs12132080	A	T	242.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=45.12;MQ0=6;OQ=964.76;QD=12.69;SB=-408.56	GT:AD:DP:GL:GQ	0/1:34,42:65:-119.34,-19.58,-129.51:99
+chr1	4208143	rs6690300	T	G	448.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.45;MQ0=0;OQ=967.38;QD=12.73;SB=-340.51	GT:AD:DP:GL:GQ	0/1:41,35:76:-122.91,-22.89,-152.81:99
+chr1	4208388	rs12239600	T	C	466.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.66;MQ0=0;OQ=937.21;QD=13.78;SB=-484.77	GT:AD:DP:GL:GQ	0/1:32,36:68:-117.50,-20.50,-127.59:99
+chr1	4208894	rs12078298	T	A	402.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=59.48;MQ0=0;OQ=1434.64;QD=16.12;SB=-624.40	GT:AD:DP:GL:GQ	0/1:43,46:88:-173.25,-26.51,-162.85:99
+chr1	4209813	rs6679489	G	A	164.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=1.52;MQ=60.00;MQ0=0;OQ=1435.86;QD=16.89;SB=-638.14	GT:AD:DP:GL:GQ	0/1:41,44:83:-171.87,-25.00,-148.88:99
+chr1	4211295	rs4654519	C	T	437.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.97;MQ0=0;OQ=1264.42;QD=19.76;SB=-439.80	GT:AD:DP:GL:GQ	0/1:26,38:62:-148.40,-18.68,-90.27:99
+chr1	4211773	rs10915487	T	G	175.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=59.23;MQ0=0;OQ=638.07;QD=10.29;SB=-306.76	GT:AD:DP:GL:GQ	0/1:37,25:61:-85.47,-18.38,-128.27:99
+chr1	4212065	rs1908490	C	T	369.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=57.82;MQ0=0;OQ=1109.73;QD=15.20;SB=-541.53	GT:AD:DP:GL:GQ	0/1:40,33:71:-135.64,-21.39,-134.48:99
+chr1	4213163	rs12741715	A	T	578.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1267.51;QD=16.90;SB=-452.19	GT:AD:DP:GL:GQ	0/1:35,40:74:-152.32,-22.29,-133.91:99
+chr1	4215064	rs966321	G	T	6.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=4;HaplotypeScore=2.95;MQ=59.70;MQ0=0;OQ=1037.52;QD=13.65;SB=-540.72	GT:AD:DP:GL:GQ	0/1:40,36:75:-129.62,-22.59,-142.94:99
+chr1	4215408	rs12691488	C	T	601.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=1073.26;QD=16.02;SB=-541.06	GT:AD:DP:GL:GQ	0/1:35,32:66:-130.50,-19.89,-109.64:99
+chr1	4216644	rs964715	T	C	389.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=939.74;QD=14.46;SB=-445.57	GT:AD:DP:GL:GQ	0/1:32,33:65:-116.84,-19.58,-130.15:99
+chr1	4217111	rs1495250	T	C	316.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=60.00;MQ0=0;OQ=777.71;QD=11.44;SB=-393.04	GT:AD:DP:GL:GQ	0/1:36,32:67:-101.25,-20.19,-143.99:99
+chr1	4218910	rs11583756	G	A	393.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=562.25;QD=10.41;SB=-300.82	GT:AD:DP:GL:GQ	0/1:33,21:51:-74.88,-15.38,-106.07:99
+chr1	4219107	rs7545415	G	A	274.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.24;MQ0=0;OQ=794.53;QD=14.45;SB=-389.90	GT:AD:DP:GL:GQ	0/1:30,25:51:-98.11,-15.38,-85.30:99
+chr1	4221548	rs1826719	G	A	1.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.02;HRun=1;HaplotypeScore=9.57;MQ=59.01;MQ0=0;OQ=1104.32;QD=16.73;SB=-370.86	GT:AD:DP:GL:GQ	0/1:31,34:63:-132.39,-18.68,-107.97:99
+chr1	4221834	rs1390137	T	A	402.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.24;MQ0=0;OQ=1338.31;QD=14.71;SB=-600.22	GT:AD:DP:GL:GQ	0/1:48,43:91:-164.52,-27.41,-184.18:99
+chr1	4222993	rs7526339	A	G	180.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=860.50;QD=13.04;SB=-424.26	GT:AD:DP:GL:GQ	0/1:36,30:65:-108.91,-19.58,-143.92:99
+chr1	4225449	rs9286982	A	C	384.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.50;MQ0=0;OQ=1099.77;QD=14.66;SB=-338.80	GT:AD:DP:GL:GQ	0/1:38,37:74:-135.55,-22.29,-134.84:99
+chr1	4226228	rs2411738	G	A	332.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=1328.38;QD=18.98;SB=-511.52	GT:AD:DP:GL:GQ	0/1:30,40:68:-156.63,-20.50,-89.85:99
+chr1	4227495	rs2101576	C	T	457.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.43;MQ0=0;OQ=1111.42;QD=15.22;SB=-551.59	GT:AD:DP:GL:GQ	0/1:39,34:73:-136.43,-22.01,-124.07:99
+chr1	4227724	rs10915493	G	A	108.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=60.00;MQ0=0;OQ=1106.23;QD=18.75;SB=-402.40	GT:AD:DP:GL:GQ	0/1:26,33:59:-131.68,-17.78,-92.93:99
+chr1	4228365	.	G	A	59.74	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=2.28;MQ=58.73;MQ0=0;OQ=1218.17;QD=16.69;SB=-516.71	GT:AD:DP:GL:GQ	0/1:36,37:71:-146.49,-21.39,-124.67:99
+chr1	4228440	rs11586171	G	A	378.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=59.25;MQ0=0;OQ=793.38;QD=14.17;SB=-261.74	GT:AD:DP:GL:GQ	0/1:30,26:52:-98.30,-15.68,-86.01:99
+chr1	4228626	rs10799221	A	G	244.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.55;MQ0=0;OQ=773.13;QD=15.16;SB=-359.35	GT:AD:DP:GL:GQ	0/1:24,27:50:-95.66,-15.07,-89.39:99
+chr1	4230147	rs6677984	A	G	313.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.80;MQ0=0;OQ=752.97;QD=10.61;SB=-294.25	GT:AD:DP:GL:GQ	0/1:36,35:64:-97.88,-19.30,-127.54:99
+chr1	4231035	.	G	A	41.87	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.60;MQ=59.27;MQ0=0;OQ=1023.37;QD=17.95;SB=-471.06	GT:AD:DP:GL:GQ	0/1:23,34:54:-121.89,-16.27,-83.08:99
+chr1	4231643	rs4654426	A	G	357.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=59.13;MQ0=0;OQ=804.91;QD=14.63;SB=-368.10	GT:AD:DP:GL:GQ	0/1:22,33:51:-99.15,-15.37,-84.11:99
+chr1	4232195	.	G	A	71.35	PASS	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=60.00;MQ0=0;OQ=896.42;QD=13.18;SB=-396.87	GT:AD:DP:GL:GQ	0/1:39,29:68:-113.42,-20.50,-128.87:99
+chr1	4232590	rs7527612	G	A	196.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.22;MQ=59.61;MQ0=0;OQ=598.22;QD=12.46;SB=-285.21	GT:AD:DP:GL:GQ	0/1:26,20:44:-76.37,-13.26,-81.07:99
+chr1	4233150	rs10737406	C	T	190.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1662.89;QD=19.34;SB=-750.79	GT:AD:DP:GL:GQ	0/1:38,48:86:-195.48,-25.90,-136.98:99
+chr1	4233365	rs10737407	T	C	106.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=59.79;MQ0=0;OQ=829.78;QD=9.43;SB=-420.85	GT:AD:DP:GL:GQ	0/1:52,36:87:-112.48,-26.22,-211.16:99
+chr1	4233528	rs10737408	T	C	490.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1057.73;QD=14.90;SB=-414.29	GT:AD:DP:GL:GQ	0/1:30,41:71:-130.46,-21.40,-122.91:99
+chr1	4233635	rs10799223	G	C	53.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=4.97;MQ=59.34;MQ0=0;OQ=1650.26;QD=16.67;SB=-729.99	GT:AD:DP:GL:GQ	0/1:53,46:99:-198.14,-29.83,-227.12:99
+chr1	4234047	rs12095914	C	T	0.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=9.26;MQ=42.37;MQ0=0;OQ=137.29;QD=9.81;SB=-42.54	GT:AD:DP:GL:GQ	0/1:9,5:10:-20.03,-3.01,-17.15:99
+chr1	4234051	rs56077919	C	T	1.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=0;HaplotypeScore=7.11;MQ=38.66;MQ0=0;OQ=106.65;QD=8.89;SB=-40.54	GT:AD:DP:GL:GQ	0/1:8,4:8:-16.36,-2.41,-14.46:99
+chr1	4234076	.	T	C	1.57	PASS	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=36.23;MQ0=1;OQ=55.15;QD=6.13;SB=-6.99	GT:AD:DP:GL:GQ	0/1:6,3:7:-10.91,-2.11,-15.53:87.98
+chr1	4234095	rs12752111	C	T	29.22	LowQual	AC=1;AF=0.50;AN=2;DB;DP=8;Dels=0.00;HRun=1;HaplotypeScore=2.44;MQ=42.08;MQ0=1;QD=3.65;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,3:6:-8.01,-1.81,-14.07:62.05
+chr1	4234115	.	T	C	41.10	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=27.16;MQ=46.57;MQ0=0;QD=2.94;SB=-6.99	GT:AD:DP:GL:GQ	0/1:10,4:11:-10.71,-3.31,-31.76:73.94
+chr1	4234119	.	T	C	26.07	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=23.15;MQ=48.70;MQ0=0;QD=1.37;SB=-6.99	GT:AD:DP:GL:GQ	0/1:13,6:15:-10.41,-4.52,-48.38:58.90
+chr1	4234123	.	T	C	99.42	SnpCluster	AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=15.26;MQ=47.83;MQ0=0;QD=4.52;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,7:16:-18.04,-4.82,-44.01:99
+chr1	4234141	.	C	T	11.93	LowQual	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=3;HaplotypeScore=2.90;MQ=45.82;MQ0=0;QD=0.38;SB=-10.00	GT:AD:DP:GL:GQ	0/1:27,4:24:-11.68,-7.23,-69.44:44.48
+chr1	4234162	rs55680202	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.02;HRun=14;HaplotypeScore=7.57;MQ=46.57;MQ0=0;OQ=162.83;QD=3.54;SB=-20.39	GT:AD:DP:GL:GQ	0/1:36,9:39:-31.01,-11.45,-100.16:99
+chr1	4234461	rs2898791	C	A	324.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=54.58;MQ0=0;OQ=1440.90;QD=17.57;SB=-669.70	GT:AD:DP:GL:GQ	0/1:33,49:78:-170.87,-23.50,-98.97:99
+chr1	4235747	rs1495243	G	A	21.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=0.87;MQ=59.34;MQ0=0;OQ=727.40;QD=20.78;SB=-304.24	GT:AD:DP:GL:GQ	0/1:14,21:34:-86.27,-10.24,-44.00:99
+chr1	4235753	rs903541	A	G	320.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=658.30;QD=17.79;SB=-304.49	GT:AD:DP:GL:GQ	0/1:15,22:36:-79.96,-10.84,-57.03:99
+chr1	4236215	rs2411739	T	C	3.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=4;HaplotypeScore=1.73;MQ=54.14;MQ0=0;OQ=570.50;QD=9.84;SB=-308.25	GT:AD:DP:GL:GQ	0/1:27,31:50:-75.41,-15.07,-105.40:99
+chr1	4243198	rs6658727	T	C	21.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.26;MQ=56.21;MQ0=0;OQ=1400.87;QD=30.45;SB=-402.32	GT:AD:DP:GL:GQ	1/1:0,46:43:-143.70,-12.96,-0.03:99
+chr1	4254604	rs1495248	G	A	254.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.88;MQ0=0;OQ=575.96;QD=13.39;SB=-220.90	GT:AD:DP:GL:GQ	0/1:24,19:42:-73.53,-12.65,-79.75:99
+chr1	4255328	rs2130621	G	A	47.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=4.28;MQ=59.31;MQ0=0;OQ=1064.10;QD=15.88;SB=-426.97	GT:AD:DP:GL:GQ	0/1:33,34:65:-129.28,-19.59,-111.47:99
+chr1	4255353	rs12123539	G	C	316.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=1198.39;QD=17.89;SB=-531.27	GT:AD:DP:GL:GQ	0/1:31,36:67:-143.33,-20.20,-136.21:99
+chr1	4255453	rs2029490	A	G	353.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=59.70;MQ0=0;OQ=1028.79;QD=13.19;SB=-497.67	GT:AD:DP:GL:GQ	0/1:34,44:74:-128.48,-22.32,-128.69:99
+chr1	4256070	rs61769407	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.03;HRun=0;HaplotypeScore=33.48;MQ=52.67;MQ0=1;OQ=340.13;QD=5.08;SB=-156.75	GT:AD:DP:GL:GQ	0/1:47,18:58:-54.18,-16.88,-142.71:99
+chr1	4256256	rs12563155	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=93.47;MQ=55.97;MQ0=0;OQ=536.64;QD=7.56;SB=-213.44	GT:AD:DP:GL:GQ	0/1:49,22:63:-75.92,-18.98,-150.16:99
+chr1	4256294	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=8.05;MQ=57.07;MQ0=1;OQ=87.19;QD=1.23;SB=41.60	GT:AD:DP:GL:GQ	0/1:61,10:65:-31.59,-19.59,-196.34:99
+chr1	4256295	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=7.58;MQ=57.07;MQ0=1;OQ=86.67;QD=1.22;SB=35.22	GT:AD:DP:GL:GQ	0/1:61,10:60:-30.03,-18.08,-181.58:99
+chr1	4256665	rs11487456	A	C	56.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=2.90;MQ=57.92;MQ0=0;OQ=976.57;QD=11.10;SB=-464.71	GT:AD:DP:GL:GQ	0/1:50,38:85:-126.54,-25.60,-185.54:99
+chr1	4258667	rs10753377	G	C	1.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=5;HaplotypeScore=1.15;MQ=59.53;MQ0=0;OQ=783.06;QD=15.98;SB=-363.09	GT:AD:DP:GL:GQ	0/1:26,23:47:-95.76,-14.17,-99.93:99
+chr1	4259991	rs592323	G	T	282.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=1759.13;QD=36.65;SB=-870.26	GT:AD:DP:GL:GQ	1/1:0,48:48:-179.51,-14.45,-0.01:99
+chr1	4261395	rs513096	G	A	177.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=58.45;MQ0=0;OQ=707.77;QD=15.73;SB=-231.55	GT:AD:DP:GL:GQ	0/1:23,22:44:-87.33,-13.26,-70.99:99
+chr1	4262899	.	A	G	18.25	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=43.81;MQ=48.38;MQ0=0;QD=0.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:50,5:40:-17.15,-12.05,-140.45:51.02
+chr1	4262904	rs28675202	G	A	73.10	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=14.98;MQ=50.70;MQ0=0;QD=1.43;SB=-10.00	GT:AD:DP:GL:GQ	0/1:40,11:45:-24.15,-13.55,-132.97:99
+chr1	4262909	.	G	A	79.12	SnpCluster	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=50.76;MQ0=0;QD=1.65;SB=-10.00	GT:AD:DP:GL:GQ	0/1:37,11:43:-24.15,-12.95,-125.43:99
+chr1	4262914	rs629808	G	A	33.56	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=52.89;MQ=50.96;MQ0=0;QD=0.68;SB=-10.00	GT:AD:DP:GL:GQ	0/1:39,10:44:-19.89,-13.25,-132.97:66.40
+chr1	4262923	.	C	T	231.89	SnpCluster	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=36.64;MQ=51.44;MQ0=0;QD=5.27;SB=-10.00	GT:AD:DP:GL:GQ	0/1:30,14:37:-37.63,-11.16,-89.50:99
+chr1	4262924	rs3124336	G	A	119.70	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=42.63;MQ=51.44;MQ0=0;QD=2.72;SB=-10.00	GT:AD:DP:GL:GQ	0/1:30,14:37:-26.40,-11.15,-102.56:99
+chr1	4262928	.	C	T	227.91	SnpCluster	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=40.91;MQ=51.65;MQ0=0;QD=5.06;SB=-10.00	GT:AD:DP:GL:GQ	0/1:31,14:38:-37.54,-11.47,-89.09:99
+chr1	4262934	.	G	A	212.81	SnpCluster	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=38.78;MQ=51.84;MQ0=0;QD=4.63;SB=-10.00	GT:AD:DP:GL:GQ	0/1:35,11:39:-36.31,-11.75,-102.65:99
+chr1	4262955	.	C	T	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=10.30;MQ=55.28;MQ0=0;OQ=119.85;QD=3.24;SB=-10.00	GT:AD:DP:GL:GQ	0/1:30,7:34:-25.51,-10.24,-106.69:99
+chr1	4262965	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=55.83;MQ0=0;OQ=58.64;QD=1.63;SB=-10.00	GT:AD:DP:GL:GQ	0/1:31,5:33:-19.09,-9.94,-116.28:91.47
+chr1	4263200	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=16.50;MQ=29.51;MQ0=20;OQ=97.44;QD=2.38;SB=-10.00	GT:AD:DP:GL:GQ	0/1:35,5:14:-17.24,-4.22,-36.40:99
+chr1	4263205	rs12035244	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=20.28;MQ=30.89;MQ0=18;OQ=95.43;QD=2.27;SB=-10.00	GT:AD:DP:GL:GQ	0/1:37,5:15:-17.34,-4.52,-40.16:99
+chr1	4263595	rs34429154	C	A	184.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=59.01;MQ0=0;OQ=488.72;QD=10.40;SB=-267.26	GT:AD:DP:GL:GQ	0/1:29,18:46:-66.01,-13.86,-101.87:99
+chr1	4263832	rs584035	G	A	216.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.61;MQ0=0;OQ=1091.44;QD=18.50;SB=-496.53	GT:AD:DP:GL:GQ	0/1:27,32:59:-130.21,-17.78,-86.40:99
+chr1	4263930	rs503536	G	A	202.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=59.57;MQ0=0;OQ=661.52;QD=12.25;SB=-344.44	GT:AD:DP:GL:GQ	0/1:32,22:49:-84.20,-14.76,-96.54:99
+chr1	4264086	rs693734	C	T	101.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.89;MQ=58.91;MQ0=0;OQ=1021.37;QD=17.02;SB=-501.11	GT:AD:DP:GL:GQ	0/1:29,31:59:-123.20,-17.78,-92.76:99
+chr1	4264332	rs1106307	A	G	290.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.63;MQ=59.33;MQ0=0;OQ=913.45;QD=14.73;SB=-354.33	GT:AD:DP:GL:GQ	0/1:28,34:58:-112.10,-17.47,-104.59:99
+chr1	4264424	rs2132176	A	G	368.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=613.38;QD=11.15;SB=-237.28	GT:AD:DP:GL:GQ	0/1:30,25:53:-80.60,-15.97,-111.46:99
+chr1	4264542	rs2132174	T	A	221.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=52.27;MQ0=0;OQ=1008.56;QD=17.69;SB=-458.63	GT:AD:DP:GL:GQ	0/1:21,35:54:-122.63,-18.49,-81.00:99
+chr1	4264801	rs3007778	G	C	66.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=58.11;MQ0=0;OQ=580.26;QD=12.35;SB=-271.29	GT:AD:DP:GL:GQ	0/1:28,19:44:-74.59,-13.28,-102.55:99
+chr1	4265009	rs3007777	C	A	272.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.09;MQ0=0;OQ=812.00;QD=17.65;SB=-415.86	GT:AD:DP:GL:GQ	0/1:19,27:45:-98.04,-13.55,-64.20:99
+chr1	4265174	.	G	A	199.75	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.87;MQ0=0;OQ=560.44;QD=13.67;SB=-202.85	GT:AD:DP:GL:GQ	0/1:23,18:41:-71.68,-12.35,-78.36:99
+chr1	4265866	rs56198562	A	G	125.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=2.61;MQ=59.78;MQ0=0;OQ=979.47;QD=11.66;SB=-298.20	GT:AD:DP:GL:GQ	0/1:43,41:82:-125.95,-24.72,-170.33:99
+chr1	4266398	rs1495240	C	T	180.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.09;MQ0=0;OQ=962.96;QD=18.88;SB=-480.01	GT:AD:DP:GL:GQ	0/1:23,28:47:-113.74,-14.16,-62.01:99
+chr1	4266494	rs1845634	G	A	227.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1124.56;QD=17.85;SB=-553.73	GT:AD:DP:GL:GQ	0/1:30,33:63:-134.72,-18.98,-108.50:99
+chr1	4267183	rs1490413	G	A	163.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=1.58;MQ=59.39;MQ0=0;OQ=1192.58;QD=17.54;SB=-578.10	GT:AD:DP:GL:GQ	0/1:31,37:66:-142.43,-19.88,-110.71:99
+chr1	4267249	rs16838591	G	A	109.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.45;MQ0=0;OQ=560.73;QD=16.49;SB=-154.59	GT:AD:DP:GL:GQ	0/1:17,17:34:-69.60,-10.24,-59.00:99
+chr1	4267670	rs17448695	C	T	256.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=2.17;MQ=59.11;MQ0=0;OQ=785.86;QD=16.72;SB=-406.95	GT:AD:DP:GL:GQ	0/1:22,24:45:-95.42,-13.55,-80.15:99
+chr1	4267782	rs1817914	T	C	324.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.97;MQ0=0;OQ=827.52;QD=14.03;SB=-394.24	GT:AD:DP:GL:GQ	0/1:29,30:58:-103.51,-17.47,-117.96:99
+chr1	4267840	rs2934983	G	A	322.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.36;MQ0=0;OQ=1060.38;QD=18.28;SB=-513.09	GT:AD:DP:GL:GQ	0/1:26,32:57:-126.49,-17.17,-95.38:99
+chr1	4267886	rs1817913	A	G	440.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=738.48;QD=13.43;SB=-393.26	GT:AD:DP:GL:GQ	0/1:24,31:50:-92.21,-15.08,-81.77:99
+chr1	4268301	rs351622	A	T	719.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=1814.47;QD=35.58;SB=-930.73	GT:AD:DP:GL:GQ	1/1:0,51:49:-185.04,-14.76,-0.01:99
+chr1	4268579	rs351621	T	C	72.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=59.25;MQ0=0;OQ=1364.91;QD=27.30;SB=-524.09	GT:AD:DP:GL:GQ	1/1:0,50:43:-140.11,-12.97,-0.04:99
+chr1	4268604	rs351620	C	T	134.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=59.46;MQ0=0;OQ=1433.75;QD=33.34;SB=-736.64	GT:AD:DP:GL:GQ	1/1:0,43:39:-146.99,-11.76,-0.03:99
+chr1	4268679	rs351619	G	A	84.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1739.98;QD=37.83;SB=-519.64	GT:AD:DP:GL:GQ	1/1:0,46:44:-177.59,-13.26,-0.01:99
+chr1	4268802	rs351618	T	C	98.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=1092.21;QD=26.64;SB=-356.42	GT:AD:DP:GL:GQ	1/1:0,41:37:-112.85,-11.17,-0.05:99
+chr1	4268811	rs351617	C	T	143.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1491.48;QD=36.38;SB=-509.63	GT:AD:DP:GL:GQ	1/1:1,40:39:-152.75,-11.76,-0.02:99
+chr1	4268960	rs2087571	C	T	152.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=53.63;MQ0=0;OQ=643.83;QD=17.40;SB=-299.23	GT:AD:DP:GL:GQ	0/1:15,22:34:-77.91,-10.25,-47.03:99
+chr1	4269767	rs351616	A	G	168.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=58.87;MQ0=0;OQ=1214.77;QD=29.63;SB=-431.27	GT:AD:DP:GL:GQ	1/1:0,41:38:-125.09,-11.46,-0.03:99
+chr1	4270245	rs351615	G	A	292.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=58.55;MQ0=0;OQ=1966.57;QD=35.76;SB=-975.01	GT:AD:DP:GL:GQ	1/1:0,54:52:-200.27,-15.67,-0.02:99
+chr1	4271723	rs351614	C	T	601.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=2473.56;QD=39.90;SB=-1111.03	GT:AD:DP:GL:GQ	1/1:0,62:62:-250.96,-18.68,-0.01:99
+chr1	4271809	rs12132314	C	T	430.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.65;MQ0=0;OQ=1181.91;QD=18.18;SB=-613.64	GT:AD:DP:GL:GQ	0/1:30,35:65:-141.06,-19.59,-97.20:99
+chr1	4273032	rs171260	A	C	300.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=60.00;MQ0=0;OQ=870.08;QD=12.08;SB=-225.83	GT:AD:DP:GL:GQ	0/1:41,31:71:-111.68,-21.38,-150.14:99
+chr1	4274131	rs351613	A	C	265.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.14;MQ0=0;OQ=2299.32;QD=35.37;SB=-1119.04	GT:AD:DP:GL:GQ	1/1:0,65:65:-233.54,-19.58,-0.02:99
+chr1	4277771	rs351596	C	T	568.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=2579.09;QD=39.68;SB=-949.23	GT:AD:DP:GL:GQ	1/1:0,65:64:-261.51,-19.28,-0.02:99
+chr1	4279737	rs876273	C	G	132.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=4.17;MQ=59.56;MQ0=0;OQ=768.76;QD=14.78;SB=-189.63	GT:AD:DP:GL:GQ	0/1:23,29:48:-94.65,-14.49,-97.38:99
+chr1	4279818	rs351598	A	T	381.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.53;MQ=59.66;MQ0=0;OQ=991.33;QD=14.58;SB=-452.46	GT:AD:DP:GL:GQ	0/1:35,33:67:-122.60,-20.18,-130.61:99
+chr1	4280055	rs1874269	C	T	619.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=2766.74;QD=39.52;SB=-1179.55	GT:AD:DP:GL:GQ	1/1:0,70:69:-280.28,-20.79,-0.02:99
+chr1	4280204	rs2411741	C	A	180.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=2;HaplotypeScore=1.15;MQ=60.13;MQ0=0;OQ=1218.75;QD=14.51;SB=-564.82	GT:AD:DP:GL:GQ	0/1:42,42:82:-149.85,-24.70,-149.73:99
+chr1	4280489	rs351599	C	T	413.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=59.72;MQ0=0;OQ=1071.03;QD=16.23;SB=-457.49	GT:AD:DP:GL:GQ	0/1:33,33:66:-130.29,-19.90,-102.77:99
+chr1	4285644	.	A	G	0.07	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=4;HaplotypeScore=2.54;MQ=57.79;MQ0=0;OQ=595.83;QD=12.16;SB=-120.71	GT:AD:DP:GL:GQ	0/1:26,23:47:-77.03,-14.16,-95.21:99
+chr1	4288221	.	G	A	0.84	PASS	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=1;HaplotypeScore=8.13;MQ=58.71;MQ0=0;OQ=1360.73;QD=16.39;SB=-394.38	GT:AD:DP:GL:GQ	0/1:43,40:81:-163.76,-24.40,-149.01:99
+chr1	4289709	.	T	G	46.86	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=1;HaplotypeScore=16.54;MQ=56.55;MQ0=0;QD=0.98;SB=53.18	GT:AD:DP:GL:GQ	0/1:27,21:32:-17.62,-9.65,-87.21:79.70
+chr1	4292594	rs34245285	G	C	0.05	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=3.96;MQ=50.65;MQ0=4;OQ=195.36;QD=3.15;SB=-102.43	GT:AD:DP:GL:GQ	0/1:47,15:34:-33.09,-10.27,-97.74:99
+chr1	4293081	rs34762254	C	G	17.74	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=35.42;MQ0=7;QD=0.43;SB=11.07	GT:AD:DP:GL:GQ	0/1:35,5:26:-12.90,-7.85,-90.70:50.51
+chr1	4293374	.	G	A	3.97	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=44.45;MQ0=2;OQ=329.37;QD=6.59;SB=0.51	GT:AD:DP:GL:GQ	0/1:31,19:40:-48.28,-12.06,-89.72:99
+chr1	4296431	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.01;HRun=0;HaplotypeScore=166.11;MQ=33.71;MQ0=1;OQ=76.77;QD=0.64;SB=116.41	GT:AD:DP:GL:GQ	0/1:95,22:100:-40.80,-29.83,-343.52:99
+chr1	4296441	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=126;Dels=0.07;HRun=0;HaplotypeScore=204.38;MQ=34.16;MQ0=1;OQ=63.06;QD=0.50;SB=111.78	GT:AD:DP:GL:GQ	0/1:104,10:96:-43.83,-34.24,-290.54:95.89
+chr1	4296449	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=184.01;MQ=35.76;MQ0=1;OQ=76.57;QD=0.81;SB=108.85	GT:AD:DP:GL:GQ	0/1:78,6:65:-53.79,-42.85,-256.56:99
+chr1	4296459	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=1;HaplotypeScore=225.82;MQ=37.43;MQ0=0;OQ=345.89;QD=3.98;SB=26.09	GT:AD:DP:GL:GQ	0/1:63,24:68:-58.36,-20.48,-198.46:99
+chr1	4296469	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=1;HaplotypeScore=189.98;MQ=37.41;MQ0=0;OQ=75.74;QD=0.80;SB=12.63	GT:AD:DP:GL:GQ	0/1:84,11:69:-31.64,-20.79,-221.92:99
+chr1	4296493	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=88.30;MQ=41.30;MQ0=0;OQ=474.04;QD=4.65;SB=-167.48	GT:AD:DP:GL:GQ	0/1:59,36:81:-93.85,-43.16,-272.31:99
+chr1	4296506	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=103;Dels=0.03;HRun=1;HaplotypeScore=78.61;MQ=43.01;MQ0=0;OQ=51.88;QD=0.50;SB=101.36	GT:AD:DP:GL:GQ	0/1:87,13:87:-34.09,-25.62,-299.11:84.72
+chr1	4296513	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=100;Dels=0.02;HRun=0;HaplotypeScore=60.45;MQ=43.56;MQ0=0;OQ=185.47;QD=1.85;SB=-3.86	GT:AD:DP:GL:GQ	0/1:80,18:74:-44.13,-22.29,-236.48:99
+chr1	4296520	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=1;HaplotypeScore=86.57;MQ=43.66;MQ0=0;OQ=90.49;QD=0.82;SB=69.81	GT:AD:DP:GL:GQ	0/1:99,12:95:-40.96,-28.62,-301.41:99
+chr1	4296571	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=100;Dels=0.02;HRun=0;HaplotypeScore=148.81;MQ=42.35;MQ0=0;OQ=149.13;QD=1.49;SB=56.28	GT:AD:DP:GL:GQ	0/1:64,20:79:-66.77,-48.58,-247.91:99
+chr1	4296587	.	G	A	55.07	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=113;Dels=0.02;HRun=0;HaplotypeScore=138.42;MQ=36.11;MQ0=2;QD=0.49;SB=3.46	GT:AD:DP:GL:GQ	0/1:83,28:77:-31.99,-23.20,-236.17:87.91
+chr1	4296590	.	A	G	63.20	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=113;Dels=0.01;HRun=1;HaplotypeScore=134.39;MQ=36.11;MQ0=2;QD=0.56;SB=44.15	GT:AD:DP:GL:GQ	0/1:101,11:84:-34.62,-25.01,-283.57:96.04
+chr1	4296596	.	G	A	133.96	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=190.44;MQ=35.58;MQ0=2;QD=1.09;SB=41.12	GT:AD:DP:GL:GQ	0/1:107,16:99:-46.51,-29.83,-296.83:99
+chr1	4296607	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=125;Dels=0.00;HRun=1;HaplotypeScore=185.73;MQ=34.74;MQ0=2;OQ=309.12;QD=2.47;SB=41.15	GT:AD:DP:GL:GQ	0/1:106,19:100:-64.31,-30.12,-298.02:99
+chr1	4296636	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=188.32;MQ=35.30;MQ0=3;OQ=116.48;QD=0.91;SB=56.18	GT:AD:DP:GL:GQ	0/1:110,17:102:-45.68,-30.75,-346.20:99
+chr1	4296642	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=1;HaplotypeScore=236.73;MQ=34.36;MQ0=5;OQ=253.36;QD=1.95;SB=47.15	GT:AD:DP:GL:GQ	0/1:113,17:102:-59.34,-30.72,-306.11:99
+chr1	4296665	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=107.40;MQ=33.96;MQ0=6;OQ=319.22;QD=2.73;SB=50.15	GT:AD:DP:GL:GQ	0/1:91,24:96:-64.13,-28.92,-272.83:99
+chr1	4296668	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=119;Dels=0.01;HRun=0;HaplotypeScore=114.24;MQ=34.12;MQ0=7;OQ=295.42;QD=2.48;SB=-19.17	GT:AD:DP:GL:GQ	0/1:99,19:98:-62.05,-29.23,-276.38:99
+chr1	4296677	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=110;Dels=0.03;HRun=0;HaplotypeScore=117.38;MQ=34.73;MQ0=5;OQ=320.24;QD=2.91;SB=47.14	GT:AD:DP:GL:GQ	0/1:86,21:91:-62.13,-26.82,-250.93:99
+chr1	4296686	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=54.93;MQ=36.96;MQ0=5;OQ=147.08;QD=1.67;SB=50.15	GT:AD:DP:GL:GQ	0/1:78,10:74:-40.29,-22.30,-219.44:99
+chr1	4308180	.	C	T	161.22	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.53;MQ0=0;OQ=1282.15;QD=17.56;SB=-488.11	GT:AD:DP:GL:GQ	0/1:35,38:73:-153.50,-22.00,-116.62:99
+chr1	4309112	.	A	C	86.02	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.15;MQ=59.03;MQ0=0;OQ=562.66;QD=13.09;SB=-287.67	GT:AD:DP:GL:GQ	0/1:22,20:43:-74.67,-15.12,-82.44:99
+chr1	4310347	.	C	T	101.72	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=59.41;MQ0=0;OQ=1172.68;QD=16.52;SB=-579.36	GT:AD:DP:GL:GQ	0/1:36,35:70:-141.64,-21.08,-130.80:99
+chr1	4314528	.	T	C	249.50	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1047.71;QD=18.38;SB=-476.64	GT:AD:DP:GL:GQ	0/1:22,35:57:-125.23,-17.17,-90.17:99
+chr1	4316332	.	T	G	43.87	PASS	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.09;MQ=59.28;MQ0=0;OQ=471.43;QD=14.73;SB=-242.41	GT:AD:DP:GL:GQ	0/1:14,18:31:-59.77,-9.34,-47.32:99
+chr1	4316334	.	C	G	15.52	PASS	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=59.32;MQ0=0;OQ=676.22;QD=19.89;SB=-323.04	GT:AD:DP:GL:GQ	0/1:15,19:34:-81.16,-10.25,-60.88:99
+chr1	4318103	rs349395	A	G	659.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=1716.14;QD=31.20;SB=-834.63	GT:AD:DP:GL:GQ	1/1:0,55:54:-175.24,-16.28,-0.05:99
+chr1	4319680	rs349393	A	C	563.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=813.26;QD=15.95;SB=-376.77	GT:AD:DP:GL:GQ	0/1:23,28:51:-99.97,-15.36,-86.41:99
+chr1	4319765	rs102083	A	T	361.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=55.80;MQ0=0;OQ=747.97;QD=14.96;SB=-385.65	GT:AD:DP:GL:GQ	0/1:24,26:48:-92.54,-14.46,-85.84:99
+chr1	4319782	rs28431405	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=20;HaplotypeScore=17.05;MQ=53.28;MQ0=0;OQ=875.22;QD=14.59;SB=-406.12	GT:AD:DP:GL:GQ	0/1:25,35:49:-105.57,-14.76,-69.63:99
+chr1	4319814	rs102085	G	A	15.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=5.54;MQ=52.08;MQ0=0;OQ=929.67;QD=17.22;SB=-462.49	GT:AD:DP:GL:GQ	0/1:25,29:49:-111.01,-14.76,-74.46:99
+chr1	4319857	rs17410050	C	T	91.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.83;MQ0=0;OQ=1009.89;QD=18.36;SB=-347.35	GT:AD:DP:GL:GQ	0/1:26,29:55:-120.84,-16.57,-94.75:99
+chr1	4320268	rs349392	G	T	359.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.27;MQ=58.71;MQ0=0;OQ=818.84;QD=15.16;SB=-433.16	GT:AD:DP:GL:GQ	0/1:23,30:49:-99.94,-14.77,-68.96:99
+chr1	4320352	rs101287	A	C	9.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=2.94;MQ=58.91;MQ0=0;OQ=686.61;QD=10.73;SB=-323.81	GT:AD:DP:GL:GQ	0/1:36,28:61:-90.33,-18.38,-119.68:99
+chr1	4321671	rs56216403	A	T	13.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=7.66;MQ=57.98;MQ0=0;OQ=569.50;QD=12.94;SB=-290.67	GT:AD:DP:GL:GQ	0/1:24,20:41:-72.59,-12.36,-76.85:99
+chr1	4321865	rs349391	T	C	61.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=58.51;MQ0=0;OQ=775.30;QD=16.50;SB=-140.34	GT:AD:DP:GL:GQ	0/1:20,26:42:-93.47,-12.66,-62.46:99
+chr1	4321866	rs56376431	G	A	8.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=58.51;MQ0=0;OQ=873.71;QD=18.59;SB=-178.26	GT:AD:DP:GL:GQ	0/1:21,26:42:-103.31,-12.65,-56.39:99
+chr1	4322006	rs56162804	C	T	116.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.53;MQ0=0;OQ=1021.04;QD=20.84;SB=-534.77	GT:AD:DP:GL:GQ	0/1:19,30:49:-120.16,-14.77,-59.62:99
+chr1	4322030	rs55838104	C	T	52.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.96;MQ=60.00;MQ0=0;OQ=1120.64;QD=21.14;SB=-534.76	GT:AD:DP:GL:GQ	0/1:20,33:52:-131.01,-15.67,-66.54:99
+chr1	4322090	rs16838800	A	G	416.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=910.62;QD=19.80;SB=-423.34	GT:AD:DP:GL:GQ	0/1:16,30:46:-108.20,-13.86,-64.49:99
+chr1	4322538	rs12403556	C	G	69.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=60.00;MQ0=0;OQ=1513.57;QD=24.81;SB=-525.74	GT:AD:DP:GL:GQ	0/1:20,41:61:-173.03,-18.39,-83.32:99
+chr1	4322543	rs12404034	A	G	25.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=3.64;MQ=60.00;MQ0=0;OQ=1221.46;QD=20.02;SB=-417.22	GT:AD:DP:GL:GQ	0/1:20,41:60:-143.50,-18.07,-80.25:99
+chr1	4322609	rs12404038	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=5;HaplotypeScore=9.16;MQ=59.56;MQ0=0;OQ=664.61;QD=12.54;SB=-143.41	GT:AD:DP:GL:GQ	0/1:24,29:49:-84.51,-14.77,-94.35:99
+chr1	4322739	rs12404366	T	C	226.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=432.95;QD=9.41;SB=-158.54	GT:AD:DP:GL:GQ	0/1:29,17:46:-60.44,-13.86,-115.98:99
+chr1	4322916	rs12402553	G	A	357.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.62;MQ0=0;OQ=842.62;QD=13.81;SB=-393.36	GT:AD:DP:GL:GQ	0/1:35,26:59:-105.32,-17.77,-117.60:99
+chr1	4323438	rs16838810	A	G	123.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=0.32;MQ=59.40;MQ0=0;OQ=808.90;QD=13.05;SB=-366.96	GT:AD:DP:GL:GQ	0/1:30,32:61:-102.56,-18.39,-119.19:99
+chr1	4323490	rs55944275	G	A	62.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.36;MQ0=0;OQ=1153.53;QD=19.89;SB=-343.36	GT:AD:DP:GL:GQ	0/1:24,34:57:-135.81,-17.17,-85.54:99
+chr1	4323756	rs349390	T	C	313.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.62;MQ0=0;OQ=671.97;QD=11.20;SB=-140.85	GT:AD:DP:GL:GQ	0/1:34,26:58:-87.95,-17.47,-136.36:99
+chr1	4323757	rs58351078	G	A	132.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.61;MQ0=0;OQ=802.14;QD=13.60;SB=-181.76	GT:AD:DP:GL:GQ	0/1:34,25:59:-101.27,-17.77,-124.39:99
+chr1	4323928	rs61676533	C	T	374.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.48;MQ0=0;OQ=1036.80;QD=14.40;SB=-477.00	GT:AD:DP:GL:GQ	0/1:40,32:72:-128.65,-21.69,-142.77:99
+chr1	4323975	rs16838812	A	G	340.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=59.17;MQ0=0;OQ=822.30;QD=12.09;SB=-364.22	GT:AD:DP:GL:GQ	0/1:38,30:68:-106.00,-20.49,-150.74:99
+chr1	4324005	rs16838813	G	A	586.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.08;MQ0=0;OQ=833.74;QD=14.13;SB=-356.82	GT:AD:DP:GL:GQ	0/1:33,26:58:-104.14,-17.48,-106.56:99
+chr1	4324062	rs56775247	A	G	352.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.86;MQ0=0;OQ=755.78;QD=11.81;SB=-150.88	GT:AD:DP:GL:GQ	0/1:37,27:64:-98.14,-19.28,-148.79:99
+chr1	4324102	rs57599092	A	T	199.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.94;MQ=53.27;MQ0=0;OQ=1008.31;QD=14.83;SB=-333.61	GT:AD:DP:GL:GQ	0/1:34,34:66:-123.99,-19.88,-127.49:99
+chr1	4324399	rs11804096	T	C	269.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=45.70;MQ0=1;OQ=598.48;QD=11.29;SB=-306.38	GT:AD:DP:GL:GQ	0/1:28,25:48:-77.59,-14.46,-100.69:99
+chr1	4324626	rs11803736	A	G	203.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=51.26;MQ0=1;OQ=569.48;QD=10.55;SB=-273.41	GT:AD:DP:GL:GQ	0/1:32,22:52:-75.89,-15.66,-126.39:99
+chr1	4324693	rs11801800	G	A	371.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=50.70;MQ0=1;OQ=920.80;QD=14.85;SB=-460.99	GT:AD:DP:GL:GQ	0/1:32,30:59:-113.14,-17.77,-113.29:99
+chr1	4324939	rs12729994	C	A	219.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=56.71;MQ0=0;OQ=746.98;QD=16.98;SB=-320.72	GT:AD:DP:GL:GQ	0/1:18,26:42:-90.63,-12.65,-55.46:99
+chr1	4325115	rs12742617	T	G	433.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.56;MQ0=0;OQ=1013.88;QD=12.07;SB=-397.13	GT:AD:DP:GL:GQ	0/1:47,37:83:-129.67,-25.00,-173.24:99
+chr1	4325508	rs34012704	A	G	166.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.90;MQ=59.63;MQ0=0;OQ=986.31;QD=19.34;SB=-504.18	GT:AD:DP:GL:GQ	0/1:17,34:49:-116.68,-14.77,-62.75:99
+chr1	4325583	.	G	A	54.73	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=60.00;MQ0=0;OQ=709.46;QD=16.50;SB=-303.82	GT:AD:DP:GL:GQ	0/1:18,25:41:-86.59,-12.36,-64.70:99
+chr1	4325707	rs12405082	A	G	0.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=6.04;MQ=58.57;MQ0=0;OQ=521.78;QD=8.42;SB=-177.38	GT:AD:DP:GL:GQ	0/1:38,24:56:-72.34,-16.88,-134.28:99
+chr1	4325759	.	C	T	1.66	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=2;HaplotypeScore=2.89;MQ=58.50;MQ0=0;OQ=768.28;QD=12.39;SB=-160.15	GT:AD:DP:GL:GQ	0/1:32,29:57:-97.29,-17.18,-106.60:99
+chr1	4325887	rs12403671	G	C	245.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.67;MQ0=0;OQ=1119.45;QD=19.64;SB=-552.71	GT:AD:DP:GL:GQ	0/1:24,33:54:-131.50,-16.27,-104.02:99
+chr1	4325945	rs12404619	C	T	347.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.65;MQ0=0;OQ=874.85;QD=15.91;SB=-387.13	GT:AD:DP:GL:GQ	0/1:26,29:53:-106.74,-15.97,-91.70:99
+chr1	4326338	rs16838819	A	C	229.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=4.02;MQ=58.63;MQ0=0;OQ=550.44;QD=10.79;SB=-296.79	GT:AD:DP:GL:GQ	0/1:29,22:49:-73.09,-14.76,-103.75:99
+chr1	4327728	rs34472761	G	C	257.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=59.05;MQ0=0;OQ=1072.08;QD=16.75;SB=-550.71	GT:AD:DP:GL:GQ	0/1:32,32:62:-129.19,-18.70,-130.17:99
+chr1	4328031	rs56108323	G	A	198.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=626.21;QD=12.28;SB=-249.12	GT:AD:DP:GL:GQ	0/1:27,24:48:-80.37,-14.46,-97.54:99
+chr1	4329322	rs483344	A	G	283.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=59.34;MQ0=0;OQ=672.82;QD=9.61;SB=-273.11	GT:AD:DP:GL:GQ	0/1:41,29:68:-91.06,-20.50,-159.89:99
+chr1	4331124	rs572439	A	C	450.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.73;MQ0=0;OQ=1069.67;QD=15.73;SB=-417.82	GT:AD:DP:GL:GQ	0/1:30,38:67:-130.43,-20.18,-110.75:99
+chr1	4331158	rs572343	G	A	289.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.72;MQ0=0;OQ=1247.65;QD=18.62;SB=-597.10	GT:AD:DP:GL:GQ	0/1:31,36:64:-147.32,-19.27,-103.83:99
+chr1	4331483	rs12750862	T	C	292.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.22;MQ=59.55;MQ0=0;OQ=752.94;QD=14.76;SB=-378.63	GT:AD:DP:GL:GQ	0/1:24,27:49:-93.35,-14.77,-86.37:99
+chr1	4331508	.	C	T	49.49	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=60.00;MQ0=0;OQ=892.12;QD=17.84;SB=-369.91	GT:AD:DP:GL:GQ	0/1:18,31:43:-105.46,-12.97,-47.94:99
+chr1	4333712	rs2926485	T	C	268.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.56;MQ=59.83;MQ0=0;OQ=1004.92;QD=15.70;SB=-484.15	GT:AD:DP:GL:GQ	0/1:28,35:61:-122.15,-18.38,-108.51:99
+chr1	4334184	rs57575485	C	T	360.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.70;MQ0=0;OQ=1292.51;QD=16.79;SB=-566.07	GT:AD:DP:GL:GQ	0/1:37,40:76:-155.43,-22.90,-133.07:99
+chr1	4334834	rs661536	A	G	714.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1993.62;QD=34.98;SB=-900.02	GT:AD:DP:GL:GQ	1/1:0,57:57:-202.97,-17.17,-0.02:99
+chr1	4339520	rs902403	T	C	449.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=846.06;QD=12.44;SB=-357.94	GT:AD:DP:GL:GQ	0/1:35,33:68:-108.38,-20.49,-140.89:99
+chr1	4339677	rs2926482	C	G	218.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2219.96;QD=42.69;SB=-974.35	GT:AD:DP:GL:GQ	1/1:0,52:52:-225.60,-15.67,-0.01:99
+chr1	4340373	rs590798	A	C	514.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=2632.91;QD=34.64;SB=-1142.61	GT:AD:DP:GL:GQ	1/1:0,76:76:-266.90,-22.89,-0.03:99
+chr1	4344158	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=3;HaplotypeScore=3.49;MQ=60.00;MQ0=0;OQ=63.29;QD=1.07;SB=56.21	GT:AD:DP:GL:GQ	0/1:42,17:47:-23.79,-14.18,-151.98:96.13
+chr1	4344566	rs349413	C	A	606.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1116.07;QD=14.69;SB=-454.53	GT:AD:DP:GL:GQ	0/1:39,37:76:-137.78,-22.89,-141.17:99
+chr1	4345038	rs164598	G	A	482.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.02;MQ0=0;OQ=1164.61;QD=17.38;SB=-524.70	GT:AD:DP:GL:GQ	0/1:32,35:67:-139.93,-20.18,-113.85:99
+chr1	4347591	rs4654526	C	T	500.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1310.21;QD=20.16;SB=-660.78	GT:AD:DP:GL:GQ	0/1:25,40:61:-152.69,-18.39,-71.94:99
+chr1	4351708	rs11585123	G	T	52.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=3;HaplotypeScore=1.96;MQ=59.43;MQ0=0;OQ=956.92;QD=13.11;SB=-391.99	GT:AD:DP:GL:GQ	0/1:39,34:73:-120.97,-21.99,-133.39:99
+chr1	4352257	rs627555	G	A	556.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.08;MQ0=0;OQ=1274.67;QD=14.01;SB=-577.49	GT:AD:DP:GL:GQ	0/1:53,38:91:-158.16,-27.41,-187.48:99
+chr1	4352698	.	A	C	145.09	PASS	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1251.00;QD=14.55;SB=-612.69	GT:AD:DP:GL:GQ	0/1:43,43:84:-153.68,-25.30,-154.64:99
+chr1	4353326	rs7523383	C	T	223.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1125.20;QD=18.75;SB=-322.36	GT:AD:DP:GL:GQ	0/1:24,35:55:-132.39,-16.58,-65.47:99
+chr1	4354986	rs55703746	G	T	228.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=1494.65;QD=18.68;SB=-625.43	GT:AD:DP:GL:GQ	0/1:32,48:80:-176.84,-24.10,-112.47:99
+chr1	4358435	.	C	T	24.59	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=3.25;MQ=55.69;MQ0=0;QD=0.61;SB=41.14	GT:AD:DP:GL:GQ	0/1:35,4:36:-16.60,-10.86,-102.91:57.41
+chr1	4358482	.	C	G	35.61	LowQual	AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=54.32;MQ0=0;QD=1.05;SB=-23.70	GT:AD:DP:GL:GQ	0/1:30,4:32:-16.49,-9.64,-124.37:68.45
+chr1	4359549	rs6679220	T	C	288.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=543.81;QD=10.66;SB=-272.37	GT:AD:DP:GL:GQ	0/1:30,21:50:-72.72,-15.06,-124.68:99
+chr1	4360825	rs56081339	G	A	327.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=59.43;MQ0=0;OQ=993.85;QD=13.61;SB=-456.06	GT:AD:DP:GL:GQ	0/1:40,33:70:-123.78,-21.11,-120.70:99
+chr1	4363525	rs349402	G	A	561.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.26;MQ0=0;OQ=1290.95;QD=16.99;SB=-425.80	GT:AD:DP:GL:GQ	0/1:36,40:74:-154.68,-22.30,-119.31:99
+chr1	4367389	rs4654429	G	A	56.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=5.58;MQ=57.65;MQ0=0;OQ=1142.68;QD=16.80;SB=-522.78	GT:AD:DP:GL:GQ	0/1:32,36:64:-136.84,-19.29,-93.56:99
+chr1	4367566	rs4654430	T	C	472.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=611.79;QD=10.92;SB=-199.58	GT:AD:DP:GL:GQ	0/1:34,22:55:-81.03,-16.57,-131.86:99
+chr1	4368744	rs547923	C	A	335.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=58.91;MQ0=0;OQ=794.59;QD=12.42;SB=-343.21	GT:AD:DP:GL:GQ	0/1:34,30:61:-101.12,-18.38,-116.77:99
+chr1	4369295	rs6687224	C	G	567.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1064.80;QD=17.75;SB=-495.28	GT:AD:DP:GL:GQ	0/1:29,31:59:-127.55,-17.78,-120.89:99
+chr1	4369728	rs733308	T	G	295.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.39;MQ=59.19;MQ0=1;OQ=894.22;QD=10.65;SB=-355.63	GT:AD:DP:GL:GQ	0/1:48,36:83:-117.71,-25.00,-176.40:99
+chr1	4370735	rs2926477	A	G	468.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=995.20;QD=15.31;SB=-357.26	GT:AD:DP:GL:GQ	0/1:29,36:64:-122.09,-19.28,-116.14:99
+chr1	4371593	rs505933	A	G	376.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.99;MQ0=0;OQ=894.44;QD=10.78;SB=-423.73	GT:AD:DP:GL:GQ	0/1:45,38:82:-117.44,-24.72,-179.72:99
+chr1	4371867	rs693045	T	C	492.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.26;MQ0=0;OQ=669.20;QD=9.99;SB=-303.21	GT:AD:DP:GL:GQ	0/1:37,30:64:-89.50,-19.29,-143.01:99
+chr1	4371873	rs10915529	G	C	482.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.33;MQ0=0;OQ=903.58;QD=12.91;SB=-393.25	GT:AD:DP:GL:GQ	0/1:40,30:69:-114.44,-20.80,-177.40:99
+chr1	4371886	rs659514	T	C	97.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=1.39;MQ=58.28;MQ0=0;OQ=683.73;QD=10.05;SB=-268.51	GT:AD:DP:GL:GQ	0/1:42,26:67:-91.84,-20.18,-171.36:99
+chr1	4372308	rs4654533	C	G	209.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.20;MQ0=0;OQ=1490.53;QD=19.61;SB=-620.61	GT:AD:DP:GL:GQ	0/1:35,41:72:-174.05,-21.72,-126.16:99
+chr1	4375044	rs349405	A	C	311.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=541.86;QD=10.62;SB=-270.89	GT:AD:DP:GL:GQ	0/1:31,20:51:-72.83,-15.36,-116.45:99
+chr1	4375626	rs349406	T	C	212.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=2.99;MQ=59.38;MQ0=0;OQ=1112.63;QD=14.84;SB=-554.63	GT:AD:DP:GL:GQ	0/1:36,39:72:-136.23,-21.69,-140.85:99
+chr1	4375771	rs12562242	G	T	432.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=59.23;MQ0=0;OQ=915.50;QD=12.54;SB=-381.76	GT:AD:DP:GL:GQ	0/1:39,34:71:-116.22,-21.39,-137.78:99
+chr1	4376133	rs349407	G	A	305.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.03;MQ0=1;OQ=1382.00;QD=18.43;SB=-530.55	GT:AD:DP:GL:GQ	0/1:31,44:71:-162.87,-21.39,-107.28:99
+chr1	4376945	rs10915530	C	T	589.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1129.31;QD=16.13;SB=-586.64	GT:AD:DP:GL:GQ	0/1:35,35:68:-136.71,-20.50,-105.26:99
+chr1	4377252	rs1490416	T	A	34.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.01;HRun=1;HaplotypeScore=4.80;MQ=59.18;MQ0=0;OQ=1402.77;QD=16.50;SB=-436.53	GT:AD:DP:GL:GQ	0/1:39,45:80:-167.66,-24.10,-131.13:99
+chr1	4377771	rs349409	C	T	337.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.02;MQ=59.15;MQ0=0;OQ=1097.95;QD=15.46;SB=-477.48	GT:AD:DP:GL:GQ	0/1:37,34:69:-133.86,-20.78,-131.05:99
+chr1	4377899	rs349410	C	A	42.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=4.55;MQ=59.19;MQ0=0;OQ=1054.50;QD=18.50;SB=-399.14	GT:AD:DP:GL:GQ	0/1:22,35:56:-125.60,-16.87,-75.99:99
+chr1	4377949	rs349411	C	T	2.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=11.72;MQ=58.87;MQ0=0;OQ=1481.01;QD=18.06;SB=-689.93	GT:AD:DP:GL:GQ	0/1:37,45:80:-175.49,-24.10,-130.86:99
+chr1	4377999	rs10915531	A	G	391.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.24;MQ0=0;OQ=1298.04;QD=16.23;SB=-576.28	GT:AD:DP:GL:GQ	0/1:36,44:80:-157.19,-24.10,-146.95:99
+chr1	4380137	rs493178	G	C	0.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.09;MQ=57.06;MQ0=0;OQ=874.81;QD=23.64;SB=-165.59	GT:AD:DP:GL:GQ	0/1:11,26:34:-101.01,-10.25,-40.96:99
+chr1	4380197	.	G	A	21.03	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=23.38;MQ=29.95;MQ0=2;QD=0.68;SB=41.12	GT:AD:DP:GL:GQ	0/1:26,5:22:-12.01,-6.63,-63.36:53.84
+chr1	4380201	rs59237016	A	T	117.83	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=21.39;MQ=30.09;MQ0=2;QD=4.36;SB=-11.73	GT:AD:DP:GL:GQ	0/1:19,6:13:-24.36,-9.29,-27.60:99
+chr1	4380203	.	A	G	41.11	LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=24.37;MQ=28.28;MQ0=2;QD=1.64;SB=-10.00	GT:AD:DP:GL:GQ	0/1:17,7:10:-10.41,-3.01,-27.49:73.95
+chr1	4380215	.	G	A	523.36	SnpCluster	AC=2;AF=1.00;AN=2;DP=19;Dels=0.05;HRun=0;HaplotypeScore=13.20;MQ=29.01;MQ0=2;QD=27.55;SB=-164.67	GT:AD:DP:GL:GQ	1/1:1,17:14:-55.92,-4.22,-0.00:42.14
+chr1	4380217	rs60888156	G	A	452.59	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.05;HRun=0;HaplotypeScore=13.68;MQ=29.01;MQ0=2;QD=23.82;SB=-163.66	GT:AD:DP:GL:GQ	1/1:4,14:14:-51.77,-4.22,-2.97:12.46
+chr1	4380219	.	G	A	274.46	SnpCluster	AC=1;AF=0.50;AN=2;DP=17;Dels=0.06;HRun=0;HaplotypeScore=11.89;MQ=29.85;MQ0=1;QD=16.14;SB=-148.61	GT:AD:DP:GL:GQ	0/1:5,11:13:-34.65,-3.92,-13.88:99
+chr1	4380249	.	G	A	49.25	LowQual	AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=16.42;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,3:2:-8.33,-0.60,-0.00:6.02
+chr1	4380271	rs6697112	G	A	9.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=37.32;MQ0=0;OQ=124.22;QD=24.84;SB=-44.55	GT:AD:DP:GL:GQ	1/1:1,4:4:-15.96,-1.21,-0.00:12.04
+chr1	4380311	rs1309838	C	A	157.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=54.85;MQ0=0;OQ=623.10;QD=14.84;SB=-208.87	GT:AD:DP:GL:GQ	0/1:19,23:41:-77.95,-12.35,-68.48:99
+chr1	4380330	rs1309839	C	T	0.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=7.73;MQ=55.45;MQ0=0;OQ=843.65;QD=20.09;SB=-255.33	GT:AD:DP:GL:GQ	0/1:15,27:37:-98.80,-11.15,-35.58:99
+chr1	4380929	.	T	C	25.32	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=2;HaplotypeScore=5.44;MQ=59.32;MQ0=0;QD=0.37;SB=122.43	GT:AD:DP:GL:GQ	0/1:48,20:54:-22.08,-16.27,-188.06:58.14
+chr1	4380941	rs349386	C	T	474.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.84;MQ0=0;OQ=1352.78;QD=17.80;SB=-554.75	GT:AD:DP:GL:GQ	0/1:36,40:74:-160.85,-22.29,-128.59:99
+chr1	4381075	rs4654432	C	T	88.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=1.63;MQ=60.32;MQ0=0;OQ=870.11;QD=12.80;SB=-258.77	GT:AD:DP:GL:GQ	0/1:40,28:66:-110.19,-19.90,-123.57:99
+chr1	4381353	rs35799150	A	G	389.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=820.10;QD=12.06;SB=-192.18	GT:AD:DP:GL:GQ	0/1:39,29:68:-105.78,-20.48,-159.19:99
+chr1	4381492	rs4654433	G	A	604.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=1070.93;QD=15.98;SB=-493.09	GT:AD:DP:GL:GQ	0/1:35,32:67:-130.57,-20.19,-112.83:99
+chr1	4382470	rs737324	G	C	535.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=1310.24;QD=17.47;SB=-409.80	GT:AD:DP:GL:GQ	0/1:38,37:74:-156.61,-22.31,-151.67:99
+chr1	4382624	rs349385	A	G	200.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=56.49;MQ0=0;OQ=1553.01;QD=28.76;SB=-619.97	GT:AD:DP:GL:GQ	1/1:0,53:51:-158.94,-15.39,-0.06:99
+chr1	4383263	rs41266223	T	C	212.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=57.69;MQ0=0;OQ=666.08;QD=11.29;SB=-355.38	GT:AD:DP:GL:GQ	0/1:32,27:53:-85.86,-15.97,-114.12:99
+chr1	4385955	rs4654537	A	G	109.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=60.00;MQ0=0;OQ=187.72;QD=8.16;SB=-92.99	GT:AD:DP:GL:GQ	0/1:12,10:21:-28.39,-6.33,-46.97:99
+chr1	4386470	rs1762818	A	G	620.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=2262.65;QD=34.81;SB=-1121.77	GT:AD:DP:GL:GQ	1/1:0,65:63:-229.87,-18.98,-0.02:99
+chr1	4386565	rs2035009	T	C	346.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=58.05;MQ0=0;OQ=655.98;QD=10.93;SB=-329.97	GT:AD:DP:GL:GQ	0/1:30,30:56:-85.78,-16.89,-109.09:99
+chr1	4386918	rs2035008	T	A	56.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=1.25;MQ=55.07;MQ0=0;OQ=728.43;QD=12.14;SB=-228.91	GT:AD:DP:GL:GQ	0/1:33,27:58:-93.60,-17.47,-122.91:99
+chr1	4387800	.	G	A	279.77	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1023.92;QD=16.25;SB=-391.36	GT:AD:DP:GL:GQ	0/1:32,31:61:-124.06,-18.39,-99.73:99
+chr1	4388151	rs4654542	C	T	244.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=60.00;MQ0=0;OQ=1264.25;QD=16.63;SB=-528.76	GT:AD:DP:GL:GQ	0/1:37,39:75:-152.31,-22.60,-121.60:99
+chr1	4388316	rs4654434	G	A	492.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1047.13;QD=14.54;SB=-490.97	GT:AD:DP:GL:GQ	0/1:40,32:72:-129.68,-21.69,-147.17:99
+chr1	4388691	rs6667927	C	T	322.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.79;MQ0=0;OQ=1604.10;QD=18.23;SB=-806.38	GT:AD:DP:GL:GQ	0/1:41,47:88:-190.20,-26.51,-149.18:99
+chr1	4388839	rs6658372	G	A	449.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.10;MQ0=0;OQ=954.40;QD=14.24;SB=-360.06	GT:AD:DP:GL:GQ	0/1:36,31:66:-118.61,-19.88,-128.27:99
+chr1	4389258	rs6678792	T	C	469.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.45;MQ0=0;OQ=1167.87;QD=15.37;SB=-534.97	GT:AD:DP:GL:GQ	0/1:37,39:76:-142.96,-22.89,-149.63:99
+chr1	4389389	rs10915533	G	A	316.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=59.63;MQ0=0;OQ=829.91;QD=13.39;SB=-417.75	GT:AD:DP:GL:GQ	0/1:33,29:58:-103.75,-17.48,-109.80:99
+chr1	4389459	rs995749	T	C	99.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.02;MQ=59.19;MQ0=0;OQ=673.64;QD=11.82;SB=-297.62	GT:AD:DP:GL:GQ	0/1:29,28:55:-87.23,-16.58,-114.38:99
+chr1	4390198	rs6676603	A	T	439.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.38;MQ0=0;OQ=1300.48;QD=17.57;SB=-634.13	GT:AD:DP:GL:GQ	0/1:32,42:73:-155.32,-21.99,-116.56:99
+chr1	4390481	rs12128251	T	C	259.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=57.96;MQ0=0;OQ=632.69;QD=11.94;SB=-295.21	GT:AD:DP:GL:GQ	0/1:28,25:50:-81.62,-15.07,-105.90:99
+chr1	4391861	rs2007533	T	A	193.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=57.74;MQ0=0;OQ=586.86;QD=11.51;SB=-140.76	GT:AD:DP:GL:GQ	0/1:30,21:48:-76.43,-14.46,-99.70:99
+chr1	4391958	rs1809702	T	C	301.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1033.40;QD=12.45;SB=-514.71	GT:AD:DP:GL:GQ	0/1:39,44:81:-131.04,-24.42,-155.02:99
+chr1	4392226	rs736265	G	A	87.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=4.07;MQ=59.56;MQ0=0;OQ=793.67;QD=14.97;SB=-313.81	GT:AD:DP:GL:GQ	0/1:27,26:51:-98.01,-15.36,-98.57:99
+chr1	4393075	rs1556691	A	G	599.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=937.52;QD=14.88;SB=-473.07	GT:AD:DP:GL:GQ	0/1:29,34:61:-115.41,-18.38,-116.29:99
+chr1	4393225	rs4654435	T	C	403.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=690.21;QD=11.50;SB=-328.14	GT:AD:DP:GL:GQ	0/1:28,31:55:-88.89,-16.58,-104.73:99
+chr1	4394358	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=18;HaplotypeScore=18.20;MQ=57.05;MQ0=0;OQ=138.13;QD=2.76;SB=68.21	GT:AD:DP:GL:GQ	0/1:39,11:43:-30.06,-12.96,-119.55:99
+chr1	4394377	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=18;HaplotypeScore=17.15;MQ=55.75;MQ0=0;OQ=145.86;QD=2.75;SB=25.24	GT:AD:DP:GL:GQ	0/1:40,13:43:-30.82,-12.95,-126.23:99
+chr1	4394834	rs12072315	G	A	483.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=835.16;QD=15.47;SB=-392.90	GT:AD:DP:GL:GQ	0/1:29,25:53:-102.78,-15.98,-90.62:99
+chr1	4394951	rs7546444	A	G	181.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.12;MQ0=0;OQ=846.04;QD=12.26;SB=-340.27	GT:AD:DP:GL:GQ	0/1:38,31:68:-108.38,-20.49,-147.54:99
+chr1	4395538	rs1591426	T	C	726.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=2474.70;QD=34.37;SB=-1102.69	GT:AD:DP:GL:GQ	1/1:0,72:71:-251.09,-21.39,-0.04:99
+chr1	4395562	rs1591425	A	G	113.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.25;MQ0=0;OQ=1914.52;QD=29.01;SB=-807.30	GT:AD:DP:GL:GQ	1/1:0,66:62:-195.10,-18.70,-0.06:99
+chr1	4396040	rs10915536	C	T	108.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.40;MQ0=0;OQ=3075.21;QD=39.94;SB=-1236.02	GT:AD:DP:GL:GQ	1/1:0,77:77:-311.12,-23.19,-0.02:99
+chr1	4396189	rs1762813	C	T	709.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.85;MQ0=0;OQ=1988.33;QD=37.52;SB=-957.81	GT:AD:DP:GL:GQ	1/1:0,52:51:-202.43,-15.36,-0.01:99
+chr1	4396377	rs1674876	G	A	690.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=3414.62;QD=39.70;SB=-1526.04	GT:AD:DP:GL:GQ	1/1:0,86:85:-340.46,-25.61,-0.02:99
+chr1	4396770	rs1335365	G	A	180.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=3218.44;QD=38.31;SB=-1546.06	GT:AD:DP:GL:GQ	1/1:0,84:82:-325.46,-24.71,-0.03:99
+chr1	4396978	rs6660514	C	T	529.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=2569.74;QD=40.15;SB=-881.18	GT:AD:DP:GL:GQ	1/1:0,64:63:-260.57,-18.97,-0.01:99
+chr1	4396990	rs1335363	G	A	705.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=2655.20;QD=39.05;SB=-1068.35	GT:AD:DP:GL:GQ	1/1:0,68:67:-269.12,-20.18,-0.02:99
+chr1	4397408	rs35211041	C	G	282.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.56;MQ0=0;OQ=845.74;QD=15.96;SB=-404.93	GT:AD:DP:GL:GQ	0/1:28,25:51:-103.22,-15.37,-116.49:99
+chr1	4397651	rs1234932	T	C	32.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=2.62;MQ=59.08;MQ0=0;OQ=2038.22;QD=30.88;SB=-895.04	GT:AD:DP:GL:GQ	1/1:0,66:64:-207.46,-19.30,-0.06:99
+chr1	4399691	rs780572	T	C	25.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=3.98;MQ=59.66;MQ0=0;OQ=2164.78;QD=32.31;SB=-610.95	GT:AD:DP:GL:GQ	1/1:0,67:65:-220.10,-19.59,-0.04:99
+chr1	4400105	rs12727067	C	T	348.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=3168.12;QD=39.11;SB=-1535.71	GT:AD:DP:GL:GQ	1/1:0,81:79:-320.41,-23.80,-0.02:99
+chr1	4400296	rs12731060	C	T	672.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2631.07;QD=38.69;SB=-901.20	GT:AD:DP:GL:GQ	1/1:0,68:67:-266.72,-20.19,-0.02:99
+chr1	4401014	rs6674190	C	T	89.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.77;MQ0=0;OQ=3223.06;QD=39.79;SB=-1621.16	GT:AD:DP:GL:GQ	1/1:0,81:80:-325.90,-24.10,-0.02:99
+chr1	4401844	rs780573	A	G	655.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=2538.38;QD=30.96;SB=-1020.34	GT:AD:DP:GL:GQ	1/1:0,82:80:-257.49,-24.12,-0.07:99
+chr1	4403585	rs780581	T	C	628.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=2729.37;QD=35.91;SB=-1251.85	GT:AD:DP:GL:GQ	1/1:0,76:75:-276.54,-22.59,-0.02:99
+chr1	4405826	rs780587	T	C	579.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=1799.99;QD=35.29;SB=-764.96	GT:AD:DP:GL:GQ	1/1:0,51:50:-183.60,-15.06,-0.02:99
+chr1	4406185	rs780588	T	G	731.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.29;MQ0=0;OQ=2276.92;QD=35.03;SB=-1150.64	GT:AD:DP:GL:GQ	1/1:0,65:65:-231.29,-19.58,-0.02:99
+chr1	4407102	rs780589	G	T	206.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.17;MQ0=0;OQ=2615.53;QD=35.83;SB=-1329.09	GT:AD:DP:GL:GQ	1/1:0,73:72:-265.16,-21.68,-0.02:99
+chr1	4407119	rs12032561	A	G	117.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.23;MQ0=0;OQ=2421.51;QD=30.65;SB=-1099.12	GT:AD:DP:GL:GQ	1/1:0,79:76:-245.80,-22.92,-0.06:99
+chr1	4407230	rs780590	C	A	140.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=2388.18;QD=35.64;SB=-981.59	GT:AD:DP:GL:GQ	1/1:0,67:66:-242.42,-19.88,-0.02:99
+chr1	4407326	rs780591	G	C	50.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.66;MQ0=0;OQ=2352.09;QD=42.77;SB=-1101.12	GT:AD:DP:GL:GQ	1/1:0,54:54:-238.81,-16.27,-0.01:99
+chr1	4407520	rs780592	G	A	361.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3300.47;QD=41.26;SB=-1496.40	GT:AD:DP:GL:GQ	1/1:0,80:80:-329.05,-24.10,-0.02:99
+chr1	4407623	rs780594	T	C	139.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=2.07;MQ=59.52;MQ0=0;OQ=2627.95;QD=34.13;SB=-1058.85	GT:AD:DP:GL:GQ	1/1:0,77:75:-266.41,-22.59,-0.03:99
+chr1	4408032	rs705684	C	T	627.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2940.63;QD=39.21;SB=-1334.78	GT:AD:DP:GL:GQ	1/1:0,75:74:-297.67,-22.29,-0.02:99
+chr1	4408272	rs780595	C	G	8.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=58.81;MQ0=0;OQ=2333.53;QD=42.43;SB=-1051.66	GT:AD:DP:GL:GQ	1/1:0,55:54:-236.95,-16.27,-0.02:99
+chr1	4408429	rs2054268	A	G	302.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=59.14;MQ0=0;OQ=2648.73;QD=34.85;SB=-1019.36	GT:AD:DP:GL:GQ	1/1:0,76:74:-268.49,-22.29,-0.03:99
+chr1	4408966	rs780596	C	G	540.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=3023.42;QD=42.58;SB=-1306.69	GT:AD:DP:GL:GQ	1/1:0,71:71:-305.95,-21.40,-0.02:99
+chr1	4409197	rs2054269	G	A	716.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=2812.55;QD=39.06;SB=-1393.37	GT:AD:DP:GL:GQ	1/1:0,72:71:-284.86,-21.39,-0.02:99
+chr1	4409239	rs2054270	C	A	370.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=2523.69;QD=36.05;SB=-1226.28	GT:AD:DP:GL:GQ	1/1:0,70:69:-255.97,-20.78,-0.02:99
+chr1	4411281	rs922114	C	T	206.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.24;MQ=60.00;MQ0=0;OQ=2458.23;QD=37.82;SB=-1122.24	GT:AD:DP:GL:GQ	1/1:0,65:63:-249.43,-18.99,-0.03:99
+chr1	4411941	rs56397589	A	G	10.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=772.90;QD=13.56;SB=-158.90	GT:AD:DP:GL:GQ	0/1:30,27:56:-97.44,-16.87,-122.46:99
+chr1	4412859	.	G	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=17.52;MQ=58.30;MQ0=0;OQ=443.68;QD=5.55;SB=107.30	GT:AD:DP:GL:GQ	0/1:54,26:67:-67.84,-20.19,-156.44:99
+chr1	4413809	rs780599	T	C	203.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=933.92;QD=15.06;SB=-130.24	GT:AD:DP:GL:GQ	0/1:31,31:62:-115.35,-18.67,-127.44:99
+chr1	4413942	rs1235308	A	G	208.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=59.56;MQ0=0;OQ=574.66;QD=10.84;SB=-295.15	GT:AD:DP:GL:GQ	0/1:24,29:45:-74.32,-13.57,-86.44:99
+chr1	4413949	rs12135334	A	G	227.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.57;MQ0=0;OQ=600.78;QD=11.13;SB=-278.65	GT:AD:DP:GL:GQ	0/1:25,29:50:-78.44,-15.07,-99.43:99
+chr1	4414313	rs11584026	G	A	462.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.70;MQ0=0;OQ=1258.44;QD=16.56;SB=-579.09	GT:AD:DP:GL:GQ	0/1:37,39:74:-151.43,-22.31,-123.49:99
+chr1	4415137	rs1213919	T	C	340.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.64;MQ0=0;OQ=1036.94;QD=16.20;SB=-428.11	GT:AD:DP:GL:GQ	0/1:27,37:63:-125.96,-18.98,-110.60:99
+chr1	4415275	rs6426411	G	A	271.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.51;MQ=58.90;MQ0=0;OQ=891.44;QD=15.11;SB=-416.76	GT:AD:DP:GL:GQ	0/1:31,28:59:-110.20,-17.77,-112.97:99
+chr1	4415367	rs6663198	A	C	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=21.51;MQ=59.22;MQ0=0;OQ=1036.43;QD=12.49;SB=-473.70	GT:AD:DP:GL:GQ	0/1:44,39:81:-131.33,-24.40,-153.13:99
+chr1	4416433	rs12131294	C	T	93.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.89;MQ=59.15;MQ0=0;OQ=414.02;QD=9.20;SB=-113.50	GT:AD:DP:GL:GQ	0/1:24,20:37:-55.83,-11.15,-84.17:99
+chr1	4416884	.	G	A	3.05	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=5.94;MQ=57.87;MQ0=0;OQ=823.53;QD=14.97;SB=-276.27	GT:AD:DP:GL:GQ	0/1:30,25:53:-101.62,-15.98,-87.09:99
+chr1	4417194	rs7550318	A	T	249.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=2.46;MQ=57.79;MQ0=0;OQ=1140.48;QD=17.28;SB=-502.48	GT:AD:DP:GL:GQ	0/1:29,37:65:-136.91,-19.58,-108.54:99
+chr1	4417494	.	G	A	25.73	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=20;HaplotypeScore=6.20;MQ=50.61;MQ0=1;QD=0.42;SB=98.27	GT:AD:DP:GL:GQ	0/1:53,9:50:-20.92,-15.07,-146.64:58.56
+chr1	4417741	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=20;HaplotypeScore=20.09;MQ=49.19;MQ0=1;OQ=84.58;QD=2.17;SB=26.11	GT:AD:DP:GL:GQ	0/1:26,12:27:-19.88,-8.14,-73.60:99
+chr1	4417905	rs642409	A	G	618.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.41;MQ0=0;OQ=2544.54;QD=34.39;SB=-1201.82	GT:AD:DP:GL:GQ	1/1:0,74:71:-258.06,-21.38,-0.02:99
+chr1	4418004	rs10127576	A	G	16.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=5.95;MQ=57.57;MQ0=1;OQ=493.53;QD=8.97;SB=-221.25	GT:AD:DP:GL:GQ	0/1:34,21:50:-67.70,-15.07,-117.20:99
+chr1	4420145	rs6426412	G	T	345.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.50;MQ0=0;OQ=1296.90;QD=17.29;SB=-663.60	GT:AD:DP:GL:GQ	0/1:33,42:75:-155.57,-22.59,-114.39:99
+chr1	4420362	.	C	T	102.52	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=60.52;MQ0=0;OQ=920.19;QD=15.34;SB=-456.47	GT:AD:DP:GL:GQ	0/1:27,31:53:-111.28,-15.98,-79.42:99
+chr1	4421024	rs12137057	A	C	291.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=701.05;QD=10.62;SB=-364.06	GT:AD:DP:GL:GQ	0/1:39,27:63:-92.36,-18.97,-137.12:99
+chr1	4421180	rs61771168	T	G	222.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.81;MQ=59.49;MQ0=0;OQ=588.51;QD=13.08;SB=-310.47	GT:AD:DP:GL:GQ	0/1:23,22:43:-75.09,-12.95,-79.35:99
+chr1	4421771	.	C	T	52.82	PASS	AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=58.00;MQ0=0;OQ=457.94;QD=13.08;SB=-230.51	GT:AD:DP:GL:GQ	0/1:18,17:32:-58.72,-9.64,-61.49:99
+chr1	4422658	.	C	T	17.02	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=3.11;MQ=59.25;MQ0=0;OQ=990.31;QD=15.97;SB=-404.43	GT:AD:DP:GL:GQ	0/1:32,30:60:-120.40,-18.09,-95.94:99
+chr1	4423184	.	G	A	28.31	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=59.25;MQ0=0;OQ=1264.58;QD=20.40;SB=-650.72	GT:AD:DP:GL:GQ	0/1:26,36:62:-148.42,-18.68,-94.18:99
+chr1	4423217	rs664520	C	T	648.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=1886.50;QD=38.50;SB=-821.33	GT:AD:DP:GL:GQ	1/1:0,49:49:-192.25,-14.76,-0.02:99
+chr1	4423270	rs17453664	G	A	225.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.40;MQ=58.29;MQ0=0;OQ=839.10;QD=16.14;SB=-245.23	GT:AD:DP:GL:GQ	0/1:25,27:50:-102.26,-15.06,-88.51:99
+chr1	4424136	.	C	G	13.14	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=4.07;MQ=59.20;MQ0=0;OQ=717.79;QD=15.27;SB=-220.02	GT:AD:DP:GL:GQ	0/1:26,21:46:-88.93,-13.87,-108.02:99
+chr1	4424195	rs16839046	G	A	266.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=59.35;MQ0=0;OQ=1078.45;QD=16.85;SB=-521.17	GT:AD:DP:GL:GQ	0/1:30,33:62:-129.81,-18.69,-96.72:99
+chr1	4424280	rs17419859	G	A	351.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.18;MQ0=0;OQ=665.56;QD=13.05;SB=-350.50	GT:AD:DP:GL:GQ	0/1:25,26:46:-83.71,-13.87,-77.13:99
+chr1	4424589	rs681175	T	C	281.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=1804.45;QD=35.38;SB=-864.37	GT:AD:DP:GL:GQ	1/1:0,51:50:-184.04,-15.06,-0.01:99
+chr1	4426611	rs16839061	C	T	6.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=8.78;MQ=59.11;MQ0=0;OQ=724.58;QD=13.42;SB=-330.47	GT:AD:DP:GL:GQ	0/1:31,23:51:-91.11,-15.37,-92.01:99
+chr1	4427201	rs350167	T	C	190.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=59.66;MQ0=0;OQ=925.11;QD=16.82;SB=-378.98	GT:AD:DP:GL:GQ	0/1:23,32:53:-111.76,-15.96,-93.83:99
+chr1	4427323	.	G	A	294.49	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=680.55;QD=13.09;SB=-356.53	GT:AD:DP:GL:GQ	0/1:28,24:44:-84.60,-13.26,-76.63:99
+chr1	4433698	.	G	A	123.19	PASS	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.52;MQ0=0;OQ=1403.52;QD=17.99;SB=-721.04	GT:AD:DP:GL:GQ	0/1:36,42:75:-166.24,-22.60,-109.14:99
+chr1	4433807	.	T	G	23.74	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=3;HaplotypeScore=5.51;MQ=60.00;MQ0=0;QD=0.37;SB=80.27	GT:AD:DP:GL:GQ	0/1:45,20:51:-21.03,-15.37,-149.91:56.55
+chr1	4434327	rs645724	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=38.18;MQ=55.12;MQ0=0;OQ=2008.88;QD=24.50;SB=-765.25	GT:AD:DP:GL:GQ	0/1:13,69:74:-226.47,-22.30,-33.80:99
+chr1	4434328	rs55641638	T	A	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=5;HaplotypeScore=34.59;MQ=55.12;MQ0=0;OQ=2483.75;QD=30.29;SB=-1104.11	GT:AD:DP:GL:GQ	1/1:7,75:79:-274.28,-23.80,-22.35:14.43
+chr1	4434380	rs350168	C	T	706.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.94;MQ0=0;OQ=2402.65;QD=38.14;SB=-988.02	GT:AD:DP:GL:GQ	1/1:0,63:61:-243.87,-18.38,-0.02:99
+chr1	4434761	.	C	A	101.78	PASS	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=59.39;MQ0=0;OQ=1132.04;QD=16.65;SB=-530.30	GT:AD:DP:GL:GQ	0/1:30,38:67:-136.67,-20.18,-105.81:99
+chr1	4435588	rs350169	T	A	602.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=1092.18;QD=14.76;SB=-420.48	GT:AD:DP:GL:GQ	0/1:38,36:74:-134.79,-22.29,-147.43:99
+chr1	4439106	rs610189	T	C	76.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.49;MQ0=0;OQ=3044.46;QD=31.07;SB=-1448.66	GT:AD:DP:GL:GQ	1/1:0,98:95:-308.11,-28.64,-0.07:99
+chr1	4440903	rs13376654	C	A	79.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=3.21;MQ=58.73;MQ0=0;OQ=748.18;QD=13.60;SB=-293.00	GT:AD:DP:GL:GQ	0/1:29,26:54:-94.37,-16.27,-89.76:99
+chr1	4440904	rs638289	A	G	184.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.21;MQ=59.14;MQ0=0;OQ=1717.40;QD=31.80;SB=-743.85	GT:AD:DP:GL:GQ	1/1:0,54:53:-175.37,-15.98,-0.04:99
+chr1	4441250	rs11799990	A	C	16.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.98;MQ=58.47;MQ0=0;OQ=285.71;QD=5.19;SB=-147.75	GT:AD:DP:GL:GQ	0/1:37,17:50:-46.92,-15.06,-127.84:99
+chr1	4441285	rs6426418	T	C	92.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.50;MQ=58.52;MQ0=0;OQ=434.66;QD=7.63;SB=-199.21	GT:AD:DP:GL:GQ	0/1:38,19:55:-63.32,-16.57,-152.10:99
+chr1	4441304	rs16839089	G	A	505.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=685.41;QD=10.71;SB=-336.42	GT:AD:DP:GL:GQ	0/1:40,24:63:-90.81,-18.98,-145.42:99
+chr1	4441520	.	C	T	159.13	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.36;MQ=59.58;MQ0=0;OQ=767.39;QD=13.95;SB=-405.80	GT:AD:DP:GL:GQ	0/1:29,25:52:-95.70,-15.68,-88.39:99
+chr1	4441584	rs28597953	G	C	102.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.54;MQ0=0;OQ=377.89;QD=7.56;SB=-189.56	GT:AD:DP:GL:GQ	0/1:35,14:50:-59.58,-18.50,-155.34:99
+chr1	4441595	rs12057544	C	T	296.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=442.52;QD=10.06;SB=-117.50	GT:AD:DP:GL:GQ	0/1:29,15:44:-60.79,-13.25,-105.58:99
+chr1	4441615	rs12094629	G	A	446.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=438.29;QD=12.17;SB=-145.60	GT:AD:DP:GL:GQ	0/1:21,15:35:-57.67,-10.56,-64.23:99
+chr1	4442760	rs705686	T	G	190.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=58.65;MQ0=0;OQ=1305.06;QD=29.00;SB=-525.86	GT:AD:DP:GL:GQ	1/1:0,45:42:-134.13,-12.66,-0.04:99
+chr1	4443102	rs16839093	T	A	368.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=60.00;MQ0=0;OQ=943.42;QD=16.85;SB=-414.85	GT:AD:DP:GL:GQ	0/1:25,31:55:-114.19,-16.57,-93.32:99
+chr1	4443523	rs6656245	A	G	229.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=4.49;MQ=59.68;MQ0=0;OQ=985.54;QD=13.50;SB=-516.93	GT:AD:DP:GL:GQ	0/1:35,37:70:-125.21,-23.37,-142.93:99
+chr1	4444038	rs350170	T	C	370.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=854.91;QD=14.49;SB=-264.93	GT:AD:DP:GL:GQ	0/1:30,29:59:-106.55,-17.78,-120.47:99
+chr1	4444166	.	C	T	124.24	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.74;MQ0=0;OQ=1098.39;QD=15.05;SB=-487.09	GT:AD:DP:GL:GQ	0/1:39,34:70:-134.21,-21.09,-126.03:99
+chr1	4446069	rs16839101	C	T	439.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.34;MQ0=0;OQ=969.43;QD=15.39;SB=-381.11	GT:AD:DP:GL:GQ	0/1:31,32:61:-118.60,-18.38,-109.31:99
+chr1	4448313	rs705687	A	G	587.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.53;MQ0=0;OQ=1218.14;QD=32.06;SB=-513.41	GT:AD:DP:GL:GQ	1/1:0,38:37:-125.42,-11.15,-0.02:99
+chr1	4448490	rs10799234	G	A	167.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=924.80;QD=18.50;SB=-481.51	GT:AD:DP:GL:GQ	0/1:22,28:50:-110.83,-15.07,-72.35:99
+chr1	4449095	.	G	T	15.09	PASS	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=59.46;MQ0=0;OQ=820.94;QD=19.09;SB=-383.80	GT:AD:DP:GL:GQ	0/1:15,28:42:-98.03,-12.65,-50.79:99
+chr1	4449190	.	G	A	102.60	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=1775.95;QD=21.93;SB=-864.43	GT:AD:DP:GL:GQ	0/1:30,51:79:-204.67,-23.80,-104.40:99
+chr1	4449240	rs705690	G	A	133.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.24;MQ0=0;OQ=3632.63;QD=39.92;SB=-1598.65	GT:AD:DP:GL:GQ	1/1:0,91:90:-362.26,-27.11,-0.03:99
+chr1	4449262	rs780606	A	G	76.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=59.06;MQ0=0;OQ=718.78;QD=9.71;SB=-329.85	GT:AD:DP:GL:GQ	0/1:44,30:73:-97.16,-22.00,-175.35:99
+chr1	4449723	.	G	A	148.11	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.81;MQ=59.52;MQ0=0;OQ=713.60;QD=14.87;SB=-335.48	GT:AD:DP:GL:GQ	0/1:25,23:48:-89.11,-14.47,-81.14:99
+chr1	4449964	rs706145	G	A	636.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2653.69;QD=37.38;SB=-1188.98	GT:AD:DP:GL:GQ	1/1:0,71:69:-268.98,-20.79,-0.03:99
+chr1	4452662	rs1878052	G	A	714.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2298.20;QD=38.95;SB=-1111.02	GT:AD:DP:GL:GQ	1/1:0,59:59:-233.42,-17.78,-0.02:99
+chr1	4454614	.	A	C	20.74	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=601.74;QD=13.68;SB=-220.89	GT:AD:DP:GL:GQ	0/1:20,24:43:-76.41,-12.95,-71.27:99
+chr1	4455561	rs10737412	T	A	735.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2244.31;QD=37.41;SB=-1132.68	GT:AD:DP:GL:GQ	1/1:0,60:60:-228.03,-18.07,-0.02:99
+chr1	4455707	rs4654547	C	T	580.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=1;OQ=2435.91;QD=38.67;SB=-681.41	GT:AD:DP:GL:GQ	1/1:0,63:61:-247.19,-18.38,-0.02:99
+chr1	4456823	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=121.08;MQ=43.96;MQ0=0;OQ=445.21;QD=5.86;SB=-205.75	GT:AD:DP:GL:GQ	0/1:54,22:71:-69.19,-21.39,-207.74:99
+chr1	4456825	rs61765158	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=3;HaplotypeScore=133.78;MQ=43.18;MQ0=0;OQ=324.30;QD=4.44;SB=-88.42	GT:AD:DP:GL:GQ	0/1:59,14:70:-56.80,-21.09,-201.65:99
+chr1	4456850	rs780601	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=50.11;MQ=42.32;MQ0=0;OQ=775.14;QD=10.77;SB=-395.42	GT:AD:DP:GL:GQ	0/1:41,31:67:-100.98,-20.18,-144.33:99
+chr1	4457263	rs780603	T	C	535.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=1544.09;QD=29.13;SB=-491.17	GT:AD:DP:GL:GQ	1/1:0,53:48:-158.03,-14.47,-0.03:99
+chr1	4457873	rs9659744	G	A	216.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.18;MQ=58.81;MQ0=0;OQ=722.66;QD=13.14;SB=-250.79	GT:AD:DP:GL:GQ	0/1:29,25:52:-94.30,-18.75,-103.70:99
+chr1	4457887	rs12029583	T	C	182.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.02;MQ=58.88;MQ0=0;OQ=815.22;QD=14.06;SB=-229.41	GT:AD:DP:GL:GQ	0/1:25,33:54:-101.08,-16.28,-89.40:99
+chr1	4458652	rs10915548	G	A	313.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=58.63;MQ0=0;OQ=1202.04;QD=18.21;SB=-612.14	GT:AD:DP:GL:GQ	0/1:31,35:64:-142.78,-19.29,-94.64:99
+chr1	4458793	rs609506	T	C	135.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=2002.23;QD=32.82;SB=-965.38	GT:AD:DP:GL:GQ	1/1:0,61:57:-203.83,-17.17,-0.03:99
+chr1	4458832	rs13374152	G	A	510.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.65;MQ0=0;OQ=1323.30;QD=19.75;SB=-559.77	GT:AD:DP:GL:GQ	0/1:28,39:65:-155.19,-19.58,-97.96:99
+chr1	4459077	rs10799235	G	C	517.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2392.46;QD=41.97;SB=-1062.67	GT:AD:DP:GL:GQ	1/1:0,57:55:-242.85,-16.57,-0.02:99
+chr1	4459761	rs4654438	T	C	731.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.40;MQ0=0;OQ=2338.83;QD=34.91;SB=-1062.10	GT:AD:DP:GL:GQ	1/1:0,67:66:-237.49,-19.88,-0.02:99
+chr1	4460253	.	G	A	71.25	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=54.34;MQ0=0;OQ=761.29;QD=16.20;SB=-383.16	GT:AD:DP:GL:GQ	0/1:23,24:45:-92.98,-13.56,-67.37:99
+chr1	4460265	rs9660574	G	A	698.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.97;MQ0=0;OQ=1971.68;QD=38.66;SB=-993.84	GT:AD:DP:GL:GQ	1/1:0,51:50:-200.77,-15.06,-0.01:99
+chr1	4460731	rs675509	A	G	75.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.19;MQ0=0;OQ=1733.09;QD=33.33;SB=-850.97	GT:AD:DP:GL:GQ	1/1:0,52:50:-176.92,-15.06,-0.02:99
+chr1	4460821	rs675641	C	T	619.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2267.76;QD=39.10;SB=-1112.00	GT:AD:DP:GL:GQ	1/1:0,58:57:-230.38,-17.17,-0.02:99
+chr1	4462336	rs4654548	G	A	293.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.55;MQ0=0;OQ=1820.62;QD=35.70;SB=-883.64	GT:AD:DP:GL:GQ	1/1:0,51:47:-185.66,-14.16,-0.02:99
+chr1	4462612	rs661886	C	G	122.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1803.84;QD=41.95;SB=-867.51	GT:AD:DP:GL:GQ	1/1:0,43:43:-183.98,-12.96,-0.01:99
+chr1	4462757	rs597453	T	C	1.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=2.36;MQ=60.00;MQ0=0;OQ=1873.91;QD=29.28;SB=-570.21	GT:AD:DP:GL:GQ	1/1:0,64:56:-191.00,-16.87,-0.03:99
+chr1	4463867	rs10799237	G	A	181.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.13;MQ0=0;OQ=2001.42;QD=37.76;SB=-711.98	GT:AD:DP:GL:GQ	1/1:0,53:51:-203.74,-15.36,-0.01:99
+chr1	4464187	.	T	C	30.12	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.10;MQ=59.33;MQ0=0;OQ=552.68;QD=8.91;SB=-289.28	GT:AD:DP:GL:GQ	0/1:39,23:60:-76.63,-18.08,-155.34:99
+chr1	4465057	rs4654549	G	A	100.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=3.11;MQ=59.46;MQ0=0;OQ=1572.23;QD=20.42;SB=-717.81	GT:AD:DP:GL:GQ	0/1:31,46:75:-183.10,-22.59,-108.27:99
+chr1	4465240	rs4654439	A	G	186.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=59.65;MQ0=0;OQ=1824.70;QD=28.07;SB=-920.11	GT:AD:DP:GL:GQ	1/1:1,64:61:-189.47,-18.40,-3.41:99
+chr1	4465350	rs4654550	C	T	464.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.14;MQ0=0;OQ=1183.55;QD=15.57;SB=-491.13	GT:AD:DP:GL:GQ	0/1:39,37:73:-143.65,-22.01,-117.80:99
+chr1	4465703	rs16839157	C	G	292.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.46;MQ0=0;OQ=1332.22;QD=15.49;SB=-637.02	GT:AD:DP:GL:GQ	0/1:48,38:85:-162.12,-25.61,-205.23:99
+chr1	4465766	rs10753381	C	T	668.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=2452.18;QD=39.55;SB=-960.97	GT:AD:DP:GL:GQ	1/1:0,62:62:-248.82,-18.68,-0.02:99
+chr1	4465913	rs10753382	A	C	344.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=42.45;MQ0=0;OQ=1152.30;QD=15.16;SB=-375.76	GT:AD:DP:GL:GQ	0/1:35,41:75:-141.10,-22.59,-129.43:99
+chr1	4465925	rs4654440	A	G	314.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=45.24;MQ0=0;OQ=2545.78;QD=35.36;SB=-1008.34	GT:AD:DP:GL:GQ	1/1:0,72:72:-258.19,-21.69,-0.03:99
+chr1	4466035	rs4654551	T	C	137.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=59.71;MQ0=0;OQ=2345.07;QD=29.31;SB=-919.32	GT:AD:DP:GL:GQ	1/1:0,80:75:-238.17,-22.62,-0.07:99
+chr1	4466375	rs4654441	A	G	153.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=1.97;MQ=59.14;MQ0=0;OQ=1252.72;QD=16.48;SB=-599.98	GT:AD:DP:GL:GQ	0/1:32,44:75:-151.15,-22.60,-128.71:99
+chr1	4466539	.	G	C	13.68	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.10;MQ=60.00;MQ0=0;OQ=1133.87;QD=19.22;SB=-442.73	GT:AD:DP:GL:GQ	0/1:26,33:58:-134.16,-17.49,-113.78:99
+chr1	4466591	rs7537577	T	C	558.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1692.69;QD=36.01;SB=-710.63	GT:AD:DP:GL:GQ	1/1:0,47:47:-172.87,-14.16,-0.01:99
+chr1	4466655	rs1870509	A	G	172.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=58.79;MQ0=0;OQ=1784.46;QD=27.04;SB=-725.30	GT:AD:DP:GL:GQ	1/1:0,66:58:-182.10,-17.50,-0.07:99
+chr1	4467025	rs1018306	G	A	522.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=2397.83;QD=37.47;SB=-678.32	GT:AD:DP:GL:GQ	1/1:0,64:61:-243.39,-18.38,-0.02:99
+chr1	4467405	.	G	A	173.51	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=60.00;MQ0=0;OQ=1037.40;QD=16.73;SB=-505.13	GT:AD:DP:GL:GQ	0/1:31,31:60:-125.11,-18.08,-96.58:99
+chr1	4467882	rs10799238	G	A	201.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=57.23;MQ0=0;OQ=2039.74;QD=37.09;SB=-730.98	GT:AD:DP:GL:GQ	1/1:0,54:52:-207.58,-15.67,-0.02:99
+chr1	4468054	rs10799239	G	T	526.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.10;MQ0=0;OQ=2381.50;QD=35.54;SB=-1199.06	GT:AD:DP:GL:GQ	1/1:0,67:66:-241.76,-19.88,-0.02:99
+chr1	4468702	rs780570	T	C	301.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.66;MQ0=0;OQ=692.07;QD=31.46;SB=-209.70	GT:AD:DP:GL:GQ	1/1:0,22:21:-72.80,-6.33,-0.01:63.17
+chr1	4468728	.	G	A	3.90	PASS	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=52.20;MQ0=0;OQ=192.92;QD=6.65;SB=-94.59	GT:AD:DP:GL:GQ	0/1:18,10:25:-30.11,-7.53,-60.00:99
+chr1	4468760	rs60725706	C	T	2.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=2.68;MQ=47.80;MQ0=0;OQ=892.66;QD=25.50;SB=-420.32	GT:AD:DP:GL:GQ	1/1:1,34:26:-92.87,-7.84,-0.02:78.22
+chr1	4468793	.	C	T	155.10	SnpCluster	AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=28.66;MQ=43.47;MQ0=0;QD=3.45;SB=-75.82	GT:AD:DP:GL:GQ	0/1:34,11:31:-28.13,-9.34,-89.19:99
+chr1	4468798	rs57105176	C	T	210.28	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=33.72;MQ=43.23;MQ0=0;QD=4.38;SB=-105.47	GT:AD:DP:GL:GQ	0/1:33,15:33:-34.25,-9.94,-88.69:99
+chr1	4468800	.	C	T	23.55	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=2;HaplotypeScore=34.30;MQ=43.63;MQ0=0;QD=0.48;SB=32.09	GT:AD:DP:GL:GQ	0/1:44,5:35:-16.18,-10.54,-113.19:56.36
+chr1	4468801	.	T	C	10.10	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=1;HaplotypeScore=35.27;MQ=44.04;MQ0=0;QD=0.21;SB=32.13	GT:AD:DP:GL:GQ	0/1:43,5:35:-14.79,-10.54,-128.12:42.49
+chr1	4469243	rs12031045	G	A	324.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=623.89;QD=15.22;SB=-230.72	GT:AD:DP:GL:GQ	0/1:20,21:41:-78.04,-12.36,-70.49:99
+chr1	4469296	rs780569	T	A	228.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.28;MQ0=0;OQ=1316.01;QD=34.63;SB=-627.73	GT:AD:DP:GL:GQ	1/1:0,38:37:-135.20,-11.15,-0.01:99
+chr1	4469318	rs12035160	A	T	129.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.81;MQ0=0;OQ=613.76;QD=19.18;SB=-234.94	GT:AD:DP:GL:GQ	0/1:11,21:31:-74.00,-9.34,-42.52:99
+chr1	4469407	rs10799241	A	G	224.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.03;MQ=57.87;MQ0=0;OQ=407.85;QD=8.87;SB=-207.21	GT:AD:DP:GL:GQ	0/1:29,17:45:-57.62,-13.55,-119.36:99
+chr1	4469520	rs16839168	G	A	432.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=846.65;QD=16.28;SB=-413.43	GT:AD:DP:GL:GQ	0/1:26,26:51:-103.31,-15.37,-89.05:99
+chr1	4469555	rs16839171	G	T	425.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.63;MQ0=0;OQ=647.76;QD=12.70;SB=-289.64	GT:AD:DP:GL:GQ	0/1:27,24:51:-83.43,-15.37,-93.72:99
+chr1	4469694	rs780568	A	G	87.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=1.60;MQ=59.63;MQ0=0;OQ=1699.95;QD=33.33;SB=-755.94	GT:AD:DP:GL:GQ	1/1:0,51:49:-173.60,-14.76,-0.02:99
+chr1	4470136	rs16839175	T	C	275.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.63;MQ0=0;OQ=746.25;QD=11.85;SB=-286.15	GT:AD:DP:GL:GQ	0/1:31,32:61:-96.29,-18.39,-125.52:99
+chr1	4470246	rs1612698	A	G	417.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.34;MQ=60.15;MQ0=0;OQ=917.82;QD=12.40;SB=-358.93	GT:AD:DP:GL:GQ	0/1:42,32:74:-117.36,-22.29,-169.05:99
+chr1	4470842	rs4654552	C	T	182.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.85;MQ=59.68;MQ0=0;OQ=1084.53;QD=15.28;SB=-349.06	GT:AD:DP:GL:GQ	0/1:37,34:71:-133.13,-21.39,-131.43:99
+chr1	4471600	rs1710415	A	G	89.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=59.45;MQ0=0;OQ=1235.30;QD=29.41;SB=-309.47	GT:AD:DP:GL:GQ	1/1:0,42:39:-127.15,-11.76,-0.03:99
+chr1	4471806	rs1762825	T	A	126.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.16;MQ0=0;OQ=1997.53;QD=36.32;SB=-643.98	GT:AD:DP:GL:GQ	1/1:0,55:54:-203.35,-16.27,-0.02:99
+chr1	4471883	rs10915549	G	A	333.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.45;MQ0=0;OQ=443.28;QD=10.55;SB=-159.64	GT:AD:DP:GL:GQ	0/1:26,16:40:-59.67,-12.06,-79.56:99
+chr1	4472000	rs4654442	G	A	195.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.37;MQ0=0;OQ=2467.21;QD=37.38;SB=-970.01	GT:AD:DP:GL:GQ	1/1:0,66:62:-250.32,-18.68,-0.02:99
+chr1	4472928	rs4568797	G	T	198.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.61;MQ=59.01;MQ0=0;OQ=1306.78;QD=17.19;SB=-394.04	GT:AD:DP:GL:GQ	0/1:30,46:73:-155.95,-21.99,-98.20:99
+chr1	4472959	rs4480324	A	G	92.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.63;MQ0=0;OQ=1914.93;QD=30.40;SB=-560.92	GT:AD:DP:GL:GQ	1/1:0,63:60:-195.13,-18.10,-0.06:99
+chr1	4472994	rs4323680	T	C	685.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1931.20;QD=32.73;SB=-824.33	GT:AD:DP:GL:GQ	1/1:0,59:55:-196.72,-16.57,-0.02:99
+chr1	4473017	rs4437847	T	C	44.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=1770.27;QD=28.55;SB=-781.74	GT:AD:DP:GL:GQ	1/1:0,62:55:-180.66,-16.58,-0.05:99
+chr1	4473102	rs4442344	T	C	686.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=1772.96;QD=35.46;SB=-792.00	GT:AD:DP:GL:GQ	1/1:0,50:50:-180.90,-15.06,-0.02:99
+chr1	4473320	rs1710418	A	G	44.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1771.10;QD=32.20;SB=-713.21	GT:AD:DP:GL:GQ	1/1:0,54:51:-180.72,-15.36,-0.02:99
+chr1	4473327	rs1762828	G	A	169.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.60;MQ0=0;OQ=2054.72;QD=36.05;SB=-823.34	GT:AD:DP:GL:GQ	1/1:0,57:53:-209.08,-15.97,-0.02:99
+chr1	4473546	rs1710419	C	A	168.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.06;MQ=57.84;MQ0=0;OQ=1495.45;QD=32.51;SB=-770.46	GT:AD:DP:GL:GQ	1/1:0,46:43:-153.15,-12.95,-0.02:99
+chr1	4473664	rs1710420	C	T	149.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=59.20;MQ0=0;OQ=902.97;QD=15.57;SB=-230.52	GT:AD:DP:GL:GQ	0/1:30,28:57:-110.76,-17.18,-94.35:99
+chr1	4473849	rs1710421	C	T	247.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.67;MQ0=0;OQ=2607.62;QD=37.79;SB=-1041.32	GT:AD:DP:GL:GQ	1/1:0,69:66:-264.37,-19.88,-0.02:99
+chr1	4473977	rs1710422	C	T	77.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=58.90;MQ0=0;OQ=2084.84;QD=37.91;SB=-795.07	GT:AD:DP:GL:GQ	1/1:0,55:54:-212.09,-16.27,-0.02:99
+chr1	4473997	rs1710423	T	C	135.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=59.07;MQ0=0;OQ=1147.64;QD=25.50;SB=-601.59	GT:AD:DP:GL:GQ	1/1:0,45:37:-118.39,-11.16,-0.04:99
+chr1	4474861	rs1710424	A	G	675.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.21;MQ0=0;OQ=2263.90;QD=31.89;SB=-1103.74	GT:AD:DP:GL:GQ	1/1:0,71:67:-230.02,-20.19,-0.04:99
+chr1	4475148	rs12036337	G	A	158.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.64;MQ=56.87;MQ0=1;OQ=1002.66;QD=14.75;SB=-286.76	GT:AD:DP:GL:GQ	0/1:34,34:59:-121.33,-17.78,-94.02:99
+chr1	4475283	.	G	A	82.68	PASS	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=59.35;MQ0=0;OQ=845.94;QD=13.22;SB=-362.87	GT:AD:DP:GL:GQ	0/1:34,30:60:-105.97,-18.09,-111.99:99
+chr1	4475382	rs10915550	C	T	345.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=58.10;MQ0=0;OQ=927.67;QD=14.96;SB=-380.90	GT:AD:DP:GL:GQ	0/1:33,29:62:-114.73,-18.68,-118.48:99
+chr1	4476131	rs10737413	C	T	15.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=59.60;MQ0=0;OQ=1742.86;QD=37.08;SB=-655.67	GT:AD:DP:GL:GQ	1/1:0,47:45:-177.88,-13.56,-0.01:99
+chr1	4476657	rs1710430	C	G	535.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2311.95;QD=41.28;SB=-1026.21	GT:AD:DP:GL:GQ	1/1:0,56:54:-234.80,-16.27,-0.02:99
+chr1	4476980	rs4654443	C	T	562.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1325.65;QD=15.60;SB=-630.22	GT:AD:DP:GL:GQ	0/1:45,40:85:-161.45,-25.60,-165.34:99
+chr1	4477487	rs12033789	G	T	214.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=60.00;MQ0=0;OQ=905.30;QD=15.34;SB=-363.43	GT:AD:DP:GL:GQ	0/1:29,30:59:-111.58,-17.77,-100.35:99
+chr1	4477488	rs12036603	C	T	258.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=60.00;MQ0=0;OQ=969.57;QD=16.16;SB=-419.81	GT:AD:DP:GL:GQ	0/1:30,30:59:-118.02,-17.78,-101.27:99
+chr1	4478406	rs596607	G	A	55.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=59.40;MQ0=0;OQ=1761.44;QD=22.88;SB=-768.34	GT:AD:DP:GL:GQ	0/1:27,50:75:-202.03,-22.60,-83.51:99
+chr1	4478558	rs12039806	T	A	70.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=6.67;MQ=59.12;MQ0=0;OQ=1156.91;QD=14.64;SB=-441.48	GT:AD:DP:GL:GQ	0/1:42,37:77:-142.17,-23.19,-150.58:99
+chr1	4478614	rs12039814	T	C	10.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=7.09;MQ=59.66;MQ0=0;OQ=671.25;QD=10.02;SB=-294.21	GT:AD:DP:GL:GQ	0/1:37,30:64:-89.71,-19.30,-136.10:99
+chr1	4478650	rs12038994	A	T	269.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.65;MQ0=0;OQ=1147.45;QD=17.39;SB=-509.94	GT:AD:DP:GL:GQ	0/1:28,38:64:-137.31,-19.28,-105.10:99
+chr1	4478709	.	A	C	2.11	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=7.65;MQ=58.73;MQ0=0;OQ=1101.58;QD=15.09;SB=-425.69	GT:AD:DP:GL:GQ	0/1:30,42:69:-134.23,-20.79,-106.44:99
+chr1	4478753	rs16839198	G	T	52.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=7.25;MQ=58.23;MQ0=0;OQ=906.23;QD=13.73;SB=-344.31	GT:AD:DP:GL:GQ	0/1:32,33:64:-113.20,-19.29,-98.09:99
+chr1	4478891	.	A	G	89.93	PASS	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=59.39;MQ0=0;OQ=917.93;QD=13.50;SB=-396.16	GT:AD:DP:GL:GQ	0/1:36,32:68:-115.57,-20.49,-141.62:99
+chr1	4478991	rs12039070	A	G	301.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=3.59;MQ=59.71;MQ0=0;OQ=1280.19;QD=16.00;SB=-441.58	GT:AD:DP:GL:GQ	0/1:37,43:80:-155.40,-24.10,-149.81:99
+chr1	4479035	rs12034930	G	A	326.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.68;MQ0=0;OQ=1133.14;QD=15.74;SB=-491.00	GT:AD:DP:GL:GQ	0/1:34,37:69:-137.39,-20.79,-119.61:99
+chr1	4479073	rs12039100	A	G	27.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=3.20;MQ=58.95;MQ0=0;OQ=915.49;QD=13.87;SB=-279.55	GT:AD:DP:GL:GQ	0/1:35,31:66:-114.72,-19.89,-140.84:99
+chr1	4479099	rs12039101	A	G	318.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=59.02;MQ0=0;OQ=1020.75;QD=14.38;SB=-348.94	GT:AD:DP:GL:GQ	0/1:36,35:70:-126.45,-21.09,-134.68:99
+chr1	4479118	rs1229148	A	G	277.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=59.11;MQ0=0;OQ=784.46;QD=10.75;SB=-374.59	GT:AD:DP:GL:GQ	0/1:37,36:67:-101.94,-20.21,-133.99:99
+chr1	4479593	rs12035830	G	A	298.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=59.59;MQ0=0;OQ=906.38;QD=16.19;SB=-375.12	GT:AD:DP:GL:GQ	0/1:28,28:56:-110.79,-16.87,-99.66:99
+chr1	4479841	rs13375249	G	C	20.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=1.63;MQ=59.73;MQ0=0;OQ=1230.24;QD=17.57;SB=-290.56	GT:AD:DP:GL:GQ	0/1:33,37:66:-146.20,-19.90,-135.57:99
+chr1	4479995	rs13375764	T	C	66.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=4.40;MQ=59.54;MQ0=0;OQ=574.33;QD=11.49;SB=-245.91	GT:AD:DP:GL:GQ	0/1:28,22:47:-74.88,-14.16,-104.49:99
+chr1	4480068	rs56226943	T	C	40.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=4.82;MQ=59.62;MQ0=0;OQ=881.12;QD=14.44;SB=-433.94	GT:AD:DP:GL:GQ	0/1:29,32:60:-109.48,-18.08,-115.28:99
+chr1	4480417	.	C	T	49.35	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=55.69;MQ0=0;OQ=1159.90;QD=16.81;SB=-282.22	GT:AD:DP:GL:GQ	0/1:33,36:66:-139.16,-19.89,-99.45:99
+chr1	4480560	rs61765366	A	G	285.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=56.94;MQ0=0;OQ=701.52;QD=11.89;SB=-268.60	GT:AD:DP:GL:GQ	0/1:29,30:57:-90.62,-17.18,-111.39:99
+chr1	4480691	rs61765367	A	G	0.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=4.75;MQ=57.81;MQ0=0;OQ=122.26;QD=1.63;SB=-4.55	GT:AD:DP:GL:GQ	0/1:63,11:59:-33.30,-17.79,-184.25:99
+chr1	4480787	rs61765379	A	G	0.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=7.68;MQ=56.41;MQ0=0;OQ=64.97;QD=0.82;SB=-50.25	GT:AD:DP:GL:GQ	0/1:64,12:67:-29.98,-20.20,-222.76:97.81
+chr1	4480849	rs549627	C	T	251.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=56.04;MQ0=0;OQ=1162.07;QD=16.37;SB=-467.11	GT:AD:DP:GL:GQ	0/1:33,37:67:-139.69,-20.20,-99.87:99
+chr1	4480920	rs548786	G	A	173	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=56.79;MQ0=1;OQ=670.11;QD=12.41;SB=-198.20	GT:AD:DP:GL:GQ	0/1:30,24:48:-84.77,-14.47,-84.01:99
+chr1	4481090	rs12039682	C	T	474.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.78;MQ0=0;OQ=980.72;QD=14.21;SB=-480.03	GT:AD:DP:GL:GQ	0/1:39,30:68:-121.84,-20.48,-138.54:99
+chr1	4481198	rs12039710	C	A	19.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=3;HaplotypeScore=2.99;MQ=59.79;MQ0=0;OQ=1468.40;QD=16.69;SB=-755.87	GT:AD:DP:GL:GQ	0/1:41,47:88:-176.63,-26.50,-144.72:99
+chr1	4481445	rs608203	T	C	400.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=60.00;MQ0=0;OQ=763.64;QD=11.93;SB=-242.90	GT:AD:DP:GL:GQ	0/1:33,31:64:-98.94,-19.29,-134.86:99
+chr1	4481949	rs518456	T	G	602.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1221.17;QD=15.26;SB=-525.73	GT:AD:DP:GL:GQ	0/1:37,43:77:-148.59,-23.19,-127.99:99
+chr1	4481956	rs57010025	C	T	238.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.40;MQ0=0;OQ=1419.96;QD=18.44;SB=-598.08	GT:AD:DP:GL:GQ	0/1:35,42:76:-168.18,-22.90,-116.42:99
+chr1	4482059	rs10489135	T	C	436.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.51;MQ0=0;OQ=1051.73;QD=13.84;SB=-549.55	GT:AD:DP:GL:GQ	0/1:39,37:73:-130.44,-21.99,-146.62:99
+chr1	4482139	rs57559146	A	C	431.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=970.54;QD=17.33;SB=-397.86	GT:AD:DP:GL:GQ	0/1:23,33:54:-116.60,-16.26,-81.57:99
+chr1	4482422	rs60071491	T	C	92.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=56.24;MQ0=0;OQ=1374.62;QD=16.76;SB=-668.88	GT:AD:DP:GL:GQ	0/1:37,45:82:-165.44,-24.69,-153.42:99
+chr1	4482693	rs4112336	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=102.81;MQ=56.77;MQ0=0;OQ=769.43;QD=9.27;SB=-197.80	GT:AD:DP:GL:GQ	0/1:55,28:82:-104.92,-24.70,-193.00:99
+chr1	4482708	.	C	A	39.18	Indel;LowQual	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=48.79;MQ=55.68;MQ0=0;QD=0.43;SB=-10.83	GT:AD:DP:GL:GQ	0/1:82,10:90:-34.30,-27.10,-291.82:72.01
+chr1	4482756	rs1229150	T	G	280.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=57.57;MQ0=0;OQ=1600.43;QD=18.83;SB=-735.72	GT:AD:DP:GL:GQ	0/1:32,53:82:-188.02,-24.70,-112.53:99
+chr1	4482784	rs1229151	A	G	1304.96	Indel	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=53.27;MQ0=0;QD=17.88;SB=-660.04	GT:AD:DP:GL:GQ	0/1:30,43:72:-155.47,-21.69,-120.71:99
+chr1	4482854	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=78.29;MQ=48.56;MQ0=0;OQ=195.41;QD=2.87;SB=-84.58	GT:AD:DP:GL:GQ	0/1:55,13:66:-42.70,-19.88,-199.63:99
+chr1	4482959	rs2097536	C	T	73.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.49;MQ0=0;OQ=999.17;QD=22.20;SB=-274.28	GT:AD:DP:GL:GQ	0/1:16,29:44:-116.46,-13.25,-55.39:99
+chr1	4486372	rs12040164	C	T	326.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=59.42;MQ0=0;OQ=1051.54;QD=14.60;SB=-388.33	GT:AD:DP:GL:GQ	0/1:40,32:72:-130.14,-21.70,-132.54:99
+chr1	4487829	rs241237	C	T	194.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.46;MQ0=0;OQ=801.99;QD=18.65;SB=-287.22	GT:AD:DP:GL:GQ	0/1:18,25:42:-96.14,-12.66,-58.53:99
+chr1	4488590	.	G	A	17.21	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1047.83;QD=22.78;SB=-295.25	GT:AD:DP:GL:GQ	0/1:15,31:44:-121.33,-13.26,-41.74:99
+chr1	4489266	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=19.48;MQ=53.94;MQ0=1;OQ=546.80;QD=8.68;SB=-157.24	GT:AD:DP:GL:GQ	0/1:31,26:42:-73.40,-15.44,-84.22:99
+chr1	4489270	rs241234	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=25.61;MQ=53.85;MQ0=1;OQ=785.85;QD=12.28;SB=-389.60	GT:AD:DP:GL:GQ	0/1:33,31:57:-99.04,-17.17,-115.38:99
+chr1	4490410	rs241233	T	C	169.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.70;MQ=59.74;MQ0=0;OQ=1074.01;QD=14.92;SB=-553.96	GT:AD:DP:GL:GQ	0/1:36,36:72:-132.37,-21.68,-149.45:99
+chr1	4490829	rs241232	G	A	84.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=59.60;MQ0=0;OQ=913.96;QD=19.45;SB=-389.16	GT:AD:DP:GL:GQ	0/1:20,27:47:-108.84,-14.16,-68.00:99
+chr1	4492019	.	C	T	107.27	PASS	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.07;MQ0=0;OQ=862.99;QD=13.28;SB=-457.42	GT:AD:DP:GL:GQ	0/1:38,27:64:-108.86,-19.28,-134.13:99
+chr1	4492104	rs241229	G	A	148.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=59.63;MQ0=0;OQ=584.46;QD=9.28;SB=-212.39	GT:AD:DP:GL:GQ	0/1:43,20:63:-80.71,-18.98,-155.69:99
+chr1	4494463	rs537398	T	C	597.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=930.45;QD=15.51;SB=-426.29	GT:AD:DP:GL:GQ	0/1:29,31:60:-114.40,-18.07,-118.90:99
+chr1	4494858	rs34231005	T	G	11.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=4;HaplotypeScore=0.14;MQ=59.76;MQ0=0;OQ=881.39;QD=11.30;SB=-322.46	GT:AD:DP:GL:GQ	0/1:45,33:76:-114.31,-22.89,-158.76:99
+chr1	4495171	rs509960	T	C	253.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.40;MQ=60.00;MQ0=0;OQ=1172.46;QD=18.04;SB=-611.00	GT:AD:DP:GL:GQ	0/1:27,38:65:-140.10,-19.58,-110.54:99
+chr1	4495869	.	C	T	861.60	Indel	AC=1;AF=0.50;AN=2;DP=74;Dels=0.04;HRun=1;HaplotypeScore=22.99;MQ=51.44;MQ0=0;QD=11.64;SB=-342.41	GT:AD:DP:GL:GQ	0/1:44,27:74:-110.83,-21.38,-161.62:99
+chr1	4495871	.	C	A	736.52	Indel	AC=1;AF=0.50;AN=2;DP=74;Dels=0.04;HRun=0;HaplotypeScore=22.99;MQ=51.44;MQ0=0;QD=9.95;SB=-304.20	GT:AD:DP:GL:GQ	0/1:44,27:74:-98.32,-21.38,-161.31:99
+chr1	4496138	rs10915553	T	C	458.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.54;MQ0=0;OQ=880.60;QD=11.90;SB=-349.17	GT:AD:DP:GL:GQ	0/1:42,32:72:-113.03,-21.69,-158.51:99
+chr1	4496148	rs10915554	G	A	271.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=55.61;MQ0=0;OQ=1132.53;QD=15.10;SB=-504.97	GT:AD:DP:GL:GQ	0/1:40,35:73:-138.53,-22.00,-129.42:99
+chr1	4496394	rs12084169	C	T	196.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=59.54;MQ0=0;OQ=1321.84;QD=16.12;SB=-685.73	GT:AD:DP:GL:GQ	0/1:41,41:80:-159.57,-24.10,-141.56:99
+chr1	4496424	rs12086217	A	G	463.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.43;MQ0=0;OQ=859.99;QD=13.23;SB=-378.26	GT:AD:DP:GL:GQ	0/1:34,31:65:-108.86,-19.58,-137.17:99
+chr1	4496942	rs623217	G	C	175.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=59.66;MQ0=0;OQ=1355.72;QD=19.94;SB=-471.80	GT:AD:DP:GL:GQ	0/1:31,37:66:-158.75,-19.89,-127.17:99
+chr1	4496949	rs472113	G	A	230.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.66;MQ0=0;OQ=1272.49;QD=18.99;SB=-462.43	GT:AD:DP:GL:GQ	0/1:30,37:67:-150.71,-20.18,-109.30:99
+chr1	4497460	rs556890	A	G	2.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=9.81;MQ=58.48;MQ0=0;OQ=661.76;QD=14.39;SB=-333.32	GT:AD:DP:GL:GQ	0/1:21,24:43:-82.42,-12.96,-78.26:99
+chr1	4497578	.	G	A	145.29	PASS	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=55.81;MQ0=2;OQ=939.73;QD=13.42;SB=-372.83	GT:AD:DP:GL:GQ	0/1:38,32:59:-115.04,-17.78,-100.90:99
+chr1	4497715	rs609304	T	C	122.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=59.55;MQ0=0;OQ=597.13;QD=11.71;SB=-145.28	GT:AD:DP:GL:GQ	0/1:26,25:50:-78.07,-15.08,-99.80:99
+chr1	4497726	rs554335	A	T	316.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=640.98;QD=12.57;SB=-272.29	GT:AD:DP:GL:GQ	0/1:29,22:51:-82.74,-15.36,-107.67:99
+chr1	4497802	rs16838465	A	G	196.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=59.68;MQ0=0;OQ=953.26;QD=13.06;SB=-260.95	GT:AD:DP:GL:GQ	0/1:33,40:71:-120.01,-21.40,-135.23:99
+chr1	4497821	rs553435	A	G	265.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=3.67;MQ=59.70;MQ0=0;OQ=1049.73;QD=13.63;SB=-281.63	GT:AD:DP:GL:GQ	0/1:34,43:75:-130.87,-22.61,-136.05:99
+chr1	4497861	rs608492	G	C	466.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.05;MQ0=0;OQ=1478.41;QD=20.82;SB=-714.38	GT:AD:DP:GL:GQ	0/1:30,41:69:-171.91,-20.79,-131.74:99
+chr1	4497881	rs12726510	T	C	431.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=56.08;MQ0=0;OQ=981.66;QD=11.69;SB=-387.89	GT:AD:DP:GL:GQ	0/1:41,43:78:-124.95,-23.50,-161.69:99
+chr1	4497887	rs12752601	C	A	191.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=56.08;MQ0=0;OQ=1107.25;QD=13.18;SB=-552.73	GT:AD:DP:GL:GQ	0/1:44,40:81:-138.40,-24.39,-157.12:99
+chr1	4497950	rs12737521	G	A	266.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.10;MQ0=0;OQ=874.33;QD=12.67;SB=-378.16	GT:AD:DP:GL:GQ	0/1:41,28:69:-111.51,-20.80,-136.23:99
+chr1	4498077	rs551359	A	G	240.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=59.32;MQ0=0;OQ=1496.06;QD=16.81;SB=-547.59	GT:AD:DP:GL:GQ	0/1:39,50:88:-179.39,-26.50,-159.21:99
+chr1	4498168	rs495682	T	C	312.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.73;MQ0=0;OQ=1219.53;QD=14.52;SB=-615.78	GT:AD:DP:GL:GQ	0/1:41,43:83:-150.24,-25.00,-166.52:99
+chr1	4498170	rs596848	G	A	305.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.72;MQ0=0;OQ=1391.50;QD=16.77;SB=-693.72	GT:AD:DP:GL:GQ	0/1:40,43:81:-166.83,-24.40,-145.63:99
+chr1	4498284	rs596360	G	A	603.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=984.96;QD=14.92;SB=-509.05	GT:AD:DP:GL:GQ	0/1:36,30:66:-121.68,-19.90,-113.72:99
+chr1	4498314	rs494638	T	C	459.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.34;MQ0=0;OQ=1145.34;QD=15.69;SB=-585.28	GT:AD:DP:GL:GQ	0/1:33,40:71:-139.20,-21.39,-128.86:99
+chr1	4498825	rs489371	A	G	35.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=1;HaplotypeScore=4.84;MQ=56.29;MQ0=0;OQ=1173.41;QD=12.62;SB=-564.58	GT:AD:DP:GL:GQ	0/1:51,42:90:-147.73,-27.11,-207.42:99
+chr1	4498854	rs489316	A	G	383.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=53.44;MQ0=0;OQ=1022.72;QD=11.24;SB=-456.67	GT:AD:DP:GL:GQ	0/1:50,41:90:-132.68,-27.12,-202.80:99
+chr1	4499103	rs592726	C	T	522.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=1251.74;QD=14.06;SB=-614.59	GT:AD:DP:GL:GQ	0/1:50,39:87:-154.68,-26.22,-160.76:99
+chr1	4499256	rs6673713	A	T	601.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.46;MQ0=0;OQ=969.14;QD=15.38;SB=-478.55	GT:AD:DP:GL:GQ	0/1:32,31:63:-119.17,-18.97,-123.21:99
+chr1	4499545	rs6677142	T	C	474.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=56.97;MQ0=0;OQ=1056.33;QD=15.77;SB=-489.28	GT:AD:DP:GL:GQ	0/1:31,36:67:-129.10,-20.18,-124.32:99
+chr1	4499557	rs10158638	A	G	600.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.01;MQ0=0;OQ=954.47;QD=14.46;SB=-498.28	GT:AD:DP:GL:GQ	0/1:33,33:66:-118.61,-19.88,-133.94:99
+chr1	4499695	rs28694108	C	T	122.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=60.16;MQ0=0;OQ=1387.28;QD=20.11;SB=-460.49	GT:AD:DP:GL:GQ	0/1:27,42:67:-162.21,-20.20,-83.84:99
+chr1	4499852	rs569392	T	C	181.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.97;MQ=59.40;MQ0=0;OQ=1301.88;QD=15.50;SB=-652.84	GT:AD:DP:GL:GQ	0/1:40,44:84:-158.78,-25.30,-162.80:99
+chr1	4499866	rs638811	G	A	371.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.47;MQ0=0;OQ=1161.22;QD=14.70;SB=-516.05	GT:AD:DP:GL:GQ	0/1:40,38:72:-141.11,-21.71,-113.94:99
+chr1	4500093	rs627374	C	A	201.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=3.04;MQ=56.24;MQ0=0;OQ=1409.06;QD=17.18;SB=-575.67	GT:AD:DP:GL:GQ	0/1:36,45:77:-170.76,-26.57,-102.66:99
+chr1	4500144	rs1612095	G	C	191.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=58.14;MQ0=0;OQ=1652.98;QD=16.87;SB=-714.30	GT:AD:DP:GL:GQ	0/1:51,47:96:-197.51,-28.93,-219.71:99
+chr1	4500181	rs1612008	C	T	343.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.55;MQ0=0;OQ=1543.90;QD=16.78;SB=-630.74	GT:AD:DP:GL:GQ	0/1:42,49:86:-183.59,-25.91,-132.31:99
+chr1	4500274	rs544513	A	G	399.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=703.77;QD=11.00;SB=-261.96	GT:AD:DP:GL:GQ	0/1:33,31:62:-92.35,-18.69,-134.62:99
+chr1	4500351	rs543653	T	G	570.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=699.52;QD=12.27;SB=-362.58	GT:AD:DP:GL:GQ	0/1:31,26:56:-90.10,-16.87,-111.77:99
+chr1	4500481	rs542688	C	G	360.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.76;MQ0=0;OQ=1267.59;QD=16.05;SB=-449.73	GT:AD:DP:GL:GQ	0/1:41,38:77:-153.25,-23.20,-181.78:99
+chr1	4500512	rs625627	C	T	286.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=59.08;MQ0=0;OQ=914.91;QD=12.89;SB=-281.75	GT:AD:DP:GL:GQ	0/1:39,32:67:-114.97,-20.19,-123.19:99
+chr1	4500529	rs541929	A	G	325.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=59.16;MQ0=0;OQ=945.37;QD=12.28;SB=-290.30	GT:AD:DP:GL:GQ	0/1:42,34:76:-120.71,-22.89,-170.67:99
+chr1	4500606	rs10915556	C	T	355.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1316.31;QD=19.65;SB=-489.56	GT:AD:DP:GL:GQ	0/1:29,38:66:-154.80,-19.88,-102.91:99
+chr1	4500644	rs2051642	G	T	498.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1142.97;QD=16.33;SB=-501.30	GT:AD:DP:GL:GQ	0/1:32,38:70:-138.67,-21.09,-110.82:99
+chr1	4500677	rs2051641	C	T	126.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=2.61;MQ=60.00;MQ0=0;OQ=1424.93;QD=18.04;SB=-396.12	GT:AD:DP:GL:GQ	0/1:37,42:79:-169.57,-23.79,-134.20:99
+chr1	4500995	rs694361	G	A	987.12	Indel	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=10;HaplotypeScore=19.73;MQ=59.67;MQ0=0;QD=14.31;SB=-451.85	GT:AD:DP:GL:GQ	0/1:36,33:64:-121.28,-19.29,-109.34:99
+chr1	4501161	rs10915557	A	C	322.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.59;MQ0=0;OQ=772.74;QD=13.80;SB=-198.82	GT:AD:DP:GL:GQ	0/1:27,28:54:-96.83,-16.27,-94.26:99
+chr1	4501182	rs10915558	G	T	398.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=829.24;QD=13.16;SB=-280.30	GT:AD:DP:GL:GQ	0/1:32,31:61:-104.58,-18.38,-107.72:99
+chr1	4501418	rs988089	G	T	231.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=59.83;MQ0=0;OQ=785.83;QD=14.29;SB=-379.13	GT:AD:DP:GL:GQ	0/1:28,27:55:-98.43,-16.57,-95.26:99
+chr1	4501445	rs988088	G	A	287.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.35;MQ0=0;OQ=635.25;QD=14.77;SB=-270.30	GT:AD:DP:GL:GQ	0/1:21,22:39:-78.57,-11.76,-58.80:99
+chr1	4501584	rs1988134	A	T	372.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.72;MQ0=0;OQ=1235.61;QD=14.89;SB=-511.29	GT:AD:DP:GL:GQ	0/1:43,40:83:-151.84,-25.00,-162.60:99
+chr1	4501936	rs508056	T	C	0.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.01;HRun=1;HaplotypeScore=15.97;MQ=59.84;MQ0=0;OQ=1145.11;QD=15.07;SB=-479.27	GT:AD:DP:GL:GQ	0/1:36,39:76:-140.39,-22.59,-147.97:99
+chr1	4501948	rs594535	A	T	38.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.01;HRun=0;HaplotypeScore=7.00;MQ=59.51;MQ0=0;OQ=1283.54;QD=17.83;SB=-623.13	GT:AD:DP:GL:GQ	0/1:31,40:72:-153.02,-21.38,-116.42:99
+chr1	4502177	rs640624	T	C	14.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=7.76;MQ=59.57;MQ0=0;OQ=1108.01;QD=16.29;SB=-573.02	GT:AD:DP:GL:GQ	0/1:30,38:66:-133.97,-19.88,-116.04:99
+chr1	4502677	.	A	G	145.65	PASS	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.30;MQ0=0;OQ=805.91;QD=12.21;SB=-395.14	GT:AD:DP:GL:GQ	0/1:37,29:66:-103.76,-19.88,-150.61:99
+chr1	4502871	rs2411775	C	T	188.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.39;MQ0=0;OQ=1230.48;QD=17.83;SB=-330.32	GT:AD:DP:GL:GQ	0/1:32,36:67:-146.52,-20.19,-100.70:99
+chr1	4503184	rs694935	T	A	28.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=2.73;MQ=59.33;MQ0=0;OQ=840.35;QD=13.55;SB=-222.90	GT:AD:DP:GL:GQ	0/1:31,31:58:-104.80,-17.48,-105.42:99
+chr1	4503230	rs694967	T	G	352.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=57.78;MQ0=0;OQ=1098.27;QD=15.25;SB=-535.44	GT:AD:DP:GL:GQ	0/1:33,39:72:-134.80,-21.69,-119.88:99
+chr1	4503601	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=1;HaplotypeScore=106.52;MQ=39.06;MQ0=0;OQ=897.90;QD=7.48;SB=-269.21	GT:AD:DP:GL:GQ	0/1:86,34:118:-128.61,-35.54,-314.22:99
+chr1	4503616	.	T	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=1;HaplotypeScore=12.83;MQ=37.47;MQ0=0;OQ=467.51;QD=3.41;SB=-122.22	GT:AD:DP:GL:GQ	0/1:111,26:134:-90.40,-40.36,-439.82:99
+chr1	4503623	rs241214	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=148;Dels=0.00;HRun=0;HaplotypeScore=94.05;MQ=37.91;MQ0=0;OQ=4273.01;QD=28.87;SB=-1538.72	GT:AD:DP:GL:GQ	0/1:32,114:147:-426.30,-51.49,-123.04:99
+chr1	4503639	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=260.99;MQ=37.36;MQ0=0;OQ=1166.38;QD=7.34;SB=-484.60	GT:AD:DP:GL:GQ	0/1:114,44:124:-157.27,-37.35,-295.16:99
+chr1	4503657	rs12754029	A	C	1394.26	DPFilter;Indel	AC=1;AF=0.50;AN=2;DB;DP=153;Dels=0.00;HRun=1;HaplotypeScore=166.14;MQ=39.29;MQ0=0;QD=9.11;SB=-599.12	GT:AD:DP:GL:GQ	0/1:73,77:122:-190.87,-48.16,-269.49:99
+chr1	4503674	rs61111938	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=147;Dels=0.00;HRun=0;HaplotypeScore=137.11;MQ=42.18;MQ0=0;OQ=392.40;QD=2.67;SB=-58.59	GT:AD:DP:GL:GQ	0/1:124,23:123:-79.58,-37.06,-405.54:99
+chr1	4503686	rs61202630	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.03;HRun=0;HaplotypeScore=163.66;MQ=45.68;MQ0=0;OQ=981.22;QD=7.91;SB=-498.66	GT:AD:DP:GL:GQ	0/1:79,40:116:-138.71,-37.31,-281.28:99
+chr1	4503715	.	T	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=16.61;MQ=53.48;MQ0=0;OQ=158.20;QD=1.86;SB=-90.66	GT:AD:DP:GL:GQ	0/1:72,13:84:-44.41,-25.30,-293.89:99
+chr1	4503964	rs241215	T	A	444.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=54.88;MQ0=0;OQ=1312.48;QD=17.50;SB=-618.08	GT:AD:DP:GL:GQ	0/1:34,41:75:-157.12,-22.59,-129.67:99
+chr1	4504029	rs241216	G	A	155.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=4.03;MQ=59.43;MQ0=0;OQ=1251.65;QD=17.15;SB=-469.46	GT:AD:DP:GL:GQ	0/1:35,38:70:-149.55,-21.10,-107.16:99
+chr1	4504349	rs241217	C	G	275.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1603.60;QD=22.59;SB=-778.42	GT:AD:DP:GL:GQ	0/1:29,42:71:-185.04,-21.39,-125.25:99
+chr1	4505282	rs241218	T	C	43.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=7.22;MQ=59.15;MQ0=0;OQ=812.13;QD=11.44;SB=-395.26	GT:AD:DP:GL:GQ	0/1:37,34:67:-104.70,-20.20,-130.72:99
+chr1	4506052	rs241219	T	C	334.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=59.17;MQ0=0;OQ=741.75;QD=13.25;SB=-389.65	GT:AD:DP:GL:GQ	0/1:27,29:55:-94.04,-16.58,-103.55:99
+chr1	4508064	rs241220	G	A	334	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=60.00;MQ0=0;OQ=1163.49;QD=17.37;SB=-431.97	GT:AD:DP:GL:GQ	0/1:32,35:66:-139.53,-19.90,-98.33:99
+chr1	4508910	rs241221	T	C	373.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.20;MQ0=0;OQ=874.89;QD=15.08;SB=-418.55	GT:AD:DP:GL:GQ	0/1:25,33:55:-107.34,-16.57,-97.13:99
+chr1	4509116	rs241222	G	C	267.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=3.24;MQ=59.18;MQ0=0;OQ=1337.43;QD=18.07;SB=-676.08	GT:AD:DP:GL:GQ	0/1:37,37:72:-158.72,-21.69,-154.68:99
+chr1	4510110	rs241244	A	T	180.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.78;MQ=60.38;MQ0=0;OQ=930.99;QD=16.33;SB=-387.46	GT:AD:DP:GL:GQ	0/1:27,30:57:-113.55,-17.17,-101.72:99
+chr1	4510493	rs241245	T	C	361.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=851.20;QD=14.43;SB=-421.93	GT:AD:DP:GL:GQ	0/1:29,30:57:-105.58,-17.17,-107.45:99
+chr1	4510920	rs241246	T	C	463.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.63;MQ0=0;OQ=864.46;QD=13.94;SB=-382.19	GT:AD:DP:GL:GQ	0/1:32,30:62:-108.40,-18.67,-129.80:99
+chr1	4510938	rs241247	G	T	223.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=4.47;MQ=59.71;MQ0=0;OQ=1111.82;QD=14.07;SB=-561.61	GT:AD:DP:GL:GQ	0/1:42,37:78:-137.96,-23.49,-147.67:99
+chr1	4511101	rs241248	G	A	90.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=4.65;MQ=58.90;MQ0=0;OQ=1137.70;QD=15.80;SB=-412.89	GT:AD:DP:GL:GQ	0/1:38,34:72:-138.74,-21.69,-139.14:99
+chr1	4512226	rs241249	C	A	118.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=2704.76;QD=36.06;SB=-1203.75	GT:AD:DP:GL:GQ	1/1:0,75:73:-274.08,-21.98,-0.01:99
+chr1	4512612	rs12117466	C	T	434.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=1595.86;QD=21.57;SB=-705.78	GT:AD:DP:GL:GQ	0/1:28,46:74:-185.16,-22.29,-104.90:99
+chr1	4512789	rs2222050	C	G	399.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=51.66;MQ0=0;OQ=560.26;QD=12.18;SB=-284.90	GT:AD:DP:GL:GQ	0/1:29,17:46:-73.17,-13.86,-129.73:99
+chr1	4512997	.	G	C	109.15	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.26;MQ0=0;OQ=1039.37;QD=14.64;SB=-540.64	GT:AD:DP:GL:GQ	0/1:41,30:70:-128.31,-21.09,-176.73:99
+chr1	4513093	rs241250	C	T	592.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.64;MQ0=0;OQ=2215.68;QD=40.29;SB=-1120.49	GT:AD:DP:GL:GQ	1/1:0,55:55:-225.17,-16.57,-0.01:99
+chr1	4513279	rs241251	T	C	191.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=56.17;MQ0=0;OQ=859.05;QD=12.10;SB=-428.93	GT:AD:DP:GL:GQ	0/1:40,31:71:-110.57,-21.39,-162.21:99
+chr1	4513371	rs241252	G	A	678.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2454.05;QD=39.58;SB=-997.85	GT:AD:DP:GL:GQ	1/1:0,61:61:-249.00,-18.37,-0.01:99
+chr1	4513556	rs56948682	G	C	523.60	Indel	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=3.31;MQ=55.31;MQ0=0;QD=11.90;SB=-218.66	GT:AD:DP:GL:GQ	0/1:25,19:40:-67.72,-12.07,-92.30:99
+chr1	4513868	rs241254	G	A	271.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=58.71;MQ0=0;OQ=649.43;QD=12.03;SB=-239.26	GT:AD:DP:GL:GQ	0/1:28,25:50:-83.30,-15.07,-98.60:99
+chr1	4513881	rs241255	G	C	176.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=58.80;MQ0=0;OQ=2370.20;QD=40.87;SB=-1167.06	GT:AD:DP:GL:GQ	1/1:0,58:55:-240.62,-16.57,-0.01:99
+chr1	4514372	rs241256	C	T	582.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=913.61;QD=13.44;SB=-345.84	GT:AD:DP:GL:GQ	0/1:39,29:68:-115.13,-20.48,-142.92:99
+chr1	4514476	rs6426419	T	A	347.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.60;MQ0=0;OQ=541.18;QD=9.33;SB=-252.68	GT:AD:DP:GL:GQ	0/1:37,21:57:-74.57,-17.17,-137.52:99
+chr1	4514682	rs241257	C	T	286.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=2358.24;QD=39.97;SB=-1174.07	GT:AD:DP:GL:GQ	1/1:0,59:59:-239.42,-17.77,-0.01:99
+chr1	4514873	rs171319	C	T	380.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.42;MQ0=0;OQ=1086.37;QD=13.58;SB=-534.53	GT:AD:DP:GL:GQ	0/1:46,34:78:-135.44,-23.52,-140.72:99
+chr1	4515369	rs241258	G	A	48.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=47.21;MQ0=0;OQ=749.09;QD=17.42;SB=-181.27	GT:AD:DP:GL:GQ	0/1:20,23:42:-90.85,-12.66,-63.49:99
+chr1	4515444	rs241259	C	G	22.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=50.43;MQ0=0;OQ=2118.85;QD=40.75;SB=-972.73	GT:AD:DP:GL:GQ	1/1:0,52:49:-215.48,-14.76,-0.01:99
+chr1	4515588	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=15;HaplotypeScore=4.97;MQ=51.27;MQ0=0;OQ=250.35;QD=4.47;SB=56.21	GT:AD:DP:GL:GQ	0/1:42,14:49:-43.09,-14.77,-129.95:99
+chr1	4515926	rs241260	C	G	33.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=2.19;MQ=55.21;MQ0=0;OQ=3292.12;QD=42.21;SB=-1616.25	GT:AD:DP:GL:GQ	1/1:0,78:75:-328.21,-22.60,-0.02:99
+chr1	4515962	rs241261	T	C	602.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.64;MQ0=0;OQ=2469.23;QD=29.75;SB=-1091.36	GT:AD:DP:GL:GQ	1/1:0,83:79:-250.58,-23.83,-0.08:99
+chr1	4516659	rs241262	T	G	634.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2557.93;QD=35.53;SB=-1149.62	GT:AD:DP:GL:GQ	1/1:0,72:72:-259.40,-21.69,-0.02:99
+chr1	4517716	rs10799244	T	C	405.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.15;MQ0=0;OQ=1346.22;QD=18.96;SB=-628.34	GT:AD:DP:GL:GQ	0/1:27,44:70:-158.99,-21.09,-107.87:99
+chr1	4518111	rs6685798	G	A	309.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.32;MQ0=0;OQ=1238.56;QD=18.21;SB=-627.62	GT:AD:DP:GL:GQ	0/1:30,37:65:-146.72,-19.58,-98.24:99
+chr1	4518139	rs916408	T	C	232.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.86;MQ=59.63;MQ0=0;OQ=609.90;QD=9.84;SB=-241.88	GT:AD:DP:GL:GQ	0/1:34,28:60:-82.36,-18.09,-138.61:99
+chr1	4518389	rs916407	C	A	294.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.44;MQ0=0;OQ=593.42;QD=10.99;SB=-258.24	GT:AD:DP:GL:GQ	0/1:32,22:53:-78.59,-15.97,-110.59:99
+chr1	4518393	rs916406	T	C	102.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.50;MQ0=0;OQ=426.60;QD=7.62;SB=-216.22	GT:AD:DP:GL:GQ	0/1:34,22:50:-61.02,-15.07,-122.30:99
+chr1	4518582	rs241263	T	C	395.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2663.66;QD=36.49;SB=-1355.60	GT:AD:DP:GL:GQ	1/1:0,73:73:-269.97,-21.98,-0.02:99
+chr1	4518898	rs241264	C	T	593.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3315.63;QD=40.93;SB=-1267.69	GT:AD:DP:GL:GQ	1/1:0,81:81:-330.56,-24.40,-0.02:99
+chr1	4519253	rs241265	G	T	396.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=442.53;QD=9.42;SB=-108.63	GT:AD:DP:GL:GQ	0/1:30,17:47:-61.69,-14.15,-109.08:99
+chr1	4520150	rs241266	G	A	572.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1309.70;QD=16.79;SB=-634.24	GT:AD:DP:GL:GQ	0/1:38,40:77:-157.45,-23.20,-135.23:99
+chr1	4520783	rs10915560	T	C	479.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=617.89;QD=10.13;SB=-279.12	GT:AD:DP:GL:GQ	0/1:36,25:60:-83.15,-18.08,-142.30:99
+chr1	4520856	rs12120353	C	A	156.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=694.57;QD=12.19;SB=-303.22	GT:AD:DP:GL:GQ	0/1:32,25:54:-89.01,-16.27,-103.65:99
+chr1	4521323	rs241267	C	T	378.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.60;MQ0=0;OQ=620.84;QD=13.21;SB=-243.25	GT:AD:DP:GL:GQ	0/1:25,22:45:-78.94,-13.58,-74.16:99
+chr1	4521646	rs12748186	C	T	419.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=983.89;QD=18.92;SB=-364.52	GT:AD:DP:GL:GQ	0/1:23,29:52:-117.34,-15.67,-75.86:99
+chr1	4522500	rs241268	A	G	490.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1548.29;QD=30.97;SB=-704.61	GT:AD:DP:GL:GQ	1/1:0,50:49:-158.46,-14.78,-0.04:99
+chr1	4523101	.	G	T	20.08	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=16;HaplotypeScore=10.17;MQ=50.32;MQ0=0;QD=0.35;SB=50.87	GT:AD:DP:GL:GQ	0/1:48,10:42:-17.95,-12.66,-121.78:52.87
+chr1	4523283	rs241269	C	T	335.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=806.86;QD=12.81;SB=-308.31	GT:AD:DP:GL:GQ	0/1:36,27:61:-102.37,-18.40,-111.88:99
+chr1	4523749	rs55956326	C	T	46.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=776.69;QD=17.65;SB=-140.14	GT:AD:DP:GL:GQ	0/1:21,23:44:-94.21,-13.26,-66.49:99
+chr1	4524365	rs497517	C	A	203.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=57.23;MQ0=0;OQ=2311.84;QD=35.57;SB=-943.65	GT:AD:DP:GL:GQ	1/1:0,65:64:-234.79,-19.27,-0.02:99
+chr1	4524639	rs190250	T	C	96.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=54.62;MQ0=1;OQ=1410.76;QD=28.22;SB=-520.24	GT:AD:DP:GL:GQ	1/1:1,49:43:-144.69,-12.96,-0.03:99
+chr1	4525049	rs241270	T	A	128.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=57.31;MQ0=0;OQ=2756.56;QD=35.80;SB=-964.62	GT:AD:DP:GL:GQ	1/1:0,76:75:-279.26,-22.59,-0.02:99
+chr1	4525775	.	C	T	82.15	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=60.00;MQ0=0;OQ=631.76;QD=12.39;SB=-287.21	GT:AD:DP:GL:GQ	0/1:28,23:47:-80.62,-14.16,-88.43:99
+chr1	4526115	rs241271	T	C	508.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=1796.29;QD=29.45;SB=-877.68	GT:AD:DP:GL:GQ	1/1:0,61:57:-183.26,-17.19,-0.05:99
+chr1	4526127	rs241272	T	G	620.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=2425.30;QD=34.16;SB=-1142.12	GT:AD:DP:GL:GQ	1/1:0,71:70:-246.14,-21.08,-0.02:99
+chr1	4526146	rs1515670	A	G	180.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=3.98;MQ=58.96;MQ0=0;OQ=860.15;QD=12.84;SB=-436.91	GT:AD:DP:GL:GQ	0/1:37,30:66:-109.18,-19.88,-145.10:99
+chr1	4526937	rs241273	A	C	421.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=1105.42;QD=16.02;SB=-515.69	GT:AD:DP:GL:GQ	0/1:31,38:69:-134.61,-20.78,-114.90:99
+chr1	4527342	rs241274	A	C	51.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1996.50;QD=32.20;SB=-821.03	GT:AD:DP:GL:GQ	1/1:0,62:58:-203.26,-17.47,-0.02:99
+chr1	4527839	rs241275	A	G	555.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=2594.28;QD=29.48;SB=-1228.48	GT:AD:DP:GL:GQ	1/1:0,88:82:-263.09,-24.73,-0.08:99
+chr1	4528191	rs28665533	G	A	434.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1407.19;QD=19.02;SB=-661.67	GT:AD:DP:GL:GQ	0/1:32,42:74:-166.29,-22.29,-115.61:99
+chr1	4528559	rs241276	C	T	153.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=4.22;MQ=59.30;MQ0=0;OQ=909.72;QD=13.78;SB=-324.82	GT:AD:DP:GL:GQ	0/1:37,29:65:-113.86,-19.61,-110.36:99
+chr1	4529046	rs241277	A	C	117.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=2.18;MQ=60.00;MQ0=0;OQ=2433.72;QD=33.34;SB=-1159.13	GT:AD:DP:GL:GQ	1/1:0,73:69:-246.98,-20.78,-0.02:99
+chr1	4529268	rs241278	T	C	273.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.43;MQ=59.61;MQ0=0;OQ=2074.79;QD=35.17;SB=-848.12	GT:AD:DP:GL:GQ	1/1:0,59:58:-211.08,-17.47,-0.02:99
+chr1	4530244	rs7531281	A	C	607.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2071.97;QD=33.42;SB=-943.11	GT:AD:DP:GL:GQ	1/1:0,62:60:-210.80,-18.07,-0.02:99
+chr1	4530343	rs7526879	C	T	127.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=59.29;MQ0=0;OQ=2841.32;QD=39.46;SB=-1410.68	GT:AD:DP:GL:GQ	1/1:0,72:71:-287.74,-21.39,-0.02:99
+chr1	4531126	rs241212	G	T	328.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=59.37;MQ0=0;OQ=847.33;QD=14.36;SB=-341.38	GT:AD:DP:GL:GQ	0/1:30,29:58:-105.49,-17.47,-104.18:99
+chr1	4531264	rs55850443	C	A	105.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=3.29;MQ=59.66;MQ0=0;OQ=907.20;QD=13.54;SB=-364.99	GT:AD:DP:GL:GQ	0/1:34,33:65:-113.58,-19.58,-115.11:99
+chr1	4532420	rs980092	A	G	568.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.63;MQ0=0;OQ=2136.98;QD=31.43;SB=-1016.73	GT:AD:DP:GL:GQ	1/1:0,68:67:-217.34,-20.21,-0.06:99
+chr1	4532678	rs34339970	T	C	238.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=59.68;MQ0=0;OQ=686.96;QD=9.41;SB=-234.24	GT:AD:DP:GL:GQ	0/1:42,31:70:-93.08,-21.10,-159.73:99
+chr1	4532688	rs171317	C	A	295.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.69;MQ0=0;OQ=2546.98;QD=34.42;SB=-1274.23	GT:AD:DP:GL:GQ	1/1:0,74:71:-258.31,-21.38,-0.02:99
+chr1	4532830	rs35748829	C	T	224.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.37;MQ0=0;OQ=1280.71;QD=19.40;SB=-516.15	GT:AD:DP:GL:GQ	0/1:29,37:64:-150.64,-19.29,-86.56:99
+chr1	4532839	rs35106071	C	T	30.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=3;HaplotypeScore=0.47;MQ=59.31;MQ0=0;OQ=1092.68;QD=17.91;SB=-426.77	GT:AD:DP:GL:GQ	0/1:29,32:61:-130.92,-18.37,-105.58:99
+chr1	4533414	rs6673089	G	A	59.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=5.78;MQ=59.66;MQ0=0;OQ=1175.25;QD=17.54;SB=-391.70	GT:AD:DP:GL:GQ	0/1:31,35:66:-140.69,-19.88,-114.80:99
+chr1	4533499	rs6426421	C	T	279.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=56.21;MQ0=0;OQ=3052.51;QD=38.64;SB=-1294.73	GT:AD:DP:GL:GQ	1/1:0,79:78:-308.86,-23.50,-0.03:99
+chr1	4533545	rs7527742	G	A	582.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.29;MQ0=0;OQ=1245.18;QD=15.19;SB=-388.08	GT:AD:DP:GL:GQ	0/1:45,37:81:-152.20,-24.40,-157.64:99
+chr1	4533745	rs241208	T	C	151.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.23;MQ0=0;OQ=641.89;QD=11.07;SB=-289.57	GT:AD:DP:GL:GQ	0/1:35,23:57:-84.64,-17.17,-139.99:99
+chr1	4533782	rs17344823	A	T	343.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=50.31;MQ0=0;OQ=1106.34;QD=17.56;SB=-567.72	GT:AD:DP:GL:GQ	0/1:26,37:60:-131.99,-18.07,-92.40:99
+chr1	4533944	rs241207	T	G	366.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.27;MQ0=0;OQ=1080.62;QD=29.21;SB=-322.00	GT:AD:DP:GL:GQ	1/1:0,37:32:-111.66,-9.64,-0.02:96.25
+chr1	4534250	rs11584033	T	C	380.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=58.88;MQ0=0;OQ=947.57;QD=16.34;SB=-494.15	GT:AD:DP:GL:GQ	0/1:26,32:58:-115.51,-17.47,-106.56:99
+chr1	4534838	rs1541318	A	G	459.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1096.76;QD=16.87;SB=-540.58	GT:AD:DP:GL:GQ	0/1:28,37:65:-132.54,-19.58,-112.37:99
+chr1	4535109	rs2411777	C	T	151.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=59.69;MQ0=0;OQ=1491.80;QD=20.16;SB=-710.25	GT:AD:DP:GL:GQ	0/1:30,44:73:-174.45,-21.99,-106.04:99
+chr1	4536054	rs10799246	T	A	279.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=56.28;MQ0=1;OQ=1123.37;QD=19.37;SB=-579.73	GT:AD:DP:GL:GQ	0/1:23,35:56:-132.49,-16.87,-78.58:99
+chr1	4536627	rs1157688	T	C	729.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2286.18;QD=34.64;SB=-1059.42	GT:AD:DP:GL:GQ	1/1:1,65:64:-232.22,-19.28,-0.02:99
+chr1	4537253	rs12746043	A	G	196.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.75;MQ0=0;OQ=742.34;QD=10.03;SB=-306.91	GT:AD:DP:GL:GQ	0/1:43,31:74:-99.82,-22.30,-175.74:99
+chr1	4537334	rs12073968	A	T	357.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1269.08;QD=15.67;SB=-567.67	GT:AD:DP:GL:GQ	0/1:40,41:80:-154.29,-24.09,-150.38:99
+chr1	4537921	rs12724503	G	A	310.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=60.00;MQ0=0;OQ=1523.81;QD=15.09;SB=-617.07	GT:AD:DP:GL:GQ	0/1:55,46:100:-185.79,-30.12,-188.53:99
+chr1	4538097	rs4654561	G	A	508.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=3756.30;QD=39.96;SB=-1777.79	GT:AD:DP:GL:GQ	1/1:0,92:93:-374.63,-34.91,-7.66:99
+chr1	4538181	rs4654562	G	A	215.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=2.80;MQ=59.13;MQ0=0;OQ=1260.80;QD=15.19;SB=-602.60	GT:AD:DP:GL:GQ	0/1:45,38:82:-154.08,-24.71,-143.05:99
+chr1	4538603	rs4654563	G	A	371.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=1202.15;QD=16.03;SB=-528.76	GT:AD:DP:GL:GQ	0/1:39,36:74:-145.80,-22.30,-125.85:99
+chr1	4538973	rs7543382	T	C	333.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=59.17;MQ0=0;OQ=1070.40;QD=14.66;SB=-356.54	GT:AD:DP:GL:GQ	0/1:37,36:73:-132.31,-21.99,-147.75:99
+chr1	4539030	rs7540656	A	G	325.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.39;MQ0=0;OQ=796.84;QD=11.72;SB=-299.04	GT:AD:DP:GL:GQ	0/1:36,32:68:-103.46,-20.49,-144.09:99
+chr1	4540675	rs1963269	C	G	227.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.54;MQ0=0;OQ=1695.02;QD=16.62;SB=-763.36	GT:AD:DP:GL:GQ	0/1:55,47:97:-202.01,-29.22,-223.35:99
+chr1	4540762	rs1024139	T	C	542	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.15;MQ0=0;OQ=842.09;QD=11.70;SB=-437.91	GT:AD:DP:GL:GQ	0/1:42,30:72:-109.18,-21.69,-170.21:99
+chr1	4541602	rs241225	G	A	260.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.63;MQ0=0;OQ=2333.57;QD=37.04;SB=-1016.38	GT:AD:DP:GL:GQ	1/1:0,63:59:-236.96,-17.77,-0.01:99
+chr1	4541659	rs241224	G	T	284.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.28;MQ0=0;OQ=2085.58;QD=35.96;SB=-859.24	GT:AD:DP:GL:GQ	1/1:0,58:57:-212.16,-17.17,-0.02:99
+chr1	4541986	rs61765446	G	A	358.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=942.30;QD=14.28;SB=-483.10	GT:AD:DP:GL:GQ	0/1:37,29:65:-117.11,-19.59,-114.27:99
+chr1	4542017	rs241223	C	T	513.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2827.32;QD=39.82;SB=-1402.70	GT:AD:DP:GL:GQ	1/1:0,71:71:-286.34,-21.39,-0.02:99
+chr1	4542337	rs184781	C	T	269.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=2680.27;QD=40.00;SB=-1072.41	GT:AD:DP:GL:GQ	1/1:0,67:66:-271.63,-19.88,-0.01:99
+chr1	4542995	.	A	T	0.76	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=53.06;MQ0=0;OQ=196.97;QD=3.28;SB=-90.71	GT:AD:DP:GL:GQ	0/1:48,11:53:-38.95,-15.97,-156.27:99
+chr1	4543292	rs2078573	A	C	86.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=6.05;MQ=56.75;MQ0=0;OQ=1341.41;QD=16.77;SB=-537.82	GT:AD:DP:GL:GQ	0/1:31,48:77:-160.62,-23.19,-115.03:99
+chr1	4543548	rs515279	T	C	17.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=59.29;MQ0=0;OQ=1923.64;QD=29.59;SB=-45.69	GT:AD:DP:GL:GQ	1/1:0,65:64:-196.03,-19.32,-0.08:99
+chr1	4543717	rs587108	T	G	137.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=716.08;QD=34.10;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,21:21:-75.20,-6.33,-0.01:63.19
+chr1	4543945	rs588347	C	T	45.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=256.94;QD=10.71;SB=-10.00	GT:AD:DP:GL:GQ	0/1:15,9:24:-36.21,-7.23,-52.03:99
+chr1	4544067	rs588861	G	A	43.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=54.12;MQ0=0;OQ=1783.57;QD=37.95;SB=-560.73	GT:AD:DP:GL:GQ	1/1:0,47:45:-181.96,-13.56,-0.01:99
+chr1	4544173	rs488684	T	A	310.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.99;MQ0=0;OQ=2644.21;QD=36.73;SB=-1277.61	GT:AD:DP:GL:GQ	1/1:0,72:70:-268.02,-21.08,-0.01:99
+chr1	4545564	rs616180	T	G	115.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=58.74;MQ0=0;OQ=2469.47;QD=35.28;SB=-1055.12	GT:AD:DP:GL:GQ	1/1:0,70:69:-250.55,-20.78,-0.02:99
+chr1	4545738	rs617046	T	C	49.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=60.00;MQ0=0;OQ=1303.79;QD=31.80;SB=-288.55	GT:AD:DP:GL:GQ	1/1:0,41:40:-133.99,-12.05,-0.02:99
+chr1	4545788	rs57374319	C	T	229.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=594.52;QD=13.51;SB=-275.28	GT:AD:DP:GL:GQ	0/1:24,20:43:-75.69,-12.95,-87.49:99
+chr1	4545807	rs563158	G	C	408.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2250.93;QD=42.47;SB=-845.32	GT:AD:DP:GL:GQ	1/1:0,53:52:-228.70,-15.67,-0.02:99
+chr1	4545915	rs617610	A	G	103.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.73;MQ0=0;OQ=1514.17;QD=27.53;SB=-766.72	GT:AD:DP:GL:GQ	1/1:0,55:49:-155.05,-14.78,-0.05:99
+chr1	4545933	rs561468	C	A	155.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.22;MQ0=0;OQ=1902.16;QD=32.24;SB=-898.65	GT:AD:DP:GL:GQ	1/1:0,59:54:-193.82,-16.27,-0.02:99
+chr1	4546125	rs538655	G	A	601.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.21;MQ0=0;OQ=2022.14;QD=38.15;SB=-935.74	GT:AD:DP:GL:GQ	1/1:0,53:52:-205.82,-15.67,-0.02:99
+chr1	4546239	rs619364	G	A	445.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=837.24;QD=13.95;SB=-392.12	GT:AD:DP:GL:GQ	0/1:34,26:60:-105.08,-18.07,-121.77:99
+chr1	4546345	rs536749	A	G	482	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1853.11;QD=30.38;SB=-858.57	GT:AD:DP:GL:GQ	1/1:0,61:58:-188.95,-17.49,-0.05:99
+chr1	4546432	rs4654446	C	T	238.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=59.28;MQ0=0;OQ=947.38;QD=16.33;SB=-474.49	GT:AD:DP:GL:GQ	0/1:28,30:56:-114.89,-16.87,-97.02:99
+chr1	4546657	rs562787	A	G	229.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=1701.20;QD=30.38;SB=-810.66	GT:AD:DP:GL:GQ	1/1:0,56:54:-173.76,-16.29,-0.05:99
+chr1	4546823	rs532259	C	T	169.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.40;MQ0=0;OQ=2521.38;QD=40.67;SB=-1140.51	GT:AD:DP:GL:GQ	1/1:0,62:62:-255.74,-18.67,-0.01:99
+chr1	4547018	rs559200	G	C	1813.47	Indel	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.18;MQ0=0;QD=40.30;SB=-734.75	GT:AD:DP:GL:GQ	1/1:0,44:43:-184.95,-12.96,-0.01:99
+chr1	4547035	rs6691728	C	T	1783.47	Indel	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.64;MQ0=0;QD=39.63;SB=-856.02	GT:AD:DP:GL:GQ	1/1:0,45:45:-181.94,-13.55,-0.01:99
+chr1	4547069	rs558411	G	C	0.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=4;HaplotypeScore=0.63;MQ=58.20;MQ0=0;OQ=1617.71;QD=41.48;SB=-687.82	GT:AD:DP:GL:GQ	1/1:0,39:38:-165.37,-11.45,-0.01:99
+chr1	4547307	rs634075	C	T	118.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=59.44;MQ0=0;OQ=1786.25;QD=34.35;SB=-705.43	GT:AD:DP:GL:GQ	1/1:0,51:47:-182.23,-14.17,-0.02:99
+chr1	4547329	rs644647	C	A	608.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=1779.42;QD=34.89;SB=-902.65	GT:AD:DP:GL:GQ	1/1:0,51:50:-181.54,-15.06,-0.02:99
+chr1	4547506	rs2674014	C	T	604.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=3048.33;QD=39.08;SB=-1465.48	GT:AD:DP:GL:GQ	1/1:0,78:77:-308.44,-23.20,-0.02:99
+chr1	4548034	rs669252	A	G	36.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=59.78;MQ0=0;OQ=2568.64;QD=30.58;SB=-1254.84	GT:AD:DP:GL:GQ	1/1:0,84:80:-260.52,-24.13,-0.08:99
+chr1	4548229	rs527146	C	T	195.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.54;MQ0=0;OQ=2361.57;QD=37.49;SB=-975.04	GT:AD:DP:GL:GQ	1/1:2,61:63:-246.39,-18.98,-6.65:99
+chr1	4548230	rs553803	A	G	202.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.54;MQ0=0;OQ=2093.62;QD=33.23;SB=-906.61	GT:AD:DP:GL:GQ	1/1:2,61:63:-221.00,-18.97,-8.05:99
+chr1	4548433	rs504274	C	T	6.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=4;HaplotypeScore=2.30;MQ=59.56;MQ0=0;OQ=3385.81;QD=39.83;SB=-1431.01	GT:AD:DP:GL:GQ	1/1:0,85:84:-337.58,-25.30,-0.02:99
+chr1	4548537	rs916404	A	G	176.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.01;MQ=59.60;MQ0=0;OQ=1563.60;QD=27.43;SB=-730.94	GT:AD:DP:GL:GQ	1/1:0,57:51:-160.00,-15.38,-0.05:99
+chr1	4548552	rs1811133	G	A	623.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=2054.70;QD=38.77;SB=-776.53	GT:AD:DP:GL:GQ	1/1:0,53:52:-209.07,-15.66,-0.01:99
+chr1	4548640	rs10915566	C	T	338.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=59.67;MQ0=0;OQ=1058.12;QD=15.12;SB=-552.39	GT:AD:DP:GL:GQ	0/1:37,33:67:-129.29,-20.20,-113.66:99
+chr1	4548685	rs2176113	C	T	467.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1206.49;QD=16.76;SB=-424.43	GT:AD:DP:GL:GQ	0/1:37,35:72:-145.62,-21.68,-138.53:99
+chr1	4548689	rs549918	C	T	547.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2745.70;QD=39.22;SB=-872.18	GT:AD:DP:GL:GQ	1/1:0,70:69:-278.17,-20.79,-0.02:99
+chr1	4548722	rs549150	C	T	597.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=3119.07;QD=40.51;SB=-1266.19	GT:AD:DP:GL:GQ	1/1:0,77:77:-315.51,-23.19,-0.01:99
+chr1	4548785	rs548958	A	C	587.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=3225.28;QD=33.25;SB=-1553.11	GT:AD:DP:GL:GQ	1/1:0,97:93:-326.16,-28.01,-0.03:99
+chr1	4548901	rs683704	G	A	493.67	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2363.22;QD=39.39;SB=-1015.37	GT:AD:DP:GL:GQ	1/1:0,60:60:-239.92,-18.08,-0.02:99
+chr1	4549335	rs572875	G	A	610.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.57;MQ0=0;OQ=2583.49;QD=39.75;SB=-1223.62	GT:AD:DP:GL:GQ	1/1:0,65:64:-261.95,-19.28,-0.01:99
+chr1	4549598	rs520532	C	T	634.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=1;OQ=2560.49;QD=37.65;SB=-1198.62	GT:AD:DP:GL:GQ	1/1:0,68:66:-259.66,-19.89,-0.02:99
+chr1	4550061	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=20;HaplotypeScore=23.52;MQ=43.78;MQ0=0;OQ=658.49;QD=6.86;SB=83.26	GT:AD:DP:GL:GQ	0/1:53,43:71:-90.53,-21.40,-163.68:99
+chr1	4550163	rs189538	T	C	1.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=4.99;MQ=53.64;MQ0=0;OQ=1059.98;QD=26.50;SB=-540.85	GT:AD:DP:GL:GQ	1/1:0,40:35:-109.62,-10.56,-0.04:99
+chr1	4550501	rs10915567	A	T	204.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.86;MQ0=0;OQ=971.67;QD=17.35;SB=-337.66	GT:AD:DP:GL:GQ	0/1:25,31:54:-116.71,-16.26,-86.04:99
+chr1	4550640	rs241213	G	A	356.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2857.67;QD=40.25;SB=-1367.83	GT:AD:DP:GL:GQ	1/1:0,71:71:-289.37,-21.39,-0.02:99
+chr1	4550851	rs164775	A	G	34.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=5.34;MQ=59.24;MQ0=0;OQ=775.11;QD=14.09;SB=-373.36	GT:AD:DP:GL:GQ	0/1:28,27:55:-97.36,-16.57,-110.68:99
+chr1	4551064	rs12079284	G	A	324.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=2.40;MQ=59.55;MQ0=0;OQ=1490.67;QD=17.96;SB=-575.98	GT:AD:DP:GL:GQ	0/1:39,44:83:-177.35,-25.00,-139.24:99
+chr1	4551090	rs164774	A	C	75.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=0.79;MQ=59.47;MQ0=0;OQ=2365.79;QD=33.80;SB=-1092.51	GT:AD:DP:GL:GQ	1/1:0,70:67:-240.18,-20.18,-0.02:99
+chr1	4551865	rs10489134	G	C	328.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=59.44;MQ0=0;OQ=1198.12;QD=16.19;SB=-348.77	GT:AD:DP:GL:GQ	0/1:36,38:72:-144.81,-21.71,-156.52:99
+chr1	4552887	rs7554766	G	A	776.54	Indel	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;QD=12.13;SB=-327.33	GT:AD:DP:GL:GQ	0/1:39,25:57:-98.11,-17.17,-116.23:99
+chr1	4552953	rs7518655	C	T	177.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=2.86;MQ=58.99;MQ0=0;OQ=677.30;QD=14.72;SB=-320.35	GT:AD:DP:GL:GQ	0/1:23,23:43:-83.97,-12.96,-72.15:99
+chr1	4553124	rs7518781	C	A	341.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=59.31;MQ0=0;OQ=849.36;QD=13.92;SB=-331.16	GT:AD:DP:GL:GQ	0/1:30,31:56:-105.09,-16.87,-90.31:99
+chr1	4553830	rs164770	A	G	0.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=3;HaplotypeScore=7.02;MQ=59.30;MQ0=0;OQ=1972.78;QD=32.88;SB=-746.94	GT:AD:DP:GL:GQ	1/1:2,57:55:-200.88,-16.57,-0.02:99
+chr1	4554084	rs61767667	T	A	362.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=502.84;QD=10.48;SB=-173.16	GT:AD:DP:GL:GQ	0/1:30,18:48:-68.02,-14.46,-113.49:99
+chr1	4554189	rs61767668	G	A	492.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=958.92;QD=14.31;SB=-387.15	GT:AD:DP:GL:GQ	0/1:38,29:66:-119.06,-19.89,-123.05:99
+chr1	4555833	rs540572	C	A	391.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=602.48;QD=12.30;SB=-99.63	GT:AD:DP:GL:GQ	0/1:24,25:46:-77.39,-13.85,-83.99:99
+chr1	4556007	rs6426423	C	A	388.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=59.29;MQ0=0;OQ=809.24;QD=15.27;SB=-378.16	GT:AD:DP:GL:GQ	0/1:24,29:51:-99.57,-15.36,-78.05:99
+chr1	4556396	rs531363	C	T	270.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=785.64;QD=14.03;SB=-358.40	GT:AD:DP:GL:GQ	0/1:30,26:54:-98.13,-16.29,-91.52:99
+chr1	4556558	rs129794	G	A	506.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=510.17;QD=11.09;SB=-262.22	GT:AD:DP:GL:GQ	0/1:29,17:46:-68.16,-13.86,-103.52:99
+chr1	4556721	rs10799248	G	A	151.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=483.34;QD=15.10;SB=-178.66	GT:AD:DP:GL:GQ	0/1:17,15:30:-60.66,-9.04,-48.95:99
+chr1	4556909	rs526695	T	C	306.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=58.98;MQ0=0;OQ=2857.53;QD=34.85;SB=-1208.70	GT:AD:DP:GL:GQ	1/1:0,82:80:-289.36,-24.10,-0.02:99
+chr1	4556982	rs516947	G	A	448.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=2681.00;QD=38.86;SB=-634.83	GT:AD:DP:GL:GQ	1/1:0,69:67:-271.71,-20.19,-0.02:99
+chr1	4556992	rs516977	A	G	448.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.27;MQ0=0;OQ=1828.72;QD=29.03;SB=-545.85	GT:AD:DP:GL:GQ	1/1:0,63:60:-186.53,-18.11,-0.07:99
+chr1	4557030	rs517092	A	C	349.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1428.85;QD=26.46;SB=-498.86	GT:AD:DP:GL:GQ	1/1:0,54:46:-146.51,-13.87,-0.04:99
+chr1	4557056	rs524982	C	T	158.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=59.64;MQ0=0;OQ=2000.95;QD=38.48;SB=-916.28	GT:AD:DP:GL:GQ	1/1:0,52:51:-203.70,-15.37,-0.02:99
+chr1	4557155	rs651695	A	T	85.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=3;HaplotypeScore=2.39;MQ=59.42;MQ0=0;OQ=1262.50;QD=15.98;SB=-615.05	GT:AD:DP:GL:GQ	0/1:40,39:78:-153.02,-23.49,-149.00:99
+chr1	4557694	rs653988	C	T	110.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.82;MQ0=0;OQ=2793.65;QD=39.91;SB=-1109.49	GT:AD:DP:GL:GQ	1/1:0,70:70:-282.97,-21.09,-0.02:99
+chr1	4558171	rs549239	T	C	727.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.17;MQ0=0;OQ=2944.97;QD=35.06;SB=-1221.82	GT:AD:DP:GL:GQ	1/1:0,84:83:-298.11,-25.00,-0.03:99
+chr1	4558199	rs12726702	T	A	2233	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=6;HaplotypeScore=61.64;MQ=53.38;MQ0=0;QD=26.58;SB=-718.98	GT:AD:DP:GL:GQ	0/1:14,70:81:-250.99,-24.40,-50.82:99
+chr1	4558206	rs549087	T	A	2870.37	Indel;SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.01;HRun=6;HaplotypeScore=46.58;MQ=52.93;MQ0=0;QD=35.88;SB=-1138.04	GT:AD:DP:GL:GQ	1/1:0,79:79:-290.65,-23.50,-0.03:99
+chr1	4558209	rs28687799	A	T	819.27	Indel;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=4;HaplotypeScore=29.81;MQ=52.84;MQ0=0;QD=10.37;SB=-175.59	GT:AD:DP:GL:GQ	0/1:49,30:77:-108.41,-23.20,-171.08:99
+chr1	4558214	rs59930628	A	T	84.16	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.03;HRun=4;HaplotypeScore=38.67;MQ=53.63;MQ0=0;QD=1.09;SB=56.66	GT:AD:DP:GL:GQ	0/1:66,9:73:-33.09,-21.39,-235.05:99
+chr1	4558250	rs666799	A	C	496.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.14;MQ0=0;OQ=2047.56;QD=34.70;SB=-847.08	GT:AD:DP:GL:GQ	1/1:0,59:58:-208.36,-17.47,-0.02:99
+chr1	4558398	rs12567277	C	T	337.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.53;MQ0=0;OQ=912.06;QD=18.61;SB=-436.84	GT:AD:DP:GL:GQ	0/1:22,27:48:-108.95,-14.46,-68.62:99
+chr1	4558676	rs553691	C	T	200.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.21;MQ0=0;OQ=1974.68;QD=37.26;SB=-1009.66	GT:AD:DP:GL:GQ	1/1:0,53:52:-201.08,-15.67,-0.02:99
+chr1	4560412	rs589176	A	G	118.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.29;MQ=58.87;MQ0=0;OQ=545.72;QD=13.31;SB=-145.53	GT:AD:DP:GL:GQ	0/1:20,21:40:-69.91,-12.06,-74.33:99
+chr1	4561004	rs602244	T	C	195.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.83;MQ=59.64;MQ0=0;OQ=1077.64;QD=16.84;SB=-452.16	GT:AD:DP:GL:GQ	0/1:26,38:63:-130.03,-18.98,-104.11:99
+chr1	4561499	rs604465	G	A	250.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=59.13;MQ0=0;OQ=735.55;QD=15.32;SB=-280.30	GT:AD:DP:GL:GQ	0/1:25,23:45:-90.40,-13.56,-80.37:99
+chr1	4561737	rs563481	C	T	22.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=747.56;QD=17.80;SB=-287.30	GT:AD:DP:GL:GQ	0/1:20,22:42:-90.69,-12.65,-73.13:99
+chr1	4562268	rs537761	C	A	317.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=820.87;QD=16.75;SB=-394.13	GT:AD:DP:GL:GQ	0/1:21,28:48:-99.83,-14.46,-74.67:99
+chr1	4562392	rs618751	G	A	349.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=60.00;MQ0=0;OQ=1032.44;QD=14.14;SB=-366.34	GT:AD:DP:GL:GQ	0/1:41,32:73:-128.52,-21.99,-148.49:99
+chr1	4562641	rs534159	C	T	355.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=808.69;QD=13.71;SB=-376.39	GT:AD:DP:GL:GQ	0/1:33,26:58:-101.65,-17.50,-100.37:99
+chr1	4565129	rs241243	A	G	370.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=694.01;QD=8.07;SB=-138.39	GT:AD:DP:GL:GQ	0/1:53,33:82:-97.39,-24.71,-212.58:99
+chr1	4565904	rs10915569	C	A	242.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.39;MQ0=0;OQ=1490.43;QD=19.61;SB=-754.94	GT:AD:DP:GL:GQ	0/1:27,49:74:-174.61,-22.29,-94.95:99
+chr1	4566354	rs164780	C	G	240.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=59.64;MQ0=0;OQ=2456.30;QD=38.38;SB=-1204.26	GT:AD:DP:GL:GQ	1/1:0,64:63:-249.27,-19.01,-0.05:99
+chr1	4566679	rs151716	A	G	365.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=59.43;MQ0=0;OQ=771.72;QD=11.87;SB=-373.98	GT:AD:DP:GL:GQ	0/1:33,32:64:-99.75,-19.29,-131.65:99
+chr1	4567238	rs4654450	G	A	244.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=59.42;MQ0=0;OQ=1219.09;QD=16.93;SB=-598.62	GT:AD:DP:GL:GQ	0/1:35,37:71:-146.59,-21.39,-121.89:99
+chr1	4567954	rs151715	A	G	136	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.44;MQ0=0;OQ=821.52;QD=10.95;SB=-417.84	GT:AD:DP:GL:GQ	0/1:41,34:74:-107.74,-22.30,-168.10:99
+chr1	4568017	rs241242	G	T	115.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=60.00;MQ0=0;OQ=1682.11;QD=33.64;SB=-638.02	GT:AD:DP:GL:GQ	1/1:0,49:48:-171.82,-14.46,-0.02:99
+chr1	4568283	rs11590266	A	G	358.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=59.56;MQ0=0;OQ=565.36;QD=10.87;SB=-241.59	GT:AD:DP:GL:GQ	0/1:27,24:51:-77.60,-17.78,-112.88:99
+chr1	4571271	rs164779	C	G	314.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.44;MQ0=0;OQ=1283.51;QD=17.11;SB=-664.28	GT:AD:DP:GL:GQ	0/1:38,37:72:-153.33,-21.69,-161.13:99
+chr1	4571572	.	C	T	90.66	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.56;MQ0=0;OQ=626.01;QD=12.04;SB=-331.33	GT:AD:DP:GL:GQ	0/1:32,20:47:-80.06,-14.17,-86.19:99
+chr1	4572354	rs164778	T	C	225.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1559.84;QD=35.45;SB=-660.32	GT:AD:DP:GL:GQ	1/1:0,44:44:-159.58,-13.25,-0.01:99
+chr1	4572615	rs6703429	T	C	577.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=862.43;QD=13.07;SB=-402.26	GT:AD:DP:GL:GQ	0/1:35,31:65:-109.11,-19.58,-142.67:99
+chr1	4574299	.	C	A	554.66	Indel	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.59;MQ0=0;QD=10.47;SB=-260.28	GT:AD:DP:GL:GQ	0/1:31,22:48:-73.21,-14.46,-96.27:99
+chr1	4576029	rs164776	C	T	259.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.56;MQ0=0;OQ=893.05;QD=17.17;SB=-421.82	GT:AD:DP:GL:GQ	0/1:24,28:50:-107.66,-15.07,-72.44:99
+chr1	4576797	rs2411886	G	C	186.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.24;MQ=59.03;MQ0=0;OQ=1978.62;QD=41.22;SB=-1006.27	GT:AD:DP:GL:GQ	1/1:0,47:46:-201.46,-13.86,-0.01:99
+chr1	4576947	rs2411887	C	T	275.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=58.35;MQ0=0;OQ=1931.75;QD=37.88;SB=-945.28	GT:AD:DP:GL:GQ	1/1:0,51:50:-196.78,-15.07,-0.02:99
+chr1	4577395	rs4403602	C	G	245.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=59.46;MQ0=0;OQ=1536.03;QD=35.72;SB=-775.22	GT:AD:DP:GL:GQ	1/1:0,43:41:-157.23,-12.38,-0.05:99
+chr1	4577589	rs7554628	T	C	1.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=57.95;MQ0=0;OQ=730.12;QD=22.82;SB=-185.76	GT:AD:DP:GL:GQ	1/1:0,31:25:-79.87,-10.17,-3.27:69.05
+chr1	4577983	rs7555011	T	C	161.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.09;MQ0=0;OQ=1457.56;QD=28.58;SB=-435.18	GT:AD:DP:GL:GQ	1/1:0,51:47:-149.39,-14.18,-0.05:99
+chr1	4578231	rs35259920	T	A	832.15	Indel	AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.20;MQ0=0;QD=28.69;SB=-10.00	GT:AD:DP:GL:GQ	1/1:1,28:26:-86.82,-7.84,-0.02:78.19
+chr1	4578361	rs7554792	A	C	303.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.92;MQ0=0;OQ=236.46;QD=26.27;SB=-138.00	GT:AD:DP:GL:GQ	1/1:0,9:8:-27.23,-2.41,-0.00:24.06
+chr1	4578400	.	A	T	84.19	Indel	AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=46.65;MQ0=0;QD=6.01;SB=-42.96	GT:AD:DP:GL:GQ	0/1:10,4:13:-15.62,-3.92,-34.97:99
+chr1	4579811	rs1905304	C	A	19.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=58.10;MQ0=0;OQ=2321.72;QD=36.28;SB=-1110.43	GT:AD:DP:GL:GQ	1/1:0,64:63:-235.77,-18.97,-0.01:99
+chr1	4580559	rs56945522	G	A	92.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=61.48;MQ0=0;OQ=2293.20;QD=38.87;SB=-907.71	GT:AD:DP:GL:GQ	1/1:0,59:58:-232.92,-17.48,-0.02:99
+chr1	4581964	rs6668002	T	C	241.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=60.00;MQ0=0;OQ=2274.26;QD=30.73;SB=-1092.12	GT:AD:DP:GL:GQ	1/1:0,73:71:-231.07,-21.41,-0.06:99
+chr1	4583570	rs1573748	A	G	1957.91	Indel	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.66;MQ=60.10;MQ0=0;QD=31.08;SB=-816.28	GT:AD:DP:GL:GQ	1/1:0,63:58:-199.41,-17.48,-0.04:99
+chr1	4584109	rs6657421	G	A	130.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.13;MQ0=0;OQ=1834.09;QD=38.21;SB=-703.35	GT:AD:DP:GL:GQ	1/1:0,48:47:-187.01,-14.16,-0.01:99
+chr1	4584165	rs6674936	T	C	66.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=2.13;MQ=59.25;MQ0=0;OQ=1819.57;QD=32.49;SB=-925.04	GT:AD:DP:GL:GQ	1/1:0,56:51:-185.56,-15.36,-0.01:99
+chr1	4585082	rs1107467	G	A	137.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=1423.05;QD=35.58;SB=-452.60	GT:AD:DP:GL:GQ	1/1:0,39:38:-145.91,-11.45,-0.02:99
+chr1	4585332	rs1483199	A	G	386.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2234.69;QD=31.04;SB=-675.88	GT:AD:DP:GL:GQ	1/1:0,72:67:-227.10,-20.19,-0.04:99
+chr1	4585508	rs875808	G	A	162.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.39;MQ=60.00;MQ0=0;OQ=2216.84;QD=38.89;SB=-1106.64	GT:AD:DP:GL:GQ	1/1:0,57:57:-225.29,-17.17,-0.02:99
+chr1	4585532	rs875807	A	G	300.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.66;MQ0=0;OQ=1870.43;QD=34.01;SB=-960.39	GT:AD:DP:GL:GQ	1/1:0,55:53:-190.65,-15.97,-0.02:99
+chr1	4585731	rs875806	G	C	165.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2133.21;QD=42.66;SB=-847.32	GT:AD:DP:GL:GQ	1/1:0,50:49:-216.92,-14.76,-0.01:99
+chr1	4586501	rs56028718	G	A	84.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=3.12;MQ=59.59;MQ0=0;OQ=1260.05;QD=18.53;SB=-634.67	GT:AD:DP:GL:GQ	0/1:31,37:66:-149.17,-19.88,-106.57:99
+chr1	4587142	rs2269620	C	T	114.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.59;MQ0=0;OQ=2196.52;QD=39.22;SB=-630.34	GT:AD:DP:GL:GQ	1/1:0,56:56:-223.26,-16.87,-0.02:99
+chr1	4587674	rs4654576	A	C	214.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=886.13;QD=32.82;SB=-420.04	GT:AD:DP:GL:GQ	1/1:0,27:26:-92.21,-7.83,-0.01:78.22
+chr1	4587807	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=2;HaplotypeScore=15.00;MQ=58.93;MQ0=0;OQ=113.78;QD=1.87;SB=74.25	GT:AD:DP:GL:GQ	0/1:34,27:42:-27.32,-12.66,-112.79:99
+chr1	4587893	rs6662425	C	G	115.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=59.36;MQ0=0;OQ=2651.42;QD=40.79;SB=-1007.19	GT:AD:DP:GL:GQ	1/1:0,65:61:-268.75,-18.38,-0.02:99
+chr1	4588021	rs6426430	G	T	639.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1436.10;QD=35.90;SB=-672.10	GT:AD:DP:GL:GQ	1/1:0,40:40:-147.21,-12.05,-0.01:99
+chr1	4590753	rs7527078	C	T	465.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.20;MQ0=0;OQ=2043.97;QD=40.08;SB=-576.76	GT:AD:DP:GL:GQ	1/1:0,51:50:-207.99,-15.06,-0.01:99
+chr1	4591042	rs4654577	A	G	251.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=58.37;MQ0=0;OQ=1466.76;QD=34.11;SB=-679.59	GT:AD:DP:GL:GQ	1/1:0,43:43:-150.28,-12.96,-0.02:99
+chr1	4592515	.	G	C	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=48.08;MQ0=6;OQ=54.55;QD=1.03;SB=38.38	GT:AD:DP:GL:GQ	0/1:45,8:39:-20.50,-11.76,-139.98:87.39
+chr1	4592571	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=14.42;MQ=41.26;MQ0=11;OQ=65.05;QD=1.07;SB=-23.62	GT:AD:DP:GL:GQ	0/1:49,12:36:-20.65,-10.86,-123.87:97.89
+chr1	4592585	.	G	C	20.06	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.14;MQ=40.25;MQ0=10;QD=0.33;SB=-5.33	GT:AD:DP:GL:GQ	0/1:54,7:37:-16.45,-11.17,-134.84:52.86
+chr1	4592620	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=1;HaplotypeScore=15.36;MQ=35.46;MQ0=10;OQ=92.00;QD=1.46;SB=0.26	GT:AD:DP:GL:GQ	0/1:54,9:42:-25.15,-12.66,-150.31:99
+chr1	4592627	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=1;HaplotypeScore=16.06;MQ=35.72;MQ0=7;OQ=153.87;QD=2.75;SB=-54.16	GT:AD:DP:GL:GQ	0/1:46,10:37:-29.82,-11.15,-128.78:99
+chr1	4592634	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=17.36;MQ=35.58;MQ0=7;OQ=255.85;QD=4.57;SB=-124.48	GT:AD:DP:GL:GQ	0/1:41,15:33:-38.82,-9.95,-100.95:99
+chr1	4592642	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=1;HaplotypeScore=28.60;MQ=35.10;MQ0=5;OQ=106.45;QD=2.01;SB=3.57	GT:AD:DP:GL:GQ	0/1:41,12:38:-25.38,-11.45,-106.45:99
+chr1	4592649	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=27.47;MQ=35.61;MQ0=5;OQ=241.86;QD=4.65;SB=-127.53	GT:AD:DP:GL:GQ	0/1:36,16:37:-38.62,-11.15,-91.45:99
+chr1	4592656	.	C	A	10.05	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=32.68;MQ=34.61;MQ0=6;QD=0.18;SB=-22.79	GT:AD:DP:GL:GQ	0/1:46,10:31:-13.58,-9.34,-92.74:42.43
+chr1	4592670	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=26.44;MQ=31.55;MQ0=8;OQ=92.67;QD=1.54;SB=-36.78	GT:AD:DP:GL:GQ	0/1:47,13:38:-24.00,-11.45,-105.70:99
+chr1	4592691	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=17.99;MQ=28.93;MQ0=15;OQ=182.04;QD=2.64;SB=-62.36	GT:AD:DP:GL:GQ	0/1:58,11:38:-32.95,-11.46,-95.16:99
+chr1	4592711	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=17.40;MQ=30.26;MQ0=13;OQ=418.56;QD=8.21;SB=-184.24	GT:AD:DP:GL:GQ	0/1:21,29:22:-51.78,-6.64,-35.47:99
+chr1	4592725	rs7533445	C	G	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=21.58;MQ=31.66;MQ0=7;OQ=325.36;QD=9.30;SB=-162.82	GT:AD:DP:GL:GQ	0/1:18,17:13:-39.75,-3.93,-11.50:75.69
+chr1	4592733	.	C	A	17.31	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=13.87;MQ=30.28;MQ0=8;QD=0.56;SB=5.02	GT:AD:DP:GL:GQ	0/1:27,3:12:-8.63,-3.62,-27.94:50.06
+chr1	4592740	rs7537972	A	C	0.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=10.05;MQ=27.67;MQ0=11;OQ=104.80;QD=3.38;SB=-67.99	GT:AD:DP:GL:GQ	0/1:22,9:8:-16.18,-2.41,-9.32:69.09
+chr1	4592747	rs7537975	A	C	18.33	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=8.21;MQ=28.35;MQ0=11;QD=0.76;SB=-7.00	GT:AD:DP:GL:GQ	0/1:17,7:4:-6.32,-1.21,-6.24:50.29
+chr1	4592767	rs7533530	C	G	42.27	HARD_TO_VALIDATE;LowQual	AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=11.04;MQ=30.06;MQ0=7;QD=3.02;SB=-43.89	GT:AD:DP:GL:GQ	1/1:8,5:2:-7.64,-0.61,-0.00:6.02
+chr1	4592837	.	C	G	13.29	LowQual	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=1;HaplotypeScore=4.96;MQ=12.04;MQ0=3;QD=2.66;SB=-10.00	GT:AD:DP:GL:GQ	0/1:4,1:1:-4.59,-0.30,-0.00:1.76
+chr1	4592901	.	T	C	5.07	PASS	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=42.32;MQ0=2;OQ=126.93;QD=6.35;SB=-77.93	GT:AD:DP:GL:GQ	0/1:9,11:15:-20.50,-4.52,-36.40:99
+chr1	4592906	.	T	C	0.11	PASS	AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=41.84;MQ0=3;OQ=578.85;QD=25.17;SB=-157.83	GT:AD:DP:GL:GQ	1/1:0,23:17:-61.47,-5.12,-0.00:51.15
+chr1	4592960	.	G	C	0.12	PASS	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=41.92;MQ0=6;OQ=217.66;QD=2.79;SB=-81.57	GT:AD:DP:GL:GQ	0/1:56,22:47:-39.23,-14.18,-153.65:99
+chr1	4592971	.	T	C	18.17	PASS	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=3.38;MQ=41.63;MQ0=7;OQ=666.60;QD=8.55;SB=-228.49	GT:AD:DP:GL:GQ	0/1:28,48:45:-83.52,-13.57,-69.37:99
+chr1	4592996	.	A	C	48.48	HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=4.82;MQ=40.87;MQ0=9;QD=0.70;SB=-26.49	GT:AD:DP:GL:GQ	0/1:54,15:47:-22.29,-14.16,-139.10:81.32
+chr1	4593024	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=14.22;MQ=41.13;MQ0=10;OQ=73.34;QD=1.41;SB=-39.79	GT:AD:DP:GL:GQ	0/1:35,17:30:-19.66,-9.04,-83.95:99
+chr1	4593037	.	G	C	11.64	DPFilter;HARD_TO_VALIDATE;LowQual	AC=1;AF=0.50;AN=2;DP=41;Dels=0.02;HRun=0;HaplotypeScore=21.01;MQ=42.10;MQ0=8;QD=0.28;SB=26.12	GT:AD:DP:GL:GQ	0/1:33,7:20:-10.45,-6.03,-72.33:44.16
+chr1	4593066	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=16.64;MQ=38.83;MQ0=9;OQ=95.97;QD=2.23;SB=-64.04	GT:AD:DP:GL:GQ	0/1:31,12:22:-19.51,-6.63,-53.44:99
+chr1	4593072	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=12.35;MQ=36.60;MQ0=11;OQ=58.68;QD=1.25;SB=-50.80	GT:AD:DP:GL:GQ	0/1:40,7:24:-16.40,-7.25,-78.79:91.52
+chr1	4593128	.	G	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=42.60;MQ0=10;OQ=87.22;QD=1.86;SB=11.06	GT:AD:DP:GL:GQ	0/1:39,8:24:-19.25,-7.24,-80.14:99
+chr1	4593184	.	G	C	48.23	LowQual	AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=5.25;MQ=50.03;MQ0=1;QD=1.51;SB=-24.84	GT:AD:DP:GL:GQ	0/1:27,5:22:-14.75,-6.64,-72.91:81.07
+chr1	4593205	.	G	C	35.18	LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.11;MQ=47.39;MQ0=4;QD=0.88;SB=-15.82	GT:AD:DP:GL:GQ	0/1:35,5:30:-15.86,-9.06,-106.35:68.02
+chr1	4593241	rs12752874	A	C	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.83;MQ=43.47;MQ0=5;OQ=55.07;QD=1.28;SB=-27.98	GT:AD:DP:GL:GQ	0/1:30,13:26:-16.62,-7.83,-74.90:87.90
+chr1	4594330	rs34642555	G	A	223.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.30;MQ=59.56;MQ0=0;OQ=741.34;QD=13.99;SB=-378.39	GT:AD:DP:GL:GQ	0/1:29,24:52:-93.10,-15.68,-88.17:99
+chr1	4599106	rs10753383	T	G	347.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.01;MQ0=0;OQ=412.58;QD=12.50;SB=-151.92	GT:AD:DP:GL:GQ	0/1:17,16:32:-54.18,-9.64,-62.40:99
+chr1	4599463	rs7513957	G	C	46.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=2;HaplotypeScore=1.18;MQ=57.56;MQ0=0;OQ=399.60;QD=12.11;SB=-196.33	GT:AD:DP:GL:GQ	0/1:20,13:31:-52.60,-9.35,-73.06:99
+chr1	4600658	rs12122002	G	A	36.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=2.74;MQ=58.47;MQ0=0;OQ=1298.26;QD=21.28;SB=-656.75	GT:AD:DP:GL:GQ	0/1:24,37:59:-150.88,-17.77,-80.26:99
+chr1	4601609	rs55711858	A	G	373.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=1068.23;QD=10.68;SB=-465.77	GT:AD:DP:GL:GQ	0/1:56,44:100:-140.25,-30.14,-225.51:99
+chr1	4601750	rs2411891	G	A	156.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1085.67;QD=16.96;SB=-561.13	GT:AD:DP:GL:GQ	0/1:31,33:63:-130.83,-18.98,-106.71:99
+chr1	4602156	rs61764994	A	G	74.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=60.00;MQ0=0;OQ=509.21;QD=7.60;SB=-244.13	GT:AD:DP:GL:GQ	0/1:40,27:63:-73.19,-18.99,-161.05:99
+chr1	4602810	rs61764995	C	T	382.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=850.22;QD=17.35;SB=-339.44	GT:AD:DP:GL:GQ	0/1:22,27:48:-102.77,-14.46,-79.78:99
+chr1	4602966	rs34993795	C	T	235.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=59.03;MQ0=0;OQ=1118.32;QD=16.69;SB=-465.43	GT:AD:DP:GL:GQ	0/1:34,33:66:-135.00,-19.88,-119.08:99
+chr1	4604462	rs2035452	C	G	271.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=397.56;QD=15.29;SB=-96.30	GT:AD:DP:GL:GQ	0/1:14,12:25:-50.58,-7.54,-52.60:99
+chr1	4606381	rs10915576	T	C	220.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=882.56;QD=16.97;SB=-410.32	GT:AD:DP:GL:GQ	0/1:21,31:51:-106.90,-15.36,-86.72:99
+chr1	4606615	rs12125737	C	T	418.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.71;MQ0=0;OQ=1209.07;QD=18.60;SB=-598.14	GT:AD:DP:GL:GQ	0/1:29,36:62:-142.87,-18.68,-88.99:99
+chr1	4607135	rs12122921	G	A	2.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=10.90;MQ=57.40;MQ0=0;OQ=881.42;QD=13.16;SB=-408.91	GT:AD:DP:GL:GQ	0/1:36,31:56:-108.31,-16.88,-93.30:99
+chr1	4607451	rs28759408	G	T	57.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=5.28;MQ=57.88;MQ0=1;OQ=710.71;QD=10.45;SB=-279.36	GT:AD:DP:GL:GQ	0/1:39,29:61:-92.73,-18.38,-123.60:99
+chr1	4608914	rs7535194	C	A	224.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=57.78;MQ0=0;OQ=1544.72;QD=16.26;SB=-662.45	GT:AD:DP:GL:GQ	0/1:44,51:95:-186.37,-28.61,-160.23:99
+chr1	4609123	.	C	T	10.31	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=56.96;MQ0=2;QD=0.17;SB=19.65	GT:AD:DP:GL:GQ	0/1:53,6:55:-20.84,-16.57,-182.90:42.72
+chr1	4609208	rs7539862	A	C	150.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=258.18;QD=5.87;SB=-149.80	GT:AD:DP:GL:GQ	0/1:32,12:43:-42.05,-12.95,-117.22:99
+chr1	4609234	.	G	A	18.35	LowQual	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.99;MQ=56.87;MQ0=1;QD=0.46;SB=-22.94	GT:AD:DP:GL:GQ	0/1:35,5:36:-15.96,-10.84,-114.15:51.13
+chr1	4609248	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=1;HaplotypeScore=35.67;MQ=56.49;MQ0=1;OQ=135.28;QD=2.42;SB=50.20	GT:AD:DP:GL:GQ	0/1:46,10:51:-32.18,-15.36,-170.39:99
+chr1	4609249	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=97.70;MQ=56.55;MQ0=1;OQ=82.36;QD=1.44;SB=50.16	GT:AD:DP:GL:GQ	0/1:47,10:52:-27.18,-15.66,-163.18:99
+chr1	4609260	rs61764999	C	T	6.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=5.81;MQ=56.56;MQ0=1;OQ=641.66;QD=10.03;SB=-130.56	GT:AD:DP:GL:GQ	0/1:42,22:63:-86.43,-18.98,-148.93:99
+chr1	4609527	rs4654581	C	G	33.46	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=59.43;MQ0=0;QD=0.67;SB=28.36	GT:AD:DP:GL:GQ	0/1:45,5:49:-21.39,-14.76,-192.44:66.29
+chr1	4610341	rs10799250	T	C	191.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.62;MQ0=0;OQ=886.46;QD=10.43;SB=-400.18	GT:AD:DP:GL:GQ	0/1:51,34:83:-116.93,-25.00,-199.77:99
+chr1	4610346	rs10915577	A	G	286.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=59.62;MQ0=0;OQ=927.42;QD=11.04;SB=-372.61	GT:AD:DP:GL:GQ	0/1:50,34:82:-120.73,-24.70,-201.64:99
+chr1	4611161	rs12405862	C	T	55.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=2.70;MQ=59.65;MQ0=0;OQ=705.61;QD=13.31;SB=-372.08	GT:AD:DP:GL:GQ	0/1:30,23:53:-89.81,-15.97,-107.55:99
+chr1	4612905	rs1466520	A	G	508.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.49;MQ0=0;OQ=1092.36;QD=32.13;SB=-567.90	GT:AD:DP:GL:GQ	1/1:0,34:32:-112.83,-9.64,-0.01:96.28
+chr1	4613357	rs4144451	T	C	2.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=4;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=378.96;QD=8.81;SB=-197.21	GT:AD:DP:GL:GQ	0/1:27,16:40:-53.24,-12.06,-95.58:99
+chr1	4616788	rs12127797	G	C	214.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=4.57;MQ=59.39;MQ0=0;OQ=1251.84;QD=16.47;SB=-458.74	GT:AD:DP:GL:GQ	0/1:41,34:72:-150.17,-21.70,-159.82:99
+chr1	4619890	rs7544371	G	A	283.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.45;MQ0=0;OQ=1234.26;QD=22.04;SB=-596.70	GT:AD:DP:GL:GQ	0/1:21,35:56:-143.59,-16.88,-63.94:99
+chr1	4621067	rs6426432	G	C	375.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=60.00;MQ0=0;OQ=975.42;QD=15.73;SB=-398.88	GT:AD:DP:GL:GQ	0/1:35,27:62:-119.51,-18.68,-150.23:99
+chr1	4621285	rs6658403	C	T	186.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.63;MQ0=0;OQ=651.01;QD=10.50;SB=-348.83	GT:AD:DP:GL:GQ	0/1:39,23:60:-86.46,-18.07,-139.05:99
+chr1	4622291	rs2035454	A	G	361.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=59.15;MQ0=0;OQ=932.32;QD=13.13;SB=-403.21	GT:AD:DP:GL:GQ	0/1:39,32:70:-117.60,-21.09,-152.00:99
+chr1	4622303	rs1531830	T	C	306.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=59.12;MQ0=0;OQ=753.21;QD=10.92;SB=-275.11	GT:AD:DP:GL:GQ	0/1:39,30:68:-99.09,-20.49,-155.18:99
+chr1	4623109	rs10799251	G	A	463.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=863.86;QD=15.43;SB=-362.38	GT:AD:DP:GL:GQ	0/1:30,26:56:-106.54,-16.87,-110.57:99
+chr1	4623282	rs10799252	G	C	114.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=53.79;MQ0=0;OQ=899.36;QD=20.92;SB=-445.94	GT:AD:DP:GL:GQ	0/1:17,26:42:-105.88,-12.66,-71.37:99
+chr1	4623298	rs10799253	T	C	313.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=52.77;MQ0=0;OQ=616.14;QD=14.00;SB=-298.33	GT:AD:DP:GL:GQ	0/1:18,26:39:-76.66,-11.76,-55.81:99
+chr1	4623777	rs10915578	A	G	84.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=0.82;MQ=58.86;MQ0=0;OQ=552.36;QD=9.69;SB=-296.32	GT:AD:DP:GL:GQ	0/1:35,22:57:-75.70,-17.18,-138.68:99
+chr1	4623873	rs10915579	T	C	271.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=57.84;MQ0=0;OQ=661.07;QD=10.17;SB=-259.38	GT:AD:DP:GL:GQ	0/1:40,25:64:-88.68,-19.29,-154.96:99
+chr1	4624091	rs12135245	G	C	41.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=1.89;MQ=59.70;MQ0=0;OQ=1186.96;QD=19.14;SB=-476.78	GT:AD:DP:GL:GQ	0/1:28,34:59:-139.77,-17.79,-108.63:99
+chr1	4624130	rs12140542	T	C	140.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=2.13;MQ=59.74;MQ0=0;OQ=656.89;QD=9.12;SB=-348.92	GT:AD:DP:GL:GQ	0/1:43,29:71:-90.37,-21.40,-172.64:99
+chr1	4624492	rs2035455	C	T	468.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=702.27;QD=12.54;SB=-335.31	GT:AD:DP:GL:GQ	0/1:34,22:55:-90.09,-16.58,-106.86:99
+chr1	4624817	rs17421247	C	T	331.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=59.65;MQ0=0;OQ=1014.16;QD=15.37;SB=-402.77	GT:AD:DP:GL:GQ	0/1:35,31:64:-123.99,-19.29,-104.67:99
+chr1	4626224	rs10915580	G	C	281.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=58.07;MQ0=0;OQ=1106.61;QD=18.14;SB=-348.42	GT:AD:DP:GL:GQ	0/1:31,30:61:-132.34,-18.40,-124.48:99
+chr1	4626314	rs12567266	T	C	443.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.48;MQ0=0;OQ=855.53;QD=18.20;SB=-345.35	GT:AD:DP:GL:GQ	0/1:19,28:47:-102.99,-14.16,-75.71:99
+chr1	4626341	rs12752003	A	G	152.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=47.43;MQ0=0;OQ=459.90;QD=12.10;SB=-75.78	GT:AD:DP:GL:GQ	0/1:17,21:35:-59.82,-10.55,-67.90:99
+chr1	4626392	rs12565906	G	A	175.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.36;MQ=51.30;MQ0=0;OQ=647.78;QD=15.42;SB=-283.17	GT:AD:DP:GL:GQ	0/1:21,21:41:-80.41,-12.35,-73.25:99
+chr1	4626545	rs12137938	T	C	1.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=2;HaplotypeScore=6.74;MQ=54.18;MQ0=1;OQ=220.73;QD=6.49;SB=-111.61	GT:AD:DP:GL:GQ	0/1:20,14:29:-34.11,-8.75,-66.24:99
+chr1	4626759	rs10799254	A	G	12.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=7.18;MQ=56.44;MQ0=0;OQ=516.47;QD=13.59;SB=-271.00	GT:AD:DP:GL:GQ	0/1:15,23:33:-64.88,-9.95,-53.03:99
+chr1	4626886	rs12137092	A	G	70.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=50.68;MQ0=3;OQ=425.89;QD=8.19;SB=-166.49	GT:AD:DP:GL:GQ	0/1:30,22:47:-60.04,-14.17,-111.36:99
+chr1	4627103	rs6663166	A	G	61.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=58.88;MQ0=0;OQ=507.83;QD=9.40;SB=-149.43	GT:AD:DP:GL:GQ	0/1:33,21:53:-70.04,-15.97,-130.76:99
+chr1	4627150	rs12138132	T	C	261.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.66;MQ0=0;OQ=429.65;QD=7.81;SB=-213.21	GT:AD:DP:GL:GQ	0/1:37,18:55:-62.82,-16.57,-149.18:99
+chr1	4627390	rs12133670	G	A	454.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.64;MQ0=0;OQ=810.38;QD=15.58;SB=-415.38	GT:AD:DP:GL:GQ	0/1:28,24:51:-99.69,-15.36,-91.80:99
+chr1	4628089	rs12133909	G	T	196.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=59.88;MQ0=0;OQ=673.35;QD=10.52;SB=-318.02	GT:AD:DP:GL:GQ	0/1:40,24:62:-89.30,-18.68,-116.17:99
+chr1	4628258	rs6703379	G	A	0.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=13.50;MQ=55.99;MQ0=1;OQ=611.30;QD=11.32;SB=-213.68	GT:AD:DP:GL:GQ	0/1:33,21:47:-78.59,-14.17,-86.02:99
+chr1	4628265	rs6672122	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.04;HRun=0;HaplotypeScore=25.47;MQ=56.13;MQ0=1;OQ=602.93;QD=10.77;SB=-162.48	GT:AD:DP:GL:GQ	0/1:29,25:52:-78.65,-15.07,-102.50:99
+chr1	4628677	rs6703802	G	A	334.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=937.15;QD=18.02;SB=-393.92	GT:AD:DP:GL:GQ	0/1:24,28:51:-112.37,-15.37,-73.40:99
+chr1	4630143	rs4654582	T	A	2.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=10.18;MQ=58.22;MQ0=0;OQ=526.78;QD=10.54;SB=-97.11	GT:AD:DP:GL:GQ	0/1:25,22:38:-67.41,-11.45,-72.86:99
+chr1	4630312	rs4654583	T	C	361.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1108.52;QD=16.07;SB=-319.34	GT:AD:DP:GL:GQ	0/1:31,38:68:-134.62,-20.48,-127.03:99
+chr1	4630977	rs12141394	A	G	593.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.47;MQ0=0;OQ=900.99;QD=13.45;SB=-440.92	GT:AD:DP:GL:GQ	0/1:31,36:65:-112.97,-19.59,-120.61:99
+chr1	4631016	rs12139858	C	T	367.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=891.25;QD=15.37;SB=-441.97	GT:AD:DP:GL:GQ	0/1:31,27:57:-109.59,-17.18,-94.97:99
+chr1	4631110	rs12141432	A	G	226.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=58.67;MQ0=0;OQ=787.70;QD=12.50;SB=-349.34	GT:AD:DP:GL:GQ	0/1:35,28:62:-100.73,-18.67,-138.62:99
+chr1	4631448	rs4144452	A	G	502.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=648.74;QD=10.64;SB=-332.00	GT:AD:DP:GL:GQ	0/1:33,28:59:-85.94,-17.78,-131.20:99
+chr1	4631992	rs12138000	G	A	396.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=1014.12;QD=15.85;SB=-413.79	GT:AD:DP:GL:GQ	0/1:32,32:63:-123.69,-18.99,-104.09:99
+chr1	4632333	rs1564667	A	G	289.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=656.79;QD=8.64;SB=-323.90	GT:AD:DP:GL:GQ	0/1:44,32:72:-90.67,-21.71,-171.92:99
+chr1	4633099	rs4654585	T	C	336.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.88;MQ=59.60;MQ0=0;OQ=968.60;QD=16.70;SB=-498.14	GT:AD:DP:GL:GQ	0/1:26,32:58:-117.61,-17.47,-104.79:99
+chr1	4633208	rs4654586	T	A	613.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2145.98;QD=37.00;SB=-956.61	GT:AD:DP:GL:GQ	1/1:0,58:58:-218.20,-17.47,-0.01:99
+chr1	4633215	rs4654455	T	C	484.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1991.47;QD=34.94;SB=-790.66	GT:AD:DP:GL:GQ	1/1:0,57:56:-202.75,-16.87,-0.02:99
+chr1	4636316	rs10915584	G	T	377.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.90;MQ=59.34;MQ0=0;OQ=844.77;QD=13.41;SB=-404.78	GT:AD:DP:GL:GQ	0/1:32,31:58:-105.23,-17.47,-102.72:99
+chr1	4637265	.	T	C	225.79	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=776.05;QD=14.64;SB=-255.94	GT:AD:DP:GL:GQ	0/1:26,27:53:-96.86,-15.97,-103.32:99
+chr1	4638345	.	G	A	67.79	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.29;MQ0=0;OQ=991.16;QD=18.70;SB=-412.80	GT:AD:DP:GL:GQ	0/1:24,29:51:-117.77,-15.37,-70.20:99
+chr1	4642883	rs2859392	C	G	348.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.26;MQ=59.71;MQ0=0;OQ=833.93;QD=12.83;SB=-304.28	GT:AD:DP:GL:GQ	0/1:37,28:61:-105.07,-18.39,-160.99:99
+chr1	4643564	rs763238	C	T	66.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.77;MQ0=0;OQ=1042.05;QD=19.66;SB=-208.90	GT:AD:DP:GL:GQ	0/1:21,32:50:-122.56,-15.07,-63.38:99
+chr1	4644154	rs4993529	C	T	334.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=60.00;MQ0=0;OQ=1314.27;QD=19.62;SB=-670.69	GT:AD:DP:GL:GQ	0/1:27,40:65:-154.30,-19.59,-85.13:99
+chr1	4646074	rs242043	T	C	1.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=13.28;MQ=59.47;MQ0=0;OQ=1026.27;QD=14.45;SB=-395.20	GT:AD:DP:GL:GQ	0/1:34,37:70:-127.00,-21.09,-134.39:99
+chr1	4646297	rs61765026	G	A	183.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=1519.28;QD=17.87;SB=-749.72	GT:AD:DP:GL:GQ	0/1:39,46:84:-180.53,-25.32,-123.19:99
+chr1	4646496	rs10915587	C	T	288.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.87;MQ=60.00;MQ0=0;OQ=1042.81;QD=16.04;SB=-490.54	GT:AD:DP:GL:GQ	0/1:32,33:64:-126.86,-19.30,-98.43:99
+chr1	4646880	rs17344953	G	A	102.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=5.33;MQ=59.62;MQ0=0;OQ=1025.96;QD=17.10;SB=-396.44	GT:AD:DP:GL:GQ	0/1:26,33:55:-122.45,-16.57,-85.52:99
+chr1	4647597	rs12747700	G	A	323.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=59.29;MQ0=0;OQ=999.88;QD=16.95;SB=-503.14	GT:AD:DP:GL:GQ	0/1:28,31:57:-120.45,-17.18,-86.54:99
+chr1	4648034	rs6684528	G	T	259.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.52;MQ0=0;OQ=808.60;QD=16.85;SB=-296.69	GT:AD:DP:GL:GQ	0/1:20,28:48:-98.60,-14.46,-70.03:99
+chr1	4648165	rs1076944	G	T	243.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=58.38;MQ0=0;OQ=602.15;QD=11.58;SB=-146.14	GT:AD:DP:GL:GQ	0/1:27,25:49:-78.26,-14.76,-94.92:99
+chr1	4648936	rs4092257	G	A	283.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=57.56;MQ0=0;OQ=450.85;QD=13.66;SB=-204.90	GT:AD:DP:GL:GQ	0/1:17,16:32:-58.02,-9.65,-54.32:99
+chr1	4649873	rs187148	C	G	93.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=3.10;MQ=59.76;MQ0=0;OQ=296.24;QD=8.98;SB=-132.74	GT:AD:DP:GL:GQ	0/1:22,11:31:-42.26,-9.35,-85.65:99
+chr1	4651624	.	C	A	146.63	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=797.72;QD=17.34;SB=-280.69	GT:AD:DP:GL:GQ	0/1:17,29:42:-95.71,-12.66,-50.88:99
+chr1	4652138	rs171380	A	G	10.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=3.45;MQ=58.45;MQ0=0;OQ=324.85;QD=10.83;SB=-162.34	GT:AD:DP:GL:GQ	0/1:14,16:28:-44.21,-8.45,-55.22:99
+chr1	4653917	rs7525374	A	G	301.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=624.45;QD=13.58;SB=-244.30	GT:AD:DP:GL:GQ	0/1:21,25:46:-79.59,-13.86,-85.75:99
+chr1	4653963	rs7528195	T	C	276.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.00;MQ0=0;OQ=479.46;QD=11.42;SB=-265.36	GT:AD:DP:GL:GQ	0/1:21,21:39:-62.99,-11.76,-78.32:99
+chr1	4654404	rs1076945	C	T	142.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=4.82;MQ=58.13;MQ0=0;OQ=818.85;QD=13.65;SB=-233.53	GT:AD:DP:GL:GQ	0/1:33,27:59:-102.95,-17.78,-107.70:99
+chr1	4655581	.	C	T	85.40	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=59.44;MQ0=0;OQ=1224.61;QD=16.55;SB=-495.16	GT:AD:DP:GL:GQ	0/1:36,38:73:-147.75,-22.00,-119.12:99
+chr1	4656328	rs10915588	T	C	75.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=629.83;QD=11.88;SB=-281.45	GT:AD:DP:GL:GQ	0/1:30,23:52:-81.93,-15.66,-115.22:99
+chr1	4656461	rs3886389	A	G	234.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.53;MQ0=0;OQ=467.67;QD=9.54;SB=-232.27	GT:AD:DP:GL:GQ	0/1:28,21:49:-64.82,-14.77,-113.76:99
+chr1	4657736	rs6669203	T	C	161.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=58.29;MQ0=0;OQ=397.97;QD=9.71;SB=-145.57	GT:AD:DP:GL:GQ	0/1:23,18:37:-54.24,-11.16,-78.29:99
+chr1	4658187	rs12121882	C	T	363.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=849.30;QD=18.07;SB=-359.52	GT:AD:DP:GL:GQ	0/1:21,26:46:-102.08,-13.87,-62.23:99
+chr1	4659178	rs242054	A	G	123.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=57.49;MQ0=0;OQ=1370.79;QD=30.46;SB=-653.90	GT:AD:DP:GL:GQ	1/1:0,45:44:-140.71,-13.27,-0.04:99
+chr1	4660176	rs61765031	A	G	230.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=59.01;MQ0=0;OQ=811.95;QD=12.30;SB=-390.16	GT:AD:DP:GL:GQ	0/1:34,31:61:-102.85,-18.37,-129.51:99
+chr1	4663049	rs6686733	T	C	216.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=4.72;MQ=59.04;MQ0=0;OQ=1082.32;QD=15.92;SB=-503.34	GT:AD:DP:GL:GQ	0/1:29,39:64:-130.80,-19.28,-107.21:99
+chr1	4663261	rs6681520	C	T	227.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1006.77;QD=22.88;SB=-416.49	GT:AD:DP:GL:GQ	0/1:15,29:43:-116.92,-12.96,-47.72:99
+chr1	4665250	rs12131565	A	G	49.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=2.95;MQ=47.43;MQ0=2;OQ=1030.19;QD=13.38;SB=-443.10	GT:AD:DP:GL:GQ	0/1:41,36:75:-128.89,-22.59,-163.25:99
+chr1	4665448	rs10915590	T	C	343.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.85;MQ0=0;OQ=469.57;QD=9.58;SB=-224.22	GT:AD:DP:GL:GQ	0/1:29,20:48:-64.71,-14.47,-110.90:99
+chr1	4665815	rs10915592	T	C	6.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=2.44;MQ=60.00;MQ0=0;OQ=940.71;QD=17.75;SB=-259.53	GT:AD:DP:GL:GQ	0/1:21,32:50:-112.42,-15.06,-71.48:99
+chr1	4667613	rs2101196	A	G	254.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=2.34;MQ=56.97;MQ0=0;OQ=1013.81;QD=15.13;SB=-354.95	GT:AD:DP:GL:GQ	0/1:32,35:65:-124.25,-19.58,-123.74:99
+chr1	4667836	.	T	C	82.17	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=758.61;QD=12.24;SB=-402.64	GT:AD:DP:GL:GQ	0/1:31,31:61:-97.53,-18.39,-127.98:99
+chr1	4667882	rs2086718	C	T	43.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.02;HRun=0;HaplotypeScore=5.21;MQ=57.79;MQ0=0;OQ=518.41;QD=9.43;SB=-229.72	GT:AD:DP:GL:GQ	0/1:31,22:40:-66.89,-11.76,-68.62:99
+chr1	4667894	.	G	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=12;HaplotypeScore=6.56;MQ=55.45;MQ0=0;OQ=63.00;QD=0.98;SB=-8.73	GT:AD:DP:GL:GQ	0/1:54,10:56:-26.47,-16.89,-148.75:95.84
+chr1	4668291	rs6670802	G	A	143.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=56.73;MQ0=0;OQ=372.96;QD=8.29;SB=-147.60	GT:AD:DP:GL:GQ	0/1:28,16:38:-52.04,-11.46,-80.12:99
+chr1	4668400	rs6688423	T	C	371.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=710.41;QD=13.16;SB=-359.33	GT:AD:DP:GL:GQ	0/1:26,28:52:-89.99,-15.67,-104.81:99
+chr1	4668882	.	T	C	49.86	LowQual	AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=3;HaplotypeScore=9.17;MQ=57.66;MQ0=0;QD=2.49;SB=-0.98	GT:AD:DP:GL:GQ	0/1:11,9:11:-11.59,-3.32,-24.54:82.70
+chr1	4669925	rs12760917	T	C	439.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.29;MQ0=0;OQ=917.38;QD=14.11;SB=-279.27	GT:AD:DP:GL:GQ	0/1:29,36:64:-114.31,-19.29,-115.57:99
+chr1	4670306	rs4654594	T	C	240.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=58.06;MQ0=0;OQ=1070.08;QD=17.54;SB=-482.88	GT:AD:DP:GL:GQ	0/1:21,40:58:-127.77,-17.48,-76.71:99
+chr1	4670764	rs1483197	T	C	225.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=4.25;MQ=58.29;MQ0=0;OQ=709.74;QD=13.65;SB=-285.29	GT:AD:DP:GL:GQ	0/1:22,29:49:-89.03,-14.77,-80.10:99
+chr1	4670879	.	G	T	21.82	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=60.00;MQ0=0;OQ=722.25;QD=15.70;SB=-186.19	GT:AD:DP:GL:GQ	0/1:22,24:42:-88.16,-12.65,-60.03:99
+chr1	4671525	rs989309	G	C	65.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=2.50;MQ=60.00;MQ0=0;OQ=327.78;QD=9.93;SB=-148.55	GT:AD:DP:GL:GQ	0/1:21,12:30:-45.12,-9.05,-74.66:99
+chr1	4671555	rs989310	G	C	120.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=60.00;MQ0=0;OQ=521.90;QD=14.11;SB=-193.59	GT:AD:DP:GL:GQ	0/1:21,16:35:-66.02,-10.55,-86.58:99
+chr1	4671913	rs1061968	T	C	32.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.55;MQ0=0;OQ=101.72;QD=6.36;SB=-10.00	GT:AD:DP:GL:GQ	0/1:10,6:16:-18.28,-4.82,-40.28:99
+chr1	4672577	rs242056	G	A	47.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.45;MQ0=0;OQ=1114.83;QD=37.16;SB=-369.99	GT:AD:DP:GL:GQ	1/1:0,30:28:-115.07,-8.43,-0.01:84.28
+chr1	4673126	rs2071999	A	C	360.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=60.00;MQ0=0;OQ=766.03;QD=12.77;SB=-408.20	GT:AD:DP:GL:GQ	0/1:27,33:59:-97.67,-17.78,-97.47:99
+chr1	4673232	rs56401224	C	G	273.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.62;MQ=59.63;MQ0=0;OQ=825.52;QD=16.51;SB=-362.08	GT:AD:DP:GL:GQ	0/1:25,25:46:-99.70,-13.86,-96.30:99
+chr1	4673712	rs242057	G	A	40.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=3;HaplotypeScore=2.46;MQ=59.65;MQ0=0;OQ=947.24;QD=14.35;SB=-485.02	GT:AD:DP:GL:GQ	0/1:36,30:63:-116.99,-18.98,-120.15:99
+chr1	4674298	rs242058	T	C	345.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=778.59;QD=15.27;SB=-272.44	GT:AD:DP:GL:GQ	0/1:23,28:50:-96.21,-15.07,-89.60:99
+chr1	4676145	rs4654595	A	C	407.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2257.07;QD=35.83;SB=-1055.12	GT:AD:DP:GL:GQ	1/1:0,63:63:-229.31,-18.97,-0.02:99
+chr1	4676402	rs4654596	G	A	207.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.44;MQ0=0;OQ=2768.52;QD=37.41;SB=-1042.40	GT:AD:DP:GL:GQ	1/1:0,74:71:-280.46,-21.39,-0.02:99
+chr1	4678092	rs3766959	C	T	358.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.73;MQ0=0;OQ=1524.54;QD=23.10;SB=-743.34	GT:AD:DP:GL:GQ	0/1:22,44:65:-175.33,-19.59,-68.56:99
+chr1	4679148	rs242040	A	G	228.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=60.00;MQ0=0;OQ=836.32;QD=13.07;SB=-312.23	GT:AD:DP:GL:GQ	0/1:34,30:63:-105.89,-18.98,-137.28:99
+chr1	4679557	rs242041	G	C	23.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=3;HaplotypeScore=1.52;MQ=58.81;MQ0=0;OQ=500.09;QD=9.81;SB=-250.11	GT:AD:DP:GL:GQ	0/1:32,19:47:-67.48,-14.18,-123.03:99
+chr1	4681011	rs3820251	C	T	321.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=59.05;MQ0=0;OQ=1264.98;QD=15.06;SB=-599.08	GT:AD:DP:GL:GQ	0/1:45,39:83:-154.80,-25.02,-140.75:99
+chr1	4683002	rs12566272	G	A	75.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=6.06;MQ=59.60;MQ0=0;OQ=811.79;QD=14.00;SB=-379.10	GT:AD:DP:GL:GQ	0/1:30,28:55:-101.04,-16.58,-98.62:99
+chr1	4683215	rs12085854	C	T	250.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.71;MQ0=0;OQ=595.12;QD=16.53;SB=-237.77	GT:AD:DP:GL:GQ	0/1:12,24:28:-71.24,-8.44,-31.48:99
+chr1	4684416	rs3820252	C	T	67.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.40;MQ=59.16;MQ0=0;OQ=1099.71;QD=21.99;SB=-407.20	GT:AD:DP:GL:GQ	0/1:18,32:50:-128.32,-15.07,-57.31:99
+chr1	4684710	rs4554693	C	T	27.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.03;MQ=59.86;MQ0=0;OQ=1309.90;QD=22.98;SB=-464.01	GT:AD:DP:GL:GQ	0/1:20,37:57:-151.45,-17.18,-62.35:99
+chr1	4685955	rs11586740	G	T	36.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=7.65;MQ=60.00;MQ0=0;OQ=1269.15;QD=17.39;SB=-560.71	GT:AD:DP:GL:GQ	0/1:30,43:69:-150.98,-20.79,-94.07:99
+chr1	4686129	.	A	G	0.31	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.20;MQ0=0;OQ=188.73;QD=3.63;SB=-3.68	GT:AD:DP:GL:GQ	0/1:41,11:52:-37.84,-15.68,-155.85:99
+chr1	4686130	.	G	C	4.40	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.20;MQ0=0;OQ=258.95;QD=4.98;SB=-16.68	GT:AD:DP:GL:GQ	0/1:42,10:52:-44.85,-15.67,-182.52:99
+chr1	4686979	rs242044	A	G	24.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=0.79;MQ=59.56;MQ0=0;OQ=1479.37;QD=27.91;SB=-538.14	GT:AD:DP:GL:GQ	1/1:0,52:45:-151.55,-13.56,-0.03:99
+chr1	4687176	rs242045	T	C	255.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1371.92;QD=34.30;SB=-697.63	GT:AD:DP:GL:GQ	1/1:0,40:40:-140.79,-12.05,-0.02:99
+chr1	4687868	rs242047	A	C	103.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=2.65;MQ=59.62;MQ0=0;OQ=770.92;QD=12.85;SB=-248.85	GT:AD:DP:GL:GQ	0/1:32,28:59:-98.15,-17.77,-114.07:99
+chr1	4688746	rs242048	A	G	112.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.71;MQ=59.36;MQ0=0;OQ=768.10;QD=21.34;SB=-331.78	GT:AD:DP:GL:GQ	1/1:0,36:26:-80.42,-7.84,-0.03:78.16
+chr1	4688889	rs242049	T	G	239.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=60.00;MQ0=0;OQ=1481.34;QD=32.92;SB=-635.03	GT:AD:DP:GL:GQ	1/1:0,45:44:-151.74,-13.26,-0.02:99
+chr1	4695274	rs446529	T	C	363.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=55.31;MQ0=0;OQ=516.35;QD=9.93;SB=-227.25	GT:AD:DP:GL:GQ	0/1:29,23:50:-69.99,-15.07,-114.97:99
+chr1	4695606	rs648712	C	T	1.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=10.04;MQ=47.15;MQ0=0;OQ=816.40;QD=17.01;SB=-434.45	GT:AD:DP:GL:GQ	0/1:23,25:46:-98.78,-13.86,-79.74:99
+chr1	4695607	.	T	G	0.18	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=11.01;MQ=47.15;MQ0=0;OQ=688.64;QD=14.35;SB=-357.86	GT:AD:DP:GL:GQ	0/1:23,25:47:-86.31,-14.16,-83.32:99
+chr1	4695638	rs432330	T	A	460.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.80;MQ0=0;OQ=772.11;QD=15.14;SB=-337.40	GT:AD:DP:GL:GQ	0/1:24,27:50:-95.56,-15.06,-90.18:99
+chr1	4695654	rs449261	T	C	245.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=2.57;MQ=53.57;MQ0=0;OQ=702.97;QD=13.52;SB=-345.62	GT:AD:DP:GL:GQ	0/1:26,26:49:-88.35,-14.77,-92.65:99
+chr1	4695676	rs435239	G	C	185.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=2.08;MQ=57.17;MQ0=0;OQ=826.31;QD=16.53;SB=-414.36	GT:AD:DP:GL:GQ	0/1:24,26:47:-100.09,-14.18,-90.75:99
+chr1	4695734	rs416953	T	C	152.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=59.13;MQ0=0;OQ=882.63;QD=16.65;SB=-283.45	GT:AD:DP:GL:GQ	0/1:22,31:50:-106.61,-15.06,-78.94:99
+chr1	4696083	rs383650	C	G	345.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=59.10;MQ0=0;OQ=1382.15;QD=17.95;SB=-715.96	GT:AD:DP:GL:GQ	0/1:38,39:75:-164.11,-22.61,-152.21:99
+chr1	4696156	rs436132	G	C	8.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1112.40;QD=19.86;SB=-564.68	GT:AD:DP:GL:GQ	0/1:25,31:56:-131.40,-16.88,-111.00:99
+chr1	4696361	.	A	C	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=2;HaplotypeScore=10.18;MQ=60.26;MQ0=0;OQ=143.73;QD=2.08;SB=104.31	GT:AD:DP:GL:GQ	0/1:45,24:52:-33.32,-15.67,-137.68:99
+chr1	4696418	rs392630	A	G	270.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=59.71;MQ0=0;OQ=1265.58;QD=13.76;SB=-582.79	GT:AD:DP:GL:GQ	0/1:45,47:87:-156.05,-26.21,-176.07:99
+chr1	4697358	rs544738	C	A	298.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=59.01;MQ0=0;OQ=538.34;QD=14.17;SB=-233.94	GT:AD:DP:GL:GQ	0/1:19,19:37:-68.26,-11.15,-60.83:99
+chr1	4697618	rs445060	G	A	155.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=2.45;MQ=59.60;MQ0=0;OQ=740.87;QD=12.77;SB=-313.26	GT:AD:DP:GL:GQ	0/1:32,26:54:-93.63,-16.26,-111.70:99
+chr1	4698713	rs578528	A	G	87.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=59.36;MQ0=0;OQ=385.70;QD=10.71;SB=-193.63	GT:AD:DP:GL:GQ	0/1:21,15:36:-52.70,-10.85,-81.97:99
+chr1	4699130	rs449181	G	A	397.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.84;MQ=59.67;MQ0=0;OQ=927.44;QD=16.56;SB=-380.14	GT:AD:DP:GL:GQ	0/1:27,29:54:-112.30,-16.28,-85.10:99
+chr1	4700289	rs13376290	T	G	0.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=4;HaplotypeScore=0.10;MQ=48.01;MQ0=0;OQ=193.53;QD=7.44;SB=-0.43	GT:AD:DP:GL:GQ	0/1:15,11:24:-29.87,-7.23,-54.19:99
+chr1	4700426	.	C	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=2;HaplotypeScore=11.52;MQ=48.42;MQ0=0;OQ=136.63;QD=5.25;SB=-6.99	GT:AD:DP:GL:GQ	0/1:7,19:10:-19.97,-3.02,-19.59:99
+chr1	4700705	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=20;HaplotypeScore=32.92;MQ=48.95;MQ0=0;OQ=199.23;QD=3.83;SB=71.25	GT:AD:DP:GL:GQ	0/1:35,17:41:-35.56,-12.35,-113.25:99
+chr1	4700881	rs529853	G	C	174.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.66;MQ=53.91;MQ0=0;OQ=810.63;QD=16.54;SB=-402.70	GT:AD:DP:GL:GQ	0/1:22,27:47:-98.53,-14.18,-93.65:99
+chr1	4701141	rs381339	T	C	9.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=2.72;MQ=59.22;MQ0=0;OQ=750.05;QD=11.54;SB=-112.61	GT:AD:DP:GL:GQ	0/1:29,33:53:-94.27,-15.98,-96.69:99
+chr1	4701497	rs382623	T	C	282.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.48;MQ0=0;OQ=1093.69;QD=13.50;SB=-513.56	GT:AD:DP:GL:GQ	0/1:38,43:80:-136.77,-24.11,-153.00:99
+chr1	4701516	rs382646	T	C	490.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1091.01;QD=14.36;SB=-413.27	GT:AD:DP:GL:GQ	0/1:38,38:75:-134.98,-22.59,-157.29:99
+chr1	4701783	rs392620	C	T	260.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.19;MQ=59.38;MQ0=0;OQ=1111.05;QD=15.01;SB=-420.88	GT:AD:DP:GL:GQ	0/1:41,33:73:-136.38,-21.99,-143.11:99
+chr1	4702373	rs448741	C	T	315.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.33;MQ0=0;OQ=1161.48;QD=16.83;SB=-516.10	GT:AD:DP:GL:GQ	0/1:33,36:68:-139.92,-20.49,-116.50:99
+chr1	4702588	rs431966	C	G	301.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.74;MQ0=0;OQ=1167.37;QD=16.21;SB=-392.89	GT:AD:DP:GL:GQ	0/1:35,37:71:-141.44,-21.42,-151.57:99
+chr1	4703125	rs367673	G	C	285.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.24;MQ0=0;OQ=1282.03;QD=21.02;SB=-602.59	GT:AD:DP:GL:GQ	0/1:26,35:61:-149.87,-18.38,-114.22:99
+chr1	4703446	rs540299	A	G	321.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=59.10;MQ0=0;OQ=1141.42;QD=14.82;SB=-449.59	GT:AD:DP:GL:GQ	0/1:36,41:75:-140.02,-22.60,-142.02:99
+chr1	4703496	rs648346	G	A	131.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=58.29;MQ0=0;OQ=1435.37;QD=17.50;SB=-321.28	GT:AD:DP:GL:GQ	0/1:40,42:79:-170.63,-23.81,-120.02:99
+chr1	4703694	rs393976	G	A	298.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.30;MQ0=0;OQ=1022.50;QD=17.04;SB=-396.14	GT:AD:DP:GL:GQ	0/1:30,30:58:-123.01,-17.47,-100.86:99
+chr1	4704145	rs375781	T	C	253.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=57.53;MQ0=0;OQ=380.91;QD=10.02;SB=-211.48	GT:AD:DP:GL:GQ	0/1:19,19:35:-51.92,-10.55,-74.06:99
+chr1	4704212	rs406065	A	T	598.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.74;MQ0=0;OQ=1026.86;QD=14.88;SB=-405.55	GT:AD:DP:GL:GQ	0/1:35,34:69:-126.75,-20.78,-135.77:99
+chr1	4704412	rs396199	G	A	86.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.14;MQ=59.62;MQ0=0;OQ=915.71;QD=18.69;SB=-324.82	GT:AD:DP:GL:GQ	0/1:21,28:47:-109.02,-14.16,-69.65:99
+chr1	4704606	rs413178	A	G	154.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=56.43;MQ0=0;OQ=958.14;QD=15.45;SB=-233.27	GT:AD:DP:GL:GQ	0/1:25,37:59:-116.89,-17.79,-90.61:99
+chr1	4704966	rs414176	A	C	426.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.63;MQ0=0;OQ=751.31;QD=11.93;SB=-297.47	GT:AD:DP:GL:GQ	0/1:31,32:62:-97.10,-18.68,-109.53:99
+chr1	4705294	rs371605	A	G	188.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.08;MQ=59.55;MQ0=0;OQ=418.07;QD=8.20;SB=-210.35	GT:AD:DP:GL:GQ	0/1:28,23:46:-58.96,-13.87,-104.25:99
+chr1	4705534	rs409048	T	C	345.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=59.35;MQ0=0;OQ=802.66;QD=12.54;SB=-363.20	GT:AD:DP:GL:GQ	0/1:35,29:64:-102.83,-19.28,-139.39:99
+chr1	4706241	rs368808	A	G	17.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=2;HaplotypeScore=4.09;MQ=59.49;MQ0=0;OQ=756.36;QD=9.22;SB=-230.86	GT:AD:DP:GL:GQ	0/1:48,34:80:-103.04,-24.12,-189.26:99
+chr1	4707706	rs368940	A	G	105.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=599.08;QD=17.12;SB=-212.56	GT:AD:DP:GL:GQ	0/1:14,21:35:-73.73,-10.54,-57.28:99
+chr1	4707911	.	C	A	31.90	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=13;HaplotypeScore=26.77;MQ=58.47;MQ0=0;QD=0.52;SB=52.91	GT:AD:DP:GL:GQ	0/1:52,9:48:-20.93,-14.46,-146.08:64.73
+chr1	4708314	rs2802721	G	A	450.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=56.44;MQ0=0;OQ=981.54;QD=15.34;SB=-489.03	GT:AD:DP:GL:GQ	0/1:28,36:59:-119.22,-17.78,-99.55:99
+chr1	4708405	rs394808	C	A	233.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.96;MQ=56.69;MQ0=0;OQ=782.76;QD=14.77;SB=-324.34	GT:AD:DP:GL:GQ	0/1:26,27:51:-96.92,-15.37,-78.87:99
+chr1	4708536	rs395145	C	T	383.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1269.10;QD=19.83;SB=-521.54	GT:AD:DP:GL:GQ	0/1:25,39:63:-149.18,-18.98,-84.36:99
+chr1	4708674	rs4654602	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=69.80;MQ=46.48;MQ0=0;OQ=293.59;QD=4.19;SB=-93.14	GT:AD:DP:GL:GQ	0/1:56,14:66:-52.53,-19.89,-198.60:99
+chr1	4708678	rs406913	A	G	32.76	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=20.07;MQ=45.13;MQ0=0;QD=0.48;SB=9.87	GT:AD:DP:GL:GQ	0/1:59,9:58:-24.04,-17.48,-194.48:65.59
+chr1	4708830	rs433427	A	G	13.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=6.55;MQ=59.08;MQ0=0;OQ=748.71;QD=10.55;SB=-350.04	GT:AD:DP:GL:GQ	0/1:40,31:70:-99.25,-21.09,-163.31:99
+chr1	4708980	rs2802720	C	T	373.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=55.41;MQ0=0;OQ=1008.97;QD=15.29;SB=-359.05	GT:AD:DP:GL:GQ	0/1:35,31:66:-124.06,-19.88,-124.56:99
+chr1	4710412	rs364642	C	T	180.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=3.52;MQ=58.91;MQ0=0;OQ=814.43;QD=13.57;SB=-402.86	GT:AD:DP:GL:GQ	0/1:32,28:58:-102.20,-17.48,-113.74:99
+chr1	4712675	rs381240	A	G	265.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=57.93;MQ0=0;OQ=805.26;QD=10.19;SB=-382.86	GT:AD:DP:GL:GQ	0/1:44,35:76:-106.72,-22.91,-172.59:99
+chr1	4712931	rs448221	T	C	105.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=56.15;MQ0=0;OQ=384.09;QD=10.38;SB=-115.63	GT:AD:DP:GL:GQ	0/1:18,19:34:-51.95,-10.25,-67.62:99
+chr1	4712934	rs431884	C	T	132.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=56.04;MQ0=0;OQ=441.73;QD=12.27;SB=-157.22	GT:AD:DP:GL:GQ	0/1:18,18:33:-57.41,-9.95,-59.19:99
+chr1	4712975	rs380239	A	G	454.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=55.78;MQ0=0;OQ=728.95;QD=12.57;SB=-369.58	GT:AD:DP:GL:GQ	0/1:31,26:56:-93.05,-16.87,-121.44:99
+chr1	4713977	rs434474	A	T	435.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.38;MQ0=0;OQ=788.95;QD=11.78;SB=-384.44	GT:AD:DP:GL:GQ	0/1:40,27:64:-101.46,-19.28,-136.23:99
+chr1	4714260	rs428001	G	A	188.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=394.17;QD=7.58;SB=-208.83	GT:AD:DP:GL:GQ	0/1:37,15:47:-56.86,-14.16,-117.42:99
+chr1	4714368	rs413383	G	C	359.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=902.57;QD=15.56;SB=-389.66	GT:AD:DP:GL:GQ	0/1:30,28:56:-110.43,-16.89,-123.48:99
+chr1	4714807	rs401110	C	T	341.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=642.13;QD=13.96;SB=-230.50	GT:AD:DP:GL:GQ	0/1:24,21:44:-80.76,-13.26,-78.68:99
+chr1	4715337	rs434504	G	A	250	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.39;MQ0=0;OQ=582.19;QD=15.32;SB=-195.19	GT:AD:DP:GL:GQ	0/1:19,19:36:-72.35,-10.85,-57.76:99
+chr1	4718265	rs423796	G	A	245.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=58.44;MQ0=0;OQ=1032.37;QD=16.92;SB=-496.08	GT:AD:DP:GL:GQ	0/1:28,33:59:-124.29,-17.77,-98.91:99
+chr1	4718977	rs41511844	A	C	15.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=3;HaplotypeScore=0.79;MQ=59.53;MQ0=0;OQ=807.51;QD=16.48;SB=-276.90	GT:AD:DP:GL:GQ	0/1:21,28:49:-98.80,-14.76,-77.17:99
+chr1	4719527	rs523141	G	A	331.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.63;MQ0=1;OQ=362.25;QD=9.29;SB=-60.24	GT:AD:DP:GL:GQ	0/1:25,14:36:-50.35,-10.84,-83.10:99
+chr1	4719663	rs368420	T	C	450.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=60.00;MQ0=0;OQ=1132.30;QD=16.90;SB=-528.33	GT:AD:DP:GL:GQ	0/1:29,38:66:-136.39,-19.88,-119.33:99
+chr1	4720200	rs34125417	T	A	155.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.33;MQ=59.59;MQ0=0;OQ=796.97;QD=13.51;SB=-224.76	GT:AD:DP:GL:GQ	0/1:29,29:54:-99.25,-16.27,-103.01:99
+chr1	4720659	rs397559	C	T	380.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.71;MQ0=0;OQ=1207.74;QD=18.87;SB=-534.79	GT:AD:DP:GL:GQ	0/1:27,37:63:-143.05,-18.99,-86.17:99
+chr1	4721157	rs443850	C	T	216.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=4.76;MQ=59.51;MQ0=0;OQ=1138.02;QD=14.97;SB=-525.69	GT:AD:DP:GL:GQ	0/1:42,34:73:-139.07,-21.99,-142.33:99
+chr1	4721448	rs9426481	G	T	366.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=988.26;QD=14.53;SB=-519.87	GT:AD:DP:GL:GQ	0/1:35,33:67:-122.29,-20.18,-120.50:99
+chr1	4722600	rs742245	A	C	591.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1064.86;QD=15.00;SB=-554.90	GT:AD:DP:GL:GQ	0/1:34,37:68:-130.25,-20.48,-117.18:99
+chr1	4722971	rs760815	C	A	224.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=59.29;MQ0=0;OQ=950.16;QD=16.10;SB=-349.23	GT:AD:DP:GL:GQ	0/1:26,33:58:-115.77,-17.47,-92.37:99
+chr1	4723061	rs2743978	G	A	259.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=60.00;MQ0=0;OQ=829.12;QD=15.07;SB=-390.87	GT:AD:DP:GL:GQ	0/1:28,27:53:-102.17,-15.97,-92.75:99
+chr1	4723683	rs411832	G	C	0.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.02;HRun=0;HaplotypeScore=12.73;MQ=59.54;MQ0=0;OQ=809.82;QD=16.20;SB=-394.90	GT:AD:DP:GL:GQ	0/1:25,24:48:-98.44,-14.17,-99.99:99
+chr1	4723923	rs425005	C	A	167.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=59.70;MQ0=0;OQ=997.52;QD=16.09;SB=-361.25	GT:AD:DP:GL:GQ	0/1:28,34:61:-121.41,-18.38,-98.67:99
+chr1	4724602	rs424723	C	T	274.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.39;MQ0=0;OQ=1215.08;QD=19.92;SB=-584.11	GT:AD:DP:GL:GQ	0/1:24,36:58:-142.27,-17.47,-75.15:99
+chr1	4725012	rs2743979	G	A	336.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.68;MQ0=0;OQ=1008.07;QD=17.38;SB=-481.48	GT:AD:DP:GL:GQ	0/1:28,30:57:-121.27,-17.17,-91.06:99
+chr1	4725752	rs57646199	C	T	319.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1002.06;QD=17.89;SB=-467.46	GT:AD:DP:GL:GQ	0/1:26,30:56:-120.36,-16.87,-93.54:99
+chr1	4725910	rs2802717	C	T	220.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=59.68;MQ0=0;OQ=1230.52;QD=17.09;SB=-300.80	GT:AD:DP:GL:GQ	0/1:35,36:70:-147.42,-21.09,-124.52:99
+chr1	4725964	rs2802716	C	A	41.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=4;HaplotypeScore=0.93;MQ=59.48;MQ0=0;OQ=1484.28;QD=18.55;SB=-734.49	GT:AD:DP:GL:GQ	0/1:32,48:80:-175.81,-24.10,-113.80:99
+chr1	4726365	rs9426502	G	A	127.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.67;MQ0=0;OQ=1140.71;QD=16.53;SB=-410.70	GT:AD:DP:GL:GQ	0/1:35,34:69:-138.14,-20.78,-128.81:99
+chr1	4726520	rs2743980	G	A	355.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.45;MQ=59.68;MQ0=0;OQ=913.23;QD=12.68;SB=-432.39	GT:AD:DP:GL:GQ	0/1:43,29:72:-116.30,-21.69,-156.11:99
+chr1	4726900	rs7548728	G	A	477.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=780.16;QD=13.69;SB=-340.47	GT:AD:DP:GL:GQ	0/1:32,25:55:-97.88,-16.58,-97.83:99
+chr1	4727923	rs426095	G	A	378.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.64;MQ0=0;OQ=878.95;QD=13.73;SB=-378.83	GT:AD:DP:GL:GQ	0/1:36,28:61:-109.56,-18.38,-120.39:99
+chr1	4728243	rs396629	C	T	353.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.62;MQ0=0;OQ=1145.27;QD=18.77;SB=-564.43	GT:AD:DP:GL:GQ	0/1:27,34:61:-136.20,-18.39,-85.13:99
+chr1	4728440	.	G	A	47.68	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=58.84;MQ0=0;OQ=1100.89;QD=19.66;SB=-554.66	GT:AD:DP:GL:GQ	0/1:23,33:56:-130.25,-16.88,-72.13:99
+chr1	4730266	rs410413	T	C	266.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=57.84;MQ0=0;OQ=500.27;QD=10.01;SB=-265.95	GT:AD:DP:GL:GQ	0/1:25,25:45:-66.88,-13.57,-94.91:99
+chr1	4730269	rs410414	T	C	250.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=57.08;MQ0=0;OQ=462.87;QD=9.85;SB=-198.61	GT:AD:DP:GL:GQ	0/1:25,22:45:-63.14,-13.57,-96.77:99
+chr1	4730645	rs395467	A	G	11.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=4.91;MQ=52.28;MQ0=0;OQ=653.20;QD=9.90;SB=-279.13	GT:AD:DP:GL:GQ	0/1:38,27:64:-87.89,-19.29,-148.52:99
+chr1	4730689	rs9426503	G	C	129.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.89;MQ=56.81;MQ0=0;OQ=1027.62;QD=14.27;SB=-322.37	GT:AD:DP:GL:GQ	0/1:41,31:67:-126.24,-20.20,-160.02:99
+chr1	4730760	rs9426483	C	T	334.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=58.90;MQ0=0;OQ=750.53;QD=13.65;SB=-332.36	GT:AD:DP:GL:GQ	0/1:31,24:54:-94.60,-16.27,-107.97:99
+chr1	4730936	rs423285	C	T	421.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=56.95;MQ0=0;OQ=670.76;QD=11.37;SB=-300.79	GT:AD:DP:GL:GQ	0/1:33,25:55:-86.95,-16.59,-101.75:99
+chr1	4730990	rs395508	G	A	57.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=59.27;MQ0=0;OQ=529.54;QD=9.29;SB=-260.10	GT:AD:DP:GL:GQ	0/1:38,19:53:-72.20,-15.97,-127.10:99
+chr1	4731053	rs418045	T	C	525.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=529.19;QD=11.50;SB=-290.44	GT:AD:DP:GL:GQ	0/1:26,20:45:-69.76,-13.55,-105.89:99
+chr1	4731180	rs396112	G	A	318.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=740.76;QD=17.64;SB=-379.17	GT:AD:DP:GL:GQ	0/1:19,23:39:-89.12,-11.76,-51.25:99
+chr1	4731341	rs406847	A	G	411.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.80;MQ0=0;OQ=513.60;QD=14.67;SB=-259.91	GT:AD:DP:GL:GQ	0/1:17,18:35:-65.19,-10.54,-67.57:99
+chr1	4731471	rs428580	C	T	186.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=867.64;QD=20.18;SB=-459.01	GT:AD:DP:GL:GQ	0/1:17,26:42:-102.70,-12.65,-55.85:99
+chr1	4731684	rs407301	C	T	107.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=57.23;MQ0=0;OQ=697.47;QD=20.51;SB=-327.88	GT:AD:DP:GL:GQ	0/1:12,22:33:-82.98,-9.95,-39.91:99
+chr1	4732014	.	T	A	875.95	Indel	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=12.12;MQ=51.16;MQ0=0;QD=14.13;SB=-350.44	GT:AD:DP:GL:GQ	0/1:31,31:60:-108.95,-18.08,-110.80:99
+chr1	4732015	.	T	A	970.99	Indel	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=9;HaplotypeScore=12.28;MQ=51.00;MQ0=0;QD=15.92;SB=-364.45	GT:AD:DP:GL:GQ	0/1:29,32:58:-117.85,-17.47,-98.32:99
+chr1	4733241	rs414434	G	C	239.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1334.69;QD=20.22;SB=-556.62	GT:AD:DP:GL:GQ	0/1:28,38:63:-155.75,-19.00,-107.17:99
+chr1	4734056	rs9426504	G	A	5.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=4;HaplotypeScore=2.44;MQ=58.18;MQ0=0;OQ=895.74;QD=16.59;SB=-312.82	GT:AD:DP:GL:GQ	0/1:25,29:51:-108.23,-15.38,-75.31:99
+chr1	4734062	rs451162	G	C	249.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=58.57;MQ0=0;OQ=977.80;QD=18.80;SB=-417.05	GT:AD:DP:GL:GQ	0/1:24,28:49:-115.83,-14.77,-93.28:99
+chr1	4734089	rs388631	T	C	200.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.48;MQ=59.01;MQ0=0;OQ=598.20;QD=12.73;SB=-188.41	GT:AD:DP:GL:GQ	0/1:21,25:44:-76.37,-13.27,-78.74:99
+chr1	4734466	rs389959	T	C	132.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=60.00;MQ0=0;OQ=323.31;QD=6.22;SB=-138.87	GT:AD:DP:GL:GQ	0/1:33,18:48:-50.08,-14.47,-128.38:99
+chr1	4734711	rs397852	T	C	337.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=60.00;MQ0=0;OQ=458.03;QD=9.35;SB=-228.25	GT:AD:DP:GL:GQ	0/1:29,20:49:-63.86,-14.77,-115.16:99
+chr1	4735235	rs399377	T	C	222.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=339.75;QD=9.71;SB=-124.62	GT:AD:DP:GL:GQ	0/1:21,14:33:-47.20,-9.94,-76.89:99
+chr1	4735981	rs394594	A	G	305.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=773.72;QD=10.46;SB=-332.92	GT:AD:DP:GL:GQ	0/1:41,33:73:-102.66,-22.01,-163.48:99
+chr1	4738101	rs414909	C	T	441.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1084.42;QD=16.19;SB=-452.94	GT:AD:DP:GL:GQ	0/1:35,32:67:-131.91,-20.18,-129.56:99
+chr1	4738908	rs381304	A	G	65.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=2;HaplotypeScore=2.37;MQ=58.77;MQ0=0;OQ=1458.03;QD=16.76;SB=-529.55	GT:AD:DP:GL:GQ	0/1:36,51:84:-174.40,-25.31,-140.93:99
+chr1	4739028	rs392984	T	C	105.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=5.08;MQ=58.80;MQ0=0;OQ=588.16;QD=10.14;SB=-181.39	GT:AD:DP:GL:GQ	0/1:30,28:53:-78.07,-15.97,-115.29:99
+chr1	4739512	rs2802719	A	G	384.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=757.23;QD=14.85;SB=-244.45	GT:AD:DP:GL:GQ	0/1:23,28:48:-93.47,-14.47,-78.98:99
+chr1	4739710	rs2802718	G	C	11.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=0.83;MQ=56.67;MQ0=0;OQ=1199.49;QD=18.74;SB=-370.48	GT:AD:DP:GL:GQ	0/1:31,33:60:-141.32,-18.09,-113.09:99
+chr1	4740018	rs7544523	T	C	161.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=58.16;MQ0=0;OQ=429.98;QD=11.94;SB=-175.51	GT:AD:DP:GL:GQ	0/1:18,18:35:-56.83,-10.55,-68.38:99
+chr1	4744236	rs9426506	C	T	327.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.29;MQ=58.57;MQ0=0;OQ=856.13;QD=13.81;SB=-428.92	GT:AD:DP:GL:GQ	0/1:35,27:62:-107.57,-18.68,-125.85:99
+chr1	4744972	rs9426484	G	A	347.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=59.65;MQ0=0;OQ=799.48;QD=12.30;SB=-407.88	GT:AD:DP:GL:GQ	0/1:38,27:60:-101.32,-18.09,-111.41:99
+chr1	4745752	rs6426434	G	A	271.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=60.00;MQ0=0;OQ=1169.68;QD=19.49;SB=-538.80	GT:AD:DP:GL:GQ	0/1:24,36:57:-137.43,-17.18,-72.34:99
+chr1	4747705	rs4654460	G	A	332.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=755.91;QD=18.90;SB=-379.91	GT:AD:DP:GL:GQ	0/1:17,23:38:-90.34,-11.46,-46.09:99
+chr1	4748668	rs12133924	A	G	455.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=1019.13;QD=13.07;SB=-468.04	GT:AD:DP:GL:GQ	0/1:42,36:77:-128.39,-23.20,-162.75:99
+chr1	4748969	rs6701069	A	G	376.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.72;MQ0=0;OQ=1003.27;QD=12.39;SB=-469.20	GT:AD:DP:GL:GQ	0/1:46,35:80:-127.71,-24.10,-182.44:99
+chr1	4749244	rs2235438	T	C	581.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=891.88;QD=13.12;SB=-467.00	GT:AD:DP:GL:GQ	0/1:32,36:65:-112.06,-19.59,-124.79:99
+chr1	4750683	rs909757	T	C	410.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.22;MQ0=0;OQ=683.00;QD=11.78;SB=-347.56	GT:AD:DP:GL:GQ	0/1:31,27:55:-88.15,-16.57,-119.32:99
+chr1	4751405	rs17345239	T	G	179.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=774.24;QD=13.12;SB=-344.85	GT:AD:DP:GL:GQ	0/1:30,29:56:-97.57,-16.87,-106.85:99
+chr1	4753272	rs742246	A	C	355.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=617.26;QD=14.03;SB=-196.34	GT:AD:DP:GL:GQ	0/1:21,23:43:-77.96,-12.95,-77.17:99
+chr1	4753548	rs932350	T	C	408.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.22;MQ0=0;OQ=924.37;QD=14.22;SB=-295.30	GT:AD:DP:GL:GQ	0/1:29,36:64:-115.01,-19.29,-116.32:99
+chr1	4753607	rs12082538	G	C	138.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.84;MQ=60.48;MQ0=0;OQ=606.35;QD=13.47;SB=-132.52	GT:AD:DP:GL:GQ	0/1:25,20:43:-76.88,-12.96,-107.57:99
+chr1	4753770	rs7519688	C	T	2.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=3;HaplotypeScore=5.33;MQ=59.09;MQ0=0;OQ=802.41;QD=15.73;SB=-282.79	GT:AD:DP:GL:GQ	0/1:25,26:48:-97.99,-14.47,-73.03:99
+chr1	4755384	rs727906	C	T	371.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=60.00;MQ0=0;OQ=954.50;QD=12.40;SB=-422.82	GT:AD:DP:GL:GQ	0/1:47,30:76:-121.64,-22.91,-153.23:99
+chr1	4756029	rs2411946	T	A	426.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.59;MQ0=0;OQ=610.43;QD=13.57;SB=-308.69	GT:AD:DP:GL:GQ	0/1:23,22:44:-77.58,-13.26,-87.22:99
+chr1	4756791	rs760816	A	G	307.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.08;MQ=60.00;MQ0=0;OQ=644.43;QD=11.51;SB=-270.35	GT:AD:DP:GL:GQ	0/1:29,27:54:-84.00,-16.27,-113.95:99
+chr1	4758251	.	A	G	4.99	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=3;HaplotypeScore=0.95;MQ=59.34;MQ0=1;OQ=796.90;QD=10.77;SB=-383.18	GT:AD:DP:GL:GQ	0/1:42,32:64:-102.26,-19.28,-139.02:99
+chr1	4758268	rs4654606	T	G	84.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=4.06;MQ=59.35;MQ0=0;OQ=681.65;QD=10.65;SB=-311.85	GT:AD:DP:GL:GQ	0/1:38,26:61:-89.83,-18.38,-124.54:99
+chr1	4759471	rs2142949	C	T	488.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=986.38;QD=17.01;SB=-326.41	GT:AD:DP:GL:GQ	0/1:27,31:57:-119.09,-17.17,-96.06:99
+chr1	4761020	rs4654607	C	T	187.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=1317.32;QD=16.67;SB=-650.17	GT:AD:DP:GL:GQ	0/1:40,39:77:-158.21,-23.19,-137.71:99
+chr1	4763236	rs2064168	C	T	278.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1185.65;QD=19.12;SB=-513.73	GT:AD:DP:GL:GQ	0/1:25,37:60:-139.92,-18.08,-90.33:99
+chr1	4763773	rs760817	T	C	455.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=59.11;MQ0=0;OQ=932.67;QD=12.78;SB=-440.55	GT:AD:DP:GL:GQ	0/1:40,33:73:-118.54,-21.99,-163.26:99
+chr1	4764845	rs10915606	A	G	585.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1075.05;QD=14.15;SB=-528.93	GT:AD:DP:GL:GQ	0/1:37,39:74:-133.08,-22.29,-148.56:99
+chr1	4765718	rs10429868	G	A	452.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1155.78;QD=15.62;SB=-602.60	GT:AD:DP:GL:GQ	0/1:39,35:74:-141.15,-22.29,-141.78:99
+chr1	4766001	rs12022466	T	A	597.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1259.06;QD=15.94;SB=-558.66	GT:AD:DP:GL:GQ	0/1:39,40:79:-152.98,-23.79,-151.51:99
+chr1	4766045	.	G	A	13.96	PASS	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=1207.52;QD=14.55;SB=-582.08	GT:AD:DP:GL:GQ	0/1:47,36:81:-148.43,-24.40,-164.42:99
+chr1	4766280	rs12752806	G	T	477.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.50;MQ0=0;OQ=1250.24;QD=15.06;SB=-480.84	GT:AD:DP:GL:GQ	0/1:42,41:81:-152.70,-24.39,-146.62:99
+chr1	4767409	rs7534770	A	T	437.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1042.20;QD=14.28;SB=-531.39	GT:AD:DP:GL:GQ	0/1:39,34:72:-129.19,-21.69,-145.29:99
+chr1	4767544	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=6;HaplotypeScore=47.32;MQ=56.17;MQ0=2;OQ=190.67;QD=2.98;SB=86.31	GT:AD:DP:GL:GQ	0/1:48,16:57:-39.52,-17.17,-173.24:99
+chr1	4769118	rs10915610	A	C	208.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=4.78;MQ=58.87;MQ0=0;OQ=1164.63;QD=14.93;SB=-551.67	GT:AD:DP:GL:GQ	0/1:37,39:77:-145.10,-25.36,-142.76:99
+chr1	4770972	.	C	A	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=2;HaplotypeScore=8.28;MQ=56.35;MQ0=0;OQ=111.37;QD=1.89;SB=65.23	GT:AD:DP:GL:GQ	0/1:35,24:40:-26.47,-12.05,-113.84:99
+chr1	4771531	rs1118009	A	G	323.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=56.74;MQ0=0;OQ=1333.25;QD=15.32;SB=-605.42	GT:AD:DP:GL:GQ	0/1:38,49:86:-162.53,-25.92,-151.96:99
+chr1	4771617	rs1118010	C	T	407.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=1431.00;QD=18.58;SB=-550.33	GT:AD:DP:GL:GQ	0/1:34,43:77:-169.58,-23.20,-123.43:99
+chr1	4772431	rs10799262	G	A	68.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=59.76;MQ0=0;OQ=1610.76;QD=20.65;SB=-755.30	GT:AD:DP:GL:GQ	0/1:32,46:78:-187.86,-23.50,-115.14:99
+chr1	4772511	rs10915611	C	T	585.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=1219.72;QD=17.42;SB=-547.54	GT:AD:DP:GL:GQ	0/1:34,36:70:-146.34,-21.08,-121.82:99
+chr1	4772916	rs10915612	A	G	195.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=58.68;MQ0=0;OQ=1058.43;QD=15.80;SB=-539.98	GT:AD:DP:GL:GQ	0/1:30,37:67:-129.31,-20.19,-122.36:99
+chr1	4773270	rs7540367	G	A	242.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.44;MQ0=0;OQ=792.22;QD=13.66;SB=-213.92	GT:AD:DP:GL:GQ	0/1:33,25:57:-99.68,-17.18,-105.56:99
+chr1	4773658	.	G	A	112.25	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.50;MQ0=0;OQ=985.30;QD=17.59;SB=-495.06	GT:AD:DP:GL:GQ	0/1:26,30:55:-118.38,-16.57,-94.83:99
+chr1	4773754	rs12120205	T	A	372.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1585.82;QD=16.18;SB=-556.42	GT:AD:DP:GL:GQ	0/1:49,49:98:-191.38,-29.51,-188.67:99
+chr1	4774287	rs10799263	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=7;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1045.47;QD=15.84;SB=-449.52	GT:AD:DP:GL:GQ	0/1:30,36:65:-127.41,-19.58,-109.32:99
+chr1	4774365	rs10915613	G	A	361.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1223.17;QD=16.31;SB=-630.64	GT:AD:DP:GL:GQ	0/1:38,37:73:-147.61,-22.01,-118.37:99
+chr1	4776755	rs12145180	C	G	356.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=59.64;MQ0=0;OQ=975.57;QD=15.24;SB=-415.28	GT:AD:DP:GL:GQ	0/1:32,32:62:-119.54,-18.70,-139.99:99
+chr1	4776903	rs10915615	C	A	330.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.69;MQ0=0;OQ=909.18;QD=12.12;SB=-404.10	GT:AD:DP:GL:GQ	0/1:43,32:72:-115.90,-21.70,-128.82:99
+chr1	4777460	rs12118812	T	G	167.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=842.15;QD=11.86;SB=-431.75	GT:AD:DP:GL:GQ	0/1:41,30:70:-108.58,-21.08,-144.58:99
+chr1	4777525	rs12118818	T	G	101.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=1.33;MQ=59.72;MQ0=0;OQ=940.16;QD=13.63;SB=-473.22	GT:AD:DP:GL:GQ	0/1:36,33:67:-117.48,-20.18,-125.31:99
+chr1	4777535	rs12143219	G	T	70.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=4;HaplotypeScore=0.27;MQ=60.00;MQ0=0;OQ=1005.40;QD=15.47;SB=-447.46	GT:AD:DP:GL:GQ	0/1:32,33:65:-123.40,-19.58,-114.32:99
+chr1	4778731	rs1120120	C	T	347.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=1.94;MQ=59.78;MQ0=0;OQ=1277.01;QD=15.02;SB=-471.94	GT:AD:DP:GL:GQ	0/1:47,38:84:-156.28,-25.30,-171.76:99
+chr1	4780340	rs10915616	C	T	196.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=881.43;QD=16.95;SB=-113.96	GT:AD:DP:GL:GQ	0/1:26,26:52:-107.09,-15.66,-92.07:99
+chr1	4780435	rs12121890	T	C	347.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.73;MQ0=0;OQ=1105.50;QD=16.26;SB=-426.60	GT:AD:DP:GL:GQ	0/1:30,38:67:-134.02,-20.18,-117.11:99
+chr1	4781127	rs12122126	T	C	314.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=58.69;MQ0=0;OQ=674.99;QD=13.50;SB=-298.62	GT:AD:DP:GL:GQ	0/1:26,24:49:-85.54,-14.76,-106.72:99
+chr1	4781899	rs12117810	G	A	242.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.88;MQ0=0;OQ=1031.36;QD=17.78;SB=-437.45	GT:AD:DP:GL:GQ	0/1:28,30:56:-123.30,-16.88,-83.86:99
+chr1	4782182	rs10915619	A	T	438.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.65;MQ0=0;OQ=1009.97;QD=12.47;SB=-431.43	GT:AD:DP:GL:GQ	0/1:47,34:80:-128.38,-24.10,-172.98:99
+chr1	4782516	rs1883345	G	A	146.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=59.45;MQ0=0;OQ=906.47;QD=11.93;SB=-338.27	GT:AD:DP:GL:GQ	0/1:44,32:71:-115.32,-21.39,-152.63:99
+chr1	4782885	rs1883346	T	A	397.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=58.75;MQ0=0;OQ=1064.02;QD=14.99;SB=-456.50	GT:AD:DP:GL:GQ	0/1:37,34:70:-130.77,-21.08,-141.61:99
+chr1	4782955	rs1883347	T	C	221.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=4.24;MQ=59.50;MQ0=0;OQ=856.09;QD=11.57;SB=-450.96	GT:AD:DP:GL:GQ	0/1:43,30:73:-110.88,-21.99,-176.74:99
+chr1	4783491	rs4654610	T	C	960.35	Indel	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=11.46;MQ=47.61;MQ0=0;QD=14.12;SB=-407.25	GT:AD:DP:GL:GQ	0/1:31,37:63:-118.30,-18.98,-112.03:99
+chr1	4793106	rs61766789	G	A	240.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=58.98;MQ0=1;OQ=1230.74;QD=17.33;SB=-554.58	GT:AD:DP:GL:GQ	0/1:35,36:69:-147.14,-20.78,-120.71:99
+chr1	4794663	.	C	T	274.23	PASS	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=833.44;QD=12.63;SB=-440.37	GT:AD:DP:GL:GQ	0/1:40,26:66:-106.51,-19.88,-144.25:99
+chr1	4794952	rs12074481	C	A	271.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=57.82;MQ0=0;OQ=1066.30;QD=15.02;SB=-452.97	GT:AD:DP:GL:GQ	0/1:33,38:69:-130.70,-20.79,-110.83:99
+chr1	4798693	rs7522386	A	G	341.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.98;MQ=58.39;MQ0=0;OQ=1056.56;QD=15.77;SB=-495.12	GT:AD:DP:GL:GQ	0/1:31,36:65:-128.52,-19.58,-122.92:99
+chr1	4801597	rs7527319	C	A	582.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=923.07;QD=13.78;SB=-344.17	GT:AD:DP:GL:GQ	0/1:34,33:66:-115.47,-19.88,-121.89:99
+chr1	4806096	rs7547779	T	C	457.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.53;MQ0=0;OQ=897.02;QD=13.39;SB=-364.21	GT:AD:DP:GL:GQ	0/1:34,33:65:-112.57,-19.58,-135.93:99
+chr1	4807563	rs11582327	T	C	467.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.73;MQ0=0;OQ=911.00;QD=13.40;SB=-422.86	GT:AD:DP:GL:GQ	0/1:32,36:67:-114.58,-20.19,-127.73:99
+chr1	4807672	rs7536960	T	C	326.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=60.00;MQ0=0;OQ=720.71;QD=12.64;SB=-286.29	GT:AD:DP:GL:GQ	0/1:27,30:55:-91.93,-16.58,-105.91:99
+chr1	4808516	rs6669130	G	A	323.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=59.98;MQ0=0;OQ=1529.46;QD=17.58;SB=-724.76	GT:AD:DP:GL:GQ	0/1:42,45:83:-181.23,-25.00,-146.35:99
+chr1	4808719	.	T	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=2;HaplotypeScore=4.69;MQ=58.91;MQ0=0;OQ=57.76;QD=0.90;SB=95.29	GT:AD:DP:GL:GQ	0/1:40,24:48:-23.52,-14.46,-139.84:90.60
+chr1	4808761	rs6683849	A	G	156.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=737.58;QD=13.17;SB=-272.54	GT:AD:DP:GL:GQ	0/1:30,26:56:-93.91,-16.87,-119.65:99
+chr1	4808953	rs12725011	G	A	96.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=1.25;MQ=59.67;MQ0=0;OQ=1362.18;QD=19.46;SB=-645.68	GT:AD:DP:GL:GQ	0/1:29,41:69:-160.29,-20.79,-101.64:99
+chr1	4808976	rs11582462	A	G	74	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=3.61;MQ=59.32;MQ0=0;OQ=923.86;QD=13.59;SB=-481.59	GT:AD:DP:GL:GQ	0/1:33,35:64:-114.94,-19.28,-135.51:99
+chr1	4809567	rs11582936	A	C	302.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=59.67;MQ0=0;OQ=605.80;QD=10.63;SB=-281.94	GT:AD:DP:GL:GQ	0/1:26,30:52:-79.53,-15.67,-97.13:99
+chr1	4809668	rs7543326	T	C	173.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=2;HaplotypeScore=1.68;MQ=59.71;MQ0=0;OQ=1092.10;QD=13.82;SB=-474.60	GT:AD:DP:GL:GQ	0/1:37,42:79:-136.31,-23.81,-148.02:99
+chr1	4811032	rs6693945	T	C	292.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=59.41;MQ0=0;OQ=916.53;QD=14.55;SB=-321.25	GT:AD:DP:GL:GQ	0/1:30,31:62:-117.13,-22.19,-125.33:99
+chr1	4811983	rs2209167	G	A	414.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.70;MQ0=0;OQ=1021.76;QD=13.10;SB=-414.40	GT:AD:DP:GL:GQ	0/1:45,33:75:-128.08,-22.62,-135.03:99
+chr1	4813003	rs6426439	C	T	133.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=3.37;MQ=59.50;MQ0=0;OQ=1367.37;QD=18.48;SB=-705.27	GT:AD:DP:GL:GQ	0/1:34,40:72:-161.71,-21.69,-122.06:99
+chr1	4813419	rs1886113	T	G	294.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=612.34;QD=12.76;SB=-248.40	GT:AD:DP:GL:GQ	0/1:25,23:47:-78.67,-14.15,-95.57:99
+chr1	4813733	rs10915628	T	C	146.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=870.49;QD=12.26;SB=-270.52	GT:AD:DP:GL:GQ	0/1:41,30:71:-111.72,-21.39,-167.00:99
+chr1	4813800	rs10915631	C	T	467.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=60.00;MQ0=0;OQ=1109.44;QD=15.20;SB=-509.01	GT:AD:DP:GL:GQ	0/1:39,34:73:-136.22,-21.99,-139.36:99
+chr1	4813826	rs10799266	A	G	440.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=1025.69;QD=13.50;SB=-528.56	GT:AD:DP:GL:GQ	0/1:40,36:76:-128.75,-22.90,-159.57:99
+chr1	4814770	rs6426440	C	A	361.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=60.00;MQ0=0;OQ=964.05;QD=12.68;SB=-378.13	GT:AD:DP:GL:GQ	0/1:42,34:76:-122.59,-22.91,-131.06:99
+chr1	4814802	rs6426441	A	T	191.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=5.04;MQ=59.57;MQ0=0;OQ=882.35;QD=13.17;SB=-416.80	GT:AD:DP:GL:GQ	0/1:37,30:65:-111.10,-19.58,-134.21:99
+chr1	4815146	rs2411949	G	T	0.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=15.15;MQ=59.31;MQ0=0;OQ=1233.12;QD=16.23;SB=-582.79	GT:AD:DP:GL:GQ	0/1:35,40:72:-148.29,-21.69,-101.37:99
+chr1	4815330	rs6658680	A	G	154.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=57.17;MQ0=0;OQ=454.29;QD=9.09;SB=-126.50	GT:AD:DP:GL:GQ	0/1:29,21:47:-62.88,-14.17,-108.85:99
+chr1	4815340	rs6692964	G	T	169.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=56.50;MQ0=0;OQ=607.11;QD=11.90;SB=-203.41	GT:AD:DP:GL:GQ	0/1:29,22:51:-79.35,-15.36,-103.70:99
+chr1	4815344	rs6692966	G	A	446.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.57;MQ0=0;OQ=669.90;QD=12.88;SB=-297.81	GT:AD:DP:GL:GQ	0/1:28,24:50:-85.35,-15.08,-90.67:99
+chr1	4815634	rs2147028	C	A	82.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=1.79;MQ=59.43;MQ0=0;OQ=1001.39;QD=15.41;SB=-277.32	GT:AD:DP:GL:GQ	0/1:32,33:62:-122.10,-18.67,-102.09:99
+chr1	4815904	rs2209166	G	A	117.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1754.50;QD=22.21;SB=-892.01	GT:AD:DP:GL:GQ	0/1:28,51:79:-202.53,-23.80,-99.82:99
+chr1	4816064	rs6693706	G	T	446.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.64;MQ0=0;OQ=733.52;QD=14.11;SB=-350.37	GT:AD:DP:GL:GQ	0/1:26,26:52:-92.30,-15.67,-93.55:99
+chr1	4816465	rs1535736	C	T	112.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=1112.33;QD=17.38;SB=-338.80	GT:AD:DP:GL:GQ	0/1:31,33:64:-133.80,-19.28,-110.54:99
+chr1	4816766	rs1535734	A	G	420.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=908.64;QD=12.62;SB=-359.52	GT:AD:DP:GL:GQ	0/1:39,33:70:-115.23,-21.09,-156.36:99
+chr1	4817101	rs6693352	A	G	227.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.68;MQ0=0;OQ=949.71;QD=13.19;SB=-443.55	GT:AD:DP:GL:GQ	0/1:38,34:70:-119.35,-21.09,-147.05:99
+chr1	4817128	rs2898848	G	A	216.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1195.65;QD=16.61;SB=-558.57	GT:AD:DP:GL:GQ	0/1:36,36:72:-144.54,-21.69,-131.83:99
+chr1	4817320	rs2209165	C	T	145.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.39;MQ0=0;OQ=1415.52;QD=20.82;SB=-731.10	GT:AD:DP:GL:GQ	0/1:27,41:68:-165.32,-20.49,-90.68:99
+chr1	4817405	rs2209164	A	G	118.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.63;MQ0=0;OQ=527.84;QD=8.51;SB=-187.44	GT:AD:DP:GL:GQ	0/1:40,22:60:-74.14,-18.07,-157.62:99
+chr1	4817514	rs2209163	G	A	238.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.72;MQ0=0;OQ=933.49;QD=13.93;SB=-217.50	GT:AD:DP:GL:GQ	0/1:38,29:66:-116.53,-19.90,-117.09:99
+chr1	4817749	rs3938469	A	G	107.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=486.41;QD=8.11;SB=-117.18	GT:AD:DP:GL:GQ	0/1:41,19:60:-70.00,-18.07,-168.54:99
+chr1	4817969	rs2093769	G	A	229.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.14;MQ=59.44;MQ0=0;OQ=1190.09;QD=14.51;SB=-381.33	GT:AD:DP:GL:GQ	0/1:44,38:79:-146.09,-23.80,-153.77:99
+chr1	4818044	rs2093768	A	G	314.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.33;MQ0=0;OQ=811.36;QD=13.09;SB=-280.55	GT:AD:DP:GL:GQ	0/1:29,33:61:-102.81,-18.39,-114.06:99
+chr1	4818509	rs10159142	G	A	308.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.55;MQ=58.95;MQ0=0;OQ=899.59;QD=15.51;SB=-448.42	GT:AD:DP:GL:GQ	0/1:30,28:58:-110.72,-17.47,-107.08:99
+chr1	4818666	rs10799268	T	C	278.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=59.42;MQ0=0;OQ=887.47;QD=13.87;SB=-404.24	GT:AD:DP:GL:GQ	0/1:33,31:62:-110.70,-18.67,-130.15:99
+chr1	4818872	rs10753387	T	C	88.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=55.54;MQ0=0;OQ=718.25;QD=13.30;SB=-324.13	GT:AD:DP:GL:GQ	0/1:25,29:53:-91.08,-15.98,-99.45:99
+chr1	4819100	rs10753388	G	A	0.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=17.64;MQ=55.33;MQ0=0;OQ=1324.27;QD=17.66;SB=-679.33	GT:AD:DP:GL:GQ	0/1:36,39:70:-156.80,-21.09,-111.06:99
+chr1	4819163	rs10753389	A	G	70.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=49.63;MQ0=1;OQ=764.05;QD=12.53;SB=-256.89	GT:AD:DP:GL:GQ	0/1:33,28:59:-97.46,-17.77,-133.52:99
+chr1	4819348	rs10915632	G	A	8.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=2;HaplotypeScore=6.46;MQ=58.48;MQ0=0;OQ=1415.77;QD=15.91;SB=-658.28	GT:AD:DP:GL:GQ	0/1:47,42:87:-171.06,-26.20,-164.95:99
+chr1	4819622	rs10799269	C	G	347.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.05;MQ0=0;OQ=934.79;QD=12.98;SB=-429.59	GT:AD:DP:GL:GQ	0/1:41,31:69:-117.56,-20.80,-181.53:99
+chr1	4819655	rs10799270	G	A	353.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.56;MQ0=0;OQ=1064.88;QD=14.39;SB=-436.38	GT:AD:DP:GL:GQ	0/1:41,33:74:-132.06,-22.29,-148.73:99
+chr1	4819737	rs2147027	T	C	200.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.22;MQ=55.94;MQ0=0;OQ=778.52;QD=14.69;SB=-321.29	GT:AD:DP:GL:GQ	0/1:25,28:51:-96.50,-15.36,-95.69:99
+chr1	4820060	rs2181701	T	C	0.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=11.39;MQ=52.25;MQ0=0;OQ=485.51;QD=9.52;SB=-244.48	GT:AD:DP:GL:GQ	0/1:29,22:49:-66.61,-14.77,-110.48:99
+chr1	4820091	rs4265399	G	A	243.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.14;MQ0=0;OQ=512.92;QD=10.06;SB=-45.99	GT:AD:DP:GL:GQ	0/1:32,19:48:-69.05,-14.48,-96.83:99
+chr1	4820096	rs2181700	T	G	75.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=50.99;MQ0=0;OQ=433.90;QD=8.34;SB=-40.01	GT:AD:DP:GL:GQ	0/1:33,19:51:-62.03,-15.36,-122.01:99
+chr1	4820154	rs9725470	C	T	281.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.90;MQ0=2;OQ=495.62;QD=9.01;SB=-102.52	GT:AD:DP:GL:GQ	0/1:37,18:51:-68.22,-15.38,-108.69:99
+chr1	4820216	rs9726479	T	G	79.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=1.15;MQ=45.62;MQ0=0;OQ=697.41;QD=12.24;SB=-299.44	GT:AD:DP:GL:GQ	0/1:30,27:55:-89.59,-16.56,-110.14:99
+chr1	4820227	rs9725796	C	A	40.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=0.33;MQ=47.59;MQ0=0;OQ=717.90;QD=11.58;SB=-300.16	GT:AD:DP:GL:GQ	0/1:34,28:59:-92.84,-17.77,-118.69:99
+chr1	4820388	rs9726805	T	C	201.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=2.98;MQ=51.02;MQ0=0;OQ=985.45;QD=12.17;SB=-457.03	GT:AD:DP:GL:GQ	0/1:42,39:76:-124.72,-22.89,-168.04:99
+chr1	4820748	.	A	G	1.13	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=35.53;MQ0=6;OQ=268.28;QD=5.37;SB=-1.83	GT:AD:DP:GL:GQ	0/1:28,21:34:-40.35,-10.24,-88.65:99
+chr1	4820850	.	T	C	0.21	PASS	AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=43.66;MQ0=1;OQ=84.14;QD=3.12;SB=-53.32	GT:AD:DP:GL:GQ	0/1:14,12:16:-16.52,-4.83,-39.77:99
+chr1	4820858	.	G	A	0.93	PASS	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=4.23;MQ=41.11;MQ0=1;OQ=153.45;QD=5.29;SB=-40.65	GT:AD:DP:GL:GQ	0/1:13,15:17:-23.75,-5.12,-38.01:99
+chr1	4820952	rs61766808	C	T	152.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=38.70;MQ0=1;OQ=409.25;QD=9.09;SB=-225.93	GT:AD:DP:GL:GQ	0/1:30,15:42:-56.86,-12.66,-95.36:99
+chr1	4821240	rs9726227	C	T	470.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=37.63;MQ0=1;OQ=887.90;QD=12.87;SB=-408.68	GT:AD:DP:GL:GQ	0/1:36,33:62:-110.75,-18.67,-130.57:99
+chr1	4821376	rs9726241	C	A	8.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=39.07;MQ0=5;OQ=305.92;QD=4.86;SB=-1.55	GT:AD:DP:GL:GQ	0/1:37,26:47:-48.04,-14.16,-121.88:99
+chr1	4821609	rs9726885	A	C	47.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=36.89;MQ0=14;OQ=448.17;QD=5.67;SB=-207.28	GT:AD:DP:GL:GQ	0/1:47,32:61:-66.47,-18.37,-159.23:99
+chr1	4821773	rs9726925	A	G	101.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=38.22;MQ0=2;OQ=859.75;QD=9.35;SB=-417.48	GT:AD:DP:GL:GQ	0/1:47,45:74:-111.55,-22.29,-173.37:99
+chr1	4821818	rs12135318	C	A	320.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=44.85;MQ0=0;OQ=1111.50;QD=12.21;SB=-470.83	GT:AD:DP:GL:GQ	0/1:41,50:79:-138.22,-23.79,-149.34:99
+chr1	4821875	rs10915634	A	G	55.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=46.72;MQ0=5;OQ=657.16;QD=7.64;SB=-166.48	GT:AD:DP:GL:GQ	0/1:46,40:75:-91.61,-22.61,-188.45:99
+chr1	4822060	rs7411909	A	G	472.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.58;MQ0=0;OQ=844.08;QD=14.07;SB=-331.93	GT:AD:DP:GL:GQ	0/1:31,29:60:-105.77,-18.08,-125.13:99
+chr1	4822115	rs4617370	G	A	221.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=59.00;MQ0=0;OQ=1387.37;QD=17.13;SB=-675.38	GT:AD:DP:GL:GQ	0/1:40,41:81:-166.44,-24.42,-127.76:99
+chr1	4822681	rs6660173	C	T	0.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.01;HRun=3;HaplotypeScore=10.96;MQ=52.45;MQ0=0;OQ=1014.70;QD=13.71;SB=-426.92	GT:AD:DP:GL:GQ	0/1:42,31:73:-126.44,-21.69,-150.88:99
+chr1	4822687	rs6660177	C	A	163.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=52.56;MQ0=0;OQ=900.97;QD=12.01;SB=-430.11	GT:AD:DP:GL:GQ	0/1:44,31:74:-115.67,-22.28,-156.45:99
+chr1	4822710	rs6668068	T	C	72.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=2.96;MQ=50.82;MQ0=0;OQ=906.69;QD=11.78;SB=-477.93	GT:AD:DP:GL:GQ	0/1:44,33:75:-116.54,-22.59,-176.01:99
+chr1	4822958	rs6665282	A	G	464.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.16;MQ0=0;OQ=785.44;QD=13.78;SB=-331.28	GT:AD:DP:GL:GQ	0/1:30,27:57:-99.00,-17.17,-122.67:99
+chr1	4823049	rs6665388	A	G	56.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=2.47;MQ=55.61;MQ0=0;OQ=907.22;QD=12.60;SB=-445.14	GT:AD:DP:GL:GQ	0/1:36,36:67:-114.19,-20.18,-139.94:99
+chr1	4823137	rs12087020	A	G	358.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=54.38;MQ0=0;OQ=1125.73;QD=15.86;SB=-588.93	GT:AD:DP:GL:GQ	0/1:32,39:69:-136.64,-20.78,-130.19:99
+chr1	4823207	rs10915638	C	T	285.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=57.74;MQ0=0;OQ=1338.14;QD=15.93;SB=-487.03	GT:AD:DP:GL:GQ	0/1:44,40:82:-161.79,-24.70,-152.84:99
+chr1	4823247	rs10915639	C	T	70.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=3;HaplotypeScore=1.40;MQ=59.24;MQ0=0;OQ=1272.31;QD=17.19;SB=-602.12	GT:AD:DP:GL:GQ	0/1:37,37:73:-152.51,-22.00,-119.03:99
+chr1	4823334	rs10915640	G	T	485.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.40;MQ0=0;OQ=978.54;QD=13.05;SB=-397.99	GT:AD:DP:GL:GQ	0/1:40,35:71:-122.52,-21.38,-136.84:99
+chr1	4823422	rs10915641	G	A	453.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.14;MQ0=3;OQ=955.26;QD=11.79;SB=-332.42	GT:AD:DP:GL:GQ	0/1:46,35:73:-120.80,-21.99,-150.35:99
+chr1	4824006	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=60;Dels=0.03;HRun=20;HaplotypeScore=17.44;MQ=44.47;MQ0=0;OQ=216.45;QD=3.61;SB=56.16	GT:AD:DP:GL:GQ	0/1:34,24:43:-37.29,-12.36,-108.08:99
+chr1	4824255	rs6656943	G	A	241.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=48.13;MQ0=0;OQ=486.99;QD=9.37;SB=-207.48	GT:AD:DP:GL:GQ	0/1:29,22:45:-65.55,-13.57,-87.60:99
+chr1	4824523	rs6674586	T	A	163.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=48.28;MQ0=0;OQ=656.95;QD=12.17;SB=-109.40	GT:AD:DP:GL:GQ	0/1:27,27:47:-83.14,-14.16,-95.96:99
+chr1	4824573	rs6674680	T	C	13.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=52.32;MQ0=0;OQ=270.57;QD=5.11;SB=-156.88	GT:AD:DP:GL:GQ	0/1:35,18:46:-44.20,-13.86,-137.80:99
+chr1	4824574	.	G	A	7.24	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=52.42;MQ0=0;OQ=361.86;QD=6.83;SB=-143.57	GT:AD:DP:GL:GQ	0/1:34,19:46:-53.32,-13.85,-117.68:99
+chr1	4824682	rs12135493	G	A	249.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=51.42;MQ0=1;OQ=988.12;QD=12.83;SB=-444.35	GT:AD:DP:GL:GQ	0/1:44,32:73:-124.08,-21.99,-153.59:99
+chr1	4824703	rs6671779	A	G	149.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.56;MQ=45.45;MQ0=6;OQ=857.95;QD=10.46;SB=-366.21	GT:AD:DP:GL:GQ	0/1:48,33:70:-110.16,-21.08,-158.61:99
+chr1	4824716	rs6674795	T	A	84.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=5.06;MQ=43.80;MQ0=7;OQ=985.67;QD=11.60;SB=-441.50	GT:AD:DP:GL:GQ	0/1:51,34:73:-123.84,-21.98,-157.76:99
+chr1	4824850	rs36062377	G	T	24.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=3;HaplotypeScore=2.62;MQ=51.81;MQ0=1;OQ=1235.06;QD=17.15;SB=-475.54	GT:AD:DP:GL:GQ	0/1:30,42:67:-146.97,-20.18,-98.26:99
+chr1	4825033	rs7529540	T	C	245.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=39.74;MQ0=8;OQ=558.43;QD=7.55;SB=-301.05	GT:AD:DP:GL:GQ	0/1:47,27:63:-78.11,-18.99,-158.23:99
+chr1	4825352	rs4559467	G	A	108.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=5.62;MQ=48.67;MQ0=0;OQ=560.80;QD=11.22;SB=-300.78	GT:AD:DP:GL:GQ	0/1:27,20:40:-71.42,-12.05,-75.01:99
+chr1	4825513	rs4638087	G	C	326.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=1176.04;QD=19.60;SB=-421.03	GT:AD:DP:GL:GQ	0/1:27,33:59:-138.66,-17.78,-117.95:99
+chr1	4825553	rs4551566	C	G	30.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.33;MQ0=0;OQ=1250.51;QD=22.33;SB=-448.38	GT:AD:DP:GL:GQ	0/1:22,34:55:-144.91,-16.57,-96.90:99
+chr1	4826034	rs7529926	A	G	223.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=2.45;MQ=57.60;MQ0=0;OQ=1139.50;QD=13.57;SB=-533.50	GT:AD:DP:GL:GQ	0/1:44,39:83:-142.23,-25.00,-178.33:99
+chr1	4826162	rs7525613	C	T	13.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=2;HaplotypeScore=3.45;MQ=59.36;MQ0=1;OQ=993.15;QD=10.80;SB=-409.28	GT:AD:DP:GL:GQ	0/1:59,33:90:-129.72,-27.12,-195.16:99
+chr1	4826345	rs2104305	G	T	184.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=57.85;MQ0=1;OQ=505.67;QD=12.64;SB=-209.45	GT:AD:DP:GL:GQ	0/1:21,19:39:-65.60,-11.75,-75.98:99
+chr1	4826423	rs2093767	G	A	138.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=58.83;MQ0=0;OQ=815.33;QD=15.68;SB=-288.73	GT:AD:DP:GL:GQ	0/1:27,25:52:-100.48,-15.67,-95.85:99
+chr1	4826585	rs2093766	C	T	86.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=59.52;MQ0=0;OQ=705.53;QD=13.07;SB=-332.40	GT:AD:DP:GL:GQ	0/1:31,23:54:-90.10,-16.27,-110.86:99
+chr1	4826810	rs10915643	T	G	203.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=57.12;MQ0=0;OQ=525.52;QD=11.94;SB=-258.86	GT:AD:DP:GL:GQ	0/1:23,21:42:-68.49,-12.65,-82.71:99
+chr1	4827586	rs55916988	A	T	25.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=889.58;QD=14.35;SB=-432.48	GT:AD:DP:GL:GQ	0/1:33,29:62:-110.92,-18.68,-123.75:99
+chr1	4827658	rs10915644	C	T	105.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=104;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=60.00;MQ0=0;OQ=1865.95;QD=17.94;SB=-912.01	GT:AD:DP:GL:GQ	0/1:46,58:101:-220.30,-30.43,-168.62:99
+chr1	4828047	rs10915645	G	T	162.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=59.35;MQ0=0;OQ=1117.38;QD=13.97;SB=-570.65	GT:AD:DP:GL:GQ	0/1:41,39:77:-138.21,-23.19,-142.58:99
+chr1	4828218	rs10915646	T	C	280.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.03;MQ=59.65;MQ0=0;OQ=827.35;QD=15.32;SB=-429.21	GT:AD:DP:GL:GQ	0/1:26,28:54:-102.28,-16.26,-103.92:99
+chr1	4829521	rs7525315	A	G	34.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=1.86;MQ=60.00;MQ0=0;OQ=437.24;QD=11.82;SB=-193.62	GT:AD:DP:GL:GQ	0/1:19,18:35:-57.55,-10.55,-75.26:99
+chr1	4829549	rs7511935	G	C	92.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=60.00;MQ0=0;OQ=512.56;QD=13.85;SB=-232.38	GT:AD:DP:GL:GQ	0/1:19,18:33:-64.49,-9.95,-73.26:99
+chr1	4829662	rs7512035	G	A	4.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=9.93;MQ=58.76;MQ0=0;OQ=838.03;QD=17.10;SB=-374.88	GT:AD:DP:GL:GQ	0/1:21,27:46:-104.45,-17.36,-74.24:99
+chr1	4830041	rs1886112	T	C	323.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=58.39;MQ0=0;OQ=754.42;QD=11.79;SB=-313.28	GT:AD:DP:GL:GQ	0/1:35,29:61:-97.11,-18.38,-135.74:99
+chr1	4830111	rs2411950	A	G	299.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=59.44;MQ0=0;OQ=788.01;QD=11.76;SB=-302.20	GT:AD:DP:GL:GQ	0/1:34,33:66:-101.98,-19.90,-134.57:99
+chr1	4831214	rs11588518	A	G	386.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.12;MQ=58.39;MQ0=0;OQ=816.62;QD=14.85;SB=-422.33	GT:AD:DP:GL:GQ	0/1:26,29:53:-100.91,-15.96,-102.18:99
+chr1	4832304	rs10915647	T	G	357.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=59.21;MQ0=0;OQ=992.87;QD=12.89;SB=-411.65	GT:AD:DP:GL:GQ	0/1:36,41:75:-125.17,-22.60,-131.25:99
+chr1	4833095	rs10489136	G	A	381.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=597.16;QD=11.94;SB=-271.12	GT:AD:DP:GL:GQ	0/1:30,20:49:-77.76,-14.76,-108.40:99
+chr1	4833385	rs11809159	G	A	313.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.57;MQ0=0;OQ=671.57;QD=12.44;SB=-350.34	GT:AD:DP:GL:GQ	0/1:33,21:52:-86.11,-15.67,-111.35:99
+chr1	4834568	rs12691490	G	A	57.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=2;HaplotypeScore=1.52;MQ=59.19;MQ0=0;OQ=1072.80;QD=14.30;SB=-179.14	GT:AD:DP:GL:GQ	0/1:41,34:74:-132.86,-22.29,-148.17:99
+chr1	4834712	rs11810903	C	T	299.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.50;MQ0=0;OQ=847.25;QD=15.99;SB=-334.31	GT:AD:DP:GL:GQ	0/1:27,26:50:-103.07,-15.06,-90.22:99
+chr1	4835505	.	G	A	70.11	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.18;MQ0=2;OQ=1406.02;QD=19.00;SB=-566.58	GT:AD:DP:GL:GQ	0/1:33,41:71:-165.27,-21.39,-109.48:99
+chr1	4835574	rs60862815	A	G	389.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.44;MQ0=0;OQ=1406.97;QD=14.66;SB=-683.24	GT:AD:DP:GL:GQ	0/1:48,48:95:-172.59,-28.61,-196.25:99
+chr1	4835660	.	A	G	23.51	PASS	AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.01;MQ0=0;OQ=1833.96;QD=19.10;SB=-522.87	GT:AD:DP:GL:GQ	0/1:39,57:96:-215.59,-28.91,-159.74:99
+chr1	4837550	rs35283465	T	G	356.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=1133.74;QD=16.67;SB=-504.82	GT:AD:DP:GL:GQ	0/1:30,38:68:-137.14,-20.48,-110.12:99
+chr1	4837913	rs10753390	T	C	137.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=2.60;MQ=60.00;MQ0=0;OQ=941.83;QD=14.72;SB=-459.61	GT:AD:DP:GL:GQ	0/1:30,34:62:-116.15,-18.68,-119.75:99
+chr1	4839426	rs942248	G	A	447.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.57;MQ=60.00;MQ0=0;OQ=1139.23;QD=16.75;SB=-553.39	GT:AD:DP:GL:GQ	0/1:34,34:68:-137.70,-20.50,-108.59:99
+chr1	4841270	rs10915651	A	G	240.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=57.66;MQ0=0;OQ=816.55;QD=11.66;SB=-378.12	GT:AD:DP:GL:GQ	0/1:39,31:68:-105.42,-20.48,-155.28:99
+chr1	4841714	rs4654463	A	C	478.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=555.94;QD=9.75;SB=-254.73	GT:AD:DP:GL:GQ	0/1:35,22:56:-75.74,-16.86,-132.35:99
+chr1	4844074	rs10733017	T	C	2.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=11.82;MQ=59.63;MQ0=0;OQ=699.51;QD=11.10;SB=-327.09	GT:AD:DP:GL:GQ	0/1:36,27:62:-91.91,-18.68,-144.88:99
+chr1	4844167	rs11576728	C	A	571.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=1050.49;QD=13.64;SB=-532.68	GT:AD:DP:GL:GQ	0/1:42,35:77:-131.52,-23.19,-153.03:99
+chr1	4844702	rs7543026	G	A	584.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.93;MQ0=0;OQ=948.11;QD=15.54;SB=-391.87	GT:AD:DP:GL:GQ	0/1:33,28:60:-116.18,-18.08,-104.09:99
+chr1	4845341	rs6658585	A	C	76.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=4.00;MQ=59.18;MQ0=0;OQ=1071.52;QD=16.74;SB=-367.56	GT:AD:DP:GL:GQ	0/1:26,38:62:-129.11,-18.67,-97.88:99
+chr1	4845498	rs12057393	G	A	364.71	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=12;HaplotypeScore=3.79;MQ=47.74;MQ0=0;QD=4.19;SB=-24.81	GT:AD:DP:GL:GQ	0/1:67,20:77:-62.95,-23.20,-211.18:99
+chr1	4845501	.	G	A	272.57	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=2;HaplotypeScore=5.43;MQ=47.58;MQ0=0;QD=3.17;SB=59.32	GT:AD:DP:GL:GQ	0/1:69,17:79:-54.34,-23.80,-226.78:99
+chr1	4845504	.	G	A	237.01	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=2;HaplotypeScore=5.58;MQ=47.42;MQ0=0;QD=2.79;SB=100.89	GT:AD:DP:GL:GQ	0/1:69,16:79:-50.79,-23.80,-233.92:99
+chr1	4846112	rs34320332	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=25.56;MQ=59.10;MQ0=1;OQ=980.42;QD=12.41;SB=-508.92	GT:AD:DP:GL:GQ	0/1:43,36:73:-123.31,-21.99,-148.19:99
+chr1	4846138	rs4141866	T	G	321.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1084.74;QD=12.91;SB=-515.88	GT:AD:DP:GL:GQ	0/1:44,39:81:-136.16,-24.40,-149.14:99
+chr1	4846537	rs2224810	C	T	118.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=2;HaplotypeScore=2.15;MQ=60.00;MQ0=0;OQ=819.69;QD=11.71;SB=-407.37	GT:AD:DP:GL:GQ	0/1:43,26:69:-109.19,-23.93,-141.50:99
+chr1	4846628	rs2209160	C	T	102.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=6.02;MQ=59.71;MQ0=0;OQ=1103.05;QD=13.96;SB=-498.70	GT:AD:DP:GL:GQ	0/1:45,34:78:-137.10,-23.51,-139.74:99
+chr1	4847013	rs4654617	G	A	341.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.65;MQ=60.12;MQ0=0;OQ=1328.73;QD=14.44;SB=-558.05	GT:AD:DP:GL:GQ	0/1:51,41:91:-163.57,-27.42,-178.46:99
+chr1	4847234	rs4654618	G	A	257.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.79;MQ0=0;OQ=1473.23;QD=16.93;SB=-644.65	GT:AD:DP:GL:GQ	0/1:44,43:86:-176.51,-25.90,-155.83:99
+chr1	4847304	rs11576619	A	C	410.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1115.68;QD=12.54;SB=-555.85	GT:AD:DP:GL:GQ	0/1:50,39:89:-141.65,-26.80,-188.69:99
+chr1	4848245	rs10915655	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.04;HRun=13;HaplotypeScore=40.55;MQ=53.84;MQ0=0;OQ=783.98;QD=11.53;SB=-399.49	GT:AD:DP:GL:GQ	0/1:35,30:57:-98.55,-16.87,-112.34:99
+chr1	4848259	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=13;HaplotypeScore=8.75;MQ=53.39;MQ0=0;OQ=145.61;QD=2.24;SB=43.71	GT:AD:DP:GL:GQ	0/1:50,15:51:-33.22,-15.38,-143.27:99
+chr1	4848272	rs59534952	C	T	83.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.85;MQ=55.61;MQ0=0;OQ=567.99;QD=11.83;SB=-226.73	GT:AD:DP:GL:GQ	0/1:29,19:46:-73.94,-13.86,-98.14:99
+chr1	4849613	rs2224809	G	T	40.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=5.98;MQ=59.05;MQ0=0;OQ=753.24;QD=11.77;SB=-371.10	GT:AD:DP:GL:GQ	0/1:36,28:62:-97.28,-18.68,-118.15:99
+chr1	4851425	rs4654464	C	A	99.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=3;HaplotypeScore=1.30;MQ=59.74;MQ0=0;OQ=1201.43;QD=13.50;SB=-585.67	GT:AD:DP:GL:GQ	0/1:47,42:87:-149.63,-26.21,-164.62:99
+chr1	4851649	rs1544062	A	C	506.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.80;MQ0=0;OQ=1031.53;QD=11.21;SB=-464.74	GT:AD:DP:GL:GQ	0/1:52,40:90:-133.54,-27.11,-194.44:99
+chr1	4852648	rs6664880	A	G	404.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=757.37;QD=15.15;SB=-338.35	GT:AD:DP:GL:GQ	0/1:21,29:49:-93.79,-14.77,-78.78:99
+chr1	4853388	rs16839786	G	T	224.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=53.58;MQ0=0;OQ=920.28;QD=16.43;SB=-211.55	GT:AD:DP:GL:GQ	0/1:26,30:55:-111.88,-16.57,-81.39:99
+chr1	4853673	rs61764897	T	A	731.06	Indel	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=49.62;MQ0=0;QD=11.25;SB=-257.66	GT:AD:DP:GL:GQ	0/1:39,26:64:-95.67,-19.28,-148.40:99
+chr1	4854729	rs11578197	G	A	258.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.65;MQ0=0;OQ=1050.33;QD=16.16;SB=-476.48	GT:AD:DP:GL:GQ	0/1:33,32:63:-127.30,-18.99,-107.48:99
+chr1	4855018	rs16839789	C	T	363.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=59.33;MQ0=0;OQ=1117.05;QD=14.70;SB=-538.76	GT:AD:DP:GL:GQ	0/1:39,37:73:-136.99,-22.00,-128.05:99
+chr1	4855722	rs6426446	C	T	346.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.43;MQ0=0;OQ=1302.13;QD=17.84;SB=-634.73	GT:AD:DP:GL:GQ	0/1:34,39:71:-154.89,-21.40,-105.41:99
+chr1	4855930	rs6426447	T	C	166.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=57.78;MQ0=0;OQ=489.14;QD=8.58;SB=-219.87	GT:AD:DP:GL:GQ	0/1:31,26:53:-68.18,-15.98,-120.90:99
+chr1	4856415	rs7547152	G	C	495.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=942.12;QD=15.20;SB=-441.90	GT:AD:DP:GL:GQ	0/1:35,27:61:-115.88,-18.38,-149.41:99
+chr1	4857229	rs58851741	C	T	459.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=966.78;QD=16.67;SB=-403.91	GT:AD:DP:GL:GQ	0/1:27,31:57:-117.15,-17.19,-83.93:99
+chr1	4857438	rs6663654	A	G	150.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.74;MQ=59.66;MQ0=0;OQ=1188.14;QD=17.73;SB=-597.99	GT:AD:DP:GL:GQ	0/1:26,41:63:-141.07,-18.98,-97.28:99
+chr1	4857938	rs4654466	T	G	14.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=3;HaplotypeScore=2.02;MQ=60.00;MQ0=0;OQ=2439.19;QD=33.41;SB=-1032.90	GT:AD:DP:GL:GQ	1/1:0,73:72:-247.54,-21.70,-0.04:99
+chr1	4857962	rs4654620	T	C	617.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2216.51;QD=34.63;SB=-1013.85	GT:AD:DP:GL:GQ	1/1:0,64:63:-225.26,-18.98,-0.03:99
+chr1	4858133	rs12026056	C	T	160.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=1391.17;QD=19.32;SB=-472.46	GT:AD:DP:GL:GQ	0/1:31,41:70:-163.49,-21.09,-105.37:99
+chr1	4858331	rs2411952	T	G	714.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2714.55;QD=33.93;SB=-941.23	GT:AD:DP:GL:GQ	1/1:0,80:78:-275.06,-23.49,-0.02:99
+chr1	4858799	rs10915656	A	G	325.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=541.63;QD=8.88;SB=-253.33	GT:AD:DP:GL:GQ	0/1:37,24:61:-75.83,-18.39,-146.51:99
+chr1	4859646	rs2031246	A	G	219.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.68;MQ0=0;OQ=1950.88;QD=29.12;SB=-966.30	GT:AD:DP:GL:GQ	1/1:0,67:62:-198.73,-18.70,-0.06:99
+chr1	4859671	.	T	C	13.11	PASS	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=3.64;MQ=59.06;MQ0=0;OQ=883.63;QD=12.81;SB=-329.17	GT:AD:DP:GL:GQ	0/1:37,32:67:-111.83,-20.19,-139.59:99
+chr1	4859954	rs34895557	G	T	206.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.25;MQ=59.24;MQ0=0;OQ=744.21;QD=13.53;SB=-251.43	GT:AD:DP:GL:GQ	0/1:28,27:52:-93.37,-15.67,-91.09:99
+chr1	4860771	rs1998542	A	G	287.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.36;MQ0=0;OQ=1092.68;QD=14.57;SB=-569.57	GT:AD:DP:GL:GQ	0/1:37,38:74:-134.84,-22.29,-148.74:99
+chr1	4861394	rs12564397	A	T	437.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=1000.40;QD=17.86;SB=-441.86	GT:AD:DP:GL:GQ	0/1:25,31:56:-120.19,-16.87,-93.72:99
+chr1	4861557	rs35411636	G	A	169.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=59.72;MQ0=0;OQ=1208.45;QD=18.04;SB=-440.97	GT:AD:DP:GL:GQ	0/1:30,37:64:-143.41,-19.28,-105.19:99
+chr1	4863429	.	C	T	229.25	PASS	AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=1493.09;QD=17.36;SB=-728.57	GT:AD:DP:GL:GQ	0/1:41,45:85:-178.20,-25.60,-151.88:99
+chr1	4863497	rs7524606	G	A	427.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=60.00;MQ0=0;OQ=1511.71;QD=17.58;SB=-634.67	GT:AD:DP:GL:GQ	0/1:42,44:85:-180.06,-25.60,-147.35:99
+chr1	4863865	rs1980722	C	T	503.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3056.08;QD=40.21;SB=-645.86	GT:AD:DP:GL:GQ	1/1:0,76:76:-309.21,-22.89,-0.02:99
+chr1	4864428	rs11580747	G	C	245.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=59.63;MQ0=0;OQ=942.97;QD=14.97;SB=-334.34	GT:AD:DP:GL:GQ	0/1:36,27:61:-115.96,-18.38,-154.60:99
+chr1	4865012	rs17345545	A	C	595.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=1349.09;QD=16.06;SB=-446.78	GT:AD:DP:GL:GQ	0/1:36,48:82:-162.89,-24.70,-132.81:99
+chr1	4865105	rs57839229	A	T	93.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=1.14;MQ=59.34;MQ0=0;OQ=1132.50;QD=17.98;SB=-522.98	GT:AD:DP:GL:GQ	0/1:27,36:62:-135.21,-18.67,-99.92:99
+chr1	4865351	rs4654467	A	G	16.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.01;HRun=0;HaplotypeScore=4.70;MQ=59.78;MQ0=0;OQ=2675.08;QD=31.11;SB=-1049.26	GT:AD:DP:GL:GQ	1/1:0,84:83:-271.15,-24.72,-0.06:99
+chr1	4866087	rs10915662	A	T	363.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.38;MQ0=0;OQ=1323.19;QD=19.75;SB=-593.71	GT:AD:DP:GL:GQ	0/1:27,40:67:-155.78,-20.18,-103.30:99
+chr1	4866400	rs12064982	G	A	103.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.34;MQ=60.00;MQ0=0;OQ=973.54;QD=18.03;SB=-247.54	GT:AD:DP:GL:GQ	0/1:25,29:53:-116.61,-15.97,-79.83:99
+chr1	4866918	rs12031154	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=24.82;MQ=54.18;MQ0=0;OQ=935.81;QD=11.27;SB=-380.06	GT:AD:DP:GL:GQ	0/1:43,40:73:-118.86,-22.00,-142.88:99
+chr1	4866921	rs12026933	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.03;HRun=18;HaplotypeScore=19.70;MQ=54.46;MQ0=0;OQ=1554.81;QD=17.87;SB=-743.33	GT:AD:DP:GL:GQ	0/1:33,51:81:-182.28,-23.51,-100.13:99
+chr1	4867019	rs11803696	A	G	583.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1173.47;QD=12.90;SB=-430.96	GT:AD:DP:GL:GQ	0/1:48,43:89:-147.44,-26.81,-193.48:99
+chr1	4867070	rs6672145	C	T	154.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=58.49;MQ0=0;OQ=2949.30;QD=37.81;SB=-1148.66	GT:AD:DP:GL:GQ	1/1:0,78:74:-298.53,-22.29,-0.02:99
+chr1	4867333	rs10737414	C	T	577.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=3774.90;QD=40.59;SB=-1090.96	GT:AD:DP:GL:GQ	1/1:0,93:91:-376.49,-27.41,-0.02:99
+chr1	4867363	rs7533707	A	T	409.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=3186.97;QD=36.63;SB=-1277.61	GT:AD:DP:GL:GQ	1/1:0,87:84:-322.30,-25.30,-0.02:99
+chr1	4867599	rs7520488	G	C	176.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.17;MQ=58.98;MQ0=0;OQ=1260.85;QD=19.70;SB=-431.87	GT:AD:DP:GL:GQ	0/1:29,35:63:-148.35,-18.98,-119.77:99
+chr1	4867836	rs10753391	C	T	252.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=58.82;MQ0=0;OQ=2192.96;QD=37.17;SB=-1090.48	GT:AD:DP:GL:GQ	1/1:0,58:57:-222.90,-17.17,-0.02:99
+chr1	4869610	rs10753392	A	G	2.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=12.66;MQ=58.15;MQ0=0;OQ=2566.56;QD=33.77;SB=-1061.07	GT:AD:DP:GL:GQ	1/1:1,75:72:-260.27,-21.69,-0.02:99
+chr1	4869715	rs10753393	A	G	57.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.94;MQ=55.52;MQ0=0;OQ=2164.34;QD=32.79;SB=-1098.81	GT:AD:DP:GL:GQ	1/1:0,66:62:-220.05,-18.68,-0.03:99
+chr1	4869773	rs10737415	G	A	79.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=59.56;MQ0=0;OQ=867.20;QD=16.36;SB=-154.19	GT:AD:DP:GL:GQ	0/1:24,29:51:-105.37,-15.37,-83.26:99
+chr1	4869802	rs10753394	T	C	256.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.38;MQ=60.00;MQ0=0;OQ=1715.99;QD=30.64;SB=-772.60	GT:AD:DP:GL:GQ	1/1:0,56:56:-175.25,-16.90,-0.06:99
+chr1	4869982	rs10915666	G	A	210.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=58.75;MQ0=0;OQ=1883.17;QD=36.21;SB=-696.34	GT:AD:DP:GL:GQ	1/1:0,50:49:-191.92,-14.76,-0.02:99
+chr1	4870346	rs6675549	G	A	170.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=4.29;MQ=57.91;MQ0=0;OQ=1211.32;QD=19.23;SB=-547.10	GT:AD:DP:GL:GQ	0/1:28,35:62:-143.11,-18.69,-84.61:99
+chr1	4870866	rs60530383	A	G	40.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=2.54;MQ=60.00;MQ0=0;OQ=824.16;QD=14.46;SB=-305.38	GT:AD:DP:GL:GQ	0/1:28,29:56:-102.57,-16.87,-109.85:99
+chr1	4871367	rs12034557	C	T	506.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1054.17;QD=18.82;SB=-458.82	GT:AD:DP:GL:GQ	0/1:25,31:55:-125.27,-16.57,-85.80:99
+chr1	4871442	rs11584441	T	G	5.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=1.95;MQ=57.60;MQ0=1;OQ=392.05;QD=7.00;SB=-149.17	GT:AD:DP:GL:GQ	0/1:35,21:54:-58.76,-16.27,-123.74:99
+chr1	4871485	rs12034590	C	T	165.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.35;MQ0=0;OQ=1273.44;QD=19.90;SB=-540.59	GT:AD:DP:GL:GQ	0/1:26,38:62:-149.30,-18.68,-91.11:99
+chr1	4871683	rs10915667	G	A	252.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.13;MQ=59.56;MQ0=0;OQ=868.47;QD=16.70;SB=-440.82	GT:AD:DP:GL:GQ	0/1:26,26:50:-105.19,-15.06,-84.43:99
+chr1	4872046	rs41524347	T	G	240.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=531.74;QD=7.28;SB=-248.55	GT:AD:DP:GL:GQ	0/1:47,26:72:-78.15,-21.69,-181.81:99
+chr1	4872269	rs7549400	A	G	96.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=1.52;MQ=58.82;MQ0=1;OQ=894.68;QD=13.76;SB=-387.61	GT:AD:DP:GL:GQ	0/1:34,31:64:-112.04,-19.29,-126.05:99
+chr1	4872967	rs11805753	C	T	385.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.68;MQ0=0;OQ=1214.98;QD=17.11;SB=-484.47	GT:AD:DP:GL:GQ	0/1:35,36:70:-145.88,-21.10,-111.38:99
+chr1	4873161	rs10915668	C	T	676.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=2872.25;QD=39.89;SB=-1024.38	GT:AD:DP:GL:GQ	1/1:0,72:72:-290.83,-21.69,-0.02:99
+chr1	4874423	rs10915669	T	C	15.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=59.06;MQ0=0;OQ=1979.91;QD=28.69;SB=-648.94	GT:AD:DP:GL:GQ	1/1:0,69:62:-201.63,-18.69,-0.05:99
+chr1	4875425	rs10157835	A	G	332.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.11;MQ0=0;OQ=1038.14;QD=16.48;SB=-539.00	GT:AD:DP:GL:GQ	0/1:28,35:63:-126.07,-18.98,-114.44:99
+chr1	4877097	rs12565275	C	G	395.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.57;MQ0=0;OQ=611.15;QD=11.32;SB=-239.42	GT:AD:DP:GL:GQ	0/1:33,21:54:-80.69,-16.29,-144.98:99
+chr1	4877956	rs2898849	G	C	124.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=59.05;MQ0=0;OQ=3110.04;QD=42.60;SB=-1016.57	GT:AD:DP:GL:GQ	1/1:0,72:72:-314.62,-21.70,-0.03:99
+chr1	4878047	rs12564793	G	C	328.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.70;MQ0=0;OQ=765.57;QD=12.15;SB=-303.80	GT:AD:DP:GL:GQ	0/1:37,26:61:-98.24,-18.40,-159.57:99
+chr1	4880219	rs11585512	A	G	134.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=3.24;MQ=59.43;MQ0=0;OQ=632.04;QD=9.58;SB=-314.90	GT:AD:DP:GL:GQ	0/1:35,31:61:-84.88,-18.39,-132.31:99
+chr1	4880279	rs11583660	G	A	590.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.47;MQ0=0;OQ=976.49;QD=13.95;SB=-412.71	GT:AD:DP:GL:GQ	0/1:40,30:69:-121.72,-20.78,-142.93:99
+chr1	4880552	rs12035499	G	A	202.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=1072.23;QD=21.02;SB=-458.86	GT:AD:DP:GL:GQ	0/1:20,31:50:-125.57,-15.06,-66.05:99
+chr1	4881363	rs942245	A	G	135.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=2549.24;QD=35.41;SB=-1267.52	GT:AD:DP:GL:GQ	1/1:0,72:71:-258.53,-21.38,-0.02:99
+chr1	4882246	rs6698453	G	A	17.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=2.99;MQ=60.00;MQ0=0;OQ=1152.61;QD=20.22;SB=-564.76	GT:AD:DP:GL:GQ	0/1:24,33:57:-135.71,-17.17,-88.68:99
+chr1	4883339	rs12043326	T	C	559.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=840.35;QD=11.84;SB=-378.86	GT:AD:DP:GL:GQ	0/1:36,35:67:-107.51,-20.19,-138.68:99
+chr1	4883603	rs10915672	C	A	302.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=917.14;QD=15.81;SB=-477.86	GT:AD:DP:GL:GQ	0/1:28,30:58:-112.47,-17.47,-92.34:99
+chr1	4883658	rs4141867	T	C	369.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=1888.75;QD=33.14;SB=-779.12	GT:AD:DP:GL:GQ	1/1:0,57:54:-192.48,-16.27,-0.02:99
+chr1	4883885	rs6702564	G	A	362.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=1074.71;QD=17.62;SB=-363.86	GT:AD:DP:GL:GQ	0/1:29,32:61:-129.13,-18.37,-105.65:99
+chr1	4884232	rs1535733	T	C	178.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.73;MQ=59.20;MQ0=1;OQ=1010.15;QD=15.08;SB=-514.02	GT:AD:DP:GL:GQ	0/1:32,35:66:-124.18,-19.88,-130.89:99
+chr1	4884527	rs6666792	C	A	73.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=1.81;MQ=60.00;MQ0=0;OQ=1017.13;QD=16.14;SB=-354.42	GT:AD:DP:GL:GQ	0/1:29,34:62:-123.67,-18.68,-100.25:99
+chr1	4884742	rs2093765	A	G	735.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=2661.52;QD=35.97;SB=-1066.10	GT:AD:DP:GL:GQ	1/1:0,74:74:-269.76,-22.29,-0.02:99
+chr1	4885223	rs6667433	C	T	727.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=1991.58;QD=36.21;SB=-991.61	GT:AD:DP:GL:GQ	1/1:1,54:54:-205.04,-16.28,-2.29:99
+chr1	4885428	rs10753395	A	C	505.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.54;MQ0=0;OQ=2504.61;QD=34.79;SB=-1254.33	GT:AD:DP:GL:GQ	1/1:0,72:71:-254.07,-21.38,-0.02:99
+chr1	4885629	rs10915675	C	T	373.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=59.20;MQ0=0;OQ=841.96;QD=14.52;SB=-410.79	GT:AD:DP:GL:GQ	0/1:31,27:56:-104.36,-16.88,-95.31:99
+chr1	4886330	rs2411956	G	T	352.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.52;MQ=59.33;MQ0=0;OQ=915.03;QD=14.76;SB=-419.13	GT:AD:DP:GL:GQ	0/1:29,33:59:-112.57,-17.78,-93.60:99
+chr1	4886464	rs2898852	G	A	427.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.69;MQ0=0;OQ=1311.14;QD=17.48;SB=-649.71	GT:AD:DP:GL:GQ	0/1:36,39:74:-156.69,-22.29,-124.22:99
+chr1	4887284	rs6666453	T	G	591.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=819.61;QD=13.22;SB=-407.64	GT:AD:DP:GL:GQ	0/1:31,31:61:-103.62,-18.37,-115.39:99
+chr1	4887891	rs61271613	G	A	361.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.32;MQ0=0;OQ=1029.14;QD=15.13;SB=-413.79	GT:AD:DP:GL:GQ	0/1:37,31:68:-126.69,-20.50,-120.37:99
+chr1	4887923	rs12567162	A	C	597.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=1047.19;QD=16.36;SB=-475.28	GT:AD:DP:GL:GQ	0/1:27,37:63:-126.98,-18.97,-102.36:99
+chr1	4888122	rs11584727	G	A	343.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=58.62;MQ0=0;OQ=960.03;QD=15.74;SB=-414.74	GT:AD:DP:GL:GQ	0/1:31,30:58:-116.76,-17.47,-107.44:99
+chr1	4888166	rs10799275	T	C	449.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=759.70;QD=14.07;SB=-405.31	GT:AD:DP:GL:GQ	0/1:28,26:54:-95.52,-16.26,-116.08:99
+chr1	4888741	rs6667349	A	G	162.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=1.54;MQ=60.00;MQ0=0;OQ=906.44;QD=15.63;SB=-403.28	GT:AD:DP:GL:GQ	0/1:26,32:57:-111.10,-17.17,-105.01:99
+chr1	4891078	rs10915677	A	C	501.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=791.64;QD=10.84;SB=-393.76	GT:AD:DP:GL:GQ	0/1:42,31:72:-104.14,-21.69,-153.97:99
+chr1	4891278	rs10753396	A	G	48.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.33;MQ=59.27;MQ0=0;OQ=705.13;QD=13.83;SB=-249.29	GT:AD:DP:GL:GQ	0/1:25,26:49:-88.56,-14.77,-92.96:99
+chr1	4892541	rs6675977	C	T	304.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.24;MQ0=0;OQ=854.23;QD=15.53;SB=-341.48	GT:AD:DP:GL:GQ	0/1:29,26:53:-104.68,-15.97,-89.47:99
+chr1	4893597	rs9426511	G	A	254.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=59.63;MQ0=0;OQ=950.24;QD=15.08;SB=-473.01	GT:AD:DP:GL:GQ	0/1:32,31:60:-116.38,-18.07,-112.58:99
+chr1	4894312	rs12409253	G	A	317.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.37;MQ0=0;OQ=1178.40;QD=17.85;SB=-478.44	GT:AD:DP:GL:GQ	0/1:31,35:66:-141.01,-19.88,-111.62:99
+chr1	4894801	rs12044092	G	A	352.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=58.46;MQ0=0;OQ=1019.91;QD=14.36;SB=-390.41	GT:AD:DP:GL:GQ	0/1:36,34:67:-125.46,-20.19,-124.85:99
+chr1	4894886	rs12049256	T	C	300.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.80;MQ=59.40;MQ0=0;OQ=829.82;QD=11.85;SB=-433.52	GT:AD:DP:GL:GQ	0/1:40,30:69:-107.05,-20.79,-158.76:99
+chr1	4895006	rs11588368	G	A	587.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=820.91;QD=16.10;SB=-424.82	GT:AD:DP:GL:GQ	0/1:26,25:51:-100.74,-15.37,-86.84:99
+chr1	4895035	rs11591047	T	C	208.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=456.13;QD=9.70;SB=-221.38	GT:AD:DP:GL:GQ	0/1:26,21:45:-62.46,-13.57,-101.40:99
+chr1	4895453	rs10915681	C	A	168.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=58.81;MQ0=0;OQ=612.66;QD=11.14;SB=-214.30	GT:AD:DP:GL:GQ	0/1:31,24:51:-79.91,-15.36,-100.29:99
+chr1	4895802	rs10915682	G	C	444.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.75;MQ0=0;OQ=770.78;QD=14.82;SB=-369.80	GT:AD:DP:GL:GQ	0/1:29,22:52:-98.80,-18.44,-131.37:99
+chr1	4896045	rs10915683	A	G	284.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.68;MQ0=0;OQ=528.33;QD=8.95;SB=-128.57	GT:AD:DP:GL:GQ	0/1:38,21:56:-72.98,-16.87,-140.47:99
+chr1	4896086	rs4654470	A	G	55.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.44;MQ=59.62;MQ0=0;OQ=494.74;QD=8.11;SB=-214.66	GT:AD:DP:GL:GQ	0/1:40,20:59:-73.24,-20.48,-157.99:99
+chr1	4896521	rs12037632	T	C	412.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.62;MQ0=0;OQ=681.99;QD=11.18;SB=-282.28	GT:AD:DP:GL:GQ	0/1:32,29:59:-89.26,-17.78,-128.31:99
+chr1	4896528	.	C	T	86.04	PASS	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=59.65;MQ0=0;OQ=946.41;QD=14.34;SB=-376.12	GT:AD:DP:GL:GQ	0/1:36,30:66:-117.81,-19.89,-127.23:99
+chr1	4896632	rs12040043	G	A	26.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=5.45;MQ=59.30;MQ0=0;OQ=1274.10;QD=19.30;SB=-654.71	GT:AD:DP:GL:GQ	0/1:28,38:65:-150.27,-19.58,-99.74:99
+chr1	4897223	rs9426467	A	G	376.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=1052.07;QD=15.47;SB=-512.94	GT:AD:DP:GL:GQ	0/1:31,37:66:-128.37,-19.88,-120.24:99
+chr1	4897430	.	C	G	135.89	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1675.35;QD=20.68;SB=-845.32	GT:AD:DP:GL:GQ	0/1:35,46:79:-194.65,-23.83,-135.28:99
+chr1	4898245	rs9426468	A	G	643.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=1735.77;QD=32.14;SB=-669.84	GT:AD:DP:GL:GQ	1/1:0,54:54:-177.21,-16.28,-0.04:99
+chr1	4899159	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=3;HaplotypeScore=6.05;MQ=46.85;MQ0=0;OQ=120.33;QD=2.27;SB=65.24	GT:AD:DP:GL:GQ	0/1:32,21:41:-27.68,-12.36,-128.17:99
+chr1	4899332	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=18.81;MQ=41.26;MQ0=0;OQ=75.19;QD=0.84;SB=83.30	GT:AD:DP:GL:GQ	0/1:74,15:82:-35.50,-24.70,-289.36:99
+chr1	4899338	rs61764934	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=1;HaplotypeScore=53.72;MQ=39.00;MQ0=0;OQ=98.84;QD=0.96;SB=80.29	GT:AD:DP:GL:GQ	0/1:81,22:86:-39.08,-25.91,-300.72:99
+chr1	4899353	.	A	G	53.98	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=1;HaplotypeScore=114.06;MQ=38.02;MQ0=0;QD=0.50;SB=80.29	GT:AD:DP:GL:GQ	0/1:92,15:73:-30.68,-22.00,-253.39:86.82
+chr1	4899362	.	C	T	241.59	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=82.55;MQ=36.98;MQ0=0;QD=2.20;SB=83.28	GT:AD:DP:GL:GQ	0/1:96,14:84:-52.74,-25.30,-256.82:99
+chr1	4899363	.	A	G	254.83	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=89.52;MQ=36.48;MQ0=0;QD=2.38;SB=77.27	GT:AD:DP:GL:GQ	0/1:93,14:79:-52.57,-23.80,-259.03:99
+chr1	4899383	.	A	G	183.41	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=35.87;MQ=33.65;MQ0=0;QD=1.73;SB=12.92	GT:AD:DP:GL:GQ	0/1:63,43:62:-40.31,-18.69,-193.47:99
+chr1	4899387	.	G	A	263.62	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=1;HaplotypeScore=43.90;MQ=33.13;MQ0=0;QD=2.66;SB=77.22	GT:AD:DP:GL:GQ	0/1:87,12:64:-48.92,-19.28,-184.60:99
+chr1	4899389	.	C	T	535.44	SnpCluster	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=0;HaplotypeScore=29.97;MQ=33.38;MQ0=0;QD=5.76;SB=-42.73	GT:AD:DP:GL:GQ	0/1:50,43:64:-76.11,-19.28,-160.16:99
+chr1	4899390	.	A	G	274.25	SnpCluster	AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=29.97;MQ=32.97;MQ0=0;QD=2.98;SB=-22.76	GT:AD:DP:GL:GQ	0/1:49,43:57:-47.88,-17.17,-174.44:99
+chr1	4899396	.	A	G	365.84	SnpCluster	AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=37.97;MQ=32.55;MQ0=0;QD=4.02;SB=-65.46	GT:AD:DP:GL:GQ	0/1:57,34:58:-57.34,-17.48,-166.05:99
+chr1	4899406	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=33.13;MQ=34.08;MQ0=0;OQ=385.33;QD=4.76;SB=65.23	GT:AD:DP:GL:GQ	0/1:64,17:63:-60.79,-18.98,-180.67:99
+chr1	4899410	.	A	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=33.12;MQ=33.37;MQ0=0;OQ=280.21;QD=3.64;SB=-127.85	GT:AD:DP:GL:GQ	0/1:61,16:68:-51.79,-20.49,-213.95:99
+chr1	4899418	rs61764937	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=24.96;MQ=35.60;MQ0=0;OQ=416.78;QD=5.56;SB=-32.80	GT:AD:DP:GL:GQ	0/1:58,17:68:-65.44,-20.48,-183.51:99
+chr1	4899454	.	A	G	399.94	SnpCluster	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=32.10;MQ=40.74;MQ0=0;QD=4.49;SB=-98.78	GT:AD:DP:GL:GQ	0/1:68,21:81:-67.68,-24.40,-246.97:99
+chr1	4899458	.	A	G	39.06	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=68.26;MQ=40.42;MQ0=0;QD=0.40;SB=83.30	GT:AD:DP:GL:GQ	0/1:88,9:79:-30.98,-23.79,-291.61:71.90
+chr1	4899460	.	A	G	118.03	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=0;HaplotypeScore=72.96;MQ=40.46;MQ0=0;QD=1.18;SB=77.27	GT:AD:DP:GL:GQ	0/1:89,11:76:-37.98,-22.90,-265.09:99
+chr1	4899462	.	C	T	72.49	SnpCluster	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=1;HaplotypeScore=75.80;MQ=40.64;MQ0=0;QD=0.70;SB=-1.28	GT:AD:DP:GL:GQ	0/1:95,8:73:-32.52,-21.98,-238.14:99
+chr1	4899467	.	A	G	135.65	SnpCluster	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=98.40;MQ=41.18;MQ0=0;QD=1.23;SB=-29.35	GT:AD:DP:GL:GQ	0/1:96,14:86:-42.76,-25.91,-295.60:99
+chr1	4899468	rs12745382	A	T	958.03	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=110;Dels=0.00;HRun=0;HaplotypeScore=107.35;MQ=41.23;MQ0=0;QD=8.71;SB=-316.45	GT:AD:DP:GL:GQ	0/1:64,46:95:-127.70,-28.61,-236.36:99
+chr1	4899487	rs12745394	A	G	720.77	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=218;Dels=0.00;HRun=0;HaplotypeScore=160.10;MQ=38.29;MQ0=1;QD=3.31;SB=-244.39	GT:AD:DP:GL:GQ	0/1:161,57:163:-124.48,-49.12,-501.88:99
+chr1	4899493	.	T	C	260.40	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=248;Dels=0.00;HRun=0;HaplotypeScore=303.17;MQ=38.85;MQ0=1;QD=1.05;SB=56.79	GT:AD:DP:GL:GQ	0/1:215,32:203:-90.48,-61.15,-713.61:99
+chr1	4899494	.	G	A	174.70	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=0;HaplotypeScore=310.33;MQ=39.06;MQ0=1;QD=0.69;SB=21.87	GT:AD:DP:GL:GQ	0/1:226,26:203:-81.91,-61.15,-646.58:99
+chr1	4899498	.	A	G	872.52	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=0;HaplotypeScore=250.40;MQ=38.78;MQ0=1;QD=3.46;SB=78.26	GT:AD:DP:GL:GQ	0/1:199,53:211:-154.09,-63.56,-686.66:99
+chr1	4899500	rs12724550	G	A	2189.95	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=250;Dels=0.00;HRun=0;HaplotypeScore=245.89;MQ=38.85;MQ0=1;QD=8.76;SB=-1087.26	GT:AD:DP:GL:GQ	0/1:149,76:205:-341.91,-119.63,-478.96:99
+chr1	4899501	.	T	G	179.31	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=1;HaplotypeScore=255.20;MQ=39.12;MQ0=1;QD=0.71;SB=215.88	GT:AD:DP:GL:GQ	0/1:226,25:204:-82.66,-61.45,-660.80:99
+chr1	4899507	.	A	G	466.12	DPFilter;Indel;SnpCluster	AC=1;AF=0.50;AN=2;DP=254;Dels=0.00;HRun=0;HaplotypeScore=236.48;MQ=39.39;MQ0=1;QD=1.84;SB=155.66	GT:AD:DP:GL:GQ	0/1:206,47:211:-113.47,-63.57,-712.04:99
+chr1	4899538	.	A	G	1219.52	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=258;Dels=0.00;HRun=0;HaplotypeScore=176.47;MQ=39.21;MQ0=0;QD=4.73;SB=-218.54	GT:AD:DP:GL:GQ	0/1:190,68:212:-189.10,-63.86,-642.45:99
+chr1	4899540	.	A	G	894.27	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=255;Dels=0.00;HRun=0;HaplotypeScore=176.74;MQ=39.03;MQ0=0;QD=3.51;SB=-184.63	GT:AD:DP:GL:GQ	0/1:181,72:195:-154.12,-61.41,-609.10:99
+chr1	4899547	rs61764939	G	A	1318.72	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=260;Dels=0.00;HRun=0;HaplotypeScore=220.06;MQ=39.48;MQ0=0;QD=5.07;SB=-35.22	GT:AD:DP:GL:GQ	0/1:180,80:174:-187.61,-52.45,-416.57:99
+chr1	4899554	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=0;HaplotypeScore=215.32;MQ=39.44;MQ0=0;OQ=71.48;QD=0.28;SB=245.79	GT:AD:DP:GL:GQ	0/1:233,19:178:-64.05,-53.62,-575.35:99
+chr1	4899560	.	A	G	527.43	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=244;Dels=0.00;HRun=0;HaplotypeScore=182.32;MQ=39.84;MQ0=0;QD=2.16;SB=62.05	GT:AD:DP:GL:GQ	0/1:191,43:207:-132.12,-76.10,-688.26:99
+chr1	4899566	.	C	T	228.85	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=230;Dels=0.00;HRun=0;HaplotypeScore=151.86;MQ=39.79;MQ0=0;QD=0.99;SB=29.83	GT:AD:DP:GL:GQ	0/1:207,23:173:-78.29,-52.12,-551.64:99
+chr1	4899567	.	A	G	591.79	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=0;HaplotypeScore=146.70;MQ=39.85;MQ0=0;QD=2.64;SB=-287.04	GT:AD:DP:GL:GQ	0/1:172,52:165:-112.16,-49.70,-538.18:99
+chr1	4899578	.	G	A	586.91	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=167;Dels=0.00;HRun=1;HaplotypeScore=122.95;MQ=41.57;MQ0=0;QD=3.51;SB=-235.54	GT:AD:DP:GL:GQ	0/1:137,30:123:-99.03,-37.05,-345.51:99
+chr1	4899580	.	G	A	442.86	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=161;Dels=0.00;HRun=0;HaplotypeScore=120.46;MQ=41.82;MQ0=0;QD=2.75;SB=-225.49	GT:AD:DP:GL:GQ	0/1:135,26:120:-83.72,-36.15,-349.19:99
+chr1	4899586	.	T	C	690.02	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=1;HaplotypeScore=129.55;MQ=42.82;MQ0=0;QD=4.63;SB=-75.61	GT:AD:DP:GL:GQ	0/1:103,46:129:-111.14,-38.86,-403.04:99
+chr1	4899587	.	G	A	484.27	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=116.82;MQ=42.67;MQ0=0;QD=3.32;SB=137.44	GT:AD:DP:GL:GQ	0/1:119,26:124:-89.06,-37.35,-358.44:99
+chr1	4899593	.	C	T	11.57	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=60.92;MQ=43.18;MQ0=0;QD=0.10;SB=158.52	GT:AD:DP:GL:GQ	0/1:100,17:99:-34.23,-29.82,-323.42:44.09
+chr1	4899594	.	A	G	11.09	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=60.92;MQ=43.00;MQ0=0;QD=0.10;SB=173.58	GT:AD:DP:GL:GQ	0/1:99,17:103:-35.39,-31.03,-369.44:43.58
+chr1	4899610	.	C	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=9.15;MQ=43.55;MQ0=0;OQ=197.17;QD=2.22;SB=-29.37	GT:AD:DP:GL:GQ	0/1:75,14:86:-48.93,-25.93,-238.79:99
+chr1	4899946	rs4654471	T	C	43.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=5.91;MQ=59.14;MQ0=0;OQ=975.13;QD=18.06;SB=-440.01	GT:AD:DP:GL:GQ	0/1:20,34:52:-116.46,-15.67,-76.61:99
+chr1	4902227	rs7555212	C	T	596.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=2926.83;QD=40.65;SB=-1218.62	GT:AD:DP:GL:GQ	1/1:0,72:72:-296.28,-21.69,-0.02:99
+chr1	4902317	rs6426367	G	T	224.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=59.74;MQ0=0;OQ=3145.50;QD=36.16;SB=-1581.61	GT:AD:DP:GL:GQ	1/1:0,87:85:-318.15,-25.60,-0.02:99
+chr1	4902486	rs6426368	C	T	717.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.86;MQ0=0;OQ=2201.20;QD=38.62;SB=-1092.00	GT:AD:DP:GL:GQ	1/1:0,57:56:-223.72,-16.87,-0.02:99
+chr1	4902573	rs6669905	T	C	700.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=2165.11;QD=36.09;SB=-859.36	GT:AD:DP:GL:GQ	1/1:0,60:59:-220.11,-17.77,-0.01:99
+chr1	4903007	rs6678838	G	T	279.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=56.35;MQ0=0;OQ=1768.51;QD=34.01;SB=-813.84	GT:AD:DP:GL:GQ	1/1:0,52:50:-180.45,-15.06,-0.02:99
+chr1	4903027	rs12142452	G	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.05;HRun=16;HaplotypeScore=13.19;MQ=49.10;MQ0=0;OQ=2384.03;QD=31.37;SB=-1040.48	GT:AD:DP:GL:GQ	1/1:0,72:70:-242.01,-20.48,-0.02:99
+chr1	4903364	rs9286971	G	A	258.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=52.70;MQ0=0;OQ=2159.66;QD=37.89;SB=-926.32	GT:AD:DP:GL:GQ	1/1:0,57:54:-219.56,-16.27,-0.01:99
+chr1	4904108	rs10799141	A	G	488.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.61;MQ0=0;OQ=2393.63;QD=33.71;SB=-1173.70	GT:AD:DP:GL:GQ	1/1:0,71:69:-242.98,-20.79,-0.03:99
+chr1	4904115	rs10753341	C	T	707.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.70;MQ0=0;OQ=2995.63;QD=39.42;SB=-1442.45	GT:AD:DP:GL:GQ	1/1:0,76:76:-303.17,-22.90,-0.02:99
+chr1	4904188	rs10753342	G	A	611.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3529.10;QD=39.65;SB=-1221.14	GT:AD:DP:GL:GQ	1/1:0,89:89:-351.91,-26.82,-0.03:99
+chr1	4905340	rs7531490	A	G	249.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.93;MQ0=0;OQ=2004.17;QD=30.83;SB=-867.03	GT:AD:DP:GL:GQ	1/1:0,65:64:-204.06,-19.31,-0.06:99
+chr1	4905635	rs7534281	T	C	82.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=2.19;MQ=59.65;MQ0=0;OQ=2315.03;QD=35.08;SB=-1175.74	GT:AD:DP:GL:GQ	1/1:0,66:65:-235.11,-19.58,-0.02:99
+chr1	4905656	rs7542048	G	A	139.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=59.63;MQ0=0;OQ=2472.89;QD=39.25;SB=-1234.03	GT:AD:DP:GL:GQ	1/1:0,62:62:-250.89,-18.68,-0.02:99
+chr1	4906196	rs6426371	T	C	169.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=58.85;MQ0=0;OQ=1914.58;QD=30.88;SB=-835.64	GT:AD:DP:GL:GQ	1/1:0,62:59:-195.09,-17.79,-0.04:99
+chr1	4906502	rs6426372	G	C	538.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.04;MQ0=0;OQ=3170.49;QD=42.84;SB=-1473.31	GT:AD:DP:GL:GQ	1/1:0,73:73:-320.65,-21.99,-0.02:99
+chr1	4907095	rs10915296	T	C	149.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=1.07;MQ=58.97;MQ0=0;OQ=3030.02;QD=34.83;SB=-1495.63	GT:AD:DP:GL:GQ	1/1:0,87:84:-306.61,-25.30,-0.03:99
+chr1	4907407	rs6702058	C	T	201.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=59.72;MQ0=0;OQ=3144.08;QD=38.34;SB=-1502.68	GT:AD:DP:GL:GQ	1/1:0,81:79:-318.01,-23.80,-0.02:99
+chr1	4907813	rs6677619	G	T	634.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2646.47;QD=36.25;SB=-1071.58	GT:AD:DP:GL:GQ	1/1:0,73:72:-268.25,-21.68,-0.02:99
+chr1	4909109	rs7413385	A	G	73.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=58.33;MQ0=0;OQ=950.25;QD=33.94;SB=-350.81	GT:AD:DP:GL:GQ	1/1:0,28:27:-98.62,-8.13,-0.01:81.24
+chr1	4909713	rs7413847	A	G	78.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=58.99;MQ0=0;OQ=2491.44;QD=34.13;SB=-1130.80	GT:AD:DP:GL:GQ	1/1:0,72:69:-252.75,-20.78,-0.02:99
+chr1	4909933	rs7411727	C	T	614.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=2836.35;QD=38.85;SB=-1407.70	GT:AD:DP:GL:GQ	1/1:0,73:71:-287.24,-21.39,-0.02:99
+chr1	4910002	rs10915297	T	C	288.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.37;MQ0=0;OQ=2563.56;QD=35.12;SB=-1064.10	GT:AD:DP:GL:GQ	1/1:0,73:72:-259.97,-21.69,-0.02:99
+chr1	4910067	rs10799142	G	A	129.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=58.55;MQ0=0;OQ=2372.23;QD=38.89;SB=-1035.39	GT:AD:DP:GL:GQ	1/1:0,61:60:-240.82,-18.08,-0.02:99
+chr1	4910738	rs6426373	T	C	29.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=4;HaplotypeScore=1.33;MQ=59.62;MQ0=0;OQ=2095.65;QD=34.35;SB=-1007.72	GT:AD:DP:GL:GQ	1/1:0,61:59:-213.17,-17.77,-0.02:99
+chr1	4910848	rs6664358	C	T	341.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=2577.25;QD=39.65;SB=-933.73	GT:AD:DP:GL:GQ	1/1:0,65:64:-261.33,-19.28,-0.02:99
+chr1	4911242	rs9426489	G	T	99.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=59.58;MQ0=0;OQ=1563.55;QD=28.43;SB=-641.98	GT:AD:DP:GL:GQ	1/1:2,53:45:-159.96,-13.56,-0.02:99
+chr1	4911262	rs9426490	A	G	133.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=1.03;MQ=60.00;MQ0=0;OQ=2076.79;QD=34.05;SB=-972.82	GT:AD:DP:GL:GQ	1/1:0,61:59:-211.29,-17.77,-0.02:99
+chr1	4911898	rs7522655	C	T	592.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2724.61;QD=40.67;SB=-1189.07	GT:AD:DP:GL:GQ	1/1:0,67:67:-276.06,-20.18,-0.01:99
+chr1	4911961	rs7544541	G	A	150.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=1.61;MQ=59.39;MQ0=0;OQ=2947.98;QD=38.79;SB=-1404.70	GT:AD:DP:GL:GQ	1/1:1,75:74:-298.40,-22.29,-0.02:99
+chr1	4911968	rs7544542	G	A	170.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.72;MQ0=0;OQ=3112.64;QD=37.96;SB=-1553.08	GT:AD:DP:GL:GQ	1/1:0,82:78:-314.87,-23.50,-0.02:99
+chr1	4912150	rs9426469	G	A	193	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.69;MQ0=0;OQ=2864.62;QD=38.19;SB=-1302.32	GT:AD:DP:GL:GQ	1/1:0,75:72:-290.07,-21.69,-0.02:99
+chr1	4913505	rs9426491	A	G	394.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.04;MQ0=0;OQ=3121.73;QD=35.88;SB=-1295.55	GT:AD:DP:GL:GQ	1/1:0,87:85:-315.78,-25.60,-0.02:99
+chr1	4914443	rs6692780	T	C	192.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=59.62;MQ0=0;OQ=3691.18;QD=35.84;SB=-1586.36	GT:AD:DP:GL:GQ	1/1:1,102:102:-368.12,-30.72,-0.04:99
+chr1	4914588	rs6701289	G	A	24.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=4;HaplotypeScore=1.20;MQ=58.58;MQ0=0;OQ=3206.41;QD=40.08;SB=-1396.85	GT:AD:DP:GL:GQ	1/1:0,80:78:-324.24,-23.49,-0.01:99
+chr1	4915327	rs6693486	A	T	79.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=0.67;MQ=59.04;MQ0=0;OQ=2495.92;QD=36.70;SB=-983.49	GT:AD:DP:GL:GQ	1/1:0,68:67:-253.20,-20.19,-0.02:99
+chr1	4915704	rs6656223	G	A	492.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1843.82;QD=39.23;SB=-720.96	GT:AD:DP:GL:GQ	1/1:0,47:46:-187.98,-13.86,-0.01:99
+chr1	4917206	rs12098076	G	A	321.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.37;MQ0=0;OQ=1024.17;QD=17.36;SB=-411.74	GT:AD:DP:GL:GQ	0/1:27,32:58:-123.18,-17.47,-93.16:99
+chr1	4918178	rs9426470	C	A	210.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=2272.14;QD=33.41;SB=-999.37	GT:AD:DP:GL:GQ	1/1:0,68:66:-230.83,-19.89,-0.03:99
+chr1	4918637	rs6696925	G	C	480.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=1020.90;QD=16.74;SB=-452.39	GT:AD:DP:GL:GQ	0/1:33,28:59:-123.15,-17.78,-134.82:99
+chr1	4920934	rs7546019	A	G	7.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=55.17;MQ0=0;OQ=1312.69;QD=25.74;SB=-576.91	GT:AD:DP:GL:GQ	1/1:0,51:42:-134.90,-12.67,-0.04:99
+chr1	4920939	rs10799143	A	G	1.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=9.55;MQ=55.37;MQ0=0;OQ=685.84;QD=14.29;SB=-109.82	GT:AD:DP:GL:GQ	1/1:0,38:24:-75.74,-10.17,-3.57:66.02
+chr1	4920972	rs10753343	C	T	150.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.67;MQ0=0;OQ=1219.60;QD=34.85;SB=-488.14	GT:AD:DP:GL:GQ	1/1:0,34:33:-125.56,-9.95,-0.02:99
+chr1	4921030	rs10799144	A	G	161.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=58.57;MQ0=0;OQ=1984.77;QD=33.64;SB=-769.10	GT:AD:DP:GL:GQ	1/1:0,59:57:-202.08,-17.17,-0.02:99
+chr1	4921060	rs10799145	T	G	245.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=58.90;MQ0=0;OQ=1759.60;QD=29.82;SB=-867.69	GT:AD:DP:GL:GQ	1/1:0,59:58:-179.61,-17.49,-0.06:99
+chr1	4921319	.	C	T	71.66	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=56.87;MQ0=0;OQ=1537.50;QD=20.78;SB=-754.34	GT:AD:DP:GL:GQ	0/1:29,45:71:-178.43,-21.40,-86.91:99
+chr1	4921542	.	G	A	297.10	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=827.15;QD=15.32;SB=-385.90	GT:AD:DP:GL:GQ	0/1:29,25:54:-102.27,-16.28,-92.99:99
+chr1	4921651	.	A	G	14.60	PASS	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=59.42;MQ0=0;OQ=1167.54;QD=16.22;SB=-587.69	GT:AD:DP:GL:GQ	0/1:31,41:71:-141.43,-21.39,-125.09:99
+chr1	4921748	.	T	C	1.07	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=7.77;MQ=59.39;MQ0=0;OQ=610.60;QD=12.72;SB=-231.30	GT:AD:DP:GL:GQ	0/1:26,22:47:-78.51,-14.17,-96.88:99
+chr1	4921801	.	A	G	290.73	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=740.93;QD=13.98;SB=-339.17	GT:AD:DP:GL:GQ	0/1:24,29:53:-93.36,-15.98,-94.97:99
+chr1	4921915	rs12118118	A	G	141.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=59.65;MQ0=0;OQ=641.25;QD=9.87;SB=-176.55	GT:AD:DP:GL:GQ	0/1:39,26:63:-86.39,-18.98,-152.81:99
+chr1	4922627	rs12119864	T	C	423.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=58.63;MQ0=0;OQ=1289.06;QD=15.17;SB=-556.56	GT:AD:DP:GL:GQ	0/1:33,52:81:-156.60,-24.41,-132.69:99
+chr1	4923016	rs6426374	A	G	591.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=2408.23;QD=29.37;SB=-1057.43	GT:AD:DP:GL:GQ	1/1:0,82:76:-244.48,-22.92,-0.07:99
+chr1	4923151	.	C	T	132.84	PASS	AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.33;MQ0=0;OQ=908.76;QD=16.23;SB=-453.45	GT:AD:DP:GL:GQ	0/1:28,28:56:-111.04,-16.88,-89.80:99
+chr1	4923249	.	A	G	76.65	PASS	AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=58.95;MQ0=0;OQ=491.85;QD=11.18;SB=-227.32	GT:AD:DP:GL:GQ	0/1:25,19:38:-63.92,-11.45,-77.07:99
+chr1	4923272	.	A	G	41.93	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=59.16;MQ0=0;OQ=549.57;QD=9.99;SB=-300.17	GT:AD:DP:GL:GQ	0/1:32,23:55:-74.82,-16.58,-127.48:99
+chr1	4923290	rs6702660	A	G	624.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1543.54;QD=30.27;SB=-737.76	GT:AD:DP:GL:GQ	1/1:0,51:50:-157.99,-15.08,-0.05:99
+chr1	4923916	.	G	A	53.20	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=57.14;MQ0=0;OQ=1330.08;QD=17.97;SB=-412.89	GT:AD:DP:GL:GQ	0/1:35,39:72:-157.99,-21.70,-107.79:99
+chr1	4923977	.	T	C	92.93	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=56.31;MQ0=0;OQ=878.08;QD=13.94;SB=-397.92	GT:AD:DP:GL:GQ	0/1:29,34:62:-109.78,-18.69,-109.67:99
+chr1	4924245	rs7523398	G	T	624.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.01;HRun=0;HaplotypeScore=0.00;MQ=52.50;MQ0=0;OQ=2976.14;QD=35.01;SB=-1222.44	GT:AD:DP:GL:GQ	1/1:0,84:82:-301.22,-24.40,-0.02:99
+chr1	4924289	.	C	T	145.80	Indel	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=20.35;MQ=47.42;MQ0=2;QD=1.80;SB=-17.33	GT:AD:DP:GL:GQ	0/1:69,12:76:-40.75,-22.89,-240.21:99
+chr1	4924318	.	A	G	303.69	PASS	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.53;MQ0=0;OQ=1150.10;QD=15.13;SB=-395.92	GT:AD:DP:GL:GQ	0/1:29,47:72:-140.00,-21.70,-115.03:99
+chr1	4924353	.	A	G	6.39	PASS	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=4.52;MQ=59.31;MQ0=0;OQ=1199.85;QD=16.00;SB=-524.06	GT:AD:DP:GL:GQ	0/1:32,42:73:-145.26,-21.99,-127.06:99
+chr1	4924370	.	T	G	76.39	PASS	AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=60.52;MQ0=0;OQ=1415.60;QD=18.15;SB=-500.81	GT:AD:DP:GL:GQ	0/1:31,47:78:-168.34,-23.49,-113.39:99
+chr1	4924651	rs140619	A	C	98.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.45;MQ=58.44;MQ0=0;OQ=1008.29;QD=14.00;SB=-504.32	GT:AD:DP:GL:GQ	0/1:36,36:69:-124.90,-20.78,-122.36:99
+chr1	4924659	rs140620	C	G	66.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=3.55;MQ=58.47;MQ0=0;OQ=1278.05;QD=17.51;SB=-626.38	GT:AD:DP:GL:GQ	0/1:37,36:72:-152.80,-21.71,-149.62:99
+chr1	4924842	rs3101217	G	A	427.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=60.00;MQ0=0;OQ=946.64;QD=12.46;SB=-438.36	GT:AD:DP:GL:GQ	0/1:44,31:68:-118.44,-20.49,-128.20:99
+chr1	4924889	rs3101218	G	C	576.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1334.27;QD=16.68;SB=-624.99	GT:AD:DP:GL:GQ	0/1:41,39:77:-159.91,-23.20,-177.20:99
+chr1	4924920	rs3101219	T	C	593.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=1041.98;QD=16.28;SB=-455.18	GT:AD:DP:GL:GQ	0/1:28,36:64:-126.76,-19.28,-110.51:99
+chr1	4924999	rs3101220	G	C	298.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.20;MQ0=0;OQ=811.79;QD=14.00;SB=-233.01	GT:AD:DP:GL:GQ	0/1:32,26:57:-101.64,-17.18,-138.57:99
+chr1	4925039	rs3128678	A	G	0.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=4;HaplotypeScore=3.38;MQ=59.22;MQ0=0;OQ=1744.26;QD=32.30;SB=-816.04	GT:AD:DP:GL:GQ	1/1:0,54:50:-178.03,-15.06,-0.02:99
+chr1	4925077	rs3101221	C	A	25.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=6.44;MQ=58.58;MQ0=0;OQ=647.61;QD=11.56;SB=-325.00	GT:AD:DP:GL:GQ	0/1:30,26:49:-82.82,-14.77,-78.79:99
+chr1	4925169	rs3128679	A	G	107.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=60.00;MQ0=0;OQ=535.15;QD=8.92;SB=-144.42	GT:AD:DP:GL:GQ	0/1:36,24:59:-74.58,-17.78,-140.21:99
+chr1	4925429	rs3128680	G	A	469.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=766.43;QD=14.46;SB=-348.86	GT:AD:DP:GL:GQ	0/1:29,24:53:-95.89,-15.97,-104.44:99
+chr1	4925430	rs3101222	C	G	427.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=771.83;QD=15.13;SB=-299.97	GT:AD:DP:GL:GQ	0/1:28,23:50:-95.55,-15.08,-110.57:99
+chr1	4925635	rs3101223	A	G	252.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.74;MQ0=0;OQ=1091.51;QD=12.26;SB=-378.11	GT:AD:DP:GL:GQ	0/1:48,41:87:-138.64,-26.21,-194.64:99
+chr1	4926101	rs3128681	G	A	350.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=59.68;MQ0=0;OQ=1174.87;QD=16.55;SB=-610.10	GT:AD:DP:GL:GQ	0/1:35,35:70:-141.86,-21.09,-114.49:99
+chr1	4926299	rs1017724	C	T	190.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1174.58;QD=15.06;SB=-383.10	GT:AD:DP:GL:GQ	0/1:41,37:77:-143.94,-23.19,-149.98:99
+chr1	4926372	rs1017726	A	G	298.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=887.74;QD=17.07;SB=-423.28	GT:AD:DP:GL:GQ	0/1:22,30:52:-107.72,-15.67,-84.02:99
+chr1	4926476	rs3128682	A	G	470.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=981.70;QD=13.27;SB=-502.91	GT:AD:DP:GL:GQ	0/1:33,41:71:-122.87,-21.41,-123.57:99
+chr1	4926532	rs3128683	G	T	372.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.69;MQ0=0;OQ=1069.82;QD=14.26;SB=-471.94	GT:AD:DP:GL:GQ	0/1:37,38:72:-131.95,-21.69,-128.03:99
+chr1	4926586	rs34841047	T	C	307.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.74;MQ0=0;OQ=1407.30;QD=15.64;SB=-662.64	GT:AD:DP:GL:GQ	0/1:42,48:89:-170.82,-26.81,-167.25:99
+chr1	4926613	rs7547938	A	C	101.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.79;MQ0=0;OQ=2670.20;QD=30.00;SB=-1246.34	GT:AD:DP:GL:GQ	1/1:1,88:87:-270.68,-26.22,-0.07:99
+chr1	4926617	.	G	A	38.65	PASS	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=1;HaplotypeScore=1.60;MQ=59.78;MQ0=0;OQ=1691.34;QD=19.90;SB=-782.69	GT:AD:DP:GL:GQ	0/1:36,49:84:-197.72,-25.30,-133.23:99
+chr1	4926705	rs10799146	C	G	149.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.64;MQ0=0;OQ=2201.93;QD=42.34;SB=-980.37	GT:AD:DP:GL:GQ	1/1:0,52:52:-223.80,-15.67,-0.02:99
+chr1	4926719	.	T	C	99.55	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=59.60;MQ0=0;OQ=721.00;QD=12.65;SB=-331.93	GT:AD:DP:GL:GQ	0/1:26,31:55:-91.96,-16.58,-103.71:99
+chr1	4926770	.	T	G	92.62	PASS	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=58.93;MQ0=0;OQ=842.91;QD=13.82;SB=-346.83	GT:AD:DP:GL:GQ	0/1:28,33:58:-105.05,-17.47,-101.93:99
+chr1	4926781	rs10915300	G	A	186.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=58.91;MQ0=0;OQ=2257.64;QD=37.63;SB=-1055.32	GT:AD:DP:GL:GQ	1/1:0,60:57:-229.37,-17.17,-0.02:99
+chr1	4927339	rs6426375	C	A	293.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=59.63;MQ0=0;OQ=1104.83;QD=17.54;SB=-437.22	GT:AD:DP:GL:GQ	0/1:25,38:59:-131.54,-17.77,-79.77:99
+chr1	4927361	rs12122012	G	C	449.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=855.62;QD=14.50;SB=-302.94	GT:AD:DP:GL:GQ	0/1:34,25:57:-106.02,-17.18,-140.73:99
+chr1	4927449	rs12129823	C	A	265.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=58.95;MQ0=0;OQ=867.88;QD=14.00;SB=-380.76	GT:AD:DP:GL:GQ	0/1:32,30:60:-108.15,-18.08,-97.33:99
+chr1	4927847	rs12122183	G	A	490.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1239.90;QD=16.31;SB=-577.98	GT:AD:DP:GL:GQ	0/1:38,38:75:-149.87,-22.60,-137.70:99
+chr1	4928324	rs10799147	T	G	316.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.64;MQ0=0;OQ=672.70;QD=12.94;SB=-277.80	GT:AD:DP:GL:GQ	0/1:27,25:51:-85.91,-15.36,-101.41:99
+chr1	4928782	.	A	T	20.70	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.98;MQ0=0;OQ=748.61;QD=18.26;SB=-256.98	GT:AD:DP:GL:GQ	0/1:17,24:41:-90.49,-12.35,-66.37:99
+chr1	4930115	rs10799148	T	G	517.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=2291.16;QD=34.71;SB=-1027.09	GT:AD:DP:GL:GQ	1/1:0,66:65:-232.72,-19.58,-0.02:99
+chr1	4930427	rs34645017	G	C	291.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=722.42;QD=16.05;SB=-202.61	GT:AD:DP:GL:GQ	0/1:25,20:45:-89.08,-13.56,-109.77:99
+chr1	4930735	rs11578909	A	G	280.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.36;MQ0=0;OQ=698.77;QD=12.05;SB=-374.99	GT:AD:DP:GL:GQ	0/1:29,28:57:-90.34,-17.18,-117.72:99
+chr1	4931239	rs10799149	G	A	641.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.08;MQ0=0;OQ=2438.74;QD=39.98;SB=-916.20	GT:AD:DP:GL:GQ	1/1:0,61:60:-247.47,-18.07,-0.01:99
+chr1	4931421	rs7518523	A	G	261.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.88;MQ0=0;OQ=2083.34;QD=31.09;SB=-1042.40	GT:AD:DP:GL:GQ	1/1:0,67:65:-211.96,-19.60,-0.05:99
+chr1	4931997	rs10753344	T	C	618.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2888.62;QD=33.98;SB=-1001.71	GT:AD:DP:GL:GQ	1/1:0,85:82:-292.48,-24.71,-0.04:99
+chr1	4932316	rs12127329	G	A	183.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=2411.54;QD=39.53;SB=-1136.02	GT:AD:DP:GL:GQ	1/1:0,61:61:-244.76,-18.38,-0.02:99
+chr1	4932881	rs11585724	C	T	291.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=59.24;MQ0=0;OQ=985.86;QD=16.16;SB=-484.11	GT:AD:DP:GL:GQ	0/1:30,31:59:-119.65,-17.78,-92.67:99
+chr1	4932899	rs56016205	G	C	205.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=58.78;MQ0=0;OQ=942.89;QD=16.54;SB=-283.52	GT:AD:DP:GL:GQ	0/1:30,27:56:-114.45,-16.88,-128.26:99
+chr1	4933102	rs56190527	G	A	17.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=7.39;MQ=59.07;MQ0=0;OQ=754.79;QD=15.10;SB=-398.92	GT:AD:DP:GL:GQ	0/1:26,24:48:-93.22,-14.46,-90.86:99
+chr1	4933190	rs56216708	T	C	104.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.13;MQ0=0;OQ=1884.00;QD=35.55;SB=-879.00	GT:AD:DP:GL:GQ	1/1:0,53:53:-192.00,-15.97,-0.02:99
+chr1	4933296	.	G	A	768.22	SnpCluster	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.45;MQ0=0;QD=12.59;SB=-376.12	GT:AD:DP:GL:GQ	0/1:35,26:58:-97.59,-17.48,-110.76:99
+chr1	4933297	.	C	T	815.45	SnpCluster	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.45;MQ0=0;QD=13.37;SB=-431.91	GT:AD:DP:GL:GQ	0/1:35,26:61:-103.20,-18.37,-126.35:99
+chr1	4933303	.	G	A	803.12	SnpCluster	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.37;MQ0=0;QD=13.39;SB=-365.85	GT:AD:DP:GL:GQ	0/1:35,25:58:-101.08,-17.48,-105.94:99
+chr1	4933521	rs7535462	G	A	371.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=1957.02;QD=39.14;SB=-986.02	GT:AD:DP:GL:GQ	1/1:0,50:49:-199.30,-14.76,-0.01:99
+chr1	4933673	.	C	G	6.69	PASS	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=58.23;MQ0=0;OQ=1494.10;QD=22.64;SB=-505.26	GT:AD:DP:GL:GQ	0/1:26,40:63:-171.68,-18.99,-100.63:99
+chr1	4934014	rs12128545	G	A	43.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.74;MQ=59.66;MQ0=0;OQ=1421.27;QD=20.90;SB=-664.71	GT:AD:DP:GL:GQ	0/1:27,41:67:-165.59,-20.18,-95.71:99
+chr1	4934078	rs12136209	C	G	149.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.61;MQ=60.00;MQ0=0;OQ=1636.42;QD=21.82;SB=-832.32	GT:AD:DP:GL:GQ	0/1:31,44:75:-189.53,-22.60,-132.33:99
+chr1	4934416	rs12126894	T	G	441.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.57;MQ0=0;OQ=586.00;QD=11.49;SB=-304.83	GT:AD:DP:GL:GQ	0/1:29,22:51:-77.25,-15.36,-105.02:99
+chr1	4935048	rs10915303	A	G	334.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=51.50;MQ0=0;OQ=770.15;QD=12.84;SB=-364.97	GT:AD:DP:GL:GQ	0/1:27,33:52:-95.98,-15.68,-87.76:99
+chr1	4935474	rs34001007	G	A	343.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=962.36;QD=16.88;SB=-495.13	GT:AD:DP:GL:GQ	0/1:27,30:56:-116.40,-16.88,-86.00:99
+chr1	4935789	rs12128035	T	C	226.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=58.94;MQ0=0;OQ=796.37;QD=12.64;SB=-306.28	GT:AD:DP:GL:GQ	0/1:34,29:62:-101.60,-18.68,-137.85:99
+chr1	4936034	rs6689050	G	C	388.76	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1874.06;QD=42.59;SB=-652.91	GT:AD:DP:GL:GQ	1/1:0,44:44:-191.00,-13.26,-0.01:99
+chr1	4936094	rs12757902	G	A	302.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=59.62;MQ0=0;OQ=578.28;QD=11.80;SB=-268.20	GT:AD:DP:GL:GQ	0/1:27,21:43:-74.09,-12.98,-70.80:99
+chr1	4936362	rs12126016	G	T	367.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.41;MQ0=0;OQ=1064.42;QD=14.99;SB=-543.63	GT:AD:DP:GL:GQ	0/1:34,37:71:-131.11,-21.39,-120.19:99
+chr1	4936409	rs11581023	G	A	329.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=58.70;MQ0=0;OQ=1088.63;QD=16.49;SB=-413.38	GT:AD:DP:GL:GQ	0/1:32,34:63:-131.13,-18.99,-102.39:99
+chr1	4936482	rs12122541	A	G	353.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.04;MQ0=0;OQ=684.77;QD=12.45;SB=-247.32	GT:AD:DP:GL:GQ	0/1:27,28:52:-87.43,-15.67,-100.04:99
+chr1	4936602	rs11584985	C	T	191.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=59.29;MQ0=0;OQ=1088.30;QD=18.45;SB=-387.41	GT:AD:DP:GL:GQ	0/1:25,34:57:-129.30,-17.18,-77.34:99
+chr1	4936637	rs898335	T	G	589.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=2347.69;QD=35.57;SB=-808.10	GT:AD:DP:GL:GQ	1/1:0,66:66:-238.37,-19.88,-0.02:99
+chr1	4937911	rs12739724	G	A	135.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=59.34;MQ0=0;OQ=1173.07;QD=20.58;SB=-518.55	GT:AD:DP:GL:GQ	0/1:24,33:57:-137.76,-17.17,-89.96:99
+chr1	4937953	rs6666618	A	C	126.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=2.81;MQ=60.00;MQ0=0;OQ=1008.55;QD=15.28;SB=-391.76	GT:AD:DP:GL:GQ	0/1:30,36:65:-123.72,-19.58,-111.64:99
+chr1	4939240	rs1841241	A	G	358.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=59.68;MQ0=0;OQ=900.69;QD=12.34;SB=-390.90	GT:AD:DP:GL:GQ	0/1:37,36:72:-115.05,-21.70,-146.81:99
+chr1	4939654	rs6660626	C	G	245.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=59.55;MQ0=0;OQ=1495.04;QD=18.01;SB=-651.03	GT:AD:DP:GL:GQ	0/1:41,42:81:-177.21,-24.42,-163.44:99
+chr1	4940611	.	A	G	75.27	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.50;MQ0=0;OQ=761.25;QD=16.55;SB=-322.41	GT:AD:DP:GL:GQ	0/1:18,28:44:-92.67,-13.26,-69.31:99
+chr1	4941180	rs12138041	C	G	147.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.43;MQ0=0;OQ=1446.36;QD=22.25;SB=-675.09	GT:AD:DP:GL:GQ	0/1:27,38:64:-167.20,-19.28,-114.12:99
+chr1	4941754	rs6426376	A	C	0.05	FDRtranche0.10to1.00	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=6;HaplotypeScore=1.65;MQ=58.89;MQ0=0;OQ=2125.54;QD=33.74;SB=-942.08	GT:AD:DP:GL:GQ	1/1:0,63:61:-216.16,-18.37,-0.02:99
+chr1	4942581	.	C	G	69.18	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.19;MQ0=0;OQ=1081.86;QD=18.98;SB=-432.32	GT:AD:DP:GL:GQ	0/1:28,29:57:-128.65,-17.18,-121.65:99
+chr1	4942801	rs12132419	G	A	594.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=1256.99;QD=16.76;SB=-497.49	GT:AD:DP:GL:GQ	0/1:35,40:73:-150.98,-21.99,-126.45:99
+chr1	4943594	rs1563791	C	A	403.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.68;MQ0=0;OQ=828.65;QD=15.63;SB=-357.20	GT:AD:DP:GL:GQ	0/1:25,28:53:-102.11,-15.96,-89.65:99
+chr1	4943942	rs10737391	T	A	518.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=2837.87;QD=37.84;SB=-993.50	GT:AD:DP:GL:GQ	1/1:0,75:74:-287.39,-22.29,-0.02:99
+chr1	4943949	rs6674570	C	G	129.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.29;MQ0=0;OQ=3029.36;QD=43.28;SB=-1059.65	GT:AD:DP:GL:GQ	1/1:0,70:69:-306.54,-20.79,-0.02:99
+chr1	4943976	rs6689766	T	C	365.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=56.77;MQ0=0;OQ=827.54;QD=14.03;SB=-391.26	GT:AD:DP:GL:GQ	0/1:29,30:57:-103.21,-17.17,-110.62:99
+chr1	4943997	rs6698166	G	T	369.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=57.73;MQ0=0;OQ=860.15;QD=13.87;SB=-411.14	GT:AD:DP:GL:GQ	0/1:31,31:60:-107.37,-18.08,-104.72:99
+chr1	4943998	rs6698167	G	A	353.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=57.73;MQ0=0;OQ=1051.24;QD=16.96;SB=-519.06	GT:AD:DP:GL:GQ	0/1:30,32:61:-126.79,-18.38,-103.11:99
+chr1	4944360	rs12131010	A	G	342.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.85;MQ0=0;OQ=760.68;QD=9.88;SB=-317.87	GT:AD:DP:GL:GQ	0/1:43,34:75:-101.96,-22.60,-172.57:99
+chr1	4944890	rs1106586	G	A	276.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=59.59;MQ0=0;OQ=802.40;QD=14.33;SB=-392.78	GT:AD:DP:GL:GQ	0/1:30,26:55:-100.10,-16.58,-95.63:99
+chr1	4945646	rs898336	G	C	25.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=96;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=56.72;MQ0=0;OQ=4154.41;QD=43.28;SB=-1921.01	GT:AD:DP:GL:GQ	1/1:0,96:94:-414.44,-28.32,-0.03:99
+chr1	4945654	rs7417805	T	C	207.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=101;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.30;MQ0=0;OQ=3685.03;QD=36.49;SB=-1843.78	GT:AD:DP:GL:GQ	1/1:0,101:100:-367.50,-30.12,-0.02:99
+chr1	4946090	rs12046931	C	T	231	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=56.28;MQ0=0;OQ=1030.23;QD=13.56;SB=-511.04	GT:AD:DP:GL:GQ	0/1:44,32:74:-128.62,-22.31,-131.20:99
+chr1	4946898	rs6679312	A	G	627.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=2846.93;QD=36.04;SB=-1277.52	GT:AD:DP:GL:GQ	1/1:0,79:79:-288.30,-23.79,-0.02:99
+chr1	4947277	.	A	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=1;HaplotypeScore=4.31;MQ=58.55;MQ0=0;OQ=58.76;QD=0.92;SB=83.26	GT:AD:DP:GL:GQ	0/1:39,25:47:-23.33,-14.17,-133.19:91.60
+chr1	4947969	rs716671	G	T	362.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=59.37;MQ0=0;OQ=959.61;QD=14.54;SB=-385.78	GT:AD:DP:GL:GQ	0/1:32,34:63:-118.22,-18.98,-106.13:99
+chr1	4948484	rs7541612	T	C	301.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.16;MQ0=0;OQ=2459.32;QD=34.16;SB=-1006.88	GT:AD:DP:GL:GQ	1/1:0,72:70:-249.54,-21.08,-0.02:99
+chr1	4948794	rs10737392	A	C	185.94	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2094.20;QD=29.50;SB=-992.36	GT:AD:DP:GL:GQ	1/1:0,71:69:-213.07,-20.80,-0.07:99
+chr1	4951092	rs12725971	A	G	439.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.52;MQ0=0;OQ=1026.84;QD=13.16;SB=-423.90	GT:AD:DP:GL:GQ	0/1:43,35:78:-129.46,-23.49,-174.67:99
+chr1	4951570	rs6683624	C	T	353.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=59.06;MQ0=0;OQ=1065.83;QD=15.45;SB=-486.02	GT:AD:DP:GL:GQ	0/1:35,34:67:-130.05,-20.19,-121.88:99
+chr1	4953123	rs7418901	T	C	620.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=2650.80;QD=31.56;SB=-1309.87	GT:AD:DP:GL:GQ	1/1:0,84:83:-268.73,-25.03,-0.06:99
+chr1	4955464	rs1459754	T	C	197.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.56;MQ0=0;OQ=2710.14;QD=31.88;SB=-1351.75	GT:AD:DP:GL:GQ	1/1:0,85:84:-274.67,-25.33,-0.07:99
+chr1	4956424	rs12566071	T	C	456.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.68;MQ0=0;OQ=1092.05;QD=27.30;SB=-412.16	GT:AD:DP:GL:GQ	1/1:0,40:36:-112.83,-10.86,-0.04:99
+chr1	4956725	rs12047194	C	T	71.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.61;MQ=60.00;MQ0=0;OQ=1049.88;QD=16.93;SB=-178.21	GT:AD:DP:GL:GQ	0/1:29,33:61:-126.65,-18.37,-103.04:99
+chr1	4957085	.	G	A	6.71	PASS	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.62;MQ0=0;OQ=1318.00;QD=21.61;SB=-441.83	GT:AD:DP:GL:GQ	0/1:23,38:60:-153.16,-18.08,-75.01:99
+chr1	4957708	rs9701766	C	T	287.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.24;MQ0=0;OQ=1921.26;QD=34.93;SB=-917.67	GT:AD:DP:GL:GQ	1/1:0,55:50:-195.73,-15.07,-0.02:99
+chr1	4957732	rs12134477	T	G	328.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=59.35;MQ0=0;OQ=737.05;QD=11.52;SB=-389.76	GT:AD:DP:GL:GQ	0/1:34,30:62:-95.67,-18.68,-123.44:99
+chr1	4960336	rs9286972	T	C	80.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=3;HaplotypeScore=0.87;MQ=59.38;MQ0=0;OQ=2352.51;QD=35.11;SB=-877.01	GT:AD:DP:GL:GQ	1/1:0,67:65:-238.86,-19.58,-0.02:99
+chr1	4960363	rs9286973	A	G	217.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.91;MQ=58.74;MQ0=0;OQ=2328.65;QD=33.27;SB=-776.20	GT:AD:DP:GL:GQ	1/1:0,68:66:-236.47,-19.88,-0.02:99
+chr1	4960544	rs10158116	T	C	435.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=930.68;QD=33.24;SB=-423.17	GT:AD:DP:GL:GQ	1/1:0,28:27:-96.66,-8.13,-0.01:81.23
+chr1	4961077	rs1380469	C	T	600.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3571.25;QD=40.58;SB=-1432.72	GT:AD:DP:GL:GQ	1/1:0,88:87:-356.13,-26.20,-0.02:99
+chr1	4961379	rs10158288	T	C	503.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2541.28;QD=30.99;SB=-793.00	GT:AD:DP:GL:GQ	1/1:0,82:80:-257.79,-24.13,-0.07:99
+chr1	4963153	rs10915307	G	A	69.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=1.45;MQ=59.07;MQ0=0;OQ=713.61;QD=14.27;SB=-252.29	GT:AD:DP:GL:GQ	0/1:25,25:45:-88.21,-13.57,-68.76:99
+chr1	4964065	rs10737393	G	C	566.31	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1749.68;QD=40.69;SB=-797.25	GT:AD:DP:GL:GQ	1/1:0,43:42:-178.57,-12.66,-0.02:99
+chr1	4964532	rs28667637	T	C	501.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1316.20;QD=16.05;SB=-509.69	GT:AD:DP:GL:GQ	0/1:33,49:82:-159.62,-24.71,-131.78:99
+chr1	4964976	rs12027167	C	T	376.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.50;MQ0=0;OQ=1085.57;QD=14.47;SB=-544.31	GT:AD:DP:GL:GQ	0/1:42,33:75:-134.44,-22.60,-148.57:99
+chr1	4965052	rs28444318	G	A	401.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.69;MQ0=0;OQ=1204.51;QD=18.82;SB=-457.96	GT:AD:DP:GL:GQ	0/1:28,36:62:-142.42,-18.68,-88.92:99
+chr1	4965449	rs10915308	C	T	686.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=2543.15;QD=38.53;SB=-937.28	GT:AD:DP:GL:GQ	1/1:0,66:64:-257.91,-19.28,-0.02:99
+chr1	4965556	rs12123277	C	A	350.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=722.36;QD=9.63;SB=-338.31	GT:AD:DP:GL:GQ	0/1:48,27:74:-97.81,-22.29,-174.39:99
+chr1	4965577	rs1380470	A	G	738.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2392.77;QD=36.25;SB=-1196.76	GT:AD:DP:GL:GQ	1/1:0,66:66:-242.88,-19.88,-0.01:99
+chr1	4965710	rs10915309	G	A	204.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=59.60;MQ0=0;OQ=2319.12;QD=39.98;SB=-986.30	GT:AD:DP:GL:GQ	1/1:0,58:58:-235.51,-17.47,-0.02:99
+chr1	4968070	rs10915310	A	G	390.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.15;MQ0=0;OQ=1179.59;QD=14.39;SB=-449.76	GT:AD:DP:GL:GQ	0/1:38,44:81:-145.65,-24.41,-157.59:99
+chr1	4968105	rs10799151	A	G	154.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=3.73;MQ=58.89;MQ0=0;OQ=1031.60;QD=12.74;SB=-406.80	GT:AD:DP:GL:GQ	0/1:40,41:78:-129.95,-23.51,-157.15:99
+chr1	4968710	.	C	G	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=53.48;MQ0=0;OQ=64.03;QD=1.56;SB=-49.12	GT:AD:DP:GL:GQ	0/1:36,5:37:-20.84,-11.15,-143.24:96.86
+chr1	4968815	rs10915311	A	C	217.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.03;MQ0=0;OQ=2004.53;QD=29.92;SB=-920.78	GT:AD:DP:GL:GQ	1/1:0,66:64:-204.09,-19.29,-0.06:99
+chr1	4969030	rs34951087	G	T	218.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.09;MQ0=0;OQ=572.86;QD=11.23;SB=-277.34	GT:AD:DP:GL:GQ	0/1:30,21:51:-75.93,-15.36,-106.99:99
+chr1	4970267	rs10915312	A	G	154.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=1.56;MQ=58.90;MQ0=0;OQ=985.64;QD=12.32;SB=-409.96	GT:AD:DP:GL:GQ	0/1:41,39:79:-125.65,-23.81,-166.76:99
+chr1	4970523	rs12045336	A	G	132	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.57;MQ=59.62;MQ0=0;OQ=1080.57;QD=17.71;SB=-383.65	GT:AD:DP:GL:GQ	0/1:25,36:60:-129.41,-18.07,-101.07:99
+chr1	4971344	.	A	C	49.60	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=0;HaplotypeScore=45.73;MQ=55.38;MQ0=0;QD=0.57;SB=95.30	GT:AD:DP:GL:GQ	0/1:77,10:78:-31.75,-23.50,-240.44:82.44
+chr1	4972155	rs1870516	C	T	119.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=2;HaplotypeScore=2.64;MQ=59.76;MQ0=0;OQ=1584.03;QD=16.67;SB=-599.54	GT:AD:DP:GL:GQ	0/1:49,46:91:-189.10,-27.42,-151.90:99
+chr1	4972838	rs1459756	T	C	570.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=978.37;QD=13.22;SB=-505.27	GT:AD:DP:GL:GQ	0/1:38,36:72:-122.81,-21.69,-153.16:99
+chr1	4972952	rs9286975	G	A	397.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2673.75;QD=39.91;SB=-1305.72	GT:AD:DP:GL:GQ	1/1:0,67:67:-270.98,-20.18,-0.02:99
+chr1	4973015	rs9662653	T	A	589.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.20;MQ0=0;OQ=1272.49;QD=16.74;SB=-576.01	GT:AD:DP:GL:GQ	0/1:36,40:76:-153.42,-22.89,-135.61:99
+chr1	4973096	rs9701780	T	C	360.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.34;MQ0=0;OQ=907.74;QD=12.97;SB=-427.52	GT:AD:DP:GL:GQ	0/1:38,32:70:-115.14,-21.08,-154.90:99
+chr1	4973099	rs1459757	A	G	435.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.36;MQ0=0;OQ=906.72;QD=12.59;SB=-477.95	GT:AD:DP:GL:GQ	0/1:40,32:72:-115.64,-21.69,-161.61:99
+chr1	4973396	rs10753346	T	C	325.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.65;MQ0=0;OQ=745.38;QD=11.29;SB=-293.22	GT:AD:DP:GL:GQ	0/1:39,27:65:-97.40,-19.58,-152.44:99
+chr1	4973518	rs10799152	A	C	461.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.77;MQ0=0;OQ=1062.89;QD=13.29;SB=-461.68	GT:AD:DP:GL:GQ	0/1:43,37:80:-133.67,-24.09,-159.84:99
+chr1	4974497	rs35292186	A	G	69.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=59.78;MQ0=0;OQ=1148.97;QD=13.84;SB=-573.87	GT:AD:DP:GL:GQ	0/1:43,40:81:-142.58,-24.40,-174.12:99
+chr1	4976182	rs10915314	G	C	291.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=1306.22;QD=17.65;SB=-415.30	GT:AD:DP:GL:GQ	0/1:38,36:73:-155.90,-22.00,-163.97:99
+chr1	4977412	rs12047764	T	C	324.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.63;MQ0=0;OQ=712.65;QD=11.49;SB=-368.84	GT:AD:DP:GL:GQ	0/1:33,29:62:-93.24,-18.69,-135.85:99
+chr1	4978209	rs10915315	A	G	314.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.17;MQ0=0;OQ=593.55;QD=8.73;SB=-263.22	GT:AD:DP:GL:GQ	0/1:42,26:67:-82.83,-20.19,-168.85:99
+chr1	4978799	rs10915316	T	C	253.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=3.42;MQ=59.03;MQ0=0;OQ=793.88;QD=11.03;SB=-421.21	GT:AD:DP:GL:GQ	0/1:40,31:69:-103.46,-20.78,-159.70:99
+chr1	4980236	.	G	A	100.41	PASS	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=1786.33;QD=21.02;SB=-886.64	GT:AD:DP:GL:GQ	0/1:34,51:83:-206.92,-25.00,-119.27:99
+chr1	4980926	rs10915317	T	C	438.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.66;MQ0=0;OQ=838.53;QD=12.33;SB=-314.09	GT:AD:DP:GL:GQ	0/1:34,34:67:-107.33,-20.19,-138.42:99
+chr1	4981033	rs898337	G	A	348.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.70;MQ0=0;OQ=1302.29;QD=16.91;SB=-502.50	GT:AD:DP:GL:GQ	0/1:36,41:75:-156.11,-22.60,-126.45:99
+chr1	4981597	rs7516703	C	T	165.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=60.19;MQ0=0;OQ=561.42;QD=9.85;SB=-184.86	GT:AD:DP:GL:GQ	0/1:36,21:54:-75.71,-16.28,-112.37:99
+chr1	4982000	rs10799153	A	G	596.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.94;MQ0=0;OQ=1157.46;QD=16.30;SB=-464.59	GT:AD:DP:GL:GQ	0/1:32,39:71:-140.42,-21.40,-120.74:99
+chr1	4983908	.	G	A	17.79	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=16;HaplotypeScore=7.18;MQ=55.71;MQ0=0;QD=0.27;SB=86.25	GT:AD:DP:GL:GQ	0/1:51,16:49:-19.83,-14.77,-145.36:50.55
+chr1	4985809	rs9439574	C	T	11.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=4;HaplotypeScore=0.16;MQ=58.95;MQ0=0;OQ=1576.28;QD=19.70;SB=-625.03	GT:AD:DP:GL:GQ	0/1:34,46:79:-184.71,-23.79,-124.63:99
+chr1	4985815	rs9439575	A	G	487	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.98;MQ0=0;OQ=1410.52;QD=17.20;SB=-545.94	GT:AD:DP:GL:GQ	0/1:36,46:82:-169.04,-24.70,-144.72:99
+chr1	4986567	rs10218468	A	C	245.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.31;MQ0=0;OQ=789.54;QD=11.78;SB=-394.67	GT:AD:DP:GL:GQ	0/1:34,33:66:-102.12,-19.88,-128.07:99
+chr1	4987124	rs10442625	A	G	373.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=59.63;MQ0=0;OQ=720.29;QD=11.43;SB=-219.26	GT:AD:DP:GL:GQ	0/1:37,26:62:-93.99,-18.68,-145.68:99
+chr1	4988477	rs2169089	A	G	373.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.69;MQ0=0;OQ=1114.19;QD=14.86;SB=-356.97	GT:AD:DP:GL:GQ	0/1:29,45:72:-136.41,-21.71,-118.67:99
+chr1	4988875	rs716112	A	G	453.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=842.62;QD=12.58;SB=-426.87	GT:AD:DP:GL:GQ	0/1:33,34:66:-107.44,-19.90,-129.75:99
+chr1	4990575	rs1459764	C	T	573.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=1234.93;QD=15.63;SB=-612.07	GT:AD:DP:GL:GQ	0/1:42,37:78:-150.28,-23.50,-132.81:99
+chr1	4990857	rs9439507	A	G	285	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.35;MQ0=0;OQ=2461.09;QD=34.66;SB=-1130.69	GT:AD:DP:GL:GQ	1/1:0,71:71:-249.72,-21.39,-0.03:99
+chr1	4991092	rs10442626	G	C	211.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.60;MQ0=0;OQ=718.97;QD=12.61;SB=-159.21	GT:AD:DP:GL:GQ	0/1:31,26:54:-91.46,-16.28,-132.88:99
+chr1	4991687	rs4949164	A	G	470.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1103.70;QD=13.80;SB=-401.93	GT:AD:DP:GL:GQ	0/1:38,42:79:-137.46,-23.80,-155.83:99
+chr1	4993546	rs7533014	T	C	526.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1036.32;QD=11.39;SB=-442.91	GT:AD:DP:GL:GQ	0/1:49,42:90:-134.04,-27.12,-197.59:99
+chr1	4993852	rs11580542	A	G	170.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=650.23;QD=9.56;SB=-317.81	GT:AD:DP:GL:GQ	0/1:43,25:66:-88.19,-19.88,-168.41:99
+chr1	4994065	.	C	T	20.53	PASS	AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1330.95;QD=18.75;SB=-592.09	GT:AD:DP:GL:GQ	0/1:33,38:71:-157.76,-21.38,-120.30:99
+chr1	4994295	rs6693990	G	A	335.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=57.88;MQ0=0;OQ=1019.69;QD=16.19;SB=-465.42	GT:AD:DP:GL:GQ	0/1:31,32:60:-123.32,-18.07,-111.15:99
+chr1	4994563	rs1459763	A	G	13.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=5.21;MQ=58.04;MQ0=0;OQ=377.66;QD=9.21;SB=-181.57	GT:AD:DP:GL:GQ	0/1:25,16:38:-52.50,-11.45,-93.25:99
+chr1	4995722	rs1459762	C	T	513.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=1249.58;QD=19.22;SB=-511.06	GT:AD:DP:GL:GQ	0/1:27,38:64:-147.53,-19.29,-84.78:99
+chr1	4996533	.	T	G	102.56	PASS	AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.08;MQ0=0;OQ=597.86;QD=9.80;SB=-320.69	GT:AD:DP:GL:GQ	0/1:35,26:61:-81.45,-18.38,-132.05:99
+chr1	4999697	.	C	G	5.71	PASS	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.53;MQ0=0;OQ=2076.06;QD=23.59;SB=-758.01	GT:AD:DP:GL:GQ	0/1:34,54:87:-237.12,-26.23,-133.95:99
+chr1	4999785	.	A	G	153.89	PASS	AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=59.42;MQ0=0;OQ=950.41;QD=13.20;SB=-485.20	GT:AD:DP:GL:GQ	0/1:39,33:71:-119.71,-21.39,-153.18:99
+chr1	5000124	rs35565495	A	G	217.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=57.68;MQ0=0;OQ=905.68;QD=12.41;SB=-443.62	GT:AD:DP:GL:GQ	0/1:40,33:73:-115.85,-22.00,-156.82:99
+chr1	5000551	rs1459761	A	G	316.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=59.68;MQ0=0;OQ=1082.64;QD=18.35;SB=-522.18	GT:AD:DP:GL:GQ	0/1:24,35:59:-129.32,-17.77,-97.53:99
+chr1	5002004	rs12403444	A	G	454.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=59.69;MQ0=0;OQ=1008.17;QD=13.62;SB=-385.25	GT:AD:DP:GL:GQ	0/1:38,36:71:-125.49,-21.39,-141.83:99
+chr1	5002384	rs12403749	A	G	334.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.18;MQ0=0;OQ=762.42;QD=12.92;SB=-306.27	GT:AD:DP:GL:GQ	0/1:32,27:59:-97.30,-17.77,-132.93:99
+chr1	5002965	rs55998096	C	T	265.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1237.12;QD=16.95;SB=-623.66	GT:AD:DP:GL:GQ	0/1:35,38:72:-148.68,-21.69,-128.69:99
+chr1	5003908	rs1459759	T	G	287.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=59.68;MQ0=0;OQ=1018.83;QD=14.15;SB=-495.74	GT:AD:DP:GL:GQ	0/1:34,38:70:-126.25,-21.08,-125.30:99
+chr1	5004548	.	C	T	0.18	PASS	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=4;HaplotypeScore=0.97;MQ=55.65;MQ0=0;OQ=1952.83;QD=19.15;SB=-933.54	GT:AD:DP:GL:GQ	0/1:44,58:102:-229.30,-30.73,-156.88:99
+chr1	5004874	rs55883351	G	A	211.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=41.17;MQ0=0;OQ=1434.24;QD=17.49;SB=-707.75	GT:AD:DP:GL:GQ	0/1:39,43:79:-170.52,-23.81,-118.83:99
+chr1	5005796	.	T	G	22.56	PASS	AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=52.68;MQ0=0;OQ=1101.12;QD=15.73;SB=-417.74	GT:AD:DP:GL:GQ	0/1:29,41:66:-133.27,-19.88,-106.95:99
+chr1	5005889	rs10737394	A	G	342.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.43;MQ0=0;OQ=434.38;QD=9.05;SB=-233.28	GT:AD:DP:GL:GQ	0/1:27,21:46:-60.59,-13.87,-106.69:99
+chr1	5006532	rs10799156	G	C	195.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=38.14;MQ0=9;OQ=508.53;QD=10.38;SB=-226.35	GT:AD:DP:GL:GQ	0/1:19,30:34:-64.39,-10.25,-81.21:99
+chr1	5007005	rs6603829	T	C	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=16.12;MQ=27.87;MQ0=17;OQ=171.08;QD=2.19;SB=-108.70	GT:AD:DP:GL:GQ	0/1:51,27:35:-30.94,-10.55,-97.26:99
+chr1	5007006	rs6603830	G	A	0.04	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=18.32;MQ=27.85;MQ0=18;OQ=165.82;QD=2.13;SB=-81.55	GT:AD:DP:GL:GQ	0/1:59,19:36:-30.72,-10.85,-97.29:99
+chr1	5007287	.	C	G	0.46	PASS	AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=8.19;MQ=48.27;MQ0=4;OQ=754.87;QD=14.52;SB=-244.08	GT:AD:DP:GL:GQ	0/1:26,25:44:-92.04,-13.27,-89.64:99
+chr1	5007421	.	A	G	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=1;HaplotypeScore=5.43;MQ=22.24;MQ0=26;OQ=110.20;QD=1.12;SB=7.49	GT:AD:DP:GL:GQ	0/1:85,12:42:-26.95,-12.65,-140.65:99
+chr1	5007424	.	G	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=2;HaplotypeScore=3.53;MQ=23.00;MQ0=24;OQ=143.47;QD=1.54;SB=3.27	GT:AD:DP:GL:GQ	0/1:81,12:42:-30.29,-12.66,-152.47:99
+chr1	5011084	.	C	G	46.29	PASS	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=45.50;MQ0=2;OQ=1885.25;QD=20.27;SB=-717.97	GT:AD:DP:GL:GQ	0/1:41,52:88:-218.32,-26.51,-163.98:99
+chr1	5011731	.	C	T	18.24	PASS	AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=2;HaplotypeScore=0.79;MQ=54.65;MQ0=1;OQ=1577.37;QD=18.13;SB=-623.62	GT:AD:DP:GL:GQ	0/1:41,46:86:-186.92,-25.90,-147.64:99
+chr1	5012084	rs10915327	C	T	347.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=48.94;MQ0=2;OQ=1240.99;QD=17.24;SB=-606.09	GT:AD:DP:GL:GQ	0/1:32,40:68:-147.88,-20.49,-101.20:99
+chr1	5012508	.	G	A	165.62	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=34.81;MQ0=2;OQ=954.73;QD=16.75;SB=-470.48	GT:AD:DP:GL:GQ	0/1:23,33:48:-113.23,-14.48,-57.23:99
+chr1	5014453	.	C	A	65.76	PASS	AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=59.79;MQ0=0;OQ=1613.72;QD=18.13;SB=-734.55	GT:AD:DP:GL:GQ	0/1:38,51:88:-191.16,-26.50,-131.97:99
+chr1	5016018	.	T	G	165.96	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=1295.09;QD=17.50;SB=-624.73	GT:AD:DP:GL:GQ	0/1:31,43:74:-155.08,-22.29,-116.52:99
+chr1	5018516	rs4262591	A	T	76.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=2;HaplotypeScore=0.94;MQ=59.27;MQ0=0;OQ=1137.62;QD=12.78;SB=-520.24	GT:AD:DP:GL:GQ	0/1:50,39:87:-143.25,-26.20,-190.22:99
+chr1	5020923	rs970119	A	C	493.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=718.78;QD=10.27;SB=-241.77	GT:AD:DP:GL:GQ	0/1:40,30:69:-95.95,-20.78,-149.31:99
+chr1	5023267	.	C	G	91.77	PASS	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=800.92;QD=19.07;SB=-315.01	GT:AD:DP:GL:GQ	0/1:20,22:41:-95.73,-12.36,-81.61:99
+chr1	5024719	rs1563792	G	A	196.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.54;MQ0=0;OQ=1348.55;QD=16.45;SB=-599.05	GT:AD:DP:GL:GQ	0/1:42,40:80:-162.25,-24.11,-132.60:99
+chr1	5027451	rs56184292	G	T	6.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=4;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1415.10;QD=15.05;SB=-721.57	GT:AD:DP:GL:GQ	0/1:44,49:93:-172.81,-28.02,-154.91:99
+chr1	5029434	rs2061494	T	A	49.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=59.72;MQ0=0;OQ=1567.79;QD=19.36;SB=-635.43	GT:AD:DP:GL:GQ	0/1:33,47:79:-183.86,-23.79,-122.93:99
+chr1	5029438	rs2061493	T	A	66.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=59.72;MQ0=0;OQ=1477.11;QD=18.24;SB=-663.80	GT:AD:DP:GL:GQ	0/1:33,48:80:-175.09,-24.10,-128.48:99
+chr1	5029774	rs55724572	C	A	223.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.17;MQ0=0;OQ=1394.44;QD=13.81;SB=-671.07	GT:AD:DP:GL:GQ	0/1:55,46:101:-173.14,-30.41,-200.20:99
+chr1	5029802	rs56297253	G	A	420.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.18;MQ0=0;OQ=1452.74;QD=14.24;SB=-632.72	GT:AD:DP:GL:GQ	0/1:58,44:100:-178.69,-30.14,-182.65:99
+chr1	5030141	rs1459758	C	G	545.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2835.80;QD=42.33;SB=-1264.90	GT:AD:DP:GL:GQ	1/1:0,67:65:-287.18,-19.58,-0.01:99
+chr1	5032542	rs977665	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=14;HaplotypeScore=4.90;MQ=58.74;MQ0=0;OQ=53.47;QD=0.58;SB=128.44	GT:AD:DP:GL:GQ	0/1:77,15:69:-29.43,-20.80,-218.90:86.30
+chr1	5036504	rs922123	T	C	526.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.12;MQ0=0;OQ=805.20;QD=10.88;SB=-361.22	GT:AD:DP:GL:GQ	0/1:44,30:74:-106.10,-22.29,-176.34:99
+chr1	5036703	rs55875722	T	A	259.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.65;MQ0=0;OQ=1241.65;QD=18.81;SB=-625.13	GT:AD:DP:GL:GQ	0/1:28,38:64:-146.72,-19.28,-96.42:99
+chr1	5036704	rs922124	T	A	61.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=59.67;MQ0=0;OQ=2561.19;QD=37.12;SB=-1099.66	GT:AD:DP:GL:GQ	1/1:0,69:68:-259.72,-20.48,-0.02:99
+chr1	5036974	rs56077964	G	A	617	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2268.61;QD=38.45;SB=-1080.42	GT:AD:DP:GL:GQ	1/1:0,59:56:-230.46,-16.87,-0.01:99
+chr1	5039060	rs56186517	C	T	567.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=3555.73;QD=39.95;SB=-1607.16	GT:AD:DP:GL:GQ	1/1:0,89:87:-354.57,-26.20,-0.02:99
+chr1	5039732	rs56347558	T	C	203.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=59.06;MQ0=0;OQ=2530.73;QD=34.20;SB=-928.36	GT:AD:DP:GL:GQ	1/1:0,73:71:-256.68,-21.39,-0.02:99
+chr1	5040152	rs3128686	G	T	232.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=59.70;MQ0=0;OQ=2534.37;QD=32.49;SB=-1255.28	GT:AD:DP:GL:GQ	1/1:1,77:71:-257.05,-21.39,-0.03:99
+chr1	5040933	rs12045197	A	T	91.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.81;MQ=44.79;MQ0=0;OQ=1582.06;QD=35.96;SB=-689.38	GT:AD:DP:GL:GQ	1/1:0,44:44:-161.81,-13.26,-0.02:99
+chr1	5041153	rs3128687	G	T	199.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=55.94;MQ0=0;OQ=2861.17;QD=36.22;SB=-1432.06	GT:AD:DP:GL:GQ	1/1:0,79:77:-289.72,-23.19,-0.02:99
+chr1	5041314	rs3128688	A	T	418.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.72;MQ0=0;OQ=2724.95;QD=37.85;SB=-1190.46	GT:AD:DP:GL:GQ	1/1:0,72:72:-276.10,-21.69,-0.02:99
+chr1	5041500	rs3128689	C	A	313.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.24;MQ=59.77;MQ0=0;OQ=2974.21;QD=36.27;SB=-1175.38	GT:AD:DP:GL:GQ	1/1:0,82:81:-301.03,-24.39,-0.02:99
+chr1	5042266	rs10915339	G	A	611.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.20;MQ0=0;OQ=2730.95;QD=39.01;SB=-1105.02	GT:AD:DP:GL:GQ	1/1:0,70:70:-276.70,-21.09,-0.02:99
+chr1	5042286	rs10915340	T	C	619.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.86;MQ0=0;OQ=2323.00;QD=35.20;SB=-939.39	GT:AD:DP:GL:GQ	1/1:0,65:65:-235.90,-19.58,-0.02:99
+chr1	5042412	rs10915341	T	G	227.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.39;MQ0=0;OQ=2175.06;QD=35.66;SB=-984.12	GT:AD:DP:GL:GQ	1/1:0,61:61:-221.11,-18.37,-0.01:99
+chr1	5042489	rs12029437	C	G	85.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=2.70;MQ=59.16;MQ0=0;OQ=2913.26;QD=40.46;SB=-1456.73	GT:AD:DP:GL:GQ	1/1:0,72:69:-294.94,-20.80,-0.03:99
+chr1	5042644	rs12047111	A	G	505.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=1237.53;QD=28.78;SB=-430.81	GT:AD:DP:GL:GQ	1/1:0,43:41:-127.38,-12.37,-0.05:99
+chr1	5042678	rs2334263	T	C	624.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=1911.69;QD=29.87;SB=-888.47	GT:AD:DP:GL:GQ	1/1:0,64:60:-194.81,-18.10,-0.06:99
+chr1	5043104	rs10799159	C	A	257.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.14;MQ0=0;OQ=3046.41;QD=35.84;SB=-1505.91	GT:AD:DP:GL:GQ	1/1:0,85:84:-308.25,-25.30,-0.02:99
+chr1	5043177	rs10799160	G	A	205.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.29;MQ0=0;OQ=2756.78;QD=37.25;SB=-1155.91	GT:AD:DP:GL:GQ	1/1:1,72:71:-282.75,-21.39,-3.49:99
+chr1	5043218	rs10799161	A	C	127.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.10;MQ0=0;OQ=2285.87;QD=29.69;SB=-810.83	GT:AD:DP:GL:GQ	1/1:0,77:71:-232.22,-21.39,-0.05:99
+chr1	5048318	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=4;HaplotypeScore=11.35;MQ=48.17;MQ0=0;OQ=57.54;QD=0.83;SB=77.27	GT:AD:DP:GL:GQ	0/1:47,22:47:-23.20,-14.17,-150.00:90.38
+chr1	5048545	rs10915343	T	C	699.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.89;MQ0=0;OQ=1690.53;QD=34.50;SB=-831.35	GT:AD:DP:GL:GQ	1/1:0,49:48:-172.65,-14.46,-0.01:99
+chr1	5050626	rs3101213	A	G	203.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=59.71;MQ0=0;OQ=2864.75;QD=36.26;SB=-1335.60	GT:AD:DP:GL:GQ	1/1:0,79:79:-290.08,-23.79,-0.02:99
+chr1	5051336	rs2199215	T	C	701.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=2974.37;QD=35.84;SB=-1419.92	GT:AD:DP:GL:GQ	1/1:0,83:83:-301.05,-25.00,-0.02:99
+chr1	5052019	rs12121092	G	T	639.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2775.75;QD=36.52;SB=-1128.45	GT:AD:DP:GL:GQ	1/1:0,76:76:-281.18,-22.89,-0.02:99
+chr1	5057740	rs55852005	G	A	37.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=3;HaplotypeScore=1.46;MQ=59.22;MQ0=0;OQ=1090.29;QD=18.48;SB=-513.03	GT:AD:DP:GL:GQ	0/1:26,33:57:-129.48,-17.17,-87.67:99
+chr1	5058085	rs4949171	C	T	168.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=59.33;MQ0=0;OQ=2116.23;QD=37.79;SB=-957.98	GT:AD:DP:GL:GQ	1/1:0,56:55:-215.23,-16.58,-0.02:99
+chr1	5058717	rs9803863	G	A	206.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.13;MQ0=0;OQ=2766.44;QD=39.52;SB=-1272.71	GT:AD:DP:GL:GQ	1/1:0,69:70:-283.01,-23.72,-2.78:99
+chr1	5059210	rs982156	T	C	60.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.49;MQ=59.24;MQ0=0;OQ=1823.01;QD=33.15;SB=-568.39	GT:AD:DP:GL:GQ	1/1:0,55:54:-185.91,-16.27,-0.03:99
+chr1	5060220	rs992597	C	T	157.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.01;MQ0=0;OQ=2915.53;QD=38.36;SB=-981.32	GT:AD:DP:GL:GQ	1/1:0,76:74:-295.16,-22.30,-0.02:99
+chr1	5060522	rs2242157	G	T	298.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.45;MQ0=0;OQ=2405.81;QD=35.38;SB=-942.03	GT:AD:DP:GL:GQ	1/1:0,68:68:-244.19,-20.49,-0.03:99
+chr1	5060591	rs1459766	T	G	395.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=2600.59;QD=35.14;SB=-1143.14	GT:AD:DP:GL:GQ	1/1:0,74:73:-263.67,-21.99,-0.02:99
+chr1	5061734	rs9439532	C	T	112.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.81;MQ=59.34;MQ0=0;OQ=2118.20;QD=37.16;SB=-1042.39	GT:AD:DP:GL:GQ	1/1:0,57:54:-215.42,-16.27,-0.02:99
+chr1	5062366	rs6683881	C	T	35.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=1.70;MQ=59.80;MQ0=0;OQ=3619.28;QD=39.77;SB=-1734.02	GT:AD:DP:GL:GQ	1/1:0,91:89:-360.93,-26.81,-0.02:99
+chr1	5062541	rs4949170	A	G	156.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=59.71;MQ0=0;OQ=2632.93;QD=33.33;SB=-1332.58	GT:AD:DP:GL:GQ	1/1:0,79:75:-266.90,-22.59,-0.03:99
+chr1	5062567	rs4949169	A	T	172.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=59.68;MQ0=0;OQ=2759.54;QD=37.80;SB=-995.13	GT:AD:DP:GL:GQ	1/1:0,73:72:-279.55,-21.68,-0.01:99
+chr1	5063485	rs9439576	C	G	98.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=59.17;MQ0=0;OQ=3111.26;QD=39.89;SB=-1145.60	GT:AD:DP:GL:GQ	1/1:0,77:71:-314.73,-21.39,-0.02:99
+chr1	5063671	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=26.54;MQ=57.06;MQ0=0;OQ=128.17;QD=2.14;SB=77.28	GT:AD:DP:GL:GQ	0/1:38,22:39:-27.89,-11.79,-122.93:99
+chr1	5064284	rs2169090	T	C	707.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=3152.45;QD=35.42;SB=-1370.23	GT:AD:DP:GL:GQ	1/1:0,89:88:-318.85,-26.50,-0.02:99
+chr1	5066340	rs57000660	A	G	484.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=766.60;QD=12.99;SB=-402.18	GT:AD:DP:GL:GQ	0/1:32,27:59:-97.71,-17.77,-131.87:99
+chr1	5066393	rs1037809	C	T	706.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3074.28;QD=39.41;SB=-1449.38	GT:AD:DP:GL:GQ	1/1:0,78:78:-311.04,-23.50,-0.02:99
+chr1	5068397	rs6659363	G	C	337.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.22;MQ0=0;OQ=768.71;QD=14.24;SB=-229.04	GT:AD:DP:GL:GQ	0/1:31,23:53:-96.12,-15.97,-137.34:99
+chr1	5068500	rs12124337	A	C	365.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=1243.29;QD=15.94;SB=-471.71	GT:AD:DP:GL:GQ	0/1:35,43:77:-150.81,-23.19,-127.77:99
+chr1	5068523	rs10733013	C	T	471.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1107.71;QD=14.39;SB=-422.79	GT:AD:DP:GL:GQ	0/1:43,34:75:-136.66,-22.60,-133.09:99
+chr1	5069554	rs2722789	G	A	592.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1009.56;QD=14.02;SB=-503.00	GT:AD:DP:GL:GQ	0/1:41,31:72:-125.95,-21.71,-131.55:99
+chr1	5070551	rs4949160	A	T	476.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.42;MQ0=0;OQ=1068.05;QD=14.83;SB=-488.53	GT:AD:DP:GL:GQ	0/1:37,35:71:-131.47,-21.38,-142.74:99
+chr1	5071819	.	G	A	258.71	PASS	AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=1213.24;QD=16.18;SB=-353.81	GT:AD:DP:GL:GQ	0/1:39,36:75:-147.20,-22.59,-142.20:99
+chr1	5071854	.	T	A	81.17	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=1149.23;QD=14.19;SB=-304.96	GT:AD:DP:GL:GQ	0/1:43,38:80:-142.31,-24.10,-164.66:99
+chr1	5072229	.	G	A	304.80	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=81;Dels=0.01;HRun=0;HaplotypeScore=64.90;MQ=44.02;MQ0=0;QD=3.76;SB=86.27	GT:AD:DP:GL:GQ	0/1:66,14:79:-57.26,-23.50,-230.57:99
+chr1	5072230	.	C	G	37.37	DPFilter;LowQual;SnpCluster	AC=1;AF=0.50;AN=2;DP=83;Dels=0.01;HRun=2;HaplotypeScore=55.89;MQ=43.72;MQ0=0;QD=0.45;SB=80.30	GT:AD:DP:GL:GQ	0/1:67,6:72:-38.59,-31.57,-277.78:70.20
+chr1	5072236	.	A	G	214.30	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=80;Dels=0.08;HRun=2;HaplotypeScore=77.80;MQ=44.49;MQ0=0;QD=2.68;SB=83.29	GT:AD:DP:GL:GQ	0/1:56,12:72:-66.82,-42.10,-235.08:99
+chr1	5072261	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=81;Dels=0.05;HRun=0;HaplotypeScore=73.45;MQ=43.15;MQ0=0;OQ=399.38;QD=4.93;SB=83.29	GT:AD:DP:GL:GQ	0/1:51,25:67:-62.51,-19.29,-172.53:99
+chr1	5072278	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=86;Dels=0.01;HRun=1;HaplotypeScore=43.28;MQ=42.83;MQ0=0;OQ=260.49;QD=3.03;SB=63.28	GT:AD:DP:GL:GQ	0/1:59,19:75:-74.72,-45.39,-204.92:99
+chr1	5072305	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=82;Dels=0.04;HRun=0;HaplotypeScore=77.14;MQ=40.79;MQ0=0;OQ=744.26;QD=9.08;SB=-270.19	GT:AD:DP:GL:GQ	0/1:44,35:70:-97.91,-20.20,-140.23:99
+chr1	5072314	.	C	A	26.92	LowQual	AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=53.92;MQ=40.19;MQ0=0;QD=0.34;SB=-28.60	GT:AD:DP:GL:GQ	0/1:60,11:56:-29.71,-23.73,-169.35:59.74
+chr1	5072329	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=71;Dels=0.01;HRun=0;HaplotypeScore=74.94;MQ=38.44;MQ0=0;OQ=775.14;QD=10.92;SB=-292.22	GT:AD:DP:GL:GQ	0/1:41,28:64:-99.78,-18.98,-129.83:99
+chr1	5072338	.	C	G	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=63;Dels=0.02;HRun=2;HaplotypeScore=51.40;MQ=37.08;MQ0=0;OQ=162.47;QD=2.58;SB=101.36	GT:AD:DP:GL:GQ	0/1:48,8:57:-50.13,-30.60,-201.42:99
+chr1	5072354	.	A	G	70.72	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=68;Dels=0.01;HRun=3;HaplotypeScore=80.87;MQ=34.07;MQ0=1;QD=1.04;SB=50.19	GT:AD:DP:GL:GQ	0/1:55,12:60:-28.14,-17.78,-195.72:99
+chr1	5072357	.	A	G	633.36	SnpCluster	AC=1;AF=0.50;AN=2;DP=67;Dels=0.01;HRun=1;HaplotypeScore=71.93;MQ=33.53;MQ0=1;QD=9.45;SB=-235.45	GT:AD:DP:GL:GQ	0/1:28,25:61:-115.70,-49.08,-135.16:99
+chr1	5072359	.	A	C	486.53	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=69;Dels=0.03;HRun=0;HaplotypeScore=52.12;MQ=33.41;MQ0=1;QD=7.05;SB=62.18	GT:AD:DP:GL:GQ	0/1:42,24:63:-73.40,-21.46,-136.62:99
+chr1	5072383	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=1;HaplotypeScore=82.78;MQ=35.86;MQ0=1;OQ=50.85;QD=0.50;SB=43.30	GT:AD:DP:GL:GQ	0/1:88,10:72:-37.48,-29.11,-217.86:83.68
+chr1	5072395	.	C	A	570.19	SnpCluster	AC=1;AF=0.50;AN=2;DP=99;Dels=0.02;HRun=1;HaplotypeScore=88.86;MQ=38.13;MQ0=1;QD=5.76;SB=-12.89	GT:AD:DP:GL:GQ	0/1:64,28:75:-96.04,-35.74,-177.41:99
+chr1	5072402	.	A	G	56.63	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=3;HaplotypeScore=106.83;MQ=38.72;MQ0=1;QD=0.58;SB=77.28	GT:AD:DP:GL:GQ	0/1:88,10:70:-30.04,-21.10,-237.13:89.47
+chr1	5072405	.	G	T	211.27	DPFilter;SnpCluster	AC=1;AF=0.50;AN=2;DP=95;Dels=0.03;HRun=0;HaplotypeScore=106.15;MQ=39.10;MQ0=1;QD=2.22;SB=86.26	GT:AD:DP:GL:GQ	0/1:74,17:80:-48.52,-24.11,-223.42:99
+chr1	5072419	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=52.76;MQ=39.26;MQ0=1;OQ=413.09;QD=4.44;SB=8.43	GT:AD:DP:GL:GQ	0/1:71,20:77:-71.28,-26.69,-194.57:99
+chr1	5072442	.	A	G	31.37	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=2;HaplotypeScore=72.31;MQ=41.30;MQ0=0;QD=0.48;SB=47.17	GT:AD:DP:GL:GQ	0/1:57,8:62:-25.11,-18.69,-212.28:64.20
+chr1	5073664	rs2611423	C	A	218.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=2432.37;QD=35.25;SB=-1208.34	GT:AD:DP:GL:GQ	1/1:0,69:67:-246.84,-20.18,-0.02:99
+chr1	5073938	rs2611424	A	G	134.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=59.25;MQ0=0;OQ=2912.91;QD=35.96;SB=-1287.55	GT:AD:DP:GL:GQ	1/1:0,81:80:-294.90,-24.09,-0.02:99
+chr1	5074030	rs2611425	C	T	598.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.51;MQ0=0;OQ=2372.22;QD=38.89;SB=-1023.68	GT:AD:DP:GL:GQ	1/1:0,61:60:-240.82,-18.07,-0.01:99
+chr1	5074510	rs9439534	C	T	637.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.93;MQ0=0;OQ=2321.21;QD=36.27;SB=-1159.05	GT:AD:DP:GL:GQ	1/1:0,64:59:-235.72,-17.77,-0.02:99
+chr1	5074638	rs57003830	G	C	372.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=43.54;MQ0=4;OQ=1370.10;QD=15.75;SB=-494.22	GT:AD:DP:GL:GQ	0/1:45,42:79:-164.10,-23.81,-179.75:99
+chr1	5075049	rs9439577	C	T	95.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=38.28;MQ0=7;OQ=1971.59;QD=31.30;SB=-484.14	GT:AD:DP:GL:GQ	1/1:0,62:51:-200.77,-15.37,-0.03:99
+chr1	5075121	rs9439535	A	G	238.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=43.82;MQ0=4;OQ=1529.43;QD=28.32;SB=-495.19	GT:AD:DP:GL:GQ	1/1:0,54:47:-156.56,-14.17,-0.03:99
+chr1	5075150	rs9439578	T	G	135.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=50.05;MQ0=3;OQ=2063.78;QD=31.75;SB=-748.06	GT:AD:DP:GL:GQ	1/1:0,65:60:-209.99,-18.08,-0.02:99
+chr1	5075197	rs10915347	C	T	55.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=2.29;MQ=47.56;MQ0=6;OQ=2171.81;QD=32.91;SB=-915.72	GT:AD:DP:GL:GQ	1/1:0,65:56:-220.79,-16.88,-0.02:99
+chr1	5075319	rs28828787	G	A	102.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=26.02;MQ0=15;OQ=432.78;QD=8.32;SB=-48.66	GT:AD:DP:GL:GQ	0/1:29,23:28:-55.00,-8.44,-46.26:99
+chr1	5075370	rs10799164	C	T	16.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=20.22;MQ0=13;OQ=746.84;QD=17.78;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,40:19:-78.27,-5.72,-0.00:57.19
+chr1	5075558	rs10799165	C	T	9.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=9.90;MQ=22.74;MQ0=30;OQ=955.91;QD=12.58;SB=-324.43	GT:AD:DP:GL:GQ	1/1:31,45:25:-99.18,-7.53,-0.01:75.24
+chr1	5075601	rs10753349	C	T	1.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=10.53;MQ=14.77;MQ0=51;OQ=525.81;QD=6.49;SB=-249.33	GT:AD:DP:GL:GQ	1/1:43,38:14:-56.17,-4.22,-0.00:42.14
+chr1	5075696	rs4949168	A	G	0.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=5.94;MQ=11.29;MQ0=39;OQ=183.21;QD=2.91;SB=-118.05	GT:AD:DP:GL:GQ	1/1:33,30:6:-21.89,-1.81,-0.00:18.06
+chr1	5075699	rs10799166	G	C	0.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=5.78;MQ=10.86;MQ0=38;OQ=173.64;QD=2.85;SB=-103.85	GT:AD:DP:GL:GQ	1/1:32,29:5:-20.93,-1.51,-0.00:15.05
+chr1	5075751	rs4949159	C	A	0.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=9.84;MQ=21.77;MQ0=1;OQ=523.96;QD=14.55;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,33:15:-55.98,-4.52,-0.00:45.14
+chr1	5075757	rs4949167	T	C	1.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=5.17;MQ=21.64;MQ0=3;OQ=605.43;QD=14.41;SB=-10.00	GT:AD:DP:GL:GQ	1/1:7,35:18:-64.13,-5.42,-0.00:54.16
+chr1	5076314	rs9439579	C	G	74.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.92;MQ=43.71;MQ0=2;OQ=2095.83;QD=33.80;SB=-956.72	GT:AD:DP:GL:GQ	1/1:3,59:49:-213.18,-14.76,-0.01:99
+chr1	5076393	rs10915349	G	A	1.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=47.36;MQ0=1;OQ=1988.87;QD=34.29;SB=-955.74	GT:AD:DP:GL:GQ	1/1:1,57:52:-202.50,-15.68,-0.03:99
+chr1	5076841	rs10799167	C	T	211.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=45.50;MQ0=4;OQ=2210.86;QD=35.66;SB=-962.98	GT:AD:DP:GL:GQ	1/1:1,61:56:-224.69,-16.87,-0.02:99
+chr1	5077036	rs10799168	A	G	167.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=21.14;MQ0=7;OQ=400.64;QD=14.84;SB=-196.71	GT:AD:DP:GL:GQ	1/1:8,19:13:-43.66,-3.92,-0.01:39.11
+chr1	5077055	rs7414866	A	G	123.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=21.33;MQ0=4;OQ=281.43;QD=13.40;SB=-64.87	GT:AD:DP:GL:GQ	1/1:4,17:10:-31.74,-3.02,-0.01:30.04
+chr1	5077077	rs7412613	C	T	3.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=1.37;MQ=22.40;MQ0=3;OQ=333.18;QD=18.51;SB=-10.00	GT:AD:DP:GL:GQ	1/1:2,15:9:-36.90,-2.71,-0.00:27.09
+chr1	5077090	.	C	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=2;HaplotypeScore=4.92;MQ=29.30;MQ0=3;OQ=51.83;QD=1.85;SB=-3.99	GT:AD:DP:GL:GQ	0/1:19,9:11:-11.79,-3.32,-22.43:84.66
+chr1	5077136	rs55919453	T	G	371.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=38.18;MQ0=2;OQ=1590.74;QD=31.81;SB=-546.07	GT:AD:DP:GL:GQ	1/1:0,50:44:-162.67,-13.25,-0.01:99
+chr1	5077346	rs28778348	C	A	55.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=26.70;MQ0=2;OQ=838.40;QD=27.95;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,29:24:-87.43,-7.23,-0.01:72.21
+chr1	5077349	rs28898289	T	G	16.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=26.06;MQ0=2;OQ=780.24;QD=25.17;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,31:23:-81.62,-6.93,-0.01:69.20
+chr1	5077435	rs7415381	A	T	121.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=26.22;MQ0=5;OQ=1349.62;QD=28.72;SB=-637.67	GT:AD:DP:GL:GQ	1/1:0,47:37:-138.56,-11.15,-0.01:99
+chr1	5077528	rs56184987	T	C	231.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.13;MQ0=2;OQ=814.91;QD=18.95;SB=-252.77	GT:AD:DP:GL:GQ	1/1:0,43:27:-85.10,-8.15,-0.03:81.19
+chr1	5077549	rs55934905	G	A	0.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=23.80;MQ0=7;OQ=1118.88;QD=22.38;SB=-246.01	GT:AD:DP:GL:GQ	1/1:0,50:29:-115.48,-8.74,-0.01:87.28
+chr1	5077770	rs60669416	C	A	584.28	Indel	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=10;HaplotypeScore=19.78;MQ=46.83;MQ0=2;QD=11.69;SB=-270.35	GT:AD:DP:GL:GQ	0/1:25,24:45:-75.27,-13.56,-79.00:99
+chr1	5077806	rs2334261	C	T	3.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.02;HRun=2;HaplotypeScore=6.33;MQ=31.47;MQ0=13;OQ=1098.90;QD=20.35;SB=-473.36	GT:AD:DP:GL:GQ	1/1:5,48:29:-113.48,-8.43,-0.01:84.27
+chr1	5077915	rs11582268	A	T	437.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.80;MQ0=5;OQ=869.48;QD=19.32;SB=-460.68	GT:AD:DP:GL:GQ	1/1:0,44:25:-90.55,-7.54,-0.02:75.21
+chr1	5078308	rs12043988	C	A	291.59	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=47.74;MQ0=0;OQ=2467.70;QD=37.39;SB=-935.67	GT:AD:DP:GL:GQ	1/1:0,66:65:-250.36,-19.57,-0.01:99
+chr1	5078509	rs9439503	T	C	20.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=38.39;MQ0=4;OQ=1877.97;QD=28.03;SB=-657.32	GT:AD:DP:GL:GQ	1/1:1,66:53:-191.40,-15.96,-0.02:99
+chr1	5078532	rs9439504	C	G	494.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.41;MQ0=3;OQ=2205.88;QD=36.16;SB=-588.53	GT:AD:DP:GL:GQ	1/1:0,61:50:-224.18,-15.06,-0.01:99
+chr1	5078612	rs10915350	C	T	169.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=47.49;MQ0=1;OQ=2196.12;QD=36.60;SB=-847.62	GT:AD:DP:GL:GQ	1/1:1,58:57:-223.22,-17.18,-0.02:99
+chr1	5079390	rs10799170	A	C	350.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.35;MQ0=0;OQ=2787.95;QD=35.29;SB=-1421.63	GT:AD:DP:GL:GQ	1/1:0,79:78:-282.40,-23.49,-0.02:99
+chr1	5079434	rs10915352	G	T	571.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.02;MQ0=0;OQ=3162.32;QD=36.77;SB=-1557.78	GT:AD:DP:GL:GQ	1/1:0,86:86:-319.84,-25.90,-0.02:99
+chr1	5079595	rs10915353	G	C	43.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.36;MQ0=0;OQ=2638.35;QD=40.59;SB=-999.16	GT:AD:DP:GL:GQ	1/1:0,65:61:-267.45,-18.39,-0.03:99
+chr1	5079666	rs6701939	T	C	563.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2172.86;QD=35.05;SB=-713.27	GT:AD:DP:GL:GQ	1/1:0,62:60:-220.89,-18.07,-0.02:99
+chr1	5080376	.	C	T	202.08	PASS	AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.09;MQ0=0;OQ=426.51;QD=11.22;SB=-188.16	GT:AD:DP:GL:GQ	0/1:24,14:37:-57.08,-11.15,-81.03:99
+chr1	5080399	.	C	A	264.12	DPFilter;Indel	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=20;HaplotypeScore=11.69;MQ=57.12;MQ0=0;QD=4.63;SB=53.19	GT:AD:DP:GL:GQ	0/1:38,19:40:-41.75,-12.05,-100.11:99
+chr1	5080680	rs10753350	A	G	105.81	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=58.32;MQ0=0;OQ=1525.28;QD=28.25;SB=-610.83	GT:AD:DP:GL:GQ	1/1:0,54:51:-156.18,-15.39,-0.07:99
+chr1	5080690	rs10753351	A	C	1.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=2.95;MQ=55.25;MQ0=0;OQ=2140.46;QD=31.48;SB=-1004.07	GT:AD:DP:GL:GQ	1/1:0,68:63:-217.66,-18.98,-0.03:99
+chr1	5081475	rs10737396	T	C	76.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=3;HaplotypeScore=0.91;MQ=60.00;MQ0=0;OQ=2367.06;QD=33.34;SB=-935.73	GT:AD:DP:GL:GQ	1/1:0,71:67:-240.32,-20.19,-0.03:99
+chr1	5081878	rs2722794	T	G	569.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.93;MQ0=0;OQ=2825.92;QD=34.89;SB=-1425.62	GT:AD:DP:GL:GQ	1/1:0,81:79:-286.20,-23.79,-0.02:99
+chr1	5081972	rs2611426	T	A	81.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.88;MQ=59.18;MQ0=0;OQ=2310.37;QD=35.01;SB=-624.95	GT:AD:DP:GL:GQ	1/1:0,66:62:-234.64,-18.68,-0.02:99
+chr1	5083407	rs2045587	A	G	34.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.31;MQ0=0;OQ=1821.48;QD=33.73;SB=-913.93	GT:AD:DP:GL:GQ	1/1:0,54:52:-185.75,-15.67,-0.02:99
+chr1	5083733	rs4313443	C	T	652.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2295.78;QD=39.58;SB=-913.70	GT:AD:DP:GL:GQ	1/1:0,58:58:-233.18,-17.47,-0.01:99
+chr1	5083785	rs4356099	G	A	29.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=60.00;MQ0=0;OQ=1676.22;QD=38.98;SB=-527.70	GT:AD:DP:GL:GQ	1/1:0,43:43:-171.22,-12.96,-0.02:99
+chr1	5083937	rs2722793	G	T	729.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=2771.95;QD=36.96;SB=-1328.90	GT:AD:DP:GL:GQ	1/1:0,75:75:-280.80,-22.59,-0.02:99
+chr1	5084549	rs10753352	G	C	80.52	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.74;MQ0=0;OQ=3116.41;QD=42.69;SB=-1439.29	GT:AD:DP:GL:GQ	1/1:0,73:73:-315.25,-22.00,-0.03:99
+chr1	5085006	rs2722792	C	A	486.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=3029.86;QD=36.95;SB=-1518.84	GT:AD:DP:GL:GQ	1/1:0,82:81:-306.59,-24.39,-0.02:99
+chr1	5085686	rs2611419	A	C	735.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2513.45;QD=35.40;SB=-1104.10	GT:AD:DP:GL:GQ	1/1:0,71:71:-254.95,-21.38,-0.02:99
+chr1	5087139	rs2611420	C	G	615.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3365.59;QD=43.15;SB=-1251.98	GT:AD:DP:GL:GQ	1/1:0,78:76:-335.56,-22.90,-0.03:99
+chr1	5087240	rs2611421	C	T	489.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=3117.95;QD=41.03;SB=-1433.39	GT:AD:DP:GL:GQ	1/1:0,76:76:-315.39,-22.89,-0.01:99
+chr1	5087511	rs2722791	G	A	190.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=59.73;MQ0=0;OQ=3174.39;QD=37.35;SB=-1593.03	GT:AD:DP:GL:GQ	1/1:0,85:81:-321.05,-24.40,-0.02:99
+chr1	5088299	rs2611422	C	T	24.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.01;HRun=4;HaplotypeScore=1.63;MQ=59.49;MQ0=0;OQ=3139.82;QD=38.29;SB=-1155.06	GT:AD:DP:GL:GQ	1/1:0,81:82:-317.60,-24.41,-0.03:99
+chr1	5088851	rs898338	G	T	586.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1967.21;QD=32.25;SB=-901.77	GT:AD:DP:GL:GQ	1/1:0,61:55:-200.32,-16.57,-0.02:99
+chr1	5091688	rs11588537	G	C	0.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=2.02;MQ=59.44;MQ0=0;OQ=1667.23;QD=40.66;SB=-503.13	GT:AD:DP:GL:GQ	1/1:0,41:41:-170.32,-12.36,-0.02:99
+chr1	5092085	rs4245628	G	A	151.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.41;MQ0=0;OQ=3066.13;QD=39.31;SB=-1187.61	GT:AD:DP:GL:GQ	1/1:0,78:77:-310.22,-23.19,-0.02:99
+chr1	5092563	rs6671889	C	A	625.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.16;MQ0=0;OQ=3060.89;QD=36.88;SB=-1358.20	GT:AD:DP:GL:GQ	1/1:0,83:82:-309.69,-24.69,-0.01:99
+chr1	5092609	rs4949165	G	C	633.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=3087.67;QD=42.88;SB=-1533.25	GT:AD:DP:GL:GQ	1/1:0,72:72:-312.37,-21.69,-0.02:99
+chr1	5092886	rs10492923	A	G	560.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=897.90;QD=12.47;SB=-469.86	GT:AD:DP:GL:GQ	0/1:34,38:69:-113.87,-20.80,-132.03:99
+chr1	5093533	rs9439505	C	T	206.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=59.13;MQ0=0;OQ=1236.94;QD=16.49;SB=-238.14	GT:AD:DP:GL:GQ	0/1:38,37:73:-148.98,-22.00,-117.20:99
+chr1	5093841	rs12143009	G	A	1328.69	Indel	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=3;HaplotypeScore=2.85;MQ=59.81;MQ0=1;QD=15.27;SB=-676.33	GT:AD:DP:GL:GQ	0/1:46,41:84:-161.46,-25.31,-156.05:99
+chr1	5094064	rs16840020	C	T	380.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=59.40;MQ0=0;OQ=843.58;QD=13.61;SB=-387.37	GT:AD:DP:GL:GQ	0/1:36,26:61:-106.01,-18.37,-128.57:99
+chr1	5094308	rs9439536	C	G	94.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=57.94;MQ0=0;OQ=2369.61;QD=43.08;SB=-1192.92	GT:AD:DP:GL:GQ	1/1:0,55:55:-240.56,-16.57,-0.02:99
+chr1	5094675	rs9439537	G	A	205.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=56.69;MQ0=0;OQ=2327.54;QD=36.95;SB=-997.02	GT:AD:DP:GL:GQ	1/1:0,63:59:-236.35,-17.77,-0.02:99
+chr1	5095027	rs10737397	A	C	379.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.02;HRun=2;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1853.36;QD=34.97;SB=-880.10	GT:AD:DP:GL:GQ	1/1:0,52:52:-188.93,-15.66,-0.01:99
+chr1	5095151	rs10915359	A	G	343.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=1130.12;QD=15.92;SB=-404.21	GT:AD:DP:GL:GQ	0/1:33,38:69:-137.08,-20.78,-130.21:99
+chr1	5095177	rs12122020	C	T	430.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1196.16;QD=13.91;SB=-341.80	GT:AD:DP:GL:GQ	0/1:49,37:84:-148.20,-25.30,-177.14:99
+chr1	5095231	rs10492925	T	C	590.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1272.89;QD=14.98;SB=-556.65	GT:AD:DP:GL:GQ	0/1:35,50:83:-155.59,-25.02,-138.70:99
+chr1	5095242	rs12045223	A	T	548.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1555.76;QD=18.52;SB=-658.48	GT:AD:DP:GL:GQ	0/1:35,49:82:-183.56,-24.70,-128.89:99
+chr1	5096599	rs9439506	A	G	501.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=607.79;QD=10.30;SB=-265.38	GT:AD:DP:GL:GQ	0/1:36,23:58:-81.54,-17.47,-140.55:99
+chr1	5097069	.	C	T	27.83	PASS	AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.95;MQ0=0;OQ=280.61;QD=35.08;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,8:8:-31.64,-2.41,-0.00:24.08
+chr1	5097076	.	C	A	58.51	PASS	AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.95;MQ0=0;OQ=242.27;QD=30.28;SB=-10.00	GT:AD:DP:GL:GQ	1/1:0,8:8:-27.81,-2.41,-0.00:24.07
+chr1	5097414	rs34593428	C	T	209.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=915.00;QD=14.52;SB=-282.17	GT:AD:DP:GL:GQ	0/1:34,29:62:-113.46,-18.67,-123.11:99
+chr1	5097811	rs10799172	T	C	730.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=2361.85;QD=34.73;SB=-1109.84	GT:AD:DP:GL:GQ	1/1:0,68:67:-239.79,-20.18,-0.02:99
+chr1	5097837	rs10799173	C	T	610.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=2894.02;QD=39.64;SB=-1458.48	GT:AD:DP:GL:GQ	1/1:0,73:72:-293.00,-21.69,-0.02:99
+chr1	5098649	rs16840051	C	T	466.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.76;MQ0=0;OQ=1115.98;QD=14.31;SB=-521.66	GT:AD:DP:GL:GQ	0/1:43,35:76:-137.77,-22.89,-150.84:99
+chr1	5099594	rs61576661	T	C	2.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.02;HRun=0;HaplotypeScore=9.91;MQ=59.43;MQ0=0;OQ=660.15;QD=12.23;SB=-250.93	GT:AD:DP:GL:GQ	0/1:29,24:54:-85.27,-15.97,-115.92:99
+chr1	5100592	rs6681359	C	T	709.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=3001.23;QD=40.02;SB=-1288.71	GT:AD:DP:GL:GQ	1/1:0,75:75:-303.72,-22.59,-0.02:99
+chr1	5102008	rs7543139	A	C	24.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=8.00;MQ=58.40;MQ0=0;OQ=1023.25;QD=14.62;SB=-311.81	GT:AD:DP:GL:GQ	0/1:35,35:67:-125.80,-20.19,-114.71:99
+chr1	5102179	rs16840055	A	G	103.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=59.41;MQ0=0;OQ=1029.92;QD=14.51;SB=-438.97	GT:AD:DP:GL:GQ	0/1:36,35:69:-127.06,-20.79,-136.54:99
+chr1	5103146	rs4484964	T	C	669.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=2031.10;QD=32.24;SB=-774.73	GT:AD:DP:GL:GQ	1/1:0,63:62:-206.74,-18.69,-0.04:99
+chr1	5103788	.	G	T	167.53	PASS	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.70;MQ0=0;OQ=1064.37;QD=14.00;SB=-541.64	GT:AD:DP:GL:GQ	0/1:38,38:74:-132.01,-22.29,-131.40:99
+chr1	5106305	rs9439509	G	A	600.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=2218.17;QD=38.92;SB=-991.33	GT:AD:DP:GL:GQ	1/1:0,57:57:-225.42,-17.18,-0.02:99
+chr1	5106499	rs4345839	A	G	149.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=59.43;MQ0=0;OQ=2177.60;QD=33.50;SB=-1108.75	GT:AD:DP:GL:GQ	1/1:0,64:62:-221.38,-18.68,-0.03:99
+chr1	5107407	rs4584438	T	G	105.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=1.66;MQ=60.00;MQ0=0;OQ=2390.91;QD=33.67;SB=-961.60	GT:AD:DP:GL:GQ	1/1:0,70:70:-246.35,-24.25,-3.68:99
+chr1	5107616	rs4543848	T	C	111.63	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=2.89;MQ=59.72;MQ0=0;OQ=2325.30;QD=34.71;SB=-962.92	GT:AD:DP:GL:GQ	1/1:0,67:66:-236.14,-19.88,-0.02:99
+chr1	5107713	.	A	C	103.40	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1036.38;QD=12.79;SB=-351.52	GT:AD:DP:GL:GQ	0/1:44,37:81:-131.32,-24.40,-159.14:99
+chr1	5109104	rs12025231	C	T	369.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=60.00;MQ0=0;OQ=1428.81;QD=14.73;SB=-339.81	GT:AD:DP:GL:GQ	0/1:53,44:96:-175.10,-28.94,-171.50:99
+chr1	5109781	rs9439510	C	G	474.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3322.39;QD=44.30;SB=-1477.33	GT:AD:DP:GL:GQ	1/1:0,75:75:-331.24,-22.59,-0.02:99
+chr1	5109984	rs12121369	C	A	599.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=1366.71;QD=15.89;SB=-516.80	GT:AD:DP:GL:GQ	0/1:40,46:85:-165.55,-25.60,-144.36:99
+chr1	5110261	rs7538704	G	C	501.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1089.65;QD=15.35;SB=-449.75	GT:AD:DP:GL:GQ	0/1:33,38:67:-132.47,-20.22,-140.33:99
+chr1	5110586	rs4462197	C	T	256.57	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2327.86;QD=37.55;SB=-1085.00	GT:AD:DP:GL:GQ	1/1:0,62:59:-236.39,-17.78,-0.02:99
+chr1	5110994	rs10753353	T	C	229.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.74;MQ0=0;OQ=2543.07;QD=35.32;SB=-1168.48	GT:AD:DP:GL:GQ	1/1:0,72:71:-257.91,-21.39,-0.02:99
+chr1	5111198	rs12027352	C	T	56.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=2;HaplotypeScore=3.00;MQ=59.50;MQ0=0;OQ=1422.29;QD=15.29;SB=-680.29	GT:AD:DP:GL:GQ	0/1:47,46:88:-172.02,-26.51,-161.50:99
+chr1	5111405	rs4314925	G	A	196.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.36;MQ0=0;OQ=2517.06;QD=38.72;SB=-1234.63	GT:AD:DP:GL:GQ	1/1:0,65:64:-255.31,-19.28,-0.02:99
+chr1	5112055	rs12145645	G	A	578.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1010.93;QD=13.66;SB=-362.83	GT:AD:DP:GL:GQ	0/1:42,32:72:-126.06,-21.69,-149.75:99
+chr1	5112088	rs61762208	G	A	38.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=2;HaplotypeScore=1.85;MQ=59.44;MQ0=0;OQ=1643.08;QD=19.80;SB=-651.68	GT:AD:DP:GL:GQ	0/1:37,46:82:-192.29,-24.70,-131.13:99
+chr1	5112135	rs12741116	A	G	713.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2397.16;QD=35.25;SB=-898.68	GT:AD:DP:GL:GQ	1/1:0,68:67:-243.32,-20.18,-0.02:99
+chr1	5113244	rs4600091	T	C	489.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2494.81;QD=29.70;SB=-1138.12	GT:AD:DP:GL:GQ	1/1:0,84:79:-253.13,-23.82,-0.07:99
+chr1	5113507	rs10753354	C	G	401.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2295.20;QD=42.50;SB=-1097.09	GT:AD:DP:GL:GQ	1/1:0,54:54:-233.13,-16.28,-0.02:99
+chr1	5113815	rs6698288	G	A	330.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2134.65;QD=39.53;SB=-887.16	GT:AD:DP:GL:GQ	1/1:0,54:54:-217.07,-16.27,-0.02:99
+chr1	5114383	rs7517431	C	G	606.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=920.14;QD=14.61;SB=-463.75	GT:AD:DP:GL:GQ	0/1:36,27:62:-113.98,-18.68,-155.27:99
+chr1	5114445	rs7517449	C	T	297.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.63;MQ0=0;OQ=2115.05;QD=38.46;SB=-1037.87	GT:AD:DP:GL:GQ	1/1:0,55:54:-215.11,-16.27,-0.02:99
+chr1	5114723	rs10915361	C	T	120.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.02;MQ=58.20;MQ0=0;OQ=931.19;QD=19.81;SB=-478.50	GT:AD:DP:GL:GQ	0/1:19,28:46:-110.26,-13.86,-62.96:99
+chr1	5115596	rs9439538	T	C	593.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1568.48;QD=30.16;SB=-606.93	GT:AD:DP:GL:GQ	1/1:0,52:50:-160.48,-15.08,-0.04:99
+chr1	5115679	rs12021698	A	T	372.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.37;MQ0=0;OQ=887.17;QD=15.04;SB=-310.70	GT:AD:DP:GL:GQ	0/1:30,29:59:-109.77,-17.77,-114.78:99
+chr1	5115822	rs56173770	C	G	132.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1600.81;QD=26.68;SB=-808.51	GT:AD:DP:GL:GQ	0/1:19,41:59:-181.14,-17.77,-78.42:99
+chr1	5115851	rs9439539	T	A	636.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=2566.28;QD=37.74;SB=-1304.50	GT:AD:DP:GL:GQ	1/1:0,68:67:-260.22,-20.18,-0.01:99
+chr1	5117179	rs5009987	A	G	1517.20	Indel	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=20.42;MQ=58.93;MQ0=0;QD=27.59;SB=-603.23	GT:AD:DP:GL:GQ	1/1:2,53:53:-162.87,-15.98,-7.57:84.15
+chr1	5117504	rs10799174	G	A	14.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=8.52;MQ=58.73;MQ0=0;OQ=1003.11;QD=18.24;SB=-483.50	GT:AD:DP:GL:GQ	0/1:24,31:52:-119.27,-15.67,-72.69:99
+chr1	5117533	rs6672724	C	T	186.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.63;MQ0=0;OQ=1901.56;QD=37.29;SB=-943.75	GT:AD:DP:GL:GQ	1/1:0,51:50:-193.77,-15.07,-0.02:99
+chr1	5118461	rs9439511	C	T	378.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=58.91;MQ0=0;OQ=1153.56;QD=14.98;SB=-536.73	GT:AD:DP:GL:GQ	0/1:42,35:77:-141.84,-23.20,-148.03:99
+chr1	5119340	rs12401983	G	A	186.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=2.35;MQ=52.79;MQ0=0;OQ=1320.64;QD=16.93;SB=-541.57	GT:AD:DP:GL:GQ	0/1:37,40:76:-158.24,-22.89,-135.98:99
+chr1	5119644	rs55835407	G	A	140.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=42.95;MQ0=4;OQ=797.21;QD=12.86;SB=-199.88	GT:AD:DP:GL:GQ	0/1:35,27:56:-99.88,-16.88,-103.36:99
+chr1	5119704	rs56293801	T	C	75.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=42.91;MQ0=1;OQ=434.63;QD=8.36;SB=-212.22	GT:AD:DP:GL:GQ	0/1:32,20:46:-60.61,-13.87,-109.45:99
+chr1	5119914	rs12097824	T	C	114	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=39.01;MQ0=0;OQ=589.79;QD=9.51;SB=-187.41	GT:AD:DP:GL:GQ	0/1:33,29:57:-79.44,-17.18,-127.34:99
+chr1	5120013	rs56126017	C	G	210.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=35.32;MQ0=0;OQ=1020.64;QD=14.38;SB=-272.51	GT:AD:DP:GL:GQ	0/1:43,28:70:-126.44,-21.09,-178.51:99
+chr1	5120085	.	G	A	0.02	FDRtranche1.00to2.00	AC=1;AF=0.50;AN=2;DP=101;Dels=0.01;HRun=0;HaplotypeScore=11.89;MQ=34.93;MQ0=0;OQ=541.17;QD=5.36;SB=13.62	GT:AD:DP:GL:GQ	0/1:77,23:97:-86.32,-28.91,-276.66:99
+chr1	5120089	.	T	A	0.03	FDRtranche0.10to1.00	AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=10.97;MQ=34.87;MQ0=0;OQ=894.55;QD=8.77;SB=-13.59	GT:AD:DP:GL:GQ	0/1:68,34:99:-122.56,-29.82,-255.26:99
+chr1	5120116	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=117;Dels=0.02;HRun=0;HaplotypeScore=143.29;MQ=34.92;MQ0=0;OQ=962.81;QD=8.23;SB=-91.05	GT:AD:DP:GL:GQ	0/1:76,37:114:-138.10,-38.53,-297.11:99
+chr1	5120146	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=141;Dels=0.01;HRun=0;HaplotypeScore=240.33;MQ=33.11;MQ0=0;OQ=492.54;QD=3.49;SB=14.98	GT:AD:DP:GL:GQ	0/1:116,23:120:-88.08,-35.54,-336.13:99
+chr1	5120150	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=150;Dels=0.03;HRun=0;HaplotypeScore=253.70;MQ=32.31;MQ0=0;OQ=526.30;QD=3.51;SB=-209.96	GT:AD:DP:GL:GQ	0/1:122,23:125:-96.24,-40.33,-348.30:99
+chr1	5120166	rs61762214	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.02;HRun=0;HaplotypeScore=340.16;MQ=31.74;MQ0=0;OQ=707.91;QD=4.19;SB=-238.38	GT:AD:DP:GL:GQ	0/1:128,38:158:-120.76,-46.69,-441.60:99
+chr1	5120182	.	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=171;Dels=0.00;HRun=0;HaplotypeScore=247.34;MQ=30.32;MQ0=1;OQ=181.12;QD=1.06;SB=99.79	GT:AD:DP:GL:GQ	0/1:146,25:160:-69.62,-48.22,-544.70:99
+chr1	5120218	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=0;HaplotypeScore=296.87;MQ=30.08;MQ0=1;OQ=467.02;QD=2.51;SB=-243.49	GT:AD:DP:GL:GQ	0/1:160,26:175:-102.70,-52.71,-541.07:99
+chr1	5120238	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=187;Dels=0.01;HRun=0;HaplotypeScore=156.33;MQ=31.62;MQ0=1;OQ=98.86;QD=0.53;SB=35.37	GT:AD:DP:GL:GQ	0/1:164,15:172:-86.49,-73.32,-562.87:99
+chr1	5120240	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=184;Dels=0.01;HRun=0;HaplotypeScore=148.66;MQ=31.61;MQ0=1;OQ=319.23;QD=1.73;SB=30.34	GT:AD:DP:GL:GQ	0/1:160,22:170:-85.81,-50.61,-526.60:99
+chr1	5120250	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=149.91;MQ=33.54;MQ0=1;OQ=262.42;QD=1.60;SB=170.48	GT:AD:DP:GL:GQ	0/1:144,20:159:-77.42,-47.90,-500.91:99
+chr1	5120252	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=0;HaplotypeScore=134.92;MQ=34.14;MQ0=1;OQ=1590.07;QD=10.46;SB=-170.99	GT:AD:DP:GL:GQ	0/1:98,53:143:-208.80,-46.51,-329.18:99
+chr1	5121185	.	T	C	32.44	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=59.52;MQ0=0;OQ=529.93;QD=11.04;SB=-169.50	GT:AD:DP:GL:GQ	0/1:26,22:46:-70.14,-13.86,-100.33:99
+chr1	5122129	rs10915363	G	C	183.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=59.47;MQ0=0;OQ=1248.82;QD=17.84;SB=-543.72	GT:AD:DP:GL:GQ	0/1:31,39:66:-148.06,-19.89,-135.32:99
+chr1	5122156	rs10915364	G	C	495.83	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=1017.04;QD=16.14;SB=-464.81	GT:AD:DP:GL:GQ	0/1:31,32:62:-123.68,-18.70,-134.13:99
+chr1	5122248	rs11804873	C	T	62.77	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.39;MQ0=0;OQ=700.13;QD=18.42;SB=-213.90	GT:AD:DP:GL:GQ	0/1:16,22:37:-84.44,-11.15,-55.54:99
+chr1	5122456	rs10915365	C	T	167.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.45;MQ=59.52;MQ0=0;OQ=504.80;QD=12.94;SB=-201.18	GT:AD:DP:GL:GQ	0/1:22,17:38:-65.21,-11.45,-78.02:99
+chr1	5122978	rs12024162	T	C	1.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=6.85;MQ=58.05;MQ0=0;OQ=2287.65;QD=35.19;SB=-898.04	GT:AD:DP:GL:GQ	1/1:1,64:63:-232.37,-18.97,-0.02:99
+chr1	5123042	rs12026730	G	A	134.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=56.89;MQ0=0;OQ=1205.15;QD=19.76;SB=-414.94	GT:AD:DP:GL:GQ	0/1:25,36:58:-141.29,-17.49,-70.06:99
+chr1	5123330	rs9439540	C	A	63.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.37;MQ0=0;OQ=975.37;QD=16.53;SB=-180.54	GT:AD:DP:GL:GQ	0/1:27,32:57:-117.99,-17.17,-89.17:99
+chr1	5124476	rs17366543	A	G	248.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=919.81;QD=12.26;SB=-428.10	GT:AD:DP:GL:GQ	0/1:42,33:74:-117.56,-22.29,-166.31:99
+chr1	5126548	rs6690311	A	G	73.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.31;MQ=60.00;MQ0=0;OQ=1952.07;QD=34.25;SB=-789.11	GT:AD:DP:GL:GQ	1/1:0,56:56:-198.81,-16.87,-0.02:99
+chr1	5126612	rs6675995	G	A	137.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=2.05;MQ=59.06;MQ0=0;OQ=2638.82;QD=38.24;SB=-1319.37	GT:AD:DP:GL:GQ	1/1:0,69:67:-267.49,-20.19,-0.02:99
+chr1	5126665	rs10799176	G	A	160.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=59.11;MQ0=0;OQ=2842.19;QD=38.93;SB=-1393.38	GT:AD:DP:GL:GQ	1/1:0,73:72:-287.83,-21.69,-0.02:99
+chr1	5126844	rs6685929	C	T	627.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2295.72;QD=37.63;SB=-1082.35	GT:AD:DP:GL:GQ	1/1:0,61:59:-233.18,-17.78,-0.02:99
+chr1	5126974	.	G	T	128.27	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.02;MQ0=0;OQ=1169.78;QD=18.87;SB=-560.81	GT:AD:DP:GL:GQ	0/1:24,38:60:-138.33,-18.07,-79.90:99
+chr1	5129269	rs11583683	C	T	146.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2126.34;QD=37.30;SB=-795.34	GT:AD:DP:GL:GQ	1/1:0,57:56:-216.24,-16.88,-0.02:99
+chr1	5129679	rs6603817	A	G	112.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.96;MQ0=0;OQ=1509.76;QD=32.82;SB=-474.53	GT:AD:DP:GL:GQ	1/1:0,46:43:-154.58,-12.95,-0.01:99
+chr1	5130606	rs4076635	G	A	636.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2562.75;QD=38.25;SB=-1303.24	GT:AD:DP:GL:GQ	1/1:0,67:65:-259.88,-19.58,-0.02:99
+chr1	5131752	rs4394703	C	A	307.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=58.90;MQ0=0;OQ=2017.11;QD=34.19;SB=-1012.79	GT:AD:DP:GL:GQ	1/1:0,58:57:-208.21,-19.84,-2.91:99
+chr1	5132477	rs6692740	A	G	667.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=2294.64;QD=31.43;SB=-1053.29	GT:AD:DP:GL:GQ	1/1:0,73:71:-233.10,-21.41,-0.05:99
+chr1	5133851	rs10492928	G	T	624.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=2734.91;QD=36.47;SB=-1337.92	GT:AD:DP:GL:GQ	1/1:0,75:75:-277.10,-22.59,-0.02:99
+chr1	5134195	rs7545119	C	A	288.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=59.11;MQ0=0;OQ=2691.33;QD=34.50;SB=-1000.80	GT:AD:DP:GL:GQ	1/1:0,78:75:-272.75,-22.59,-0.03:99
+chr1	5135504	rs10915369	C	T	488.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.87;MQ0=0;OQ=1900.03;QD=39.58;SB=-759.52	GT:AD:DP:GL:GQ	1/1:0,48:48:-193.60,-14.46,-0.01:99
+chr1	5135682	rs11583044	G	A	156.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=56.88;MQ0=0;OQ=1535.65;QD=34.90;SB=-689.33	GT:AD:DP:GL:GQ	1/1:0,44:41:-157.17,-12.36,-0.02:99
+chr1	5135692	rs10915370	C	T	137.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.35;MQ0=0;OQ=2137.06;QD=38.16;SB=-962.28	GT:AD:DP:GL:GQ	1/1:0,56:55:-217.31,-16.57,-0.02:99
+chr1	5138733	rs10915371	G	A	186.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=58.20;MQ0=0;OQ=3762.30;QD=40.02;SB=-1754.36	GT:AD:DP:GL:GQ	1/1:0,94:93:-375.23,-28.01,-0.02:99
+chr1	5139307	rs9439541	A	T	634.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3003.64;QD=37.55;SB=-1255.20	GT:AD:DP:GL:GQ	1/1:0,80:79:-303.97,-23.79,-0.02:99
+chr1	5139791	rs6603818	C	T	714.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=2781.44;QD=39.73;SB=-1291.72	GT:AD:DP:GL:GQ	1/1:0,70:70:-281.75,-21.09,-0.02:99
+chr1	5140071	rs7547229	C	T	724.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3128.00;QD=38.62;SB=-1344.39	GT:AD:DP:GL:GQ	1/1:0,81:78:-316.40,-23.49,-0.02:99
+chr1	5140234	.	A	C	162.19	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=858.81;QD=15.61;SB=-394.78	GT:AD:DP:GL:GQ	0/1:24,31:53:-105.13,-15.96,-88.06:99
+chr1	5141171	rs6688418	G	A	695.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2832.24;QD=40.46;SB=-1208.37	GT:AD:DP:GL:GQ	1/1:0,70:70:-286.82,-21.08,-0.01:99
+chr1	5141665	.	C	T	43.31	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.95;MQ0=0;OQ=985.11;QD=18.24;SB=-409.92	GT:AD:DP:GL:GQ	0/1:25,29:53:-117.76,-15.96,-94.79:99
+chr1	5141935	rs6701052	C	T	100.43	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.66;MQ=49.80;MQ0=8;OQ=1859.57;QD=32.06;SB=-869.02	GT:AD:DP:GL:GQ	1/1:8,50:47:-189.55,-14.16,-0.01:99
+chr1	5142041	rs12072516	A	T	329.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.00;MQ0=0;OQ=266.78;QD=9.53;SB=-152.82	GT:AD:DP:GL:GQ	0/1:16,12:25:-37.49,-7.53,-57.93:99
+chr1	5142287	rs9286978	G	A	22.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=23.68;MQ0=8;OQ=873.11;QD=24.95;SB=-85.33	GT:AD:DP:GL:GQ	1/1:3,32:23:-90.90,-6.93,-0.01:69.22
+chr1	5143205	rs6664086	T	C	86.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=3.60;MQ=58.49;MQ0=0;OQ=2734.43;QD=33.76;SB=-1255.67	GT:AD:DP:GL:GQ	1/1:1,80:78:-277.05,-23.49,-0.03:99
+chr1	5144621	rs6603819	C	A	635.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2574.32;QD=36.78;SB=-1238.13	GT:AD:DP:GL:GQ	1/1:0,70:70:-261.03,-21.08,-0.02:99
+chr1	5146701	rs6669501	C	T	700.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=3011.38;QD=38.61;SB=-1500.64	GT:AD:DP:GL:GQ	1/1:0,78:76:-304.75,-22.90,-0.03:99
+chr1	5146942	rs10492930	A	G	610.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2413.30;QD=30.17;SB=-1138.47	GT:AD:DP:GL:GQ	1/1:0,79:77:-244.99,-23.23,-0.08:99
+chr1	5147215	rs10492931	G	A	723.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2807.87;QD=39.00;SB=-1216.01	GT:AD:DP:GL:GQ	1/1:0,72:71:-284.39,-21.39,-0.02:99
+chr1	5148161	.	G	A	24.17	PASS	AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=59.39;MQ0=0;OQ=1450.62;QD=19.09;SB=-417.73	GT:AD:DP:GL:GQ	0/1:33,43:74:-170.64,-22.29,-112.74:99
+chr1	5148401	rs6665697	T	C	269.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.48;MQ0=0;OQ=2231.09;QD=30.99;SB=-952.42	GT:AD:DP:GL:GQ	1/1:0,72:70:-226.75,-21.11,-0.06:99
+chr1	5150357	rs10915375	A	G	529.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.37;MQ0=0;OQ=1555.45;QD=31.74;SB=-790.64	GT:AD:DP:GL:GQ	1/1:0,49:49:-159.17,-14.78,-0.04:99
+chr1	5150590	.	G	T	11.56	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=20;HaplotypeScore=36.67;MQ=54.55;MQ0=0;QD=0.17;SB=69.39	GT:AD:DP:GL:GQ	0/1:49,15:42:-26.08,-21.67,-128.29:44.08
+chr1	5150765	rs9439543	T	C	624.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=2519.73;QD=35.49;SB=-971.41	GT:AD:DP:GL:GQ	1/1:0,71:70:-255.58,-21.09,-0.03:99
+chr1	5150768	rs9439544	C	T	629.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=2827.18;QD=38.21;SB=-1183.08	GT:AD:DP:GL:GQ	1/1:0,74:71:-286.33,-21.39,-0.02:99
+chr1	5150948	rs11583754	A	G	125.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=56.88;MQ0=0;OQ=1724.72;QD=34.49;SB=-813.67	GT:AD:DP:GL:GQ	1/1:0,50:49:-176.07,-14.76,-0.02:99
+chr1	5153524	rs7536712	T	C	117.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=59.77;MQ0=0;OQ=2818.40;QD=35.23;SB=-1399.67	GT:AD:DP:GL:GQ	1/1:1,78:79:-289.59,-27.33,-4.17:99
+chr1	5155164	rs2722780	G	T	611.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2724.16;QD=35.38;SB=-1305.24	GT:AD:DP:GL:GQ	1/1:0,77:77:-276.03,-23.20,-0.03:99
+chr1	5155635	rs2018394	C	G	496.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.82;MQ0=0;OQ=3565.75;QD=43.48;SB=-1230.53	GT:AD:DP:GL:GQ	1/1:0,82:80:-355.57,-24.10,-0.02:99
+chr1	5156126	rs2679215	G	C	570.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2670.60;QD=41.73;SB=-1328.91	GT:AD:DP:GL:GQ	1/1:0,64:63:-270.67,-18.98,-0.02:99
+chr1	5156634	rs1320179	T	A	161.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=59.60;MQ0=0;OQ=1611.01;QD=34.28;SB=-497.40	GT:AD:DP:GL:GQ	1/1:0,47:44:-164.71,-13.26,-0.02:99
+chr1	5157054	.	G	A	104.21	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.46;MQ=58.03;MQ0=0;OQ=746.35;QD=13.09;SB=-370.87	GT:AD:DP:GL:GQ	0/1:33,24:57:-95.09,-17.17,-121.22:99
+chr1	5157089	rs2722781	C	T	248.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.68;MQ0=0;OQ=2013.78;QD=38.00;SB=-852.01	GT:AD:DP:GL:GQ	1/1:0,53:51:-204.98,-15.36,-0.01:99
+chr1	5158014	rs2679216	A	G	582.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=2870.64;QD=35.01;SB=-1392.56	GT:AD:DP:GL:GQ	1/1:0,82:80:-290.67,-24.10,-0.03:99
+chr1	5158416	rs2722782	T	C	292.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=59.74;MQ0=0;OQ=2481.35;QD=34.95;SB=-1226.71	GT:AD:DP:GL:GQ	1/1:0,71:71:-251.75,-21.39,-0.03:99
+chr1	5158842	rs2679217	A	C	278.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=2099.17;QD=33.86;SB=-765.90	GT:AD:DP:GL:GQ	1/1:0,62:61:-213.53,-18.38,-0.03:99
+chr1	5160232	rs2722783	T	C	124.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.20;MQ=59.02;MQ0=0;OQ=2420.10;QD=34.09;SB=-1200.16	GT:AD:DP:GL:GQ	1/1:1,69:68:-249.06,-23.31,-3.46:99
+chr1	5162761	rs2679218	T	C	309.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.65;MQ0=0;OQ=2240.61;QD=34.47;SB=-957.91	GT:AD:DP:GL:GQ	1/1:0,65:65:-227.67,-19.58,-0.02:99
+chr1	5164088	rs2722786	A	G	678.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2134.58;QD=34.99;SB=-757.97	GT:AD:DP:GL:GQ	1/1:0,61:60:-217.06,-18.07,-0.02:99
+chr1	5164377	rs2722787	T	C	664.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1994.32;QD=31.16;SB=-946.38	GT:AD:DP:GL:GQ	1/1:0,64:63:-203.07,-19.00,-0.06:99
+chr1	5164508	.	G	A	21.64	PASS	AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1023.93;QD=15.51;SB=-404.39	GT:AD:DP:GL:GQ	0/1:35,31:64:-124.97,-19.29,-108.14:99
+chr1	5165252	rs2679219	A	G	545.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2430.87;QD=31.16;SB=-1145.16	GT:AD:DP:GL:GQ	1/1:0,78:76:-246.73,-22.91,-0.06:99
+chr1	5165298	rs2722788	C	T	111.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.52;MQ0=0;OQ=3387.05;QD=38.93;SB=-1669.69	GT:AD:DP:GL:GQ	1/1:0,87:85:-337.71,-25.61,-0.03:99
+chr1	5166378	rs2722790	C	T	150.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=59.01;MQ0=0;OQ=2739.21;QD=39.13;SB=-1381.68	GT:AD:DP:GL:GQ	1/1:0,70:69:-277.52,-20.79,-0.02:99
+chr1	5170379	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=20;HaplotypeScore=3.49;MQ=51.63;MQ0=1;OQ=52.88;QD=0.64;SB=122.38	GT:AD:DP:GL:GQ	0/1:61,22:64:-27.86,-19.28,-197.27:85.72
+chr1	5172063	rs56164612	G	A	177.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=59.16;MQ0=0;OQ=776.89;QD=15.54;SB=-274.16	GT:AD:DP:GL:GQ	0/1:24,26:48:-95.43,-14.46,-86.73:99
+chr1	5191577	rs471824	A	G	242.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.16;MQ0=0;OQ=1721.79;QD=27.77;SB=-749.45	GT:AD:DP:GL:GQ	1/1:1,61:57:-179.88,-17.20,-4.11:99
+chr1	5191739	rs632051	C	A	18.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=2;HaplotypeScore=4.23;MQ=58.83;MQ0=0;OQ=3137.26;QD=37.35;SB=-891.27	GT:AD:DP:GL:GQ	1/1:0,84:83:-317.33,-25.00,-0.02:99
+chr1	5193545	rs566114	T	G	200.45	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=2400.30;QD=34.29;SB=-1100.14	GT:AD:DP:GL:GQ	1/1:0,70:68:-243.64,-20.48,-0.02:99
+chr1	5194097	rs56295354	C	T	367.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.98;MQ0=0;OQ=896.66;QD=14.01;SB=-471.46	GT:AD:DP:GL:GQ	0/1:34,30:62:-111.63,-18.68,-121.51:99
+chr1	5195036	rs677735	A	G	310.10	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.68;MQ0=0;OQ=2493.12;QD=34.15;SB=-981.71	GT:AD:DP:GL:GQ	1/1:0,73:71:-252.92,-21.39,-0.03:99
+chr1	5195467	rs2986186	T	A	311.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=2846.52;QD=37.45;SB=-1332.00	GT:AD:DP:GL:GQ	1/1:0,76:75:-288.25,-22.59,-0.02:99
+chr1	5196704	rs2353169	T	C	724.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=2499.39;QD=34.71;SB=-983.95	GT:AD:DP:GL:GQ	1/1:0,72:72:-253.55,-21.69,-0.02:99
+chr1	5197705	rs473104	A	G	598.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2654.56;QD=34.93;SB=-1319.89	GT:AD:DP:GL:GQ	1/1:0,76:74:-269.06,-22.29,-0.02:99
+chr1	5197747	rs586165	T	C	721.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2710.69;QD=35.20;SB=-1278.13	GT:AD:DP:GL:GQ	1/1:0,77:76:-274.68,-22.89,-0.03:99
+chr1	5198145	rs584402	C	T	717.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2714.09;QD=39.33;SB=-1353.02	GT:AD:DP:GL:GQ	1/1:0,69:69:-275.01,-20.79,-0.02:99
+chr1	5198627	rs679712	T	A	207.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=59.36;MQ0=0;OQ=2332.10;QD=35.88;SB=-1044.59	GT:AD:DP:GL:GQ	1/1:0,65:63:-236.81,-18.97,-0.02:99
+chr1	5198919	rs551536	T	C	66.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=59.68;MQ0=0;OQ=2254.50;QD=31.75;SB=-1121.22	GT:AD:DP:GL:GQ	1/1:0,71:70:-229.09,-21.11,-0.06:99
+chr1	5198972	rs551376	G	A	527.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2736.21;QD=38.54;SB=-1372.67	GT:AD:DP:GL:GQ	1/1:0,71:69:-277.22,-20.79,-0.02:99
+chr1	5199041	rs550558	G	A	271.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.75;MQ0=0;OQ=2982.88;QD=39.25;SB=-1518.69	GT:AD:DP:GL:GQ	1/1:0,75:75:-301.89,-22.59,-0.02:99
+chr1	5199083	rs549773	C	A	400.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2265.19;QD=35.39;SB=-1149.37	GT:AD:DP:GL:GQ	1/1:0,64:63:-230.13,-18.98,-0.02:99
+chr1	5199801	rs663998	C	G	667.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.24;MQ0=1;OQ=2933.78;QD=41.91;SB=-1382.38	GT:AD:DP:GL:GQ	1/1:0,70:68:-296.98,-20.49,-0.02:99
+chr1	5199984	rs663142	G	T	300.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=57.88;MQ0=0;OQ=2524.52;QD=34.58;SB=-1263.12	GT:AD:DP:GL:GQ	1/1:0,73:71:-256.06,-21.39,-0.02:99
+chr1	5200020	rs663106	T	C	288.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.94;MQ0=0;OQ=2324.56;QD=29.06;SB=-1068.20	GT:AD:DP:GL:GQ	1/1:0,80:72:-236.10,-21.71,-0.06:99
+chr1	5201096	rs35339923	C	T	25.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.74;MQ=59.27;MQ0=0;OQ=2513.57;QD=39.90;SB=-919.70	GT:AD:DP:GL:GQ	1/1:0,63:63:-254.96,-18.98,-0.02:99
+chr1	5201932	rs611422	T	C	369.89	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2205.79;QD=33.94;SB=-980.06	GT:AD:DP:GL:GQ	1/1:0,65:62:-224.19,-18.68,-0.02:99
+chr1	5201978	rs534321	A	C	83.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.68;MQ0=0;OQ=2498.46;QD=34.23;SB=-901.19	GT:AD:DP:GL:GQ	1/1:0,73:73:-253.46,-21.99,-0.03:99
+chr1	5202029	rs534188	C	T	644.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=2223.00;QD=39.70;SB=-899.19	GT:AD:DP:GL:GQ	1/1:0,56:56:-225.90,-16.87,-0.02:99
+chr1	5202175	rs12125575	G	A	578.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.13;MQ0=0;OQ=1740.25;QD=37.03;SB=-800.07	GT:AD:DP:GL:GQ	1/1:0,47:44:-177.62,-13.25,-0.01:99
+chr1	5202200	rs610133	T	C	141.51	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=49.73;MQ0=0;OQ=1399.83;QD=30.43;SB=-711.63	GT:AD:DP:GL:GQ	1/1:0,46:41:-143.59,-12.36,-0.02:99
+chr1	5202222	rs511282	G	T	609.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=50.02;MQ0=0;OQ=2299.71;QD=34.32;SB=-1138.31	GT:AD:DP:GL:GQ	1/1:0,67:64:-233.58,-19.28,-0.02:99
+chr1	5202265	rs599481	G	T	595.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=49.58;MQ0=0;OQ=2113.87;QD=33.55;SB=-993.43	GT:AD:DP:GL:GQ	1/1:0,63:58:-214.99,-17.47,-0.02:99
+chr1	5202388	rs12066405	A	G	127.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=51.98;MQ0=0;OQ=2322.85;QD=33.66;SB=-1080.10	GT:AD:DP:GL:GQ	1/1:0,69:65:-235.89,-19.58,-0.02:99
+chr1	5202422	.	T	G	419.39	Indel	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=66.39;MQ=43.53;MQ0=0;QD=7.23;SB=-202.77	GT:AD:DP:GL:GQ	0/1:38,20:51:-60.59,-15.36,-121.07:99
+chr1	5202441	rs12071111	G	A	97.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=40.65;MQ0=0;OQ=1838.51;QD=34.69;SB=-927.74	GT:AD:DP:GL:GQ	1/1:1,52:48:-187.45,-14.46,-0.02:99
+chr1	5202467	rs12067585	T	G	27.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.10;MQ=52.14;MQ0=0;OQ=1141.50;QD=32.61;SB=-417.26	GT:AD:DP:GL:GQ	1/1:0,35:33:-117.74,-9.94,-0.01:99
+chr1	5202510	rs10915390	T	C	6.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=45.77;MQ0=0;OQ=1492.54;QD=28.70;SB=-582.99	GT:AD:DP:GL:GQ	1/1:0,52:46:-152.88,-13.87,-0.04:99
+chr1	5202536	rs10915391	A	G	576.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.09;MQ0=0;OQ=1719.08;QD=33.06;SB=-769.98	GT:AD:DP:GL:GQ	1/1:0,52:48:-175.51,-14.46,-0.01:99
+chr1	5202563	.	A	G	1303.98	SnpCluster	AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=5.87;MQ=34.10;MQ0=0;QD=25.08;SB=-434.46	GT:AD:DP:GL:GQ	1/1:0,52:39:-134.00,-11.75,-0.02:99
+chr1	5202564	.	T	C	1560.70	SnpCluster	AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;HRun=2;HaplotypeScore=5.87;MQ=34.10;MQ0=0;QD=30.01;SB=-450.83	GT:AD:DP:GL:GQ	1/1:1,51:44:-159.67,-13.26,-0.02:99
+chr1	5202566	.	C	T	1713.62	SnpCluster	AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=34.87;MQ0=0;QD=32.95;SB=-454.10	GT:AD:DP:GL:GQ	1/1:0,51:43:-174.96,-12.95,-0.01:99
+chr1	5202576	rs12134110	C	T	0.75	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=6.13;MQ=37.89;MQ0=0;OQ=1873.93;QD=33.46;SB=-544.73	GT:AD:DP:GL:GQ	1/1:1,55:47:-190.99,-14.16,-0.01:99
+chr1	5202767	rs2986185	A	G	288.60	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=54.20;MQ0=0;OQ=2264.33;QD=34.84;SB=-1153.44	GT:AD:DP:GL:GQ	1/1:0,65:64:-230.04,-19.28,-0.02:99
+chr1	5202796	rs2945617	T	C	352.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.10;MQ0=0;OQ=1791.40;QD=27.99;SB=-839.97	GT:AD:DP:GL:GQ	1/1:0,64:58:-182.79,-17.50,-0.06:99
+chr1	5202844	rs2986184	C	G	260.78	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=52.86;MQ0=0;OQ=2380.85;QD=40.35;SB=-1080.09	GT:AD:DP:GL:GQ	1/1:0,59:56:-241.69,-16.88,-0.02:99
+chr1	5202908	.	C	T	49.09	PASS	AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=56.41;MQ0=0;OQ=1679.71;QD=37.33;SB=-834.36	GT:AD:DP:GL:GQ	1/1:0,45:42:-171.56,-12.65,-0.01:99
+chr1	5203231	rs480807	G	A	112.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=59.13;MQ0=0;OQ=2991.96;QD=39.89;SB=-1079.44	GT:AD:DP:GL:GQ	1/1:0,75:75:-302.81,-22.60,-0.03:99
+chr1	5203306	rs6687834	C	T	621.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3055.40;QD=39.68;SB=-1315.34	GT:AD:DP:GL:GQ	1/1:0,77:77:-309.15,-23.20,-0.02:99
+chr1	5203354	rs584498	C	T	147.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=2983.67;QD=38.25;SB=-1435.37	GT:AD:DP:GL:GQ	1/1:0,78:75:-301.97,-22.59,-0.02:99
+chr1	5203671	rs582779	C	A	167.92	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=2146.95;QD=35.78;SB=-804.85	GT:AD:DP:GL:GQ	1/1:0,60:60:-218.30,-18.08,-0.02:99
+chr1	5203886	rs474456	G	C	148.15	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.48;MQ=58.03;MQ0=0;OQ=2254.35;QD=39.55;SB=-1087.49	GT:AD:DP:GL:GQ	1/1:0,57:55:-229.05,-16.59,-0.04:99
+chr1	5203943	rs473685	T	C	568.01	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.84;MQ0=0;OQ=1941.75;QD=35.30;SB=-734.93	GT:AD:DP:GL:GQ	1/1:0,55:55:-197.78,-16.57,-0.02:99
+chr1	5204037	rs472768	C	A	257.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=53.49;MQ0=0;OQ=2116.13;QD=35.87;SB=-808.86	GT:AD:DP:GL:GQ	1/1:0,59:58:-215.21,-17.47,-0.01:99
+chr1	5204179	rs561169	C	T	180.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.63;MQ0=0;OQ=1666.79;QD=32.68;SB=-839.97	GT:AD:DP:GL:GQ	1/1:0,51:44:-170.29,-13.26,-0.02:99
+chr1	5204268	rs677650	G	C	32.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=41.36;MQ0=0;OQ=1911.63;QD=39.01;SB=-915.40	GT:AD:DP:GL:GQ	1/1:0,49:46:-194.77,-13.87,-0.02:99
+chr1	5204556	rs676589	T	A	738.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.27;MQ0=0;OQ=2559.35;QD=36.56;SB=-1189.80	GT:AD:DP:GL:GQ	1/1:0,70:69:-259.54,-20.78,-0.02:99
+chr1	5204733	rs675738	T	C	27.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=2.20;MQ=59.17;MQ0=0;OQ=1658.38;QD=29.61;SB=-662.81	GT:AD:DP:GL:GQ	1/1:0,56:52:-169.47,-15.68,-0.05:99
+chr1	5204883	rs9439546	G	A	532.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2940.91;QD=38.70;SB=-1192.36	GT:AD:DP:GL:GQ	1/1:0,76:75:-297.70,-22.60,-0.03:99
+chr1	5204955	rs674820	A	G	79.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=59.62;MQ0=0;OQ=2113.60;QD=34.65;SB=-990.71	GT:AD:DP:GL:GQ	1/1:0,61:60:-214.97,-18.07,-0.02:99
+chr1	5204998	rs674421	C	T	11.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=4.18;MQ=59.19;MQ0=0;OQ=2200.64;QD=38.61;SB=-746.99	GT:AD:DP:GL:GQ	1/1:0,57:55:-223.66,-16.57,-0.01:99
+chr1	5205224	rs673451	T	G	405.18	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=1733.87;QD=28.90;SB=-756.83	GT:AD:DP:GL:GQ	1/1:0,60:55:-177.02,-16.58,-0.05:99
+chr1	5206120	rs56397638	C	T	43.03	Indel;LowQual	AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=3.09;MQ=48.93;MQ0=0;QD=2.39;SB=-0.99	GT:AD:DP:GL:GQ	0/1:15,3:17:-12.71,-5.12,-48.36:75.87
+chr1	5206410	.	T	C	0.40	PASS	AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=1.63;MQ=56.77;MQ0=0;OQ=1364.10;QD=34.98;SB=-316.12	GT:AD:DP:GL:GQ	1/1:0,39:38:-140.01,-11.45,-0.01:99
+chr1	5206681	rs12121640	A	C	71.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.51;MQ0=0;OQ=1679.67;QD=32.93;SB=-387.04	GT:AD:DP:GL:GQ	1/1:0,51:47:-171.57,-14.16,-0.01:99
+chr1	5206700	rs12125074	G	A	98.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.12;MQ0=0;OQ=2000.17;QD=37.74;SB=-489.65	GT:AD:DP:GL:GQ	1/1:0,53:50:-203.61,-15.06,-0.01:99
+chr1	5208394	rs7549686	T	C	327.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=94;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3436.97;QD=36.56;SB=-1599.67	GT:AD:DP:GL:GQ	1/1:0,94:93:-342.70,-28.01,-0.02:99
+chr1	5209527	rs12135834	C	T	124.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=2736.25;QD=39.66;SB=-1253.04	GT:AD:DP:GL:GQ	1/1:0,69:68:-277.22,-20.48,-0.01:99
+chr1	5209757	rs12128282	G	A	708.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2355.65;QD=38.62;SB=-1039.67	GT:AD:DP:GL:GQ	1/1:0,61:59:-239.17,-17.77,-0.02:99
+chr1	5210118	rs4465222	T	C	132.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.97;MQ0=0;OQ=1268.12;QD=28.18;SB=-489.53	GT:AD:DP:GL:GQ	1/1:0,45:42:-130.45,-12.68,-0.06:99
+chr1	5210152	rs4465223	T	C	176.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.16;MQ0=0;OQ=1621.75;QD=29.49;SB=-654.28	GT:AD:DP:GL:GQ	1/1:0,55:51:-165.81,-15.38,-0.05:99
+chr1	5210469	rs6686714	G	T	712.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1971.04;QD=35.20;SB=-893.62	GT:AD:DP:GL:GQ	1/1:0,56:56:-200.71,-16.87,-0.02:99
+chr1	5211244	rs6603825	T	C	594.56	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2173.03;QD=35.62;SB=-828.31	GT:AD:DP:GL:GQ	1/1:0,61:60:-220.91,-18.07,-0.02:99
+chr1	5211435	.	C	T	25.65	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.22;MQ=59.65;MQ0=0;OQ=960.07;QD=17.78;SB=-418.78	GT:AD:DP:GL:GQ	0/1:25,29:53:-115.26,-15.97,-85.03:99
+chr1	5212025	rs4475768	T	G	354.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=695.32;QD=14.19;SB=-234.36	GT:AD:DP:GL:GQ	0/1:24,25:49:-87.57,-14.76,-89.97:99
+chr1	5212226	rs494046	T	C	148.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=2779.20;QD=29.88;SB=-1328.52	GT:AD:DP:GL:GQ	1/1:0,93:88:-281.58,-26.54,-0.08:99
+chr1	5213428	.	A	G	11.97	PASS	AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=58.55;MQ0=0;OQ=408.80;QD=8.52;SB=-93.78	GT:AD:DP:GL:GQ	0/1:27,21:44:-57.43,-13.27,-96.36:99
+chr1	5213524	.	T	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=71.93;MQ=50.54;MQ0=0;OQ=502.87;QD=9.14;SB=-189.21	GT:AD:DP:GL:GQ	0/1:37,18:47:-67.73,-14.16,-102.82:99
+chr1	5213770	rs6658152	C	T	45.87	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=1572.39;QD=38.35;SB=-554.31	GT:AD:DP:GL:GQ	1/1:0,41:41:-160.84,-12.35,-0.02:99
+chr1	5215271	.	A	G	38.30	PASS	AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=59.60;MQ0=0;OQ=1692.08;QD=29.17;SB=-770.59	GT:AD:DP:GL:GQ	1/1:0,57:55:-172.85,-16.59,-0.06:99
+chr1	5217813	.	G	C	1.18	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=9.11;MQ=58.35;MQ0=1;OQ=1164.43;QD=14.38;SB=-426.29	GT:AD:DP:GL:GQ	0/1:49,32:77:-142.93,-23.20,-194.98:99
+chr1	5217931	rs4847582	C	G	145.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.66;MQ0=0;OQ=1509.42;QD=22.20;SB=-480.86	GT:AD:DP:GL:GQ	0/1:26,42:66:-174.11,-19.89,-110.01:99
+chr1	5218042	rs4847581	A	T	229.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.31;MQ0=0;OQ=560.70;QD=9.19;SB=-151.08	GT:AD:DP:GL:GQ	0/1:39,22:59:-77.12,-17.77,-150.88:99
+chr1	5218412	rs12089315	C	T	695.85	PASS	AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2655.40;QD=40.23;SB=-1167.53	GT:AD:DP:GL:GQ	1/1:0,66:65:-269.14,-19.58,-0.01:99
+chr1	5218922	rs55929300	C	T	250.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=58.35;MQ0=0;OQ=749.84;QD=14.42;SB=-372.87	GT:AD:DP:GL:GQ	0/1:29,23:51:-93.64,-15.37,-91.04:99
+chr1	5218923	rs2945619	A	G	55.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.25;MQ=58.42;MQ0=0;OQ=1817.82;QD=33.66;SB=-828.90	GT:AD:DP:GL:GQ	1/1:0,54:53:-185.39,-15.97,-0.03:99
+chr1	5219162	.	C	T	26.36	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=2;HaplotypeScore=0.93;MQ=59.78;MQ0=0;OQ=1260.89;QD=15.01;SB=-475.42	GT:AD:DP:GL:GQ	0/1:46,38:84:-154.67,-25.30,-167.04:99
+chr1	5220394	rs632798	A	G	319.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1931.82;QD=32.74;SB=-775.98	GT:AD:DP:GL:GQ	1/1:0,59:54:-196.78,-16.27,-0.02:99
+chr1	5221239	rs11584035	A	G	510.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2162.59;QD=34.33;SB=-1003.74	GT:AD:DP:GL:GQ	1/1:0,63:61:-219.86,-18.37,-0.02:99
+chr1	5221301	rs11585734	G	C	28.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.47;MQ0=0;OQ=2416.76;QD=43.16;SB=-843.33	GT:AD:DP:GL:GQ	1/1:0,56:55:-245.27,-16.57,-0.01:99
+chr1	5221482	rs34835703	A	T	2939.50	Indel	AC=2;AF=1.00;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=3.98;MQ=58.65;MQ0=0;QD=31.95;SB=-1078.25	GT:AD:DP:GL:GQ	1/1:2,89:87:-306.96,-29.45,-9.42:99
+chr1	5221725	.	G	A	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=60;Dels=0.03;HRun=18;HaplotypeScore=39.80;MQ=52.31;MQ0=0;OQ=152.15;QD=2.54;SB=47.14	GT:AD:DP:GL:GQ	0/1:40,18:43:-30.85,-12.35,-114.35:99
+chr1	5222078	rs972257	T	A	639.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.18;MQ0=0;OQ=3168.88;QD=37.28;SB=-1120.55	GT:AD:DP:GL:GQ	1/1:0,85:85:-320.49,-25.60,-0.02:99
+chr1	5222126	rs972256	A	G	626.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=2639.54;QD=35.19;SB=-1126.78	GT:AD:DP:GL:GQ	1/1:0,75:75:-267.56,-22.59,-0.03:99
+chr1	5224091	rs499416	T	C	297.77	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.44;MQ0=0;OQ=2957.76;QD=36.07;SB=-1259.50	GT:AD:DP:GL:GQ	1/1:0,82:82:-299.39,-24.70,-0.03:99
+chr1	5224457	rs681122	A	G	116.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.67;MQ0=0;OQ=2663.18;QD=31.70;SB=-1024.35	GT:AD:DP:GL:GQ	1/1:0,84:81:-269.96,-24.42,-0.06:99
+chr1	5224547	rs503246	T	C	2.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=6.13;MQ=59.67;MQ0=0;OQ=2425.86;QD=34.66;SB=-1136.77	GT:AD:DP:GL:GQ	1/1:0,69:69:-249.69,-23.90,-3.52:99
+chr1	5224600	rs504015	G	A	107.71	PASS	AC=2;AF=1.00;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=59.36;MQ0=0;OQ=3623.40;QD=38.14;SB=-1734.33	GT:AD:DP:GL:GQ	1/1:1,94:92:-361.34,-27.72,-0.04:99
+chr1	5225244	rs34916930	A	G	210.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=59.23;MQ0=0;OQ=766.73;QD=12.78;SB=-281.64	GT:AD:DP:GL:GQ	0/1:31,29:57:-97.13,-17.17,-122.94:99
+chr1	5225286	rs1614164	A	G	116.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.11;MQ0=0;OQ=1503.00;QD=28.90;SB=-584.52	GT:AD:DP:GL:GQ	1/1:0,52:49:-153.94,-14.79,-0.06:99
+chr1	5225305	rs531507	T	C	127.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=59.05;MQ0=0;OQ=1485.28;QD=30.31;SB=-700.80	GT:AD:DP:GL:GQ	1/1:0,49:47:-152.15,-14.18,-0.04:99
+chr1	5225319	rs531541	G	A	341.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.53;MQ0=0;OQ=776.62;QD=15.85;SB=-311.30	GT:AD:DP:GL:GQ	0/1:25,24:46:-94.81,-13.86,-73.71:99
+chr1	5225584	rs12139398	G	T	64.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=3;HaplotypeScore=2.68;MQ=59.09;MQ0=0;OQ=1255.53;QD=16.52;SB=-636.75	GT:AD:DP:GL:GQ	0/1:35,41:76:-151.73,-22.89,-120.82:99
+chr1	5225784	rs648378	G	A	217.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=3051.49;QD=38.63;SB=-1366.03	GT:AD:DP:GL:GQ	1/1:0,79:77:-308.76,-23.20,-0.02:99
+chr1	5225910	rs536995	T	C	659.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2238.13;QD=31.52;SB=-1141.80	GT:AD:DP:GL:GQ	1/1:0,71:69:-227.45,-20.80,-0.05:99
+chr1	5226194	rs646542	C	A	53.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.51;MQ=59.52;MQ0=0;OQ=616.21;QD=12.84;SB=-186.21	GT:AD:DP:GL:GQ	0/1:25,23:46:-78.77,-13.86,-80.93:99
+chr1	5227007	rs17422703	C	T	447.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=653.00;QD=13.89;SB=-346.50	GT:AD:DP:GL:GQ	0/1:27,20:47:-82.75,-14.17,-88.07:99
+chr1	5227141	rs479689	T	C	634.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2577.54;QD=35.80;SB=-1149.80	GT:AD:DP:GL:GQ	1/1:0,72:72:-261.36,-21.69,-0.02:99
+chr1	5227198	rs631837	T	G	470.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=1038.21;QD=12.98;SB=-481.28	GT:AD:DP:GL:GQ	0/1:42,38:78:-130.60,-23.49,-142.85:99
+chr1	5227509	rs2945620	A	G	463.41	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=1887.53;QD=34.95;SB=-718.20	GT:AD:DP:GL:GQ	1/1:0,54:53:-192.35,-15.96,-0.02:99
+chr1	5227512	rs2986190	C	G	581.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=2178.35;QD=38.90;SB=-696.39	GT:AD:DP:GL:GQ	1/1:0,56:54:-221.45,-16.29,-0.03:99
+chr1	5227592	rs484203	C	G	505.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.30;MQ0=0;OQ=1740.53;QD=36.26;SB=-435.04	GT:AD:DP:GL:GQ	1/1:0,48:44:-177.67,-13.27,-0.03:99
+chr1	5227620	rs2945621	C	T	184.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.52;MQ0=0;OQ=2108.36;QD=38.33;SB=-729.97	GT:AD:DP:GL:GQ	1/1:0,54:54:-216.99,-18.70,-2.57:99
+chr1	5228455	rs605572	G	A	158.70	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.08;MQ0=0;OQ=2364.59;QD=38.76;SB=-1049.40	GT:AD:DP:GL:GQ	1/1:0,61:59:-240.06,-17.77,-0.01:99
+chr1	5228485	rs547366	A	G	151.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=59.32;MQ0=0;OQ=1644.48;QD=29.90;SB=-746.94	GT:AD:DP:GL:GQ	1/1:0,55:53:-168.09,-15.99,-0.05:99
+chr1	5228494	rs547375	T	C	432.28	PASS	AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=1148.89;QD=28.72;SB=-518.83	GT:AD:DP:GL:GQ	1/1:0,40:38:-118.51,-11.46,-0.04:99
+chr1	5228675	rs549178	A	C	608.96	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1844.59;QD=34.16;SB=-895.07	GT:AD:DP:GL:GQ	1/1:0,54:53:-188.06,-15.96,-0.02:99
+chr1	5229041	rs552154	A	G	144.86	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=58.33;MQ0=0;OQ=2394.34;QD=35.74;SB=-1030.76	GT:AD:DP:GL:GQ	1/1:0,67:67:-243.04,-20.18,-0.02:99
+chr1	5229075	rs694316	A	G	16.95	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=2.71;MQ=58.29;MQ0=0;OQ=1696.38;QD=32.62;SB=-808.31	GT:AD:DP:GL:GQ	1/1:0,52:49:-173.25,-14.76,-0.02:99
+chr1	5229079	rs574063	A	C	47.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=2.27;MQ=58.29;MQ0=0;OQ=1690.52;QD=32.51;SB=-775.03	GT:AD:DP:GL:GQ	1/1:0,52:50:-172.66,-15.06,-0.02:99
+chr1	5229195	rs2986189	T	C	594.24	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1695.13;QD=33.24;SB=-849.99	GT:AD:DP:GL:GQ	1/1:0,50:49:-173.12,-14.76,-0.02:99
+chr1	5229410	rs590229	A	G	533.32	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.69;MQ0=0;OQ=1626.39;QD=32.53;SB=-702.18	GT:AD:DP:GL:GQ	1/1:0,50:47:-166.24,-14.16,-0.02:99
+chr1	5229454	rs576935	T	C	291.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=2227.88;QD=34.81;SB=-1091.09	GT:AD:DP:GL:GQ	1/1:0,64:63:-226.40,-18.98,-0.03:99
+chr1	5229643	rs589314	C	T	702.68	PASS	AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3349.31;QD=39.87;SB=-1157.05	GT:AD:DP:GL:GQ	1/1:0,84:83:-333.93,-25.00,-0.02:99
+chr1	5229725	rs579467	T	C	242.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=59.13;MQ0=0;OQ=1575.01;QD=29.72;SB=-809.29	GT:AD:DP:GL:GQ	1/1:0,53:51:-161.14,-15.39,-0.05:99
+chr1	5229840	rs580404	G	A	618.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=2841.67;QD=38.93;SB=-1151.68	GT:AD:DP:GL:GQ	1/1:0,73:73:-287.78,-22.00,-0.03:99
+chr1	5229963	rs587619	A	G	627.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=1527.65;QD=31.18;SB=-661.80	GT:AD:DP:GL:GQ	1/1:0,49:48:-156.40,-14.48,-0.05:99
+chr1	5230068	rs684796	A	G	654.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1910.04;QD=31.31;SB=-776.75	GT:AD:DP:GL:GQ	1/1:0,61:59:-194.63,-17.79,-0.04:99
+chr1	5230099	rs493993	T	C	52.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.40;MQ=60.00;MQ0=0;OQ=1531.39;QD=30.03;SB=-555.88	GT:AD:DP:GL:GQ	1/1:0,51:49:-156.77,-14.78,-0.05:99
+chr1	5230146	rs494138	C	T	565.44	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1901.52;QD=38.03;SB=-812.08	GT:AD:DP:GL:GQ	1/1:0,50:49:-193.76,-14.77,-0.02:99
+chr1	5230400	rs683361	C	T	576.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=2445.96;QD=38.22;SB=-885.63	GT:AD:DP:GL:GQ	1/1:0,64:64:-248.21,-19.29,-0.03:99
+chr1	5230419	rs683326	A	C	444.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=2097.81;QD=32.78;SB=-733.04	GT:AD:DP:GL:GQ	1/1:0,64:59:-213.39,-17.77,-0.02:99
+chr1	5230522	rs497780	C	T	280.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=59.44;MQ0=0;OQ=2456.36;QD=36.66;SB=-1135.53	GT:AD:DP:GL:GQ	1/1:0,66:64:-249.25,-19.29,-0.03:99
+chr1	5230617	rs682425	A	C	128.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=60.00;MQ0=0;OQ=2329.64;QD=34.26;SB=-803.08	GT:AD:DP:GL:GQ	1/1:1,67:66:-236.57,-19.88,-0.02:99
+chr1	5230727	rs499639	G	A	152.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.28;MQ0=0;OQ=1710.74;QD=26.73;SB=-582.87	GT:AD:DP:GL:GQ	1/1:0,37:64:-256.74,-99.73,-82.08:99
+chr1	5230993	rs17423021	C	T	275.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=60.00;MQ0=0;OQ=870.39;QD=18.52;SB=-403.16	GT:AD:DP:GL:GQ	0/1:21,26:47:-104.48,-14.16,-73.19:99
+chr1	5231281	rs695100	T	C	614.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1962.66;QD=33.84;SB=-961.65	GT:AD:DP:GL:GQ	1/1:0,58:57:-199.88,-17.17,-0.03:99
+chr1	5231434	rs2860250	T	G	608.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1940.74;QD=34.66;SB=-919.09	GT:AD:DP:GL:GQ	1/1:0,56:55:-197.68,-16.57,-0.02:99
+chr1	5231440	rs2353173	G	T	713.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2174.12;QD=33.45;SB=-1013.52	GT:AD:DP:GL:GQ	1/1:0,65:62:-221.02,-18.68,-0.02:99
+chr1	5231533	rs4290073	G	A	106.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=59.20;MQ0=0;OQ=1041.27;QD=12.86;SB=-342.41	GT:AD:DP:GL:GQ	0/1:49,32:81:-131.81,-24.39,-179.39:99
+chr1	5231729	rs2945622	G	A	619.13	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=2286.02;QD=38.75;SB=-1132.51	GT:AD:DP:GL:GQ	1/1:0,59:57:-232.20,-17.17,-0.01:99
+chr1	5231775	rs4633300	T	C	80.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=2.27;MQ=58.86;MQ0=0;OQ=2147.74;QD=35.21;SB=-1067.79	GT:AD:DP:GL:GQ	1/1:0,61:61:-218.38,-18.38,-0.02:99
+chr1	5231808	rs10799186	T	C	608.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=2059.90;QD=33.22;SB=-1027.00	GT:AD:DP:GL:GQ	1/1:0,62:60:-209.61,-18.08,-0.04:99
+chr1	5231809	rs10799187	G	C	596.93	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=2598.74;QD=40.61;SB=-1318.71	GT:AD:DP:GL:GQ	1/1:0,64:61:-263.48,-18.38,-0.02:99
+chr1	5231833	rs530731	G	C	494.40	PASS	AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2447.16;QD=42.19;SB=-1018.28	GT:AD:DP:GL:GQ	1/1:0,58:58:-248.32,-17.48,-0.02:99
+chr1	5231988	rs614111	C	A	590.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1949.76;QD=35.45;SB=-809.87	GT:AD:DP:GL:GQ	1/1:0,55:54:-198.57,-16.26,-0.01:99
+chr1	5231995	rs614102	A	G	590.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=2129.07;QD=36.09;SB=-828.32	GT:AD:DP:GL:GQ	1/1:0,59:59:-216.51,-17.77,-0.02:99
+chr1	5232537	rs558175	T	A	537.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2470.42;QD=36.33;SB=-1158.53	GT:AD:DP:GL:GQ	1/1:0,68:67:-250.65,-20.18,-0.02:99
+chr1	5232779	rs560794	T	A	637.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2459.58;QD=36.17;SB=-1165.07	GT:AD:DP:GL:GQ	1/1:0,68:66:-249.56,-19.88,-0.02:99
+chr1	5232782	rs600322	G	A	160.84	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.65;MQ0=0;OQ=2495.29;QD=38.39;SB=-1228.15	GT:AD:DP:GL:GQ	1/1:0,65:64:-253.13,-19.28,-0.02:99
+chr1	5232864	rs599884	A	G	212.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.42;MQ0=0;OQ=2139.99;QD=35.08;SB=-951.99	GT:AD:DP:GL:GQ	1/1:0,61:60:-217.60,-18.07,-0.02:99
+chr1	5233339	rs598031	G	A	300.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.38;MQ0=0;OQ=2603.20;QD=38.85;SB=-1265.68	GT:AD:DP:GL:GQ	1/1:0,66:66:-263.92,-19.88,-0.02:99
+chr1	5233376	rs587228	C	T	292.53	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=2392.78;QD=39.88;SB=-1196.59	GT:AD:DP:GL:GQ	1/1:0,60:60:-242.88,-18.07,-0.02:99
+chr1	5233377	rs476866	A	G	630.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=2129.35;QD=34.91;SB=-1082.46	GT:AD:DP:GL:GQ	1/1:0,61:60:-216.54,-18.07,-0.02:99
+chr1	5233422	rs476993	T	C	95.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=58.92;MQ0=0;OQ=1891.61;QD=33.78;SB=-702.84	GT:AD:DP:GL:GQ	1/1:1,55:55:-192.78,-16.58,-0.03:99
+chr1	5233779	rs56260836	C	T	250.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=59.69;MQ0=0;OQ=907.86;QD=15.13;SB=-369.08	GT:AD:DP:GL:GQ	0/1:31,29:57:-111.25,-17.18,-100.79:99
+chr1	5234072	rs504647	G	A	600.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2853.54;QD=40.19;SB=-1415.37	GT:AD:DP:GL:GQ	1/1:0,71:71:-288.96,-21.39,-0.02:99
+chr1	5234128	rs7551166	T	C	37.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=4.51;MQ=60.00;MQ0=0;OQ=837.05;QD=13.29;SB=-326.85	GT:AD:DP:GL:GQ	0/1:34,29:63:-105.96,-18.97,-138.54:99
+chr1	5234274	rs583170	C	A	510.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=1124.36;QD=17.57;SB=-381.75	GT:AD:DP:GL:GQ	0/1:28,36:64:-134.99,-19.28,-100.59:99
+chr1	5234483	rs12746195	G	T	448	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=60.00;MQ0=0;OQ=907.18;QD=14.87;SB=-443.17	GT:AD:DP:GL:GQ	0/1:30,31:60:-112.07,-18.07,-106.20:99
+chr1	5234497	rs12732868	T	G	365.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.80;MQ=60.00;MQ0=0;OQ=834.65;QD=13.04;SB=-431.76	GT:AD:DP:GL:GQ	0/1:33,31:62:-105.43,-18.68,-118.96:99
+chr1	5234595	rs12747559	C	T	411.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=59.66;MQ0=0;OQ=1103.55;QD=16.23;SB=-461.98	GT:AD:DP:GL:GQ	0/1:32,36:64:-132.93,-19.29,-98.65:99
+chr1	5234628	rs12746515	G	A	395.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.70;MQ0=0;OQ=1407.50;QD=18.04;SB=-722.08	GT:AD:DP:GL:GQ	0/1:37,41:75:-166.64,-22.60,-112.02:99
+chr1	5234751	rs12747870	C	T	314.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=2.20;MQ=59.17;MQ0=0;OQ=991.08;QD=14.57;SB=-434.89	GT:AD:DP:GL:GQ	0/1:38,30:67:-122.57,-20.18,-136.08:99
+chr1	5234796	rs12729227	A	T	285.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=58.68;MQ0=0;OQ=635.81;QD=9.49;SB=-240.21	GT:AD:DP:GL:GQ	0/1:44,23:66:-86.75,-19.88,-161.14:99
+chr1	5234855	rs12746867	G	A	137.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=3;HaplotypeScore=0.48;MQ=58.86;MQ0=0;OQ=803.94;QD=13.18;SB=-392.38	GT:AD:DP:GL:GQ	0/1:35,26:59:-101.45,-17.77,-122.51:99
+chr1	5234867	rs12729373	A	G	399.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=739.47;QD=12.12;SB=-312.22	GT:AD:DP:GL:GQ	0/1:35,26:61:-95.60,-18.37,-142.14:99
+chr1	5235030	rs55729623	C	G	87.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=4.84;MQ=59.98;MQ0=0;OQ=961.43;QD=16.30;SB=-383.64	GT:AD:DP:GL:GQ	0/1:26,33:53:-115.42,-16.00,-99.45:99
+chr1	5235034	.	G	A	5.72	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=5.25;MQ=59.98;MQ0=0;OQ=618.09;QD=9.97;SB=-190.00	GT:AD:DP:GL:GQ	0/1:34,27:51:-82.91,-17.82,-96.99:99
+chr1	5235136	rs17457156	T	C	138.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=59.24;MQ0=0;OQ=556.94;QD=9.13;SB=-82.80	GT:AD:DP:GL:GQ	0/1:34,26:58:-79.46,-20.48,-139.05:99
diff --git a/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap b/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap
new file mode 100644
index 000000000..cd0a1f9ad
--- /dev/null
+++ b/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap
@@ -0,0 +1,500 @@
+rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode NA19625 NA19700 NA19701 NA19702 NA19703 NA19704 NA19705 NA19708 NA19712 NA19711 NA19818 NA19819 NA19828 NA19835 NA19834 NA19836 NA19902 NA19901 NA19900 NA19904 NA19919 NA19908 NA19909 NA19914 NA19915 NA19916 NA19917 NA19918 NA19921 NA20129 NA19713 NA19982 NA19983 NA19714 NA19985 NA19984 NA20128 NA20126 NA20127 NA20277 NA20276 NA20279 NA20282 NA20281 NA20284 NA20287 NA20288 NA20290 NA20289 NA20291 NA20292 NA20295 NA20294 NA20297 NA20300 NA20298 NA20301 NA20302 NA20317 NA20319 NA20322 NA20333 NA20332 NA20335 NA20334 NA20337 NA20336 NA20340 NA20341 NA20343 NA20342 NA20344 NA20345 NA20346 NA20347 NA20348 NA20349 NA20350 NA20351 NA20357 NA20356 NA20358 NA20359 NA20360 NA20363 NA20364 NA20412
+rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
+rs11510103 A/G chr1 557616 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11510103:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA NN AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
+rs11240767 C/T chr1 718814 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11240767:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CT CC CC CT CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CT CT CC CC CC CT CC CC CC CC NN CC CT CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CT CT CC CC CT CT CC
+rs3131972 A/G chr1 742584 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3131972:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG AG AA AA AA AA GG AG AG AG AA AG GG AG GG AG AG AG AA GG GG AG AG AG AA AA AA GG AG AA AG AG AG AA AG AG AG GG AA AG AG AG AA GG AA AA GG AG AG AA AA AA AA AA AG GG GG GG AG AA AA AA AA AG AA AG GG AG AG AG AG AG AG AG AG AG AG AA AG AA AG AA AG AA AA AA
+rs3131969 A/G chr1 744045 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3131969:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG AG AA AA AA AA GG AG GG AG AA AG GG AG GG AG AG AG AA GG GG AG AG AG AA AA AA GG AG AA AG AG AG AA NN AG AG GG AG GG GG AG AA GG AA AA GG AG AG NN AA AG AA AA AG GG GG GG AG AA AA NN AA AG AA AG GG AG AG AG AG AG GG AG AG AG AG AA AG AA AG AA AG AA AA AA
+rs1048488 C/T chr1 750775 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1048488:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT TT CT CC CC CC TT CT TT CT CC CT TT CT TT CT CT TT CC TT TT CT CT CT CC CC CC TT CT CC TT CT CT CC CT CT CT TT CT TT CT CT CC TT CC CC TT CT CT CC CT CT CT CC CT TT TT TT CT CC CC CT CT TT CC CT TT CT CT CT CT CT CT CT CT CT CT CC CT CC CT CC CT CC CC CC
+rs12562034 A/G chr1 758311 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12562034:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG GG GG GG GG NN GG AG GG GG GG AG AG AG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AG GG GG GG GG GG AG GG GG AG
+rs12124819 A/G chr1 766409 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12124819:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AG AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
+rs4040617 A/G chr1 769185 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4040617:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG AA AG GG GG GG AA AG AA AG GG AG AA AG AA AG AG AA GG AA AA AG AG AG AG GG AG AA AG GG AA AG NN GG AG AG AG AA AG AA AA AG AG AA GG GG AA AG AG GG AG AG AG GG AG AA AA AA AG AA GG AG AG AA GG AG AA AG AG AG AG AG AA AA AG AG AG GG AG AG AA GG AG AG GG GG
+rs2905036 C/T chr1 782343 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2905036:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT CT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT CC TT TT TT TT TT TT TT CT TT TT TT TT TT CT TT TT TT TT TT CT CT TT TT CT TT TT
+rs4245756 C/T chr1 789326 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4245756:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CT CT CT CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
+rs12086311 A/G chr1 798632 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12086311:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
+rs4970383 A/C chr1 828418 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4970383:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC AC CC CC CC AA AC AC CC AC CC CC CC AC AC AC AC AC CC AA CC AC CC CC AC AA CC AC CC CC AC AC CC AA AA AC AC CC AC AA AC AA AC AC AC CC AC CC CC AC AC CC AC AC CC AC AC AA AC CC CC CC AC CC CC CC CC AC CC AC AA AC AC CC CC CC AC CC AC AA AC AC AC AC CC AC AC
+rs4475691 C/T chr1 836671 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4475691:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CT CT CC CC CC TT CT CC CC CT CC CT TT CT CC CC CT CC CC CC CC CT CC CT CT TT CC CC CT CC CT CT CT CT TT CT CT CT CT CT TT CC CT CT CT CT CT CC CC CT TT CT CC TT TT TT CT CC CT TT CT CT CC CC CT CT CT CC CT CC CC CC CT CT CC CT CT CT CC CT CC CT CT CT CT
+rs1806509 A/C chr1 843817 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1806509:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC CC CC CC CC AC AC CC CC AA AC AC CC CC CC CC AC AC AA AC AA AC AC AC AA AA CC AC AA AC AC CC CC AC AC AC CC AC AC AC AC AC CC CC AC AC AC AC CC AC AA CC CC AC CC CC CC CC AC AC CC CC AC AC AA CC CC CC CC AC AC CC CC AC AC AC CC CC AC AC AC CC AA AC AC AA CC
+rs7537756 A/G chr1 844113 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7537756:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA GG AG AG AG AA AG AA AA AG AG GG AA AG AA AG AG AA AA AA AA AA AG AA AA AG AG AA AA AA AG AA AG AA AA GG AG AG AA AA AG AG AG AG AA AA AG AG AA AA AA AA AG AA GG GG GG AG AA AG AA AA AG AA AG GG GG AG AA AG AG AG AA AG AG AG AA AA AG AA AG AA AA AG AA AG
+rs6694982 A/G chr1 847691 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6694982:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AG AA AA AA AA AG AG AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AG AG AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA
+rs13302982 A/G chr1 851671 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs13302982:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AA AA AG AA AG AG AG AA AA AA AA AA AG AA AG AA AG AA AG AG AG GG AG AA AA AA GG GG AA AG AG AG AG AG GG AG GG AA AG GG AG AA GG AA AA AG AA AG AG AG AG AG GG GG AG GG GG GG AA AA AA GG GG AG AA AA AA AG AG AG AG AG AA AA AG AG AG GG AA AG AG AA AG AG AG
+rs4040604 G/T chr1 852987 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4040604:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GT GG GG GT GG GT GT GT GG GG GG GG GG GT GG GT GG GT GG GT GT GT TT GT GG GG GG TT TT GG GT GT GT GT GT TT GT TT GG GT TT GT GG TT GG GG GT GG GT GT GT GT GT TT TT GT TT TT TT GG GG GG TT TT GT GG GG GG GT GT GT GT GT GG GG GT GT GT TT GG GT GT GG GT GT GT
+rs2340587 A/G chr1 854801 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2340587:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG GG AG GG AG GG AG GG GG GG GG GG AG GG AG GG AG GG AG AG AG AG AG GG GG GG AA AG GG AG AG GG GG AG GG GG AG GG AG AG GG GG AG GG GG AG GG AG AG AG AG GG AG AG GG GG AA AA GG GG GG AG AG AG GG GG GG AG GG AG AG AG GG GG AG AG AG AA GG AG AG GG AG AG GG
+rs28576697 C/T chr1 860508 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28576697:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT CC CT CT TT TT CT CT TT CT TT TT TT TT TT TT TT TT TT TT TT CT CC TT TT TT TT TT TT TT CT TT TT TT CT CT CT CT CT TT TT CT CT TT TT TT TT TT TT TT TT CT
+rs1110052 G/T chr1 863421 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1110052:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GT GG GG GT GG GT GG GG GG GG GG GG GG GT GG GT GG GT GG GT GT GT GT TT GG GG GG TT GT GT GT TT GT GG GT GG GG GT GG GT GT GG GG GT GG GG GT GG GT GT GG GG GG GT GG GG GG TT TT GG GG GG GT GT GG GG GT GG GG GG GG GG GG GG GG GG GG GT TT GG GT GT GG GT GT GT
+rs7523549 C/T chr1 869180 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7523549:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CC CT CC CT CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CT CC CT CC CC CC CC CC CT TT TT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CT CC CC CC CT CT CC CC CC CT CC CC CC CT CC CC CC CC CC CC CC CC CC CC CT CC CC CC CT CC CT CT CT
+rs3748592 A/G chr1 870101 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3748592:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG AG AG AG AA AG AG AG GG GG
+rs3748593 A/C chr1 870253 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3748593:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC AC CC CC AC CC AC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC AC CC CC CC CC CC AC AA AA CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC AC CC CC CC AC CC CC CC AC AC CC CC CC AC CC CC CC AC CC CC CC CC CC CC CC CC CC CC AC CC CC CC AC CC AC AC AC
+rs2272756 A/G chr1 871896 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2272756:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG AG GG GG GG GG GG GG GG GG GG GG GG AG AA GG GG GG GG GG GG GG AG GG GG GG AG AG AG AG AG GG GG AG AG GG GG GG GG GG GG GG GG AG
+rs2340582 A/G chr1 872666 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2340582:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG AG AG AG AA AG AG AG GG GG
+rs4246503 A/G chr1 874678 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4246503:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG AG AG AG AA AG AG AG GG GG
+rs3748594 A/G chr1 876247 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3748594:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG GG AG GG AG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG AG AA AA GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG AG GG GG GG AG AG GG GG GG AG GG GG GG AG GG GG GG GG GG GG GG GG GG GG AG GG GG GG AG GG AG AG AG
+rs17160698 C/T chr1 877025 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs17160698:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT CT TT CT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT TT TT TT CT TT TT TT CT CC TT CT CT CT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT
+rs3748595 A/C chr1 877423 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3748595:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC CC AC AC CC AC CC CC CC CC AC CC AC CC AC CC AC AC CC AC CC CC CC CC CC CC CC CC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC CC CC CC AC CC CC AC AC CC CC AC CC CC CC CC AC CC CC CC CC CC CC CC AC CC CC CC CC CC AC AC CC CC AC AC AC AA AC AC AC AC CC
+rs13303106 A/G chr1 881808 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs13303106:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AG AG AA AA AA AA AA AA AA AA AA AG AG AG AA GG AG AG AG AG AA AG AA GG AG AG AA AA GG AG NN AG GG AG AG AG AG AA AA AG AG AA AG AA AA AA AA AA AA AA AA AA AA AG AG AA AA AG AA AG AA AA AA AA AA AA AA AA AG AG AA AA AA AA AG AG AA AA AA AA AA AA
+rs28415373 C/T chr1 883844 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28415373:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
+rs13303010 A/G chr1 884436 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs13303010:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG AG AG AG GG GG GG AG GG GG GG GG AG AG AG GG AA AG AG AA AG AG AG AG AA AG AG GG GG AA AG AG AA AA AA AG AG AA AG GG AA AG GG AA AG GG GG GG GG GG GG AG AG AA AG AG GG GG AG GG AG AG GG GG GG AG AG AG AG AA AG GG AG AG GG AG AG GG GG GG GG GG AG
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