diff --git a/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java b/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
index b25da688d91..ee7539d6b82 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
@@ -1,10 +1,11 @@
 package org.broadinstitute.hellbender.engine;
 
+import com.intel.genomicsdb.model.GenomicsDBExportConfiguration;
+import com.intel.genomicsdb.reader.GenomicsDBFeatureReader;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.util.IOUtil;
 import htsjdk.tribble.*;
 import htsjdk.variant.bcf2.BCF2Codec;
-import htsjdk.variant.variantcontext.GenotypeLikelihoods;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFHeader;
 import org.apache.logging.log4j.LogManager;
@@ -19,25 +20,18 @@
 import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
 import org.broadinstitute.hellbender.utils.nio.SeekableByteChannelPrefetcher;
-
-import com.intel.genomicsdb.model.GenomicsDBExportConfiguration;
-import com.intel.genomicsdb.reader.GenomicsDBFeatureReader;
-import com.googlecode.protobuf.format.JsonFormat;
-import com.intel.genomicsdb.model.GenomicsDBVidMapProto;
+import static org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBUtils.*;
 
 import java.io.File;
 import java.io.IOException;
 import java.nio.channels.SeekableByteChannel;
-import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Optional;
 import java.util.function.Function;
-import java.io.FileReader;
-import java.util.HashMap;
-import java.util.Map;
+
+
 
 /**
  * Enables traversals and queries over sources of Features, which are metadata associated with a location
@@ -68,11 +62,6 @@
 public final class FeatureDataSource<T extends Feature> implements GATKDataSource<T>, AutoCloseable {
     private static final Logger logger = LogManager.getLogger(FeatureDataSource.class);
 
-    /**
-     * identifies a path as a GenomicsDB URI
-     */
-    public static final String GENOMIC_DB_URI_SCHEME = "gendb://";
-
     /**
      * Feature reader used to retrieve records from our file
      */
@@ -288,14 +277,6 @@ public FeatureDataSource(final FeatureInput<T> featureInput, final int queryLook
         this.queryLookaheadBases = queryLookaheadBases;
     }
 
-    /**
-     * @param path String containing the path to test
-     * @return true if path represent a GenomicsDB URI, otherwise false
-     */
-    public static boolean isGenomicsDBPath(final String path) {
-        return path != null && path.startsWith(GENOMIC_DB_URI_SCHEME);
-    }
-
     @SuppressWarnings("unchecked")
     private static <T extends Feature> FeatureReader<T> getFeatureReader(final FeatureInput<T> featureInput, final Class<? extends Feature> targetFeatureType,
                                                                          final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper,
@@ -368,7 +349,7 @@ private static <T extends Feature> FeatureReader<T> getFeatureReader(final Featu
         }
     }
 
-    private static FeatureReader<VariantContext> getGenomicsDBFeatureReader(final String path, final File reference) {
+    protected static FeatureReader<VariantContext> getGenomicsDBFeatureReader(final String path, final File reference) {
         if (!isGenomicsDBPath(path)) {
             throw new IllegalArgumentException("Trying to create a GenomicsDBReader from a non-GenomicsDB input");
         }
@@ -404,149 +385,6 @@ private static FeatureReader<VariantContext> getGenomicsDBFeatureReader(final St
         }
     }
 
-    private static GenomicsDBExportConfiguration.ExportConfiguration createExportConfiguration(final File reference, final File workspace,
-                                                                                               final File callsetJson, final File vidmapJson,
-                                                                                               final File vcfHeader) {
-        final GenomicsDBExportConfiguration.ExportConfiguration.Builder exportConfigurationBuilder =
-                GenomicsDBExportConfiguration.ExportConfiguration.newBuilder()
-                        .setWorkspace(workspace.getAbsolutePath())
-                        .setReferenceGenome(reference.getAbsolutePath())
-                        .setVidMappingFile(vidmapJson.getAbsolutePath())
-                        .setCallsetMappingFile(callsetJson.getAbsolutePath())
-                        .setVcfHeaderFilename(vcfHeader.getAbsolutePath())
-                        .setProduceGTField(false)
-                        .setProduceGTWithMinPLValueForSpanningDeletions(false)
-                        .setSitesOnlyQuery(false)
-                        .setMaxDiploidAltAllelesThatCanBeGenotyped(GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
-        final Path arrayFolder = Paths.get(workspace.getAbsolutePath(), GenomicsDBConstants.DEFAULT_ARRAY_NAME).toAbsolutePath();
-
-        // For the multi-interval support, we create multiple arrays (directories) in a single workspace -
-        // one per interval. So, if you wish to import intervals ("chr1", [ 1, 100M ]) and ("chr2", [ 1, 100M ]),
-        // you end up with 2 directories named chr1$1$100M and chr2$1$100M. So, the array names depend on the
-        // partition bounds.
-
-        // During the read phase, the user only supplies the workspace. The array names are obtained by scanning
-        // the entries in the workspace and reading the right arrays. For example, if you wish to read ("chr2",
-        // 50, 50M), then only the second array is queried.
-
-        // In the previous version of the tool, the array name was a constant - genomicsdb_array. The new version
-        // will be backward compatible with respect to reads. Hence, if a directory named genomicsdb_array is found,
-        // the array name is passed to the GenomicsDBFeatureReader otherwise the array names are generated from the
-        // directory entries.
-        if (Files.exists(arrayFolder)) {
-            exportConfigurationBuilder.setArrayName(GenomicsDBConstants.DEFAULT_ARRAY_NAME);
-        } else {
-            exportConfigurationBuilder.setGenerateArrayNameFromPartitionBounds(true);
-        }
-
-        //Sample code snippet to show how combine operations for INFO fields can be specified using the Protobuf
-        //API
-        //
-        //References
-        //GenomicsDB Protobuf structs: https://github.com/Intel-HLS/GenomicsDB/blob/master/src/resources/genomicsdb_vid_mapping.proto
-        //Protobuf generated Java code guide:
-        //https://developers.google.com/protocol-buffers/docs/javatutorial#the-protocol-buffer-api
-        //https://developers.google.com/protocol-buffers/docs/reference/java-generated
-
-        //Parse the vid json and create an in-memory Protobuf structure representing the
-        //information in the JSON file
-        GenomicsDBVidMapProto.VidMappingPB vidMapPB;
-        try {
-            vidMapPB = getProtobufVidMappingFromJsonFile(vidmapJson);
-        } catch (final IOException e) {
-            throw new UserException("Could not open vid json file " + vidmapJson, e);
-        }
-
-        //In vidMapPB, fields is a list of GenomicsDBVidMapProto.GenomicsDBFieldInfo objects
-        //Each GenomicsDBFieldInfo object contains information about a specific field in the TileDB/GenomicsDB store
-        //We iterate over the list and create a field name to list index map
-        final HashMap<String, Integer> fieldNameToIndexInVidFieldsList =
-                getFieldNameToListIndexInProtobufVidMappingObject(vidMapPB);
-
-        //Example: set MQ combine operation to median (default is also median, but this is just an example)
-        vidMapPB = updateINFOFieldCombineOperation(vidMapPB, fieldNameToIndexInVidFieldsList,
-                "MQ", "median");
-        if (vidMapPB != null) {
-            //Use rebuilt vidMap in exportConfiguration
-            //NOTE: this does NOT update the JSON file, the vidMapPB is a temporary structure that's passed to
-            //C++ modules of GenomicsDB for this specific query. Other queries will continue to use the information
-            //in the JSON file
-            exportConfigurationBuilder.setVidMapping(vidMapPB);
-        }
-
-        return exportConfigurationBuilder.build();
-    }
-
-    /**
-     * Parse the vid json and create an in-memory Protobuf structure representing the
-     * information in the JSON file
-     *
-     * @param vidmapJson vid JSON file
-     * @return Protobuf object
-     */
-    public static GenomicsDBVidMapProto.VidMappingPB getProtobufVidMappingFromJsonFile(final File vidmapJson)
-            throws IOException {
-        final GenomicsDBVidMapProto.VidMappingPB.Builder vidMapBuilder = GenomicsDBVidMapProto.VidMappingPB.newBuilder();
-        try (final FileReader reader = new FileReader(vidmapJson)) {
-            JsonFormat.merge(reader, vidMapBuilder);
-        }
-        return vidMapBuilder.build();
-    }
-
-    /**
-     * In vidMapPB, fields is a list of GenomicsDBVidMapProto.GenomicsDBFieldInfo objects
-     * Each GenomicsDBFieldInfo object contains information about a specific field in the TileDB/GenomicsDB store
-     * We iterate over the list and create a field name to list index map
-     *
-     * @param vidMapPB Protobuf vid mapping object
-     * @return map from field name to index in vidMapPB.fields list
-     */
-    public static HashMap<String, Integer> getFieldNameToListIndexInProtobufVidMappingObject(
-            final GenomicsDBVidMapProto.VidMappingPB vidMapPB) {
-        final HashMap<String, Integer> fieldNameToIndexInVidFieldsList = new HashMap<>();
-        for (int fieldIdx = 0; fieldIdx < vidMapPB.getFieldsCount(); ++fieldIdx) {
-            fieldNameToIndexInVidFieldsList.put(vidMapPB.getFields(fieldIdx).getName(), fieldIdx);
-        }
-        return fieldNameToIndexInVidFieldsList;
-    }
-
-    /**
-     * Update vid Protobuf object with new combine operation for field
-     *
-     * @param vidMapPB                        input vid object
-     * @param fieldNameToIndexInVidFieldsList name to index in list
-     * @param fieldName                       INFO field name
-     * @param newCombineOperation             combine op ("sum", "median")
-     * @return updated vid Protobuf object if field exists, else null
-     */
-    public static GenomicsDBVidMapProto.VidMappingPB updateINFOFieldCombineOperation(
-            final GenomicsDBVidMapProto.VidMappingPB vidMapPB,
-            final Map<String, Integer> fieldNameToIndexInVidFieldsList,
-            final String fieldName,
-            final String newCombineOperation) {
-        final int fieldIdx = fieldNameToIndexInVidFieldsList.containsKey(fieldName)
-                ? fieldNameToIndexInVidFieldsList.get(fieldName) : -1;
-        if (fieldIdx >= 0) {
-            //Would need to rebuild vidMapPB - so get top level builder first
-            final GenomicsDBVidMapProto.VidMappingPB.Builder updatedVidMapBuilder = vidMapPB.toBuilder();
-            //To update the list element corresponding to fieldName, we get the builder for that specific list element
-            final GenomicsDBVidMapProto.GenomicsDBFieldInfo.Builder fieldBuilder =
-                    updatedVidMapBuilder.getFieldsBuilder(fieldIdx);
-            //And update its combine operation
-            fieldBuilder.setVCFFieldCombineOperation(newCombineOperation);
-
-            //Shorter way of writing the same operation
-            /*
-            updatedVidMapBuilder.getFieldsBuilder(fieldIdx)
-                .setVCFFieldCombineOperation(newCombineOperation);
-            */
-
-            //Rebuild full vidMap
-            return updatedVidMapBuilder.build();
-        }
-        return null;
-    }
-
     /**
      * Returns the sequence dictionary for this source of Features.
      * Uses the dictionary from the VCF header (if present) for variant inputs,
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/FeatureInput.java b/src/main/java/org/broadinstitute/hellbender/engine/FeatureInput.java
index 320f9c6ef94..a1112153f48 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/FeatureInput.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/FeatureInput.java
@@ -4,6 +4,7 @@
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.FeatureCodec;
 import org.broadinstitute.barclay.argparser.CommandLineException;
+import org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBUtils;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
 
@@ -244,8 +245,8 @@ public void setFeatureCodecClass(final Class<FeatureCodec<T, ?>> featureCodecCla
      * creates a name from the given filePath by finding the absolute path of the given input
      */
     private static String makeIntoAbsolutePath(final String filePath){
-        if(FeatureDataSource.isGenomicsDBPath(filePath)){
-            return FeatureDataSource.GENOMIC_DB_URI_SCHEME + new File(filePath.replace(FeatureDataSource.GENOMIC_DB_URI_SCHEME,"")).getAbsolutePath();
+        if(GenomicsDBUtils.isGenomicsDBPath(filePath)){
+            return GenomicsDBUtils.GENOMIC_DB_URI_SCHEME + new File(filePath.replace(GenomicsDBUtils.GENOMIC_DB_URI_SCHEME,"")).getAbsolutePath();
         } else if (URI.create(filePath).getScheme() != null) {
             return IOUtils.getPath(filePath).toAbsolutePath().toUri().toString();
         } else {
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java
new file mode 100644
index 00000000000..0ce0adcc500
--- /dev/null
+++ b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java
@@ -0,0 +1,180 @@
+package org.broadinstitute.hellbender.tools.genomicsdb;
+
+import com.googlecode.protobuf.format.JsonFormat;
+import com.intel.genomicsdb.model.GenomicsDBExportConfiguration;
+import com.intel.genomicsdb.model.GenomicsDBVidMapProto;
+import htsjdk.variant.variantcontext.GenotypeLikelihoods;
+import org.broadinstitute.hellbender.exceptions.UserException;
+import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Utility class containing various methods for working with GenomicsDB
+ * Contains code to modify the GenomicsDB query output format using the Protobuf API
+ *
+ * References:
+ * GenomicsDB Protobuf structs: https://github.com/Intel-HLS/GenomicsDB/blob/master/src/resources/genomicsdb_vid_mapping.proto
+ * Protobuf generated Java code guide:
+ * https://developers.google.com/protocol-buffers/docs/javatutorial#the-protocol-buffer-api
+ * https://developers.google.com/protocol-buffers/docs/reference/java-generated
+ */
+public class GenomicsDBUtils {
+
+    /**
+     * identifies a path as a GenomicsDB URI
+     */
+    public static final String GENOMIC_DB_URI_SCHEME = "gendb://";
+
+    /**
+     * @param path String containing the path to test
+     * @return true if path represent a GenomicsDB URI, otherwise false
+     */
+    public static boolean isGenomicsDBPath(final String path) {
+        return path != null && path.startsWith(GENOMIC_DB_URI_SCHEME);
+    }
+
+    /**
+     *
+     * @param reference reference sequence
+     * @param workspace path to the GenomicsDB workspace
+     * @param callsetJson path to the GenomicsDB callset JSON
+     * @param vidmapJson path to the GenomicsDB vidmap JSON
+     * @param vcfHeader VCF with header information to use for header lines on export
+     * @return a configuration to determine the output format when the GenomicsDB is queried
+     */
+    public static GenomicsDBExportConfiguration.ExportConfiguration createExportConfiguration(final File reference, final File workspace,
+                                                                                               final File callsetJson, final File vidmapJson,
+                                                                                               final File vcfHeader) {
+        final GenomicsDBExportConfiguration.ExportConfiguration.Builder exportConfigurationBuilder =
+                GenomicsDBExportConfiguration.ExportConfiguration.newBuilder()
+                        .setWorkspace(workspace.getAbsolutePath())
+                        .setReferenceGenome(reference.getAbsolutePath())
+                        .setVidMappingFile(vidmapJson.getAbsolutePath())
+                        .setCallsetMappingFile(callsetJson.getAbsolutePath())
+                        .setVcfHeaderFilename(vcfHeader.getAbsolutePath())
+                        .setProduceGTField(false)
+                        .setProduceGTWithMinPLValueForSpanningDeletions(false)
+                        .setSitesOnlyQuery(false)
+                        .setMaxDiploidAltAllelesThatCanBeGenotyped(GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
+        final Path arrayFolder = Paths.get(workspace.getAbsolutePath(), GenomicsDBConstants.DEFAULT_ARRAY_NAME).toAbsolutePath();
+
+        // For the multi-interval support, we create multiple arrays (directories) in a single workspace -
+        // one per interval. So, if you wish to import intervals ("chr1", [ 1, 100M ]) and ("chr2", [ 1, 100M ]),
+        // you end up with 2 directories named chr1$1$100M and chr2$1$100M. So, the array names depend on the
+        // partition bounds.
+
+        // During the read phase, the user only supplies the workspace. The array names are obtained by scanning
+        // the entries in the workspace and reading the right arrays. For example, if you wish to read ("chr2",
+        // 50, 50M), then only the second array is queried.
+
+        // In the previous version of the tool, the array name was a constant - genomicsdb_array. The new version
+        // will be backward compatible with respect to reads. Hence, if a directory named genomicsdb_array is found,
+        // the array name is passed to the GenomicsDBFeatureReader otherwise the array names are generated from the
+        // directory entries.
+        if (Files.exists(arrayFolder)) {
+            exportConfigurationBuilder.setArrayName(GenomicsDBConstants.DEFAULT_ARRAY_NAME);
+        } else {
+            exportConfigurationBuilder.setGenerateArrayNameFromPartitionBounds(true);
+        }
+
+        //Parse the vid json and create an in-memory Protobuf structure representing the information in the JSON file
+        GenomicsDBVidMapProto.VidMappingPB vidMapPB;
+        try {
+            vidMapPB = getProtobufVidMappingFromJsonFile(vidmapJson);
+        } catch (final IOException e) {
+            throw new UserException("Could not open vid json file " + vidmapJson, e);
+        }
+
+        //In vidMapPB, fields is a list of GenomicsDBVidMapProto.GenomicsDBFieldInfo objects
+        //Each GenomicsDBFieldInfo object contains information about a specific field in the TileDB/GenomicsDB store
+        //We iterate over the list and create a field name to list index map
+        final HashMap<String, Integer> fieldNameToIndexInVidFieldsList =
+                getFieldNameToListIndexInProtobufVidMappingObject(vidMapPB);
+
+        vidMapPB = updateINFOFieldCombineOperation(vidMapPB, fieldNameToIndexInVidFieldsList,
+                GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, "element_wise_sum");
+
+
+        if (vidMapPB != null) {
+            //Use rebuilt vidMap in exportConfiguration
+            //NOTE: this does NOT update the JSON file, the vidMapPB is a temporary structure that's passed to
+            //C++ modules of GenomicsDB for this specific query. Other queries will continue to use the information
+            //in the JSON file
+            exportConfigurationBuilder.setVidMapping(vidMapPB);
+        }
+
+        return exportConfigurationBuilder.build();
+    }
+
+    /**
+     * Parse the vid json and create an in-memory Protobuf structure representing the
+     * information in the JSON file
+     *
+     * @param vidmapJson vid JSON file
+     * @return Protobuf object
+     */
+    public static GenomicsDBVidMapProto.VidMappingPB getProtobufVidMappingFromJsonFile(final File vidmapJson)
+            throws IOException {
+        final GenomicsDBVidMapProto.VidMappingPB.Builder vidMapBuilder = GenomicsDBVidMapProto.VidMappingPB.newBuilder();
+        try (final FileReader reader = new FileReader(vidmapJson)) {
+            JsonFormat.merge(reader, vidMapBuilder);
+        }
+        return vidMapBuilder.build();
+    }
+
+    /**
+     * In vidMapPB, fields is a list of GenomicsDBVidMapProto.GenomicsDBFieldInfo objects
+     * Each GenomicsDBFieldInfo object contains information about a specific field in the TileDB/GenomicsDB store
+     * We iterate over the list and create a field name to list index map
+     *
+     * @param vidMapPB Protobuf vid mapping object
+     * @return map from field name to index in vidMapPB.fields list
+     */
+    public static HashMap<String, Integer> getFieldNameToListIndexInProtobufVidMappingObject(
+            final GenomicsDBVidMapProto.VidMappingPB vidMapPB) {
+        final HashMap<String, Integer> fieldNameToIndexInVidFieldsList = new HashMap<>();
+        for (int fieldIdx = 0; fieldIdx < vidMapPB.getFieldsCount(); ++fieldIdx) {
+            fieldNameToIndexInVidFieldsList.put(vidMapPB.getFields(fieldIdx).getName(), fieldIdx);
+        }
+        return fieldNameToIndexInVidFieldsList;
+    }
+
+    /**
+     * Update vid Protobuf object with new combine operation for field
+     *
+     * @param vidMapPB                        input vid object
+     * @param fieldNameToIndexInVidFieldsList name to index in list
+     * @param fieldName                       INFO field name
+     * @param newCombineOperation             combine op ("sum", "median")
+     * @return updated vid Protobuf object if field exists, else null
+     */
+    public static GenomicsDBVidMapProto.VidMappingPB updateINFOFieldCombineOperation(
+            final GenomicsDBVidMapProto.VidMappingPB vidMapPB,
+            final Map<String, Integer> fieldNameToIndexInVidFieldsList,
+            final String fieldName,
+            final String newCombineOperation) {
+        final int fieldIdx = fieldNameToIndexInVidFieldsList.containsKey(fieldName)
+                ? fieldNameToIndexInVidFieldsList.get(fieldName) : -1;
+        if (fieldIdx >= 0) {
+            //Would need to rebuild vidMapPB - so get top level builder first
+            final GenomicsDBVidMapProto.VidMappingPB.Builder updatedVidMapBuilder = vidMapPB.toBuilder();
+            //To update the list element corresponding to fieldName, we get the builder for that specific list element
+            final GenomicsDBVidMapProto.GenomicsDBFieldInfo.Builder fieldBuilder =
+                    updatedVidMapBuilder.getFieldsBuilder(fieldIdx);
+            //And update its combine operation
+            fieldBuilder.setVCFFieldCombineOperation(newCombineOperation);
+
+            //Rebuild full vidMap
+            return updatedVidMapBuilder.build();
+        }
+        return null;
+    }
+}
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java
index eb49a7096b5..a998c1c3823 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java
@@ -8,6 +8,8 @@
 import htsjdk.variant.vcf.VCFConstants;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
 import htsjdk.variant.vcf.VCFStandardHeaderLines;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.engine.ReferenceContext;
 import org.broadinstitute.hellbender.exceptions.UserException;
@@ -17,6 +19,7 @@
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods;
 import org.broadinstitute.hellbender.utils.help.HelpConstants;
+import org.broadinstitute.hellbender.utils.logging.OneShotLogger;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
 import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines;
@@ -30,6 +33,8 @@
  *
  * <p>This annotation provides an estimation of the overall mapping quality of reads supporting a variant call, averaged over all samples in a cohort.</p>
  *
+ * <p>The raw data format for this annotation consists of a list of two entries: the sum of the squared mapping qualities and the number of reads across variant (not homRef) genotypes</p>
+ *
  * <h3>Statistical notes</h3>
  * <p>The root mean square is equivalent to the mean of the mapping qualities plus the standard deviation of the mapping qualities.</p>
  *
@@ -41,10 +46,16 @@
  */
 @DocumentedFeature(groupName=HelpConstants.DOC_CAT_ANNOTATORS, groupSummary=HelpConstants.DOC_CAT_ANNOTATORS_SUMMARY, summary="Root mean square of the mapping quality of reads across all samples (MQ)")
 public final class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation, ReducibleAnnotation {
+    private static final OneShotLogger logger = new OneShotLogger(RMSMappingQuality.class);
     private static final RMSMappingQuality instance = new RMSMappingQuality();
+    public static final int NUM_LIST_ENTRIES = 2;
+    public static final int SUM_OF_SQUARES_INDEX = 0;
+    public static final int TOTAL_DEPTH_INDEX = 1;
 
     @Override
-    public String getRawKeyName() { return GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY;}
+    public String getRawKeyName() { return GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY;}   //new key for the two-value MQ data to prevent version mismatch catastrophes
+
+    public static String getDeprecatedRawKeyName() { return GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY;}   //new key for the two-value MQ data to prevent version mismatch catastrophes
 
     @Override
     public List<String> getKeyNames() {
@@ -74,9 +85,9 @@ public Map<String, Object> annotateRawData(final ReferenceContext ref,
         }
 
         final Map<String, Object> annotations = new HashMap<>();
-        final ReducibleAnnotationData<Number> myData = new ReducibleAnnotationData<>(null);
+        final ReducibleAnnotationData<List<Integer>> myData = new ReducibleAnnotationData<>(null);
         calculateRawData(vc, likelihoods, myData);
-        final String annotationString = formattedValue((double) myData.getAttributeMap().get(Allele.NO_CALL));
+        final String annotationString = makeRawAnnotationString(vc.getAlleles(), myData.getAttributeMap());
         annotations.put(getRawKeyName(), annotationString);
         return annotations;
     }
@@ -90,7 +101,6 @@ public Map<String, Object> combineRawData(final List<Allele> vcAlleles, final Li
         for (final ReducibleAnnotationData currentValue : annotationList) {
             parseRawDataString(currentValue);
             combineAttributeMap(currentValue, combinedData);
-
         }
         final Map<String, Object> annotations = new HashMap<>();
         String annotationString = makeRawAnnotationString(vcAlleles, combinedData.getAttributeMap());
@@ -98,34 +108,67 @@ public Map<String, Object> combineRawData(final List<Allele> vcAlleles, final Li
         return annotations;
     }
 
-    public String makeRawAnnotationString(final List<Allele> vcAlleles, final Map<Allele, Number> perAlleleData) {
-        return String.format("%.2f", perAlleleData.get(Allele.NO_CALL));
+    public String makeRawAnnotationString(final List<Allele> vcAlleles, final Map<Allele, List<Integer>> perAlleleData) {
+        return String.format("%d,%d", perAlleleData.get(Allele.NO_CALL).get(0), perAlleleData.get(Allele.NO_CALL).get(1));
     }
 
     @Override
     @SuppressWarnings({"unchecked", "rawtypes"})//FIXME generics here blow up
     public Map<String, Object> finalizeRawData(final VariantContext vc, final VariantContext originalVC) {
-        if (!vc.hasAttribute(getRawKeyName()))
+        String rawMQdata;
+        if (vc.hasAttribute(getRawKeyName())) {
+            rawMQdata = vc.getAttributeAsString(getRawKeyName(), null);
+        }
+        else if (vc.hasAttribute(getDeprecatedRawKeyName())) {
+            rawMQdata = vc.getAttributeAsString(getDeprecatedRawKeyName(), null);
+            //the original version of ReblockGVCF produces a different MQ format -- try to handle that gracefully here just in case those files go through GenotypeGVCFs
+            if (vc.hasAttribute("MQ_DP")) {
+                logger.warn("Presence of MQ_DP key indicates that this tool may be running on an older output of ReblockGVCF " +
+                        "that may not have compatible annotations with this GATK version. Attempting to reformat MQ data.");
+                final String rawMQdepth = vc.getAttributeAsString("MQ_DP",null);
+                if (rawMQdepth == null) {
+                    throw new UserException.BadInput("MQ annotation data is not properly formatted. This version expects an " +
+                            "int tuple of sum of squared MQ values and total reads over variant genotypes.");
+                }
+                rawMQdata = Math.round(Double.parseDouble(rawMQdata)) + "," + rawMQdepth;  //deprecated format was double so it needs to be converted to int
+            }
+            else {
+                logger.warn("MQ annotation data is not properly formatted. This GATK version expects key "
+                        + getRawKeyName() + " with an int tuple of sum of squared MQ values and total reads over variant "
+                        + "genotypes as the value. Attempting to use deprecated MQ calculation.");
+                final int numOfReads = getNumOfReads(vc, null);
+                rawMQdata = Math.round(Double.parseDouble(rawMQdata)) + "," + numOfReads;   //deprecated format was double so it needs to be converted to int
+            }
+        }
+        else {
             return new HashMap<>();
-        String rawMQdata = vc.getAttributeAsString(getRawKeyName(),null);
-        if (rawMQdata == null)
+        }
+        if (rawMQdata == null) {
             return new HashMap<>();
+        }
 
-        ReducibleAnnotationData myData = new ReducibleAnnotationData(rawMQdata);
+        ReducibleAnnotationData<List<Integer>> myData = new ReducibleAnnotationData(rawMQdata);
         parseRawDataString(myData);
 
-        String annotationString = makeFinalizedAnnotationString(getNumOfReads(vc, null), myData.getAttributeMap());
+        final String annotationString = makeFinalizedAnnotationString(myData.getAttribute(Allele.NO_CALL).get(TOTAL_DEPTH_INDEX), myData.getAttribute(Allele.NO_CALL).get(SUM_OF_SQUARES_INDEX));
         return Collections.singletonMap(getKeyNames().get(0), annotationString);
     }
 
-    public String makeFinalizedAnnotationString(final int numOfReads, final Map<Allele, Double> perAlleleData) {
-        return String.format("%.2f", Math.sqrt(perAlleleData.get(Allele.NO_CALL)/numOfReads));
+    public String makeFinalizedAnnotationString(final int numOfReads, final int sumOfSquaredMQs) {
+        return String.format("%.2f", Math.sqrt(sumOfSquaredMQs/(double)numOfReads));
     }
 
 
-    public void combineAttributeMap(ReducibleAnnotationData<Double> toAdd, ReducibleAnnotationData<Double> combined) {
+    /**
+     * Combine the int tuples: sum of squared mapping quality and read counts over variant genotypes
+     * Since this is not an allele-specific annotation, store the result with the NO_CALL allele key.
+     * @param toAdd new data
+     * @param combined passed in as previous data, modified to store the combined result
+     */
+    public void combineAttributeMap(ReducibleAnnotationData<List<Integer>> toAdd, ReducibleAnnotationData<List<Integer>> combined) {
         if (combined.getAttribute(Allele.NO_CALL) != null) {
-            combined.putAttribute(Allele.NO_CALL, combined.getAttribute(Allele.NO_CALL) + toAdd.getAttribute(Allele.NO_CALL));
+            combined.putAttribute(Allele.NO_CALL, Arrays.asList(combined.getAttribute(Allele.NO_CALL).get(0) + toAdd.getAttribute(Allele.NO_CALL).get(0),
+                    combined.getAttribute(Allele.NO_CALL).get(1) + toAdd.getAttribute(Allele.NO_CALL).get(1)));
         } else {
             combined.putAttribute(Allele.NO_CALL, toAdd.getAttribute(Allele.NO_CALL));
         }
@@ -135,14 +178,19 @@ public void combineAttributeMap(ReducibleAnnotationData<Double> toAdd, Reducible
     public void calculateRawData(final VariantContext vc,
                                  final ReadLikelihoods<Allele> likelihoods,
                                  final ReducibleAnnotationData rawAnnotations){
-        //put this as a double, like GATK3.5
-        final double squareSum = IntStream.range(0, likelihoods.numberOfSamples()).boxed()
-                .flatMap(s -> likelihoods.sampleReads(s).stream())
-                .map(GATKRead::getMappingQuality)
-                .filter(mq -> mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE)
-                .mapToDouble(mq -> mq * mq).sum();
-
-        rawAnnotations.putAttribute(Allele.NO_CALL, squareSum);
+        //GATK3.5 had a double, but change this to an int for the tuple representation (square sum, read count)
+        int squareSum = 0;
+        int numReadsUsed = 0;
+        for (int i = 0; i < likelihoods.numberOfSamples(); i++) {
+            for (final GATKRead read : likelihoods.sampleReads(i)) {
+                int mq = read.getMappingQuality();
+                if (mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE) {
+                    squareSum += mq * mq;
+                    numReadsUsed++;
+                }
+            }
+        }
+        rawAnnotations.putAttribute(Allele.NO_CALL, Arrays.asList(squareSum, numReadsUsed));
     }
 
     @Override
@@ -155,9 +203,9 @@ public Map<String, Object> annotate(final ReferenceContext ref,
         }
 
         final Map<String, Object> annotations = new HashMap<>();
-        final ReducibleAnnotationData<Double> myData = new ReducibleAnnotationData<>(null);
+        final ReducibleAnnotationData<List<Integer>> myData = new ReducibleAnnotationData<>(null);
         calculateRawData(vc, likelihoods, myData);
-        final String annotationString = makeFinalizedAnnotationString(getNumOfReads(vc, likelihoods), myData.getAttributeMap());
+        final String annotationString = makeFinalizedAnnotationString(myData.getAttribute(Allele.NO_CALL).get(TOTAL_DEPTH_INDEX), myData.getAttribute(Allele.NO_CALL).get(SUM_OF_SQUARES_INDEX));
         annotations.put(getKeyNames().get(0), annotationString);
         return annotations;
     }
@@ -168,9 +216,10 @@ static String formattedValue(double rms) {
     }
 
     /**
-     * converts {@link GATKVCFConstants#RAW_RMS_MAPPING_QUALITY_KEY} into  {@link VCFConstants#RMS_MAPPING_QUALITY_KEY}  annotation if present
+     * converts {@link GATKVCFConstants#RAW_MAPPING_QUALITY_WITH_DEPTH_KEY} into  {@link VCFConstants#RMS_MAPPING_QUALITY_KEY}  annotation if present
+     * NOTE: this is currently only used by HaplotypeCaller in VCF mode
      * @param vc which potentially contains rawMQ
-     * @return if vc contained {@link GATKVCFConstants#RAW_RMS_MAPPING_QUALITY_KEY} it will be replaced with {@link VCFConstants#RMS_MAPPING_QUALITY_KEY}
+     * @return if vc contained {@link GATKVCFConstants#RAW_MAPPING_QUALITY_WITH_DEPTH_KEY} it will be replaced with {@link VCFConstants#RMS_MAPPING_QUALITY_KEY}
      * otherwise return the original vc
      */
     public VariantContext finalizeRawMQ(final VariantContext vc) {
@@ -178,9 +227,8 @@ public VariantContext finalizeRawMQ(final VariantContext vc) {
         if (rawMQdata == null) {
             return vc;
         } else {
-            final double squareSum = parseRawDataString(rawMQdata);
-            final int numOfReads = getNumOfReads(vc, null);
-            final double rms = Math.sqrt(squareSum / (double)numOfReads);
+            final List<Integer> SSQMQandDP = parseRawDataString(rawMQdata);
+            final double rms = Math.sqrt(SSQMQandDP.get(SUM_OF_SQUARES_INDEX) / (double)SSQMQandDP.get(TOTAL_DEPTH_INDEX));
             final String finalizedRMSMAppingQuality = formattedValue(rms);
             return new VariantContextBuilder(vc)
                     .rmAttribute(getRawKeyName())
@@ -189,24 +237,20 @@ public VariantContext finalizeRawMQ(final VariantContext vc) {
         }
     }
 
-    protected void parseRawDataString(ReducibleAnnotationData<Number> myData) {
-        final String rawDataString = myData.getRawData();
-        String[] rawMQdataAsStringVector;
-        rawMQdataAsStringVector = rawDataString.split(",");
-        double squareSum = Double.parseDouble(rawMQdataAsStringVector[0]);
-        myData.putAttribute(Allele.NO_CALL, squareSum);
+    protected void parseRawDataString(ReducibleAnnotationData<List<Integer>> myData) {
+        myData.putAttribute(Allele.NO_CALL, parseRawDataString(myData.getRawData()));
     }
 
     //TODO once the AS annotations have been added genotype gvcfs this can be removed for a more generic approach
-    private static double parseRawDataString(String rawDataString) {
+    private static List<Integer> parseRawDataString(String rawDataString) {
         try {
-            /*
-             * TODO: this is copied from gatk3 where it ignored all but the first value, we should figure out if this is
-             * the right thing to do or if it should just convert the string without trying to split it and fail if
-             * there is more than one value
-             */
-            final double squareSum = Double.parseDouble(rawDataString.split(",")[0]);
-            return squareSum;
+            final String[] parsed = rawDataString.split(",");
+            if (parsed.length != NUM_LIST_ENTRIES) {
+                throw new UserException.BadInput("Raw value for annotation has " + parsed.length + " values, expected " + NUM_LIST_ENTRIES);
+            }
+            final int squareSum = Integer.parseInt(parsed[SUM_OF_SQUARES_INDEX]);
+            final int totalDP = Integer.parseInt(parsed[TOTAL_DEPTH_INDEX]);
+            return Arrays.asList(squareSum,totalDP);
         } catch (final NumberFormatException e) {
             throw new UserException.BadInput("malformed " + GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY + " annotation: " + rawDataString);
         }
@@ -215,14 +259,22 @@ private static double parseRawDataString(String rawDataString) {
 
     /**
      *
-     * @return the number of reads at the given site, calculated as InfoField {@link VCFConstants#DEPTH_KEY} minus the
+     * @return the number of reads at the given site, trying first {@Link GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY},
+     * falling back to calculating the value as InfoField {@link VCFConstants#DEPTH_KEY} minus the
      * format field {@link GATKVCFConstants#MIN_DP_FORMAT_KEY} or DP of each of the HomRef genotypes at that site.
-     * Will fall back to calculating the reads from the stratifiedContexts then AlleleLikelyhoods data if provided.
+     * If neither of those is possible, will fall back to calculating the reads from the ReadLikelihoods data if provided.
      * @throws UserException.BadInput if the {@link VCFConstants#DEPTH_KEY} is missing or if the calculated depth is <= 0
      */
     @VisibleForTesting
     static int getNumOfReads(final VariantContext vc,
                              final ReadLikelihoods<Allele> likelihoods) {
+        if(vc.hasAttribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY)) {
+            List<Integer> MQtuple = vc.getAttributeAsIntList(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY,0);
+            if (MQtuple.get(TOTAL_DEPTH_INDEX) > 0) {
+                return MQtuple.get(TOTAL_DEPTH_INDEX);
+            }
+        }
+
         int numOfReads = 0;
         if (vc.hasAttribute(VCFConstants.DEPTH_KEY)) {
             numOfReads = vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, -1);
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
index 5cdb257ea7b..ad6d2434cd4 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
@@ -149,7 +149,11 @@ public void onTraversalStart() {
         headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY));   // needed for gVCFs without DP tags
         headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_QUAL_APPROX_KEY));
         headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.VARIANT_DEPTH_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MAPPING_QUALITY_DEPTH));
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY));
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MAPPING_QUALITY_DEPTH));  //NOTE: this is deprecated, but keep until we reprocess all GVCFs
+        if (inputHeader.hasInfoLine(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY)) {
+            headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY));  //NOTE: this is deprecated, but keep until we reprocess all GVCFs
+        }
 
         if ( dbsnp.dbsnp != null  ) {
             VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.DBSNP_KEY);
@@ -404,8 +408,17 @@ protected VariantContext cleanUpHighQualityVariant(final VariantContext result,
             genotypesArray.add(g);
         }
 
-        //we're going to approximate MQ_DP with the site-level DP (should be informative and uninformative reads), which is pretty safe because it will only differ if reads are missing MQ
-        attrMap.put(GATKVCFConstants.MAPPING_QUALITY_DEPTH, originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY,0));
+        //we're going to approximate depth for MQ calculation with the site-level DP (should be informative and uninformative reads), which is pretty safe because it will only differ if reads are missing MQ
+        final Double rawMqValue = originalVC.hasAttribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY) ?
+                originalVC.getAttributeAsDouble(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, 0) :
+                originalVC.getAttributeAsDouble(VCFConstants.RMS_MAPPING_QUALITY_KEY, 60.0) *
+                        originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY,0);
+        attrMap.put(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY,
+                 String.format("%.2f,%d", rawMqValue, originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY,0)));
+        attrMap.put(GATKVCFConstants.MAPPING_QUALITY_DEPTH, originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY,0)); //NOTE: this annotation is deprecated, but keep it here so we don't have to reprocess gnomAD v3 GVCFs again
+        if (originalVC.hasAttribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY)) {
+            attrMap.put(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, originalVC.getAttributeAsDouble(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, 0)); //NOTE: this annotation is deprecated, but keep it here so we don't have to reprocess gnomAD v3 GVCFs again
+        }
 
         if(allelesNeedSubsetting) {
             List<Allele> newAlleleSet = new ArrayList<>();
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
index db2474e937b..b522056aff1 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
@@ -20,7 +20,8 @@ public final class GATKVCFConstants {
     public static final String ALLELE_SPECIFIC_PREFIX =             "AS_";
     public static final String AS_FILTER_STATUS_KEY =               "AS_FilterStatus";
     public static final String RAW_RMS_MAPPING_QUALITY_KEY =        "RAW_MQ";
-    public static final String MAPPING_QUALITY_DEPTH =              "MQ_DP";
+    public static final String MAPPING_QUALITY_DEPTH =              "MQ_DP";  //NOTE: this is deprecated in favor of the new RAW_MQandDP below
+    public static final String RAW_MAPPING_QUALITY_WITH_DEPTH_KEY = "RAW_MQandDP";
     public static final String AS_RMS_MAPPING_QUALITY_KEY =         "AS_MQ";
     public static final String AS_RAW_RMS_MAPPING_QUALITY_KEY =     "AS_RAW_MQ";
     public static final String AS_CULPRIT_KEY =                     "AS_culprit";
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
index d4150e53750..5547e655067 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.hellbender.utils.variant;
 
 import htsjdk.variant.vcf.*;
-import org.broadinstitute.hellbender.exceptions.GATKException;
+import org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality;
 import org.broadinstitute.hellbender.utils.Utils;
 
 import java.util.*;
@@ -141,8 +141,9 @@ private static void addFilterLine(final VCFFilterHeaderLine line) {
         addInfoLine(new VCFInfoHeaderLine(LIKELIHOOD_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref haplotype likelihoods"));
         addInfoLine(new VCFInfoHeaderLine(MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"));
         addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score From Wilcoxon rank sum test of each Alt vs. Ref read mapping qualities"));
-        addInfoLine(new VCFInfoHeaderLine(RAW_RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Raw data for RMS Mapping Quality"));
-        addInfoLine(new VCFInfoHeaderLine(MAPPING_QUALITY_DEPTH, 1, VCFHeaderLineType.Integer, "Depth over variant samples for better MQ calculation"));
+        addInfoLine(new VCFInfoHeaderLine(MAPPING_QUALITY_DEPTH, 1, VCFHeaderLineType.Integer, "Depth over variant samples for better MQ calculation (deprecated -- use " + RAW_MAPPING_QUALITY_WITH_DEPTH_KEY + " instead."));
+        addInfoLine(new VCFInfoHeaderLine(RAW_RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.Integer, "Raw data for RMS Mapping Quality (deprecated -- use " + RAW_MAPPING_QUALITY_WITH_DEPTH_KEY + " instead."));
+        addInfoLine(new VCFInfoHeaderLine(RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated " + RMSMappingQuality.getDeprecatedRawKeyName() + " formulation."));
         addInfoLine(new VCFInfoHeaderLine(AS_RAW_RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.String, "Allele-specfic raw data for RMS Mapping Quality"));
         addInfoLine(new VCFInfoHeaderLine(AS_RMS_MAPPING_QUALITY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific RMS Mapping Quality"));
         addInfoLine(new VCFInfoHeaderLine(AS_RAW_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "Allele-specfic raw data for Mapping Quality Rank Sum"));
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
index fc648ed28c7..e0658652c23 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.tools.genomicsdb;
 
 import com.intel.genomicsdb.model.GenomicsDBExportConfiguration;
+import com.intel.genomicsdb.model.GenomicsDBVidMapProto;
 import com.intel.genomicsdb.reader.GenomicsDBFeatureReader;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
@@ -17,6 +18,7 @@
 import org.broadinstitute.hellbender.CommandLineProgramTest;
 import org.broadinstitute.hellbender.Main;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.engine.FeatureDataSource;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.IntervalUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
@@ -26,6 +28,7 @@
 import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
 import org.broadinstitute.hellbender.testutils.BaseTest;
 import org.broadinstitute.hellbender.testutils.VariantContextTestUtils;
+import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
 import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
@@ -113,6 +116,11 @@ public final class GenomicsDBImportIntegrationTest extends CommandLineProgramTes
     private static final String SAMPLE_NAME_KEY = "SN";
     private static final String ANOTHER_ATTRIBUTE_KEY = "AA";
 
+    private static final List<String> GVCFS_WITH_NEW_MQ = Arrays.asList(toolsTestDir + "/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf", getTestDataDir() + "/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf");
+    private static final String COMBINED_WITH_NEW_MQ = toolsTestDir + "/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf";
+    private static final List<SimpleInterval> INTERVAL2 = Arrays.asList(new SimpleInterval("20", 1, 11_000_000));
+    private static final List<String> ATTRIBUTES_TO_IGNORE = Arrays.asList("RAW_MQ","RAW_MQandDP");  //CombineGVCFs doesn't support the old RAW_MQ anymore
+
     @Override
     public String getTestedClassName() {
         return GenomicsDBImport.class.getSimpleName();
@@ -134,6 +142,11 @@ public void testGenomicsDBImportFileInputs() throws IOException {
         testGenomicsDBImporter(LOCAL_GVCFS, INTERVAL, COMBINED, b38_reference_20_21, true, 1);
     }
 
+    @Test
+    public void testGenomicsDBImportFileInputs_newMQ() throws IOException {
+        testGenomicsDBImporter_newMQ(GVCFS_WITH_NEW_MQ, INTERVAL2, COMBINED_WITH_NEW_MQ, b37_reference_20_21, true, Collections.emptyList());
+    }
+
     @Test
     public void testGenomicsDBImportFileInputsWithMultipleIntervals() throws IOException {
         testGenomicsDBImporter(LOCAL_GVCFS, MULTIPLE_INTERVALS, COMBINED_MULTI_INTERVAL, b38_reference_20_21, true, 1);
@@ -255,7 +268,7 @@ private void testGenomicsDBImporterWithGenotypes(final List<String> vcfInputs, f
 
         writeToGenomicsDB(vcfInputs, intervals, workspace, 0, false, 0, 1);
         checkJSONFilesAreWritten(workspace);
-        checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, referenceFile, testAll, produceGTField, sitesOnlyQuery);
+        checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, referenceFile, testAll, ATTRIBUTES_TO_IGNORE, produceGTField, sitesOnlyQuery);
     }
 
     private File runCombineGVCFs(final List<String> inputs, final List<SimpleInterval> intervals, final String reference, final String[] extraArgs) {
@@ -284,7 +297,7 @@ private void testGenomicsDBAgainstCombineGVCFs(final List<String> vcfInputs, fin
         for(SimpleInterval currInterval : intervals) {
             List<SimpleInterval> tmpList = new ArrayList<SimpleInterval>(Arrays.asList(currInterval));
             File expectedCombinedVCF = runCombineGVCFs(vcfInputs, tmpList, referenceFile, CombineGVCFArgs);
-            checkGenomicsDBAgainstExpected(workspace, tmpList, expectedCombinedVCF.getAbsolutePath(), referenceFile, true);
+            checkGenomicsDBAgainstExpected(workspace, tmpList, expectedCombinedVCF.getAbsolutePath(), referenceFile, true, ATTRIBUTES_TO_IGNORE);
         }
     }
 
@@ -301,7 +314,7 @@ public void testGenomicsDBAbsolutePathDepndency() throws IOException {
         writeToGenomicsDB(LOCAL_GVCFS, INTERVAL, workspace.getAbsolutePath() + "/workspace", 0, false, 0, 1);
         checkJSONFilesAreWritten(workspace.getAbsolutePath() + "/workspace");
         Files.move(workspace.toPath(), workspace2.toPath(), StandardCopyOption.REPLACE_EXISTING);
-        checkGenomicsDBAgainstExpected(workspace2.getAbsolutePath() + "/workspace", INTERVAL, COMBINED, b38_reference_20_21, true);
+        checkGenomicsDBAgainstExpected(workspace2.getAbsolutePath() + "/workspace", INTERVAL, COMBINED, b38_reference_20_21, true, ATTRIBUTES_TO_IGNORE);
     }
 
     @Test (enabled = true)
@@ -356,7 +369,7 @@ public void testDifferentThreadValuesFromABucket(final int threads) throws IOExc
 
         writeToGenomicsDB(vcfInputs, INTERVAL, workspace, 0, false, 0, threads);
         checkJSONFilesAreWritten(workspace);
-        checkGenomicsDBAgainstExpected(workspace, INTERVAL, COMBINED, b38_reference_20_21, true);
+        checkGenomicsDBAgainstExpected(workspace, INTERVAL, COMBINED, b38_reference_20_21, true, ATTRIBUTES_TO_IGNORE);
     }
 
     @Test(dataProvider = "getThreads")
@@ -366,7 +379,7 @@ public void testDifferentThreadValuesLocally(final int threads) throws IOExcepti
 
         writeToGenomicsDB(vcfInputs, INTERVAL, workspace, 0, false, 0, threads);
         checkJSONFilesAreWritten(workspace);
-        checkGenomicsDBAgainstExpected(workspace, INTERVAL, COMBINED, b38_reference_20_21, true);
+        checkGenomicsDBAgainstExpected(workspace, INTERVAL, COMBINED, b38_reference_20_21, true, ATTRIBUTES_TO_IGNORE);
     }
     /**
      *
@@ -382,10 +395,20 @@ private void testGenomicsDBImporter(final List<String> vcfInputs, final List<Sim
                                         final String expectedCombinedVCF, final String referenceFile,
                                         final boolean testAll, final int threads) throws IOException {
         final String workspace = createTempDir("genomicsdb-tests-").getAbsolutePath() + "/workspace";
+        writeToGenomicsDB(vcfInputs, intervals, workspace, 0, false, 0, 1);
 
-        writeToGenomicsDB(vcfInputs, intervals, workspace, 0, false, 0, threads);
+        checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, referenceFile, testAll, ATTRIBUTES_TO_IGNORE);
+    }
+
+    private void testGenomicsDBImporter_newMQ(final List<String> vcfInputs, final List<SimpleInterval> intervals,
+                                        final String expectedCombinedVCF, final String referenceFile,
+                                        final boolean testAll, final List<String> attributesToIgnore) throws IOException {
+        final String workspace = createTempDir("genomicsdb-tests-").getAbsolutePath() + "/workspace";
+
+        writeToGenomicsDB(vcfInputs, intervals, workspace, 0, false, 0, 1);
         checkJSONFilesAreWritten(workspace);
-        checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, referenceFile, testAll);
+
+        checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, referenceFile, testAll, attributesToIgnore);
     }
 
     private void testGenomicsDBImporterWithBatchSize(final List<String> vcfInputs, final List<SimpleInterval> intervals,
@@ -394,7 +417,7 @@ private void testGenomicsDBImporterWithBatchSize(final List<String> vcfInputs, f
 
         writeToGenomicsDB(vcfInputs, intervals, workspace, batchSize, false, 0, 1);
         checkJSONFilesAreWritten(workspace);
-        checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, b38_reference_20_21, true);
+        checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, b38_reference_20_21, true, ATTRIBUTES_TO_IGNORE);
     }
 
     private void testGenomicsDBImportWithZeroBufferSize(final List<String> vcfInputs, final List<SimpleInterval> intervals,
@@ -403,7 +426,7 @@ private void testGenomicsDBImportWithZeroBufferSize(final List<String> vcfInputs
 
         writeToGenomicsDB(vcfInputs, intervals, workspace, 0, true, 0, 1);
         checkJSONFilesAreWritten(workspace);
-        checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, b38_reference_20_21, true);
+        checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, b38_reference_20_21, true, ATTRIBUTES_TO_IGNORE);
 
     }
 
@@ -429,10 +452,11 @@ private static void checkJSONFilesAreWritten(final String workspace) {
 
     private static void checkGenomicsDBAgainstExpected(final String workspace, final List<SimpleInterval> intervals,
                                                        final String expectedCombinedVCF, final String referenceFile,
-                                                       final boolean testAll) throws IOException {
+                                                       final boolean testAll, final List<String> attributesToIgnore) throws IOException {
         checkGenomicsDBAgainstExpected(workspace, intervals,
                 expectedCombinedVCF, referenceFile,
                 testAll,
+                attributesToIgnore,
                 false,
                 false);
     }
@@ -440,6 +464,7 @@ private static void checkGenomicsDBAgainstExpected(final String workspace, final
     private static void checkGenomicsDBAgainstExpected(final String workspace, final List<SimpleInterval> intervals,
                                                        final String expectedCombinedVCF, final String referenceFile,
                                                        final boolean testAll,
+                                                       final List<String> attributesToIgnore,
                                                        final boolean produceGTField,
                                                        final boolean sitesOnlyQuery) throws IOException {
         final GenomicsDBFeatureReader<VariantContext, PositionalBufferedStream> genomicsDBFeatureReader =
@@ -465,7 +490,7 @@ private static void checkGenomicsDBAgainstExpected(final String workspace, final
                                 .map(g -> g.getGenotypeString().equals(".")?new GenotypeBuilder(g).alleles(GATKVariantContextUtils.noCallAlleles(2)).make():g)
                                 .collect(Collectors.toList());
                         a = new VariantContextBuilder(a).genotypes(genotypes).make();
-                        VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, Collections.emptyList(), VCF_HEADER);
+                        VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, attributesToIgnore, VCF_HEADER);
 
                         // Test only that the genotypes match
                     } else {
@@ -542,7 +567,7 @@ public void testSampleNameWithSpaces() throws IOException {
 
         runCommandLine(args);
         checkJSONFilesAreWritten(workspace);
-        checkGenomicsDBAgainstExpected(workspace, SMALLER_INTERVAL, COMBINED_WITHSPACES, b38_reference_20_21, true);
+        checkGenomicsDBAgainstExpected(workspace, SMALLER_INTERVAL, COMBINED_WITHSPACES, b38_reference_20_21, true, ATTRIBUTES_TO_IGNORE);
     }
 
     @Test(dataProvider = "getOrderingTests")
@@ -554,7 +579,7 @@ public void testSampleNameOrdering(final ArgumentsBuilder args) throws IOExcepti
 
         runCommandLine(args);
         checkJSONFilesAreWritten(workspace);
-        checkGenomicsDBAgainstExpected(workspace, INTERVAL, COMBINED, b38_reference_20_21, true);
+        checkGenomicsDBAgainstExpected(workspace, INTERVAL, COMBINED, b38_reference_20_21, true, ATTRIBUTES_TO_IGNORE);
     }
 
     private static File createInOrderSampleMap() {
@@ -777,7 +802,7 @@ private static GenomicsDBFeatureReader<VariantContext, PositionalBufferedStream>
             final String workspace, final String reference,
             final boolean produceGTField,
             final boolean sitesOnlyQuery) throws IOException {
-       GenomicsDBExportConfiguration.ExportConfiguration exportConfiguration = GenomicsDBExportConfiguration.ExportConfiguration.newBuilder()
+        GenomicsDBExportConfiguration.ExportConfiguration.Builder exportConfigurationBuilder = GenomicsDBExportConfiguration.ExportConfiguration.newBuilder()
                 .setWorkspace(workspace)
                 .setReferenceGenome(reference)
                 .setVidMappingFile(new File(workspace, GenomicsDBConstants.DEFAULT_VIDMAP_FILE_NAME).getAbsolutePath())
@@ -785,10 +810,25 @@ private static GenomicsDBFeatureReader<VariantContext, PositionalBufferedStream>
                 .setVcfHeaderFilename(new File(workspace, GenomicsDBConstants.DEFAULT_VCFHEADER_FILE_NAME).getAbsolutePath())
                 .setProduceGTField(produceGTField)
                 .setSitesOnlyQuery(sitesOnlyQuery)
-                .setGenerateArrayNameFromPartitionBounds(true)
-                .build();
+               .setGenerateArrayNameFromPartitionBounds(true);
+        GenomicsDBVidMapProto.VidMappingPB vidMapPB = null;
+        try {
+            vidMapPB = GenomicsDBUtils.getProtobufVidMappingFromJsonFile(new File(workspace, GenomicsDBConstants.DEFAULT_VIDMAP_FILE_NAME));
+        }
+        catch (final IOException e) {
+            throw new UserException("Could not open vid json file "+GenomicsDBConstants.DEFAULT_VIDMAP_FILE_NAME, e);
+        }
+        HashMap<String, Integer> fieldNameToIndexInVidFieldsList =
+                GenomicsDBUtils.getFieldNameToListIndexInProtobufVidMappingObject(vidMapPB);
+
+        vidMapPB = GenomicsDBUtils.updateINFOFieldCombineOperation(vidMapPB, fieldNameToIndexInVidFieldsList,
+                GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, "element_wise_sum");
+
+        if(vidMapPB != null) {
+            exportConfigurationBuilder.setVidMapping(vidMapPB);
+        }
 
-       return new GenomicsDBFeatureReader<>(exportConfiguration, new BCF2Codec(), Optional.empty());
+        return new GenomicsDBFeatureReader<>(exportConfigurationBuilder.build(), new BCF2Codec(), Optional.empty());
     }
 
     private static GenomicsDBFeatureReader<VariantContext, PositionalBufferedStream> getGenomicsDBFeatureReader(
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java
index e3bfac8ba1d..52ec50ab653 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java
@@ -31,6 +31,10 @@
 
 public class CombineGVCFsIntegrationTest extends CommandLineProgramTest {
     private static final List<String> NO_EXTRA_ARGS = Collections.emptyList();
+    private static final List<String> ATTRIBUTES_TO_IGNORE = Arrays.asList(
+            "RAW_MQ"); //MQ data format and key have changed since GATK3
+    private static final File NA12878_HG37 = new File(toolsTestDir + "haplotypecaller/expected.testGVCFMode.gatk4.g.vcf");
+
 
     private static <T> void assertForEachElementInLists(final List<T> actual, final List<T> expected, final BiConsumer<T, T> assertion) {
         Assert.assertEquals(actual.size(), expected.size(), "different number of elements in lists:\n"
@@ -77,6 +81,7 @@ public Object[][] gvcfsToCombine() {
                         getTestFile("gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf"),
                         Arrays.asList("--" + CombineGVCFs.BREAK_BANDS_LONG_NAME, "2000000"),
                         b38_reference_20_21},
+                {new File[]{NA12878_HG37, getTestFile("YRIoffspring.chr20snippet.g.vcf")}, getTestFile("newMQcalc.combined.g.vcf"), NO_EXTRA_ARGS, b37_reference_20_21},
         };
     }
 
@@ -122,12 +127,12 @@ public void compareToGATK3(File[] inputs, File outputFile, List<String> extraArg
             System.out.println("Found precomputed gatk3Result");
         }
 
-        assertVariantContextsMatch(Arrays.asList(inputs), gatk3Result, extraArgs, reference);
+        assertVariantContextsMatch(Arrays.asList(inputs), gatk3Result, extraArgs, reference, ATTRIBUTES_TO_IGNORE);
     }
 
     @Test(dataProvider = "gvcfsToCombine")
     public void compareToGATK3ExpectedResults(File[] inputs, File outputFile, List<String> extraArgs, String reference) throws IOException, NoSuchAlgorithmException {
-        assertVariantContextsMatch(Arrays.asList(inputs), outputFile, extraArgs, reference);
+        assertVariantContextsMatch(Arrays.asList(inputs), outputFile, extraArgs, reference, ATTRIBUTES_TO_IGNORE);
     }
 
     public static void runProcess(ProcessController processController, String[] command) {
@@ -139,15 +144,15 @@ public static void runProcess(ProcessController processController, String[] comm
     }
 
 
-
-    private void assertVariantContextsMatch(List<File> inputs, File expected, List<String> extraArgs, String reference) throws IOException {
+    public void assertVariantContextsMatch(List<File> inputs, File expected, List<String> extraArgs, String reference, List<String> attributesToIgnore) throws IOException {
         final VCFHeader header = getHeaderFromFile(expected);
 
         runCombineGVCFSandAssertSomething(inputs, expected, extraArgs, (a, e) -> {
-            VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, Arrays.asList(), header);
+            VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, attributesToIgnore, header);
         }, reference);
     }
 
+
     public void runCombineGVCFSandAssertSomething(List<File> inputs, File expected, List<String> additionalArguments, BiConsumer<VariantContext, VariantContext> assertion, String reference) throws IOException {
         final File output = createTempFile("combinegvcfs", ".vcf");
 
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
index 60440ffe4be..5ac020bd672 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
@@ -11,6 +11,7 @@
 import org.broadinstitute.hellbender.CommandLineProgramTest;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.engine.FeatureDataSource;
+import org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBConstants;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
@@ -46,10 +47,12 @@ public class GenotypeGVCFsIntegrationTest extends CommandLineProgramTest {
 
     private static final File CEUTRIO_20_21_GATK3_4_G_VCF = new File(largeFileTestDir, "gvcfs/CEUTrio.20.21.gatk3.4.g.vcf");
     private static final String CEUTRIO_20_21_EXPECTED_VCF = "CEUTrio.20.21.gatk3.7_30_ga4f720357.expected.vcf";
-    private static final List<String> ATTRIBUTES_TO_IGNORE = Arrays.asList(
+    private static final File NA12878_HG37 = new File(toolsTestDir + "haplotypecaller/expected.testGVCFMode.gatk4.g.vcf");
+    private static final List<String> ATTRIBUTES_WITH_JITTER = Arrays.asList(
             "AS_QD",
             "QD",//TODO QD and AS_QD have cap values and anything that reaches that is randomized.  It's difficult to reproduce the same random numbers across gatk3 -> 4
             "FS");//TODO There's some bug in either gatk3 or gatk4 fisherstrand that's making them not agree still, I'm not sure which is correct
+    private static final List<String> ATTRIBUTES_TO_IGNORE = Arrays.asList("AS_QD","QD","FS","RAW_MQ","MQ"); //MQ data format and key have changed since GATK3
 
     private static final String ALLELE_SPECIFIC_DIRECTORY = toolsTestDir + "walkers/annotator/allelespecific";
 
@@ -73,7 +76,6 @@ public Object[][] gvcfsToGenotype() {
                 {getTestFile("testUpdatePGT.gvcf"), getTestFile( "testUpdatePGT.gatk3.7_30_ga4f720357.output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21},   //testUpdatePGT
                 {getTestFile("gvcfExample1.vcf"), getTestFile( "gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //single sample vcf
                 {getTestFile("gvcfExample1.vcf"), getTestFile( "gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("-L", "20"), b37_reference_20_21}, //single sample vcf with -L
-                {getTestFile("mnp.input.g.vcf"), getTestFile("mnp.expected.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, // Testing that MNPs can be genotyped correctly
                 {getTestFile("combined_genotype_gvcf_exception.original.vcf"), getTestFile( "combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //test that an input vcf with 0/0 already in GT field is overwritten
                 {getTestFile("combined_genotype_gvcf_exception.nocall.vcf"), getTestFile( "combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21},  //same test as above but with ./.
                 {getTestFile(BASE_PAIR_GVCF), getTestFile("ndaTest.gatk3.7_30_ga4f720357.expected.vcf"), Collections.singletonList("--annotate-with-num-discovered-alleles"), b37_reference_20_21},  //annotating with the number of alleles discovered option
@@ -105,6 +107,20 @@ public Object[][] gvcfWithPPs() {
         };
     }
 
+    @DataProvider(name = "singleSampleGVCFWithNewMQFormat")
+    public Object[][] singleSampleGVCFWithNewMQFormat() {
+        return new Object[][]{
+                {NA12878_HG37, getTestFile("newMQcalc.singleSample.genotyped.vcf"), new SimpleInterval("20", 1, 11_000_000), b37_reference_20_21}
+        };
+    }
+
+    @DataProvider(name = "GVCFsWithNewMQFormat")
+    public Object[][] GVCFsWithNewMQFormat() {
+        return new Object[][]{
+                {NA12878_HG37, getTestFile("newMQcalc.singleSample.genotyped.vcf"), new SimpleInterval("20", 1, 11_000_000), b37_reference_20_21},
+                {new File(getTestDataDir() + "/walkers/CombineGVCFs/newMQcalc.combined.g.vcf"), getTestFile("newMQcalc.combined.genotyped.vcf"), new SimpleInterval("20", 1, 11_000_000), b37_reference_20_21}
+        };
+    }
 
     /*
     This test is useful for testing changes in GATK4 versus different versions of GATK3.
@@ -170,7 +186,7 @@ public Object[][] getGVCFsForGenomicsDB(){
         };
     }
 
-
+    //this only tests single-sample
     @Test(dataProvider = "getGVCFsForGenomicsDB")
     public void assertMatchingGenotypesFromTileDB(File input, File expected, Locatable interval, String reference) throws IOException {
         final File tempGenomicsDB = GenomicsDBTestUtils.createTempGenomicsDB(input, interval);
@@ -178,6 +194,16 @@ public void assertMatchingGenotypesFromTileDB(File input, File expected, Locatab
         runGenotypeGVCFSAndAssertSomething(genomicsDBUri, expected, NO_EXTRA_ARGS, VariantContextTestUtils::assertVariantContextsHaveSameGenotypes, reference);
     }
 
+    //this tests single-sample with new MQ format
+    @Test (dataProvider = "singleSampleGVCFWithNewMQFormat")
+    public void assertMatchingAnnotationsFromGenomicsDB_newMQformat(File input, File expected, Locatable interval, String reference) throws IOException {
+        final File tempGenomicsDB = GenomicsDBTestUtils.createTempGenomicsDB(input, interval);
+        final String genomicsDBUri = GenomicsDBTestUtils.makeGenomicsDBUri(tempGenomicsDB);
+        
+        final VCFHeader header = VCFHeaderReader.readHeaderFrom(new SeekablePathStream(IOUtils.getPath(expected.getAbsolutePath())));
+        runGenotypeGVCFSAndAssertSomething(genomicsDBUri, expected, NO_EXTRA_ARGS, (a, e) -> VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_WITH_JITTER, header), reference);
+    }
+
     @Test(dataProvider = "gvcfsToGenotype")
     public void testEntireVariantContext(File input, File expected, List<String> extraArgs, String reference) throws IOException {
         assertVariantContextsMatch(input, expected, extraArgs, reference);
@@ -202,6 +228,12 @@ public void assertPPsAreStripped(File input, File expected, List<String> extraAr
         runGenotypeGVCFSAndAssertSomething(input, expected, extraArgs, VariantContextTestUtils::assertGenotypePosteriorsAttributeWasRemoved, reference);
     }
 
+    //this test is separate because all the others use old data and ignore the MQ annotations
+    @Test(dataProvider = "GVCFsWithNewMQFormat")
+    public void assertNewMQWorks(File input, File expected, Locatable interval, String reference) throws IOException {
+        final VCFHeader header = VCFHeaderReader.readHeaderFrom(new SeekablePathStream(IOUtils.getPath(expected.getAbsolutePath())));
+        runGenotypeGVCFSAndAssertSomething(input, expected, NO_EXTRA_ARGS, (a, e) -> VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_WITH_JITTER, header), reference);
+    }
 
     private void runGenotypeGVCFSAndAssertSomething(File input, File expected, List<String> additionalArguments, BiConsumer<VariantContext, VariantContext> assertion, String reference) throws IOException {
         runGenotypeGVCFSAndAssertSomething(input.getAbsolutePath(), expected, additionalArguments, assertion, reference
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java
index 471a3417df1..ff0f1b159cd 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java
@@ -9,6 +9,7 @@
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality;
 import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation;
+import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData;
 import org.broadinstitute.hellbender.utils.MathUtils;
 import org.broadinstitute.hellbender.utils.QualityUtils;
 import org.broadinstitute.hellbender.utils.genotyper.AlleleList;
@@ -37,25 +38,25 @@ public void testAllNull() throws Exception {
 
     @Test
     public void testDescriptions() throws Exception {
-        final InfoFieldAnnotation cov = new RMSMappingQuality();
+        final RMSMappingQuality cov = new RMSMappingQuality();
         Assert.assertEquals(cov.getDescriptions().size(), 1);
         Assert.assertEquals(cov.getDescriptions().get(0).getID(), VCFConstants.RMS_MAPPING_QUALITY_KEY);
-        Assert.assertEquals(((RMSMappingQuality)cov).getRawDescriptions().get(0).getID(), GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY);
-        Assert.assertEquals(new RMSMappingQuality().getRawKeyName(), GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY);
-        Assert.assertEquals(new RMSMappingQuality().getKeyNames(), Sets.newHashSet(VCFConstants.RMS_MAPPING_QUALITY_KEY, GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY));
+        Assert.assertEquals(cov.getRawDescriptions().size(), 1);
+        Assert.assertEquals(cov.getRawDescriptions().get(0).getID(), GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY);
+        Assert.assertEquals(new RMSMappingQuality().getRawKeyName(), GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY);
+        Assert.assertEquals(new RMSMappingQuality().getKeyNames(), Sets.newHashSet(VCFConstants.RMS_MAPPING_QUALITY_KEY, GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY));
     }
 
     @Test
     public void testNullLikelihoods() throws Exception {
         final VariantContext vc= makeVC();
         final ReferenceContext referenceContext= null;
-        final InfoFieldAnnotation cov = new RMSMappingQuality();
+        final RMSMappingQuality cov = new RMSMappingQuality();
         final Map<String, Object> annotate = cov.annotate(referenceContext, vc, null);
         Assert.assertTrue(annotate.isEmpty());
 
         Assert.assertEquals(cov.getDescriptions().get(0).getID(), VCFConstants.RMS_MAPPING_QUALITY_KEY);
-        Assert.assertEquals(((RMSMappingQuality)cov).getRawDescriptions().get(0).getID(), GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY);
-        Assert.assertEquals(cov.getDescriptions().get(0).getID(), VCFConstants.RMS_MAPPING_QUALITY_KEY);
+        Assert.assertEquals(cov.getRawDescriptions().get(0).getID(), GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY);
     }
 
     /**
@@ -98,7 +99,7 @@ public void testLikelihoods(){
         Assert.assertEquals(annotate.size(), 1, "size");
         Assert.assertEquals(annotate.keySet(), Collections.singleton(VCFConstants.RMS_MAPPING_QUALITY_KEY), "annots");
         final double rms= MathUtils.sumOfSquares(MQsListOK); //only those are MQ0
-        Assert.assertNull(annotate.get(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY));
+        Assert.assertNull(annotate.get(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY));
         Assert.assertEquals(annotate.get(VCFConstants.RMS_MAPPING_QUALITY_KEY), String.format("%.2f", Math.sqrt(rms/(reads.size()-1))));
     }
 
@@ -193,25 +194,46 @@ public void testLikelihoodsEmpty_AS() throws Exception {
         Assert.assertEquals(split[1], String.format("%.2f", 0.0));
     }
 
+    @Test
+    public void testCombineAndFinalize() {
+        final List<Allele> vcAlleles = Arrays.asList(Allele.create("A", true), Allele.create("T", false));
+        final List<ReducibleAnnotationData<?>> combinedVCdata = new ArrayList<>();
+        combinedVCdata.add(new ReducibleAnnotationData<>("33640,10"));  //10 MQ58 reads
+        combinedVCdata.add(new ReducibleAnnotationData<>("36000,10"));  //10 MQ60 reads
+
+        final RMSMappingQuality annotator = RMSMappingQuality.getInstance();
+
+        final Map<String, Object> combined = annotator.combineRawData(vcAlleles, combinedVCdata);
+        final String combinedListString = (String)combined.get(annotator.getRawKeyName());
+        Assert.assertEquals(combinedListString, "69640,20");
+
+        final VariantContext vc = new VariantContextBuilder(makeVC())
+                .attribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, combinedListString)
+                .make();
+        final VariantContext originalVC = null;
+        final Map<String, Object> output = new RMSMappingQuality().finalizeRawData(vc, originalVC);
+        Assert.assertEquals(Double.parseDouble((String)output.get("MQ")), 59.01);
+    }
+
     @Test
     public void testFinalizeRawData(){
         final VariantContext vc = new VariantContextBuilder(makeVC())
-                .attribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, "2000,100,20")
+                .attribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, "43732,13")
                 .attribute(VCFConstants.DEPTH_KEY, 20)
                 .make();
         final VariantContext originalVC = null;
         final Map<String, Object> output = new RMSMappingQuality().finalizeRawData(vc, originalVC);
-        Assert.assertEquals(output.get("MQ"), "10.00");
+        Assert.assertEquals(output.get("MQ"), "58.00");
     }
 
     @Test
     public void testFinalizeRawMQ(){
         final VariantContext vc = new VariantContextBuilder(makeVC())
-                .attribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, "2000")
+                .attribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, "2000,20")
                 .attribute(VCFConstants.DEPTH_KEY, 20)
                 .make();
         final VariantContext output = new RMSMappingQuality().finalizeRawMQ(vc);
-        Assert.assertFalse(output.hasAttribute( GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY));
+        Assert.assertFalse(output.hasAttribute( GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY));
         Assert.assertTrue(output.hasAttribute(VCFConstants.RMS_MAPPING_QUALITY_KEY));
         Assert.assertEquals(output.getAttributeAsDouble(VCFConstants.RMS_MAPPING_QUALITY_KEY, -1.0), 10.0, 0.01);
     }
@@ -220,31 +242,17 @@ public void testFinalizeRawMQ(){
     @Test(expectedExceptions = UserException.BadInput.class)
     public void testBadRawMQ(){
         final VariantContext vc = new VariantContextBuilder(makeVC())
-                .attribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, "fiftyeight")
+                .attribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, "fiftyeight")
                 .make();
         new RMSMappingQuality().finalizeRawMQ(vc);
     }
 
-    @Test
-    public void testNoDepth() {
-        final VariantContext vc = new VariantContextBuilder(makeVC())
-                .attribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, "2000")
-                .make();
-        Assert.assertTrue(new RMSMappingQuality().finalizeRawMQ(vc).hasAttribute(VCFConstants.RMS_MAPPING_QUALITY_KEY));
-        Assert.assertTrue(Double.isNaN(new RMSMappingQuality().finalizeRawMQ(vc).getAttributeAsDouble(VCFConstants.RMS_MAPPING_QUALITY_KEY, 0)));
-    }
-
-    @Test
-    //this test mimics the behavior in gatk3, it's not necessarily the right thing to do
-    public void testMultipleRawMQOnlyFirstIsSeen(){
+    @Test(expectedExceptions = UserException.BadInput.class)
+    public void testNoDepth(){
         final VariantContext vc = new VariantContextBuilder(makeVC())
-                .attribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, "2000,1000,")
-                .attribute(VCFConstants.DEPTH_KEY, 20)
+                .attribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, "20000")
                 .make();
-        final VariantContext output = new RMSMappingQuality().finalizeRawMQ(vc);
-        Assert.assertFalse(output.hasAttribute( GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY));
-        Assert.assertTrue(output.hasAttribute(VCFConstants.RMS_MAPPING_QUALITY_KEY));
-        Assert.assertEquals(output.getAttributeAsDouble(VCFConstants.RMS_MAPPING_QUALITY_KEY, -1.0), 10.0, 0.01);
+        new RMSMappingQuality().finalizeRawMQ(vc);
     }
 
     @Test
@@ -256,7 +264,7 @@ public void testNoRawMQ(){
                     .make();
         final VariantContext output = new RMSMappingQuality().finalizeRawMQ(vc);
         Assert.assertFalse(output.hasAttribute(VCFConstants.RMS_MAPPING_QUALITY_KEY));
-        Assert.assertFalse(output.hasAttribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY));
+        Assert.assertFalse(output.hasAttribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY));
         Assert.assertEquals(output.getAttribute(OTHER_KEY), VALUE);
     }
 
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java
index a87fe974159..9cc4d922b2f 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java
@@ -22,7 +22,7 @@ public class ReblockGVCFIntegrationTest extends CommandLineProgramTest {
     private static final String hg38_reference_20_21 = largeFileTestDir + "Homo_sapiens_assembly38.20.21.fasta";
     private static final String b37_reference_20_21 = largeFileTestDir + "human_g1k_v37.20.21.fasta";
 
-    @Test
+    @Test  //covers inputs with "MQ" annotation
     public void testJustOneSample() throws Exception {
         final IntegrationTestSpec spec = new IntegrationTestSpec(
                 "-L chr20:69485-69791 -O %s -R " + hg38_reference_20_21 +
@@ -35,7 +35,7 @@ public void testJustOneSample() throws Exception {
     @Test
     public void testGVCFReblockingIsContiguous() throws Exception {
         final File output = createTempFile("reblockedgvcf", ".vcf");
-        final File expected = new File(largeFileTestDir + "testProductionGVCF.expected.g.vcf.gz");
+        final File expected = new File(largeFileTestDir + "testProductionGVCF.expected.g.vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(b37_reference_20_21))
@@ -80,4 +80,14 @@ public void testNonRefADCorrection() throws Exception {
                 Arrays.asList(getToolTestDataDir() + "testNonRefADCorrection.expected.g.vcf"));
         spec.executeTest("testNonRefADCorrection", this);
     }
+
+    @Test //covers inputs with "RAW_MQ" annotation
+    public void testRawMQInput() throws Exception {
+        final IntegrationTestSpec spec = new IntegrationTestSpec(
+                "-O %s -R " + hg38_reference_20_21 +
+                        " -V " + getToolTestDataDir() + "prod.chr20snippet.withRawMQ.g.vcf" +
+                        " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false",
+                Arrays.asList(getToolTestDataDir() + "prod.chr20snippet.withRawMQ.expected.g.vcf"));
+        spec.executeTest("testNonRefADCorrection", this);
+    }
 }
\ No newline at end of file
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFUnitTest.java
index fd1b22370ef..e652e167f02 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFUnitTest.java
@@ -41,8 +41,8 @@ public void testCleanUpHighQualityVariant() {
         Assert.assertTrue(cleaned1.getAttribute(GATKVCFConstants.RAW_QUAL_APPROX_KEY).equals(41));
         Assert.assertTrue(cleaned1.hasAttribute(GATKVCFConstants.VARIANT_DEPTH_KEY));
         Assert.assertTrue(cleaned1.getAttribute(GATKVCFConstants.VARIANT_DEPTH_KEY).equals(30));
-        Assert.assertTrue(cleaned1.hasAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH));
-        Assert.assertTrue(cleaned1.getAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH).equals(32));
+        Assert.assertTrue(cleaned1.hasAttribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY));
+        Assert.assertTrue(cleaned1.getAttributeAsString(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY,"").split(",")[1].equals("32"));
 
         final Genotype hetNonRef = makeG("sample2", DELETION, LONG_SNP, 891,879,1128,84,0,30,891,879,84,891);
         final VariantContext keepAlts = makeDeletionVC("keepAllAlts", Arrays.asList(LONG_REF, DELETION, LONG_SNP, Allele.NON_REF_ALLELE), LONG_REF.length(), hetNonRef);
diff --git a/src/test/resources/large/testProductionGVCF.expected.g.vcf b/src/test/resources/large/testProductionGVCF.expected.g.vcf
new file mode 100644
index 00000000000..fa793c12aef
--- /dev/null
+++ b/src/test/resources/large/testProductionGVCF.expected.g.vcf
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f131b56912c5fb62dd1f5d5e5135d6cb3371fe6ea07a8b7d2e90743e070df4d9
+size 1383772
diff --git a/src/test/resources/large/testProductionGVCF.expected.g.vcf.gz b/src/test/resources/large/testProductionGVCF.expected.g.vcf.gz
deleted file mode 100644
index 62298071799..00000000000
--- a/src/test/resources/large/testProductionGVCF.expected.g.vcf.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:3434135510e78426cc1c1f5ad552956fc9094d56b7d60bf778778753f8da43a9
-size 272188
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf
index 6206edc8981..82278df5e9a 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf
@@ -91,29 +91,29 @@
 ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
 ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
 ##contig=<ID=20,length=63025520>
 ##contig=<ID=21,length=48129895>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 20	10000000	.	T	<NON_REF>	.	.	END=10000116	GT:DP:GQ:MIN_DP:PL	0/0:84:99:64:0,120,1800
-20	10000117	.	C	T,<NON_REF>	905.77	.	AS_RAW_BaseQRankSum=|2.1,1|NaN;AS_RAW_MQ=127369.00|100800.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=16,20|19,9|0,0;BaseQRankSum=2.136;DP=64;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.913;RAW_MQ=228169.00;ReadPosRankSum=-0.223	GT:AD:DP:GQ:PL:SB	0/1:36,28,0:64:99:934,0,1248,1042,1332,2374:16,20,19,9
+20	10000117	.	C	T,<NON_REF>	905.77	.	AS_RAW_BaseQRankSum=|2.1,1|NaN;AS_RAW_MQ=127369.00|100800.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=16,20|19,9|0,0;BaseQRankSum=2.136;DP=64;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.913;RAW_MQandDP=228169,64;ReadPosRankSum=-0.223	GT:AD:DP:GQ:PL:SB	0/1:36,28,0:64:99:934,0,1248,1042,1332,2374:16,20,19,9
 20	10000118	.	T	<NON_REF>	.	.	END=10000210	GT:DP:GQ:MIN_DP:PL	0/0:52:99:44:0,108,1620
-20	10000211	.	C	T,<NON_REF>	941.77	.	AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=91369.00|97200.00|0.00;AS_RAW_MQRankSum=|1.0,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=15,11|11,16|0,0;BaseQRankSum=1.867;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.057;RAW_MQ=188569.00;ReadPosRankSum=0.703	GT:AD:DP:GQ:PL:SB	0/1:26,27,0:53:99:970,0,906,1049,988,2036:15,11,11,16
+20	10000211	.	C	T,<NON_REF>	941.77	.	AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=91369.00|97200.00|0.00;AS_RAW_MQRankSum=|1.0,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=15,11|11,16|0,0;BaseQRankSum=1.867;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.057;RAW_MQandDP=188569,53;ReadPosRankSum=0.703	GT:AD:DP:GQ:PL:SB	0/1:26,27,0:53:99:970,0,906,1049,988,2036:15,11,11,16
 20	10000212	.	A	<NON_REF>	.	.	END=10000438	GT:DP:GQ:MIN_DP:PL	0/0:79:99:55:0,120,1800
-20	10000439	.	T	G,<NON_REF>	2804.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|279076.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|49,31|0,0;DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=279076.00	GT:AD:DP:GQ:PL:SB	1/1:0,80,0:80:99:2833,240,0,2833,240,2833:0,0,49,31
+20	10000439	.	T	G,<NON_REF>	2804.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|279076.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|49,31|0,0;DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=279076,80	GT:AD:DP:GQ:PL:SB	1/1:0,80,0:80:99:2833,240,0,2833,240,2833:0,0,49,31
 20	10000440	.	T	<NON_REF>	.	.	END=10000585	GT:DP:GQ:MIN_DP:PL	0/0:55:99:41:0,102,1530
 20	10000586	.	C	<NON_REF>	.	.	END=10000586	GT:DP:GQ:MIN_DP:PL	0/0:44:93:44:0,93,1503
 20	10000587	.	G	<NON_REF>	.	.	END=10000597	GT:DP:GQ:MIN_DP:PL	0/0:46:99:42:0,108,1620
-20	10000598	.	T	A,<NON_REF>	1941.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|149628.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|19,30|0,0;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=149628.00	GT:AD:DP:GQ:PL:SB	1/1:0,49,0:49:99:1970,147,0,1970,147,1970:0,0,19,30
+20	10000598	.	T	A,<NON_REF>	1941.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|149628.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|19,30|0,0;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=149628,49	GT:AD:DP:GQ:PL:SB	1/1:0,49,0:49:99:1970,147,0,1970,147,1970:0,0,19,30
 20	10000599	.	T	<NON_REF>	.	.	END=10000693	GT:DP:GQ:MIN_DP:PL	0/0:72:99:48:0,120,1800
-20	10000694	.	G	A,<NON_REF>	1008.77	.	AS_RAW_BaseQRankSum=|3.5,1|NaN;AS_RAW_MQ=135228.00|58968.00|0.00;AS_RAW_MQRankSum=|-5.2,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=25,20|18,19|0,0;BaseQRankSum=3.599;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.114;RAW_MQ=194196.00;ReadPosRankSum=0.657	GT:AD:DP:GQ:PL:SB	0/1:45,37,0:82:99:1037,0,1601,1173,1712,2885:25,20,18,19
+20	10000694	.	G	A,<NON_REF>	1008.77	.	AS_RAW_BaseQRankSum=|3.5,1|NaN;AS_RAW_MQ=135228.00|58968.00|0.00;AS_RAW_MQRankSum=|-5.2,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=25,20|18,19|0,0;BaseQRankSum=3.599;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.114;RAW_MQandDP=194196,82;ReadPosRankSum=0.657	GT:AD:DP:GQ:PL:SB	0/1:45,37,0:82:99:1037,0,1601,1173,1712,2885:25,20,18,19
 20	10000695	.	G	<NON_REF>	.	.	END=10000757	GT:DP:GQ:MIN_DP:PL	0/0:89:99:79:0,120,1800
-20	10000758	.	T	A,<NON_REF>	3838.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|270581.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|45,50|0,0;DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=270581.00	GT:AD:DP:GQ:PL:SB	1/1:0,95,0:95:99:3867,286,0,3867,286,3867:0,0,45,50
+20	10000758	.	T	A,<NON_REF>	3838.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|270581.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|45,50|0,0;DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=270581,95	GT:AD:DP:GQ:PL:SB	1/1:0,95,0:95:99:3867,286,0,3867,286,3867:0,0,45,50
 20	10000759	.	A	<NON_REF>	.	.	END=10001018	GT:DP:GQ:MIN_DP:PL	0/0:66:99:52:0,120,1800
-20	10001019	.	T	G,<NON_REF>	650.77	.	AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=137329.00|21866.00|0.00;AS_RAW_MQRankSum=|-7.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=17,22|14,12|0,0;BaseQRankSum=-2.541;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-7.498;RAW_MQ=159195.00;ReadPosRankSum=-0.925	GT:AD:DP:GQ:PL:SB	0/1:39,26,0:65:99:679,0,1426,796,1504,2300:17,22,14,12
+20	10001019	.	T	G,<NON_REF>	650.77	.	AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=137329.00|21866.00|0.00;AS_RAW_MQRankSum=|-7.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=17,22|14,12|0,0;BaseQRankSum=-2.541;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-7.498;RAW_MQandDP=159195,65;ReadPosRankSum=-0.925	GT:AD:DP:GQ:PL:SB	0/1:39,26,0:65:99:679,0,1426,796,1504,2300:17,22,14,12
 20	10001020	.	C	<NON_REF>	.	.	END=10001297	GT:DP:GQ:MIN_DP:PL	0/0:68:99:46:0,117,1755
-20	10001298	.	T	A,<NON_REF>	2917.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|217124.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|41,32|0,0;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=218493.00	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2946,220,0,2946,220,2946:0,0,41,32
+20	10001298	.	T	A,<NON_REF>	2917.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|217124.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|41,32|0,0;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=218493,74	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2946,220,0,2946,220,2946:0,0,41,32
 20	10001299	.	C	<NON_REF>	.	.	END=10001426	GT:DP:GQ:MIN_DP:PL	0/0:63:99:49:0,111,1800
 20	10001427	.	T	<NON_REF>	.	.	END=10001427	GT:DP:GQ:MIN_DP:PL	0/0:53:5:53:0,5,1899
 20	10001428	.	T	<NON_REF>	.	.	END=10001429	GT:DP:GQ:MIN_DP:PL	0/0:54:99:53:0,120,1800
@@ -122,25 +122,25 @@
 20	10001433	.	T	<NON_REF>	.	.	END=10001433	GT:DP:GQ:MIN_DP:PL	0/0:56:0:56:0,0,1779
 20	10001434	.	G	<NON_REF>	.	.	END=10001434	GT:DP:GQ:MIN_DP:PL	0/0:56:99:56:0,120,1800
 20	10001435	.	A	<NON_REF>	.	.	END=10001435	GT:DP:GQ:MIN_DP:PL	0/0:55:0:55:0,0,1790
-20	10001436	.	A	AAGGCT,<NON_REF>	2301.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|76986.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,7|0,0;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=92755.00	GT:AD:DP:GQ:PL:SB	1/1:0,50,0:50:99:2339,156,0,2340,157,2340:0,0,43,7
+20	10001436	.	A	AAGGCT,<NON_REF>	2301.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|76986.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,7|0,0;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=92755,55	GT:AD:DP:GQ:PL:SB	1/1:0,50,0:50:99:2339,156,0,2340,157,2340:0,0,43,7
 20	10001437	.	A	<NON_REF>	.	.	END=10001473	GT:DP:GQ:MIN_DP:PL	0/0:61:99:51:0,120,1800
-20	10001474	.	C	T,<NON_REF>	2640.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|140615.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|48,25|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=140615.00	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2669,219,0,2669,219,2669:0,0,48,25
+20	10001474	.	C	T,<NON_REF>	2640.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|140615.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|48,25|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=140615,73	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2669,219,0,2669,219,2669:0,0,48,25
 20	10001475	.	G	<NON_REF>	.	.	END=10001616	GT:DP:GQ:MIN_DP:PL	0/0:95:99:72:0,120,1800
-20	10001617	.	C	A,<NON_REF>	1731.77	.	AS_RAW_BaseQRankSum=|1.2,1|NaN;AS_RAW_MQ=177220.00|181369.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=23,29|33,18|0,0;BaseQRankSum=1.261;DP=103;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.373;RAW_MQ=358589.00;ReadPosRankSum=-0.280	GT:AD:DP:GQ:PL:SB	0/1:52,51,0:103:99:1760,0,1781,1916,1935,3851:23,29,33,18
+20	10001617	.	C	A,<NON_REF>	1731.77	.	AS_RAW_BaseQRankSum=|1.2,1|NaN;AS_RAW_MQ=177220.00|181369.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=23,29|33,18|0,0;BaseQRankSum=1.261;DP=103;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.373;RAW_MQandDP=358589,103;ReadPosRankSum=-0.280	GT:AD:DP:GQ:PL:SB	0/1:52,51,0:103:99:1760,0,1781,1916,1935,3851:23,29,33,18
 20	10001618	.	T	<NON_REF>	.	.	END=10001627	GT:DP:GQ:MIN_DP:PL	0/0:100:99:94:0,120,1800
-20	10001628	.	G	A,<NON_REF>	3898.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|332548.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|55,40|0,0;DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=332548.00	GT:AD:DP:GQ:PL:SB	1/1:0,95,0:95:99:3927,285,0,3927,285,3927:0,0,55,40
+20	10001628	.	G	A,<NON_REF>	3898.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|332548.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|55,40|0,0;DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=332548,95	GT:AD:DP:GQ:PL:SB	1/1:0,95,0:95:99:3927,285,0,3927,285,3927:0,0,55,40
 20	10001629	.	G	<NON_REF>	.	.	END=10001660	GT:DP:GQ:MIN_DP:PL	0/0:81:99:76:0,120,1800
-20	10001661	.	T	C,<NON_REF>	3606.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|275574.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|49,32|0,0;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=275574.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,81,0:81:99:0|1:10001661_T_C:3635,249,0,3635,249,3635:0,0,49,32
+20	10001661	.	T	C,<NON_REF>	3606.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|275574.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|49,32|0,0;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=275574,81	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,81,0:81:99:0|1:10001661_T_C:3635,249,0,3635,249,3635:0,0,49,32
 20	10001662	.	T	<NON_REF>	.	.	END=10001669	GT:DP:GQ:MIN_DP:PL	0/0:82:99:81:0,120,1800
-20	10001670	.	T	G,<NON_REF>	3673.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|267297.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|46,35|0,0;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=267297.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,81,0:81:99:0|1:10001661_T_C:3702,253,0,3702,253,3702:0,0,46,35
+20	10001670	.	T	G,<NON_REF>	3673.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|267297.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|46,35|0,0;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=267297,81	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,81,0:81:99:0|1:10001661_T_C:3702,253,0,3702,253,3702:0,0,46,35
 20	10001671	.	G	<NON_REF>	.	.	END=10002057	GT:DP:GQ:MIN_DP:PL	0/0:76:99:57:0,120,1800
-20	10002058	.	T	G,<NON_REF>	2963.77	.	AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=841.00|249365.00|0.00;AS_RAW_MQRankSum=|3.0,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=1,0|51,23|0,0;BaseQRankSum=1.931;DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=3.068;RAW_MQ=250206.00;ReadPosRankSum=0.624	GT:AD:DP:GQ:PL:SB	1/1:1,74,0:75:99:2992,216,0,2994,223,3001:1,0,51,23
+20	10002058	.	T	G,<NON_REF>	2963.77	.	AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=841.00|249365.00|0.00;AS_RAW_MQRankSum=|3.0,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=1,0|51,23|0,0;BaseQRankSum=1.931;DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=3.068;RAW_MQandDP=250206,75;ReadPosRankSum=0.624	GT:AD:DP:GQ:PL:SB	1/1:1,74,0:75:99:2992,216,0,2994,223,3001:1,0,51,23
 20	10002059	.	A	<NON_REF>	.	.	END=10002098	GT:DP:GQ:MIN_DP:PL	0/0:77:99:65:0,120,1800
-20	10002099	.	C	T,<NON_REF>	1194.77	.	AS_RAW_BaseQRankSum=|-0.3,1|NaN;AS_RAW_MQ=88923.00|117006.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=19,8|23,15|0,0;BaseQRankSum=-0.282;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.850;RAW_MQ=205929.00;ReadPosRankSum=0.173	GT:AD:DP:GQ:PL:SB	0/1:27,38,0:65:99:1223,0,844,1304,958,2262:19,8,23,15
+20	10002099	.	C	T,<NON_REF>	1194.77	.	AS_RAW_BaseQRankSum=|-0.3,1|NaN;AS_RAW_MQ=88923.00|117006.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=19,8|23,15|0,0;BaseQRankSum=-0.282;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.850;RAW_MQandDP=205929,65;ReadPosRankSum=0.173	GT:AD:DP:GQ:PL:SB	0/1:27,38,0:65:99:1223,0,844,1304,958,2262:19,8,23,15
 20	10002100	.	T	<NON_REF>	.	.	END=10002137	GT:DP:GQ:MIN_DP:PL	0/0:59:99:49:0,120,1800
-20	10002138	.	C	G,<NON_REF>	2443.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|168463.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,26|0,0;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=168463.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,53,0:53:99:0|1:10002138_C_G:2472,169,0,2472,169,2472:0,0,27,26
+20	10002138	.	C	G,<NON_REF>	2443.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|168463.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,26|0,0;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=168463,53	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,53,0:53:99:0|1:10002138_C_G:2472,169,0,2472,169,2472:0,0,27,26
 20	10002139	.	A	<NON_REF>	.	.	END=10002141	GT:DP:GQ:MIN_DP:PL	0/0:54:99:52:0,120,1800
-20	10002142	.	G	C,<NON_REF>	2407.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|164863.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|24,28|0,0;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=164863.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,52,0:52:99:0|1:10002138_C_G:2436,166,0,2436,166,2436:0,0,24,28
+20	10002142	.	G	C,<NON_REF>	2407.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|164863.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|24,28|0,0;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=164863,52	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,52,0:52:99:0|1:10002138_C_G:2436,166,0,2436,166,2436:0,0,24,28
 20	10002143	.	T	<NON_REF>	.	.	END=10002201	GT:DP:GQ:MIN_DP:PL	0/0:48:99:42:0,105,1575
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 20	10002204	.	G	<NON_REF>	.	.	END=10002212	GT:DP:GQ:MIN_DP:PL	0/0:46:99:45:0,99,1485
@@ -149,13 +149,13 @@
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 20	10002456	.	T	<NON_REF>	.	.	END=10002456	GT:DP:GQ:MIN_DP:PL	0/0:52:78:52:0,78,1170
 20	10002457	.	A	<NON_REF>	.	.	END=10002457	GT:DP:GQ:MIN_DP:PL	0/0:52:0:52:0,0,1572
-20	10002458	.	G	GT,GTTT,GTTTTT,<NON_REF>	2135.73	.	AS_RAW_BaseQRankSum=||||;AS_RAW_MQ=0.00|18441.00|16082.00|3364.00|0.00;AS_RAW_MQRankSum=||||;AS_RAW_ReadPosRankSum=||||;AS_SB_TABLE=0,0|3,3|5,1|4,0|0,0;DP=47;ExcessHet=3.0103;MLEAC=1,1,0,0;MLEAF=0.500,0.500,0.00,0.00;RAW_MQ=127415.00	GT:AD:DP:GQ:PL:SB	1/2:0,6,6,4,0:16:9:2172,654,493,249,0,82,353,33,9,214,876,512,168,254,730:0,0,12,4
+20	10002458	.	G	GT,GTTT,GTTTTT,<NON_REF>	2135.73	.	AS_RAW_BaseQRankSum=||||;AS_RAW_MQ=0.00|18441.00|16082.00|3364.00|0.00;AS_RAW_MQRankSum=||||;AS_RAW_ReadPosRankSum=||||;AS_SB_TABLE=0,0|3,3|5,1|4,0|0,0;DP=47;ExcessHet=3.0103;MLEAC=1,1,0,0;MLEAF=0.500,0.500,0.00,0.00;RAW_MQandDP=127415,47	GT:AD:DP:GQ:PL:SB	1/2:0,6,6,4,0:16:9:2172,654,493,249,0,82,353,33,9,214,876,512,168,254,730:0,0,12,4
 20	10002459	.	T	<NON_REF>	.	.	END=10002459	GT:DP:GQ:MIN_DP:PL	0/0:58:78:58:0,78,1170
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 20	10002468	.	T	<NON_REF>	.	.	END=10002468	GT:DP:GQ:MIN_DP:PL	0/0:64:99:64:0,99,1485
 20	10002469	.	T	<NON_REF>	.	.	END=10002469	GT:DP:GQ:MIN_DP:PL	0/0:62:81:62:0,81,1215
-20	10002470	.	C	T,<NON_REF>	2522.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|144226.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|34,27|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=144226.00	GT:AD:DP:GQ:PL:SB	1/1:0,61,0:61:99:2551,189,0,2551,189,2551:0,0,34,27
+20	10002470	.	C	T,<NON_REF>	2522.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|144226.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|34,27|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=144226,61	GT:AD:DP:GQ:PL:SB	1/1:0,61,0:61:99:2551,189,0,2551,189,2551:0,0,34,27
 20	10002471	.	T	<NON_REF>	.	.	END=10002471	GT:DP:GQ:MIN_DP:PL	0/0:63:84:63:0,84,1260
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 20	10002475	.	T	<NON_REF>	.	.	END=10002477	GT:DP:GQ:MIN_DP:PL	0/0:70:99:66:0,102,1530
@@ -184,9 +184,9 @@
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-20	10002625	.	G	T,<NON_REF>	2665.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|223179.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|26,38|0,0;DP=64;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=223179.00	GT:AD:DP:GQ:PL:SB	1/1:0,64,0:64:99:2694,193,0,2694,193,2694:0,0,26,38
+20	10002625	.	G	T,<NON_REF>	2665.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|223179.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|26,38|0,0;DP=64;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=223179,64	GT:AD:DP:GQ:PL:SB	1/1:0,64,0:64:99:2694,193,0,2694,193,2694:0,0,26,38
 20	10002626	.	G	<NON_REF>	.	.	END=10003020	GT:DP:GQ:MIN_DP:PL	0/0:65:99:52:0,120,1800
-20	10003021	.	C	T,<NON_REF>	2383.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|208779.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,25|0,0;DP=60;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=208779.00	GT:AD:DP:GQ:PL:SB	1/1:0,60,0:60:99:2412,181,0,2412,181,2412:0,0,35,25
+20	10003021	.	C	T,<NON_REF>	2383.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|208779.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,25|0,0;DP=60;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=208779,60	GT:AD:DP:GQ:PL:SB	1/1:0,60,0:60:99:2412,181,0,2412,181,2412:0,0,35,25
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@@ -194,114 +194,114 @@
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 20	10003123	.	A	<NON_REF>	.	.	END=10003357	GT:DP:GQ:MIN_DP:PL	0/0:88:99:55:0,120,1800
-20	10003358	.	A	C,<NON_REF>	1454.77	.	AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=159769.00|158400.00|0.00;AS_RAW_MQRankSum=|1.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=31,14|29,15|0,0;BaseQRankSum=0.004;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.011;RAW_MQ=318169.00;ReadPosRankSum=-1.355	GT:AD:DP:GQ:PL:SB	0/1:45,44,0:89:99:1483,0,1477,1618,1609,3227:31,14,29,15
+20	10003358	.	A	C,<NON_REF>	1454.77	.	AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=159769.00|158400.00|0.00;AS_RAW_MQRankSum=|1.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=31,14|29,15|0,0;BaseQRankSum=0.004;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.011;RAW_MQandDP=318169,89;ReadPosRankSum=-1.355	GT:AD:DP:GQ:PL:SB	0/1:45,44,0:89:99:1483,0,1477,1618,1609,3227:31,14,29,15
 20	10003359	.	C	<NON_REF>	.	.	END=10003650	GT:DP:GQ:MIN_DP:PL	0/0:78:99:50:0,120,1800
-20	10003651	.	T	C,<NON_REF>	3620.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|325876.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|32,61|0,0;DP=93;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=325876.00	GT:AD:DP:GQ:PL:SB	1/1:0,93,0:93:99:3649,279,0,3649,279,3649:0,0,32,61
+20	10003651	.	T	C,<NON_REF>	3620.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|325876.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|32,61|0,0;DP=93;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=325876,93	GT:AD:DP:GQ:PL:SB	1/1:0,93,0:93:99:3649,279,0,3649,279,3649:0,0,32,61
 20	10003652	.	C	<NON_REF>	.	.	END=10003691	GT:DP:GQ:MIN_DP:PL	0/0:79:99:70:0,120,1800
-20	10003692	.	A	G,<NON_REF>	2609.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|240338.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|25,43|0,0;DP=68;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=240338.00	GT:AD:DP:GQ:PL:SB	1/1:0,68,0:68:99:2638,205,0,2638,205,2638:0,0,25,43
+20	10003692	.	A	G,<NON_REF>	2609.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|240338.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|25,43|0,0;DP=68;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=240338,68	GT:AD:DP:GQ:PL:SB	1/1:0,68,0:68:99:2638,205,0,2638,205,2638:0,0,25,43
 20	10003693	.	T	<NON_REF>	.	.	END=10003831	GT:DP:GQ:MIN_DP:PL	0/0:53:99:46:0,111,1665
-20	10003832	.	G	A,<NON_REF>	2705.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|215436.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|23,43|0,0;DP=66;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=215436.00	GT:AD:DP:GQ:PL:SB	1/1:0,66,0:66:99:2734,199,0,2734,199,2734:0,0,23,43
+20	10003832	.	G	A,<NON_REF>	2705.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|215436.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|23,43|0,0;DP=66;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=215436,66	GT:AD:DP:GQ:PL:SB	1/1:0,66,0:66:99:2734,199,0,2734,199,2734:0,0,23,43
 20	10003833	.	T	<NON_REF>	.	.	END=10004093	GT:DP:GQ:MIN_DP:PL	0/0:69:99:43:0,108,1620
-20	10004094	.	A	C,<NON_REF>	1825.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|147492.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,18|0,0;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=147492.00	GT:AD:DP:GQ:PL:SB	1/1:0,53,0:53:99:1854,157,0,1854,157,1854:0,0,35,18
+20	10004094	.	A	C,<NON_REF>	1825.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|147492.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,18|0,0;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=147492,53	GT:AD:DP:GQ:PL:SB	1/1:0,53,0:53:99:1854,157,0,1854,157,1854:0,0,35,18
 20	10004095	.	C	<NON_REF>	.	.	END=10004146	GT:DP:GQ:MIN_DP:PL	0/0:51:99:45:0,109,1596
-20	10004147	.	A	G,<NON_REF>	1837.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|157262.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|21,31|0,0;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=157262.00	GT:AD:DP:GQ:PL:SB	1/1:0,52,0:52:99:1866,156,0,1866,156,1866:0,0,21,31
+20	10004147	.	A	G,<NON_REF>	1837.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|157262.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|21,31|0,0;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=157262,52	GT:AD:DP:GQ:PL:SB	1/1:0,52,0:52:99:1866,156,0,1866,156,1866:0,0,21,31
 20	10004148	.	G	<NON_REF>	.	.	END=10004192	GT:DP:GQ:MIN_DP:PL	0/0:49:99:45:0,106,1637
-20	10004193	.	G	T,<NON_REF>	918.77	.	AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=70129.00|112740.00|0.00;AS_RAW_MQRankSum=|3.4,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=12,11|12,17|0,0;BaseQRankSum=-0.504;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.421;RAW_MQ=182869.00;ReadPosRankSum=1.512	GT:AD:DP:GQ:PL:SB	0/1:23,29,0:52:99:947,0,775,1016,860,1876:12,11,12,17
+20	10004193	.	G	T,<NON_REF>	918.77	.	AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=70129.00|112740.00|0.00;AS_RAW_MQRankSum=|3.4,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=12,11|12,17|0,0;BaseQRankSum=-0.504;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.421;RAW_MQandDP=182869,52;ReadPosRankSum=1.512	GT:AD:DP:GQ:PL:SB	0/1:23,29,0:52:99:947,0,775,1016,860,1876:12,11,12,17
 20	10004194	.	C	<NON_REF>	.	.	END=10004221	GT:DP:GQ:MIN_DP:PL	0/0:50:99:46:0,105,1575
-20	10004222	.	C	CA,<NON_REF>	12.96	.	AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=121951.00|23791.00|0.00;AS_RAW_MQRankSum=|-2.1,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=18,13|4,4|0,0;BaseQRankSum=0.335;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.042;RAW_MQ=194729.00;ReadPosRankSum=1.271	GT:AD:DP:GQ:PL:SB	0/1:31,8,0:39:50:50,0,923,153,952,1105:18,13,4,4
-20	10004223	.	A	AG,<NON_REF>	47.73	.	AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=108277.00|39441.00|0.00;AS_RAW_MQRankSum=|1.8,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,20|5,6|0,0;BaseQRankSum=-0.480;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.886;RAW_MQ=210769.00;ReadPosRankSum=0.339	GT:AD:DP:GQ:PL:SB	0/1:36,11,0:47:85:85,0,982,193,1017,1210:16,20,5,6
+20	10004222	.	C	CA,<NON_REF>	12.96	.	AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=121951.00|23791.00|0.00;AS_RAW_MQRankSum=|-2.1,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=18,13|4,4|0,0;BaseQRankSum=0.335;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.042;RAW_MQandDP=194729,54;ReadPosRankSum=1.271	GT:AD:DP:GQ:PL:SB	0/1:31,8,0:39:50:50,0,923,153,952,1105:18,13,4,4
+20	10004223	.	A	AG,<NON_REF>	47.73	.	AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=108277.00|39441.00|0.00;AS_RAW_MQRankSum=|1.8,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,20|5,6|0,0;BaseQRankSum=-0.480;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.886;RAW_MQandDP=210769,62;ReadPosRankSum=0.339	GT:AD:DP:GQ:PL:SB	0/1:36,11,0:47:85:85,0,982,193,1017,1210:16,20,5,6
 20	10004224	.	A	<NON_REF>	.	.	END=10004224	GT:DP:GQ:MIN_DP:PL	0/0:66:0:66:0,0,1403
 20	10004225	.	A	<NON_REF>	.	.	END=10004240	GT:DP:GQ:MIN_DP:PL	0/0:70:99:65:0,117,1755
 20	10004241	.	G	<NON_REF>	.	.	END=10004241	GT:DP:GQ:MIN_DP:PL	0/0:66:0:66:0,0,1965
 20	10004242	.	A	<NON_REF>	.	.	END=10004350	GT:DP:GQ:MIN_DP:PL	0/0:73:99:58:0,120,1800
-20	10004351	.	C	G,<NON_REF>	2755.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|243987.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,32|0,0;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=243987.00	GT:AD:DP:GQ:PL:SB	1/1:0,70,0:70:99:2784,211,0,2784,211,2784:0,0,38,32
+20	10004351	.	C	G,<NON_REF>	2755.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|243987.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,32|0,0;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=243987,70	GT:AD:DP:GQ:PL:SB	1/1:0,70,0:70:99:2784,211,0,2784,211,2784:0,0,38,32
 20	10004352	.	A	<NON_REF>	.	.	END=10004388	GT:DP:GQ:MIN_DP:PL	0/0:65:99:62:0,120,1800
-20	10004389	.	T	G,<NON_REF>	2494.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|199570.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|25,37|0,0;DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=199570.00	GT:AD:DP:GQ:PL:SB	1/1:0,62,0:62:99:2523,187,0,2523,187,2523:0,0,25,37
+20	10004389	.	T	G,<NON_REF>	2494.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|199570.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|25,37|0,0;DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=199570,62	GT:AD:DP:GQ:PL:SB	1/1:0,62,0:62:99:2523,187,0,2523,187,2523:0,0,25,37
 20	10004390	.	G	<NON_REF>	.	.	END=10004609	GT:DP:GQ:MIN_DP:PL	0/0:73:99:58:0,120,1800
-20	10004610	.	A	C,<NON_REF>	3625.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|306605.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|46,43|0,0;DP=89;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=306605.00	GT:AD:DP:GQ:PL:SB	1/1:0,89,0:89:99:3654,267,0,3654,267,3654:0,0,46,43
+20	10004610	.	A	C,<NON_REF>	3625.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|306605.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|46,43|0,0;DP=89;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=306605,89	GT:AD:DP:GQ:PL:SB	1/1:0,89,0:89:99:3654,267,0,3654,267,3654:0,0,46,43
 20	10004611	.	C	<NON_REF>	.	.	END=10004724	GT:DP:GQ:MIN_DP:PL	0/0:75:99:64:0,120,1800
-20	10004725	.	A	G,<NON_REF>	951.77	.	AS_RAW_BaseQRankSum=|-2.2,1|NaN;AS_RAW_MQ=92793.00|105769.00|0.00;AS_RAW_MQRankSum=|3.0,1|NaN;AS_RAW_ReadPosRankSum=|2.0,1|NaN;AS_SB_TABLE=10,25|17,13|0,0;BaseQRankSum=-2.154;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.008;RAW_MQ=198562.00;ReadPosRankSum=2.087	GT:AD:DP:GQ:PL:SB	0/1:35,30,0:65:99:980,0,1168,1085,1258,2343:10,25,17,13
+20	10004725	.	A	G,<NON_REF>	951.77	.	AS_RAW_BaseQRankSum=|-2.2,1|NaN;AS_RAW_MQ=92793.00|105769.00|0.00;AS_RAW_MQRankSum=|3.0,1|NaN;AS_RAW_ReadPosRankSum=|2.0,1|NaN;AS_SB_TABLE=10,25|17,13|0,0;BaseQRankSum=-2.154;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.008;RAW_MQandDP=198562,65;ReadPosRankSum=2.087	GT:AD:DP:GQ:PL:SB	0/1:35,30,0:65:99:980,0,1168,1085,1258,2343:10,25,17,13
 20	10004726	.	T	<NON_REF>	.	.	END=10004768	GT:DP:GQ:MIN_DP:PL	0/0:66:99:62:0,120,1800
-20	10004769	.	TAAAACTATGC	T,<NON_REF>	981.73	.	AS_RAW_BaseQRankSum=|1.6,1|NaN;AS_RAW_MQ=133200.00|32185.00|0.00;AS_RAW_MQRankSum=|-6.7,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=14,23|7,20|0,0;BaseQRankSum=1.603;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.625;RAW_MQ=216626.00;ReadPosRankSum=1.879	GT:AD:DP:GQ:PL:SB	0/1:37,27,0:64:99:1019,0,1471,1130,1554,2684:14,23,7,20
+20	10004769	.	TAAAACTATGC	T,<NON_REF>	981.73	.	AS_RAW_BaseQRankSum=|1.6,1|NaN;AS_RAW_MQ=133200.00|32185.00|0.00;AS_RAW_MQRankSum=|-6.7,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=14,23|7,20|0,0;BaseQRankSum=1.603;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.625;RAW_MQandDP=216626,79;ReadPosRankSum=1.879	GT:AD:DP:GQ:PL:SB	0/1:37,27,0:64:99:1019,0,1471,1130,1554,2684:14,23,7,20
 20	10004780	.	A	<NON_REF>	.	.	END=10004873	GT:DP:GQ:MIN_DP:PL	0/0:77:99:69:0,120,1800
-20	10004874	.	A	C,<NON_REF>	3602.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|306223.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|54,33|0,0;DP=87;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=306223.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:0,0,54,33
+20	10004874	.	A	C,<NON_REF>	3602.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|306223.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|54,33|0,0;DP=87;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=306223,87	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:0,0,54,33
 20	10004875	.	T	<NON_REF>	.	.	END=10004886	GT:DP:GQ:MIN_DP:PL	0/0:86:99:85:0,120,1800
-20	10004887	.	A	G,<NON_REF>	1323.77	.	AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=159241.00|141241.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=24,21|24,16|0,0;BaseQRankSum=0.356;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.067;RAW_MQ=300482.00;ReadPosRankSum=-1.114	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:45,40,0:85:99:0|1:10004874_A_C:1352,0,1542,1487,1662,3149:24,21,24,16
+20	10004887	.	A	G,<NON_REF>	1323.77	.	AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=159241.00|141241.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=24,21|24,16|0,0;BaseQRankSum=0.356;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.067;RAW_MQandDP=300482,85;ReadPosRankSum=-1.114	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:45,40,0:85:99:0|1:10004874_A_C:1352,0,1542,1487,1662,3149:24,21,24,16
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-20	10005010	.	C	T,<NON_REF>	2934.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|256441.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|44,28|0,0;DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=256441.00	GT:AD:DP:GQ:PL:SB	1/1:0,72,0:72:99:2963,217,0,2963,217,2963:0,0,44,28
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-20	10005427	.	C	T,<NON_REF>	2214.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|195241.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,28|0,0;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=195241.00	GT:AD:DP:GQ:PL:SB	1/1:0,55,0:55:99:2243,165,0,2243,165,2243:0,0,27,28
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 20	10005500	.	T	<NON_REF>	.	.	END=10005586	GT:DP:GQ:MIN_DP:PL	0/0:71:99:66:0,120,1800
-20	10005587	.	A	G,<NON_REF>	1229.77	.	AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=129600.00|127369.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=19,17|16,20|0,0;BaseQRankSum=-0.834;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.972;RAW_MQ=256969.00;ReadPosRankSum=0.248	GT:AD:DP:GQ:PL:SB	0/1:36,36,0:72:99:1258,0,1236,1366,1345,2710:19,17,16,20
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-20	10005723	.	A	G,<NON_REF>	3062.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|307369.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|48,38|0,0;DP=86;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=307369.00	GT:AD:DP:GQ:PL:SB	1/1:0,86,0:86:99:3091,258,0,3091,258,3091:0,0,48,38
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-20	10006291	.	G	A,<NON_REF>	978.77	.	AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=188569.00|106610.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|NaN;AS_SB_TABLE=25,28|16,15|0,0;BaseQRankSum=0.311;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.081;RAW_MQ=295179.00;ReadPosRankSum=-1.447	GT:AD:DP:GQ:PL:SB	0/1:53,31,0:84:99:1007,0,1905,1167,1998,3165:25,28,16,15
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-20	10006404	.	A	C,<NON_REF>	2928.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|268082.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,49|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=269451.00	GT:AD:DP:GQ:PL:SB	1/1:0,76,0:76:99:2957,228,0,2957,228,2957:0,0,27,49
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 20	10006405	.	C	<NON_REF>	.	.	END=10006681	GT:DP:GQ:MIN_DP:PL	0/0:78:99:65:0,120,1800
-20	10006682	.	T	A,<NON_REF>	2874.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|257810.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|44,29|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=257810.00	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2903,219,0,2903,219,2903:0,0,44,29
+20	10006682	.	T	A,<NON_REF>	2874.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|257810.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|44,29|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=257810,73	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2903,219,0,2903,219,2903:0,0,44,29
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-20	10006819	.	AAAAC	A,<NON_REF>	2531.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|219200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,28|0,0;DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=284000.00	GT:AD:DP:GQ:PL:SB	1/1:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28
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-20	10007150	.	G	C,<NON_REF>	669.77	.	AS_RAW_BaseQRankSum=|-4.5,1|NaN;AS_RAW_MQ=136800.00|90000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=16,22|14,11|0,0;BaseQRankSum=-4.476;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=226800.00;ReadPosRankSum=-0.077	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:38,25,0:63:99:0|1:10007150_G_C:698,0,1479,813,1554,2366:16,22,14,11
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-20	10007175	.	C	T,<NON_REF>	1350.77	.	AS_RAW_BaseQRankSum=|2.2,1|NaN;AS_RAW_MQ=80041.00|136800.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=9,14|18,20|0,0;BaseQRankSum=2.249;DP=61;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.319;RAW_MQ=216841.00;ReadPosRankSum=-1.213	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:23,38,0:61:99:1|0:10007150_G_C:1379,0,780,1448,894,2343:9,14,18,20
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-20	10007352	.	C	T,<NON_REF>	2764.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|245641.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|29,40|0,0;DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=245641.00	GT:AD:DP:GQ:PL:SB	1/1:0,69,0:69:99:2793,208,0,2793,208,2793:0,0,29,40
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-20	10007980	.	A	C,<NON_REF>	3524.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|331800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|39,51|0,0;DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=331800.00	GT:AD:DP:GQ:PL:SB	1/1:0,90,0:90:99:3553,270,0,3553,270,3553:0,0,39,51
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-20	10008029	.	T	TA,<NON_REF>	1986.73	.	AS_RAW_BaseQRankSum=|0.4,1|NaN;AS_RAW_MQ=10800.00|268510.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=1,2|27,45|0,0;BaseQRankSum=0.409;DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.576;RAW_MQ=327251.00;ReadPosRankSum=-1.326	GT:AD:DP:GQ:PL:SB	1/1:3,72,0:75:99:2024,145,0,2033,222,2110:1,2,27,45
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+20	10008221	.	T	C,<NON_REF>	3224.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|289669.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,37|0,0;DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=289669,80	GT:AD:DP:GQ:PL:SB	1/1:0,80,0:80:99:3253,240,0,3253,240,3253:0,0,43,37
 20	10008222	.	T	<NON_REF>	.	.	END=10008457	GT:DP:GQ:MIN_DP:PL	0/0:64:99:45:0,108,1620
-20	10008458	.	T	G,<NON_REF>	2654.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|191842.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,39|0,0;DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=191842.00	GT:AD:DP:GQ:PL:SB	1/1:0,69,0:69:99:2683,207,0,2683,207,2683:0,0,30,39
+20	10008458	.	T	G,<NON_REF>	2654.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|191842.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,39|0,0;DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=191842,69	GT:AD:DP:GQ:PL:SB	1/1:0,69,0:69:99:2683,207,0,2683,207,2683:0,0,30,39
 20	10008459	.	A	<NON_REF>	.	.	END=10008732	GT:DP:GQ:MIN_DP:PL	0/0:70:99:40:0,105,1575
 20	10008733	.	T	<NON_REF>	.	.	END=10008733	GT:DP:GQ:MIN_DP:PL	0/0:47:94:47:0,94,1689
 20	10008734	.	G	<NON_REF>	.	.	END=10008741	GT:DP:GQ:MIN_DP:PL	0/0:48:99:47:0,120,1800
-20	10008742	.	G	T,<NON_REF>	715.77	.	AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=37586.00|30288.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=10,13|11,15|0,0;BaseQRankSum=3.893;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQ=67874.00;ReadPosRankSum=0.190	GT:AD:DP:GQ:PL:SB	0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15
+20	10008742	.	G	T,<NON_REF>	715.77	.	AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=37586.00|30288.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=10,13|11,15|0,0;BaseQRankSum=3.893;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQandDP=67874,49;ReadPosRankSum=0.190	GT:AD:DP:GQ:PL:SB	0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15
 20	10008743	.	T	<NON_REF>	.	.	END=10008757	GT:DP:GQ:MIN_DP:PL	0/0:46:99:42:0,99,1485
-20	10008758	.	C	CA,<NON_REF>	684.14	.	AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=6578.00|37631.00|0.00;AS_RAW_MQRankSum=|-1.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=3,1|16,15|0,0;BaseQRankSum=0.130;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-1.168;RAW_MQ=54656.00;ReadPosRankSum=-0.052	GT:AD:DP:GQ:PL:SB	1/1:4,31,0:35:10:721,10,0,733,102,825:3,1,16,15
+20	10008758	.	C	CA,<NON_REF>	684.14	.	AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=6578.00|37631.00|0.00;AS_RAW_MQRankSum=|-1.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=3,1|16,15|0,0;BaseQRankSum=0.130;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-1.168;RAW_MQandDP=54656,44;ReadPosRankSum=-0.052	GT:AD:DP:GQ:PL:SB	1/1:4,31,0:35:10:721,10,0,733,102,825:3,1,16,15
 20	10008759	.	A	<NON_REF>	.	.	END=10008772	GT:DP:GQ:MIN_DP:PL	0/0:55:99:53:0,120,1800
 20	10008773	.	T	<NON_REF>	.	.	END=10008773	GT:DP:GQ:MIN_DP:PL	0/0:54:0:54:0,0,1660
 20	10008774	.	T	<NON_REF>	.	.	END=10008774	GT:DP:GQ:MIN_DP:PL	0/0:55:99:55:0,117,1755
 20	10008775	.	A	<NON_REF>	.	.	END=10008775	GT:DP:GQ:MIN_DP:PL	0/0:55:60:55:0,60,1923
 20	10008776	.	G	<NON_REF>	.	.	END=10008920	GT:DP:GQ:MIN_DP:PL	0/0:54:99:45:0,99,1480
-20	10008921	.	C	CA,<NON_REF>	253.73	.	AS_RAW_BaseQRankSum=|0.6,1|NaN;AS_RAW_MQ=62041.00|43805.00|0.00;AS_RAW_MQRankSum=|-2.0,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=10,8|8,8|0,0;BaseQRankSum=0.610;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.906;RAW_MQ=155512.00;ReadPosRankSum=0.173	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:10,8,8,8
+20	10008921	.	C	CA,<NON_REF>	253.73	.	AS_RAW_BaseQRankSum=|0.6,1|NaN;AS_RAW_MQ=62041.00|43805.00|0.00;AS_RAW_MQRankSum=|-2.0,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=10,8|8,8|0,0;BaseQRankSum=0.610;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.906;RAW_MQandDP=155512,49;ReadPosRankSum=0.173	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:10,8,8,8
 20	10008922	.	A	<NON_REF>	.	.	END=10008942	GT:DP:GQ:MIN_DP:PL	0/0:53:99:47:0,114,1710
 20	10008943	.	A	<NON_REF>	.	.	END=10008944	GT:DP:GQ:MIN_DP:PL	0/0:47:78:47:0,78,1170
 20	10008945	.	A	<NON_REF>	.	.	END=10008947	GT:DP:GQ:MIN_DP:PL	0/0:47:81:46:0,81,1215
-20	10008948	.	TA	T,<NON_REF>	2057.73	.	AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=625.00|134397.00|0.00;AS_RAW_MQRankSum=|2.0,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=1,0|35,15|0,0;BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQ=138622.00;ReadPosRankSum=0.884	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15
+20	10008948	.	TA	T,<NON_REF>	2057.73	.	AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=625.00|134397.00|0.00;AS_RAW_MQRankSum=|2.0,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=1,0|35,15|0,0;BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQandDP=138622,52;ReadPosRankSum=0.884	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15
 20	10008950	.	A	<NON_REF>	.	.	END=10008950	GT:DP:GQ:MIN_DP:PL	0/0:52:99:52:0,99,1485
 20	10008951	.	A	<NON_REF>	.	.	END=10008951	GT:DP:GQ:MIN_DP:PL	0/0:51:93:51:0,93,1395
-20	10008952	.	CACACACACACACA	C,CCA,CCACACACACA,CCACACACACACA,<NON_REF>	1666.73	.	AS_RAW_BaseQRankSum=|0.3,1|0.3,1|0.6,1|1.9,1|NaN;AS_RAW_MQ=625.00|2523.00|11774.00|12125.00|39600.00|0.00;AS_RAW_MQRankSum=|1.1,1|4.0,1|0.6,1|3.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|1.0,1|-0.3,1|0.8,1|NaN;AS_SB_TABLE=1,0|2,1|8,6|4,1|11,0|0,0;BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQ=154068.00;ReadPosRankSum=0.716	GT:AD:DP:GQ:PL:SB	2/4:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8
+20	10008952	.	CACACACACACACA	C,CCA,CCACACACACA,CCACACACACACA,<NON_REF>	1666.73	.	AS_RAW_BaseQRankSum=|0.3,1|0.3,1|0.6,1|1.9,1|NaN;AS_RAW_MQ=625.00|2523.00|11774.00|12125.00|39600.00|0.00;AS_RAW_MQRankSum=|1.1,1|4.0,1|0.6,1|3.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|1.0,1|-0.3,1|0.8,1|NaN;AS_SB_TABLE=1,0|2,1|8,6|4,1|11,0|0,0;BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=154068,59;ReadPosRankSum=0.716	GT:AD:DP:GQ:PL:SB	2/4:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8
 20	10008966	.	C	<NON_REF>	.	.	END=10008986	GT:DP:GQ:MIN_DP:PL	0/0:58:99:56:0,120,1800
 20	10008987	.	A	<NON_REF>	.	.	END=10008989	GT:DP:GQ:MIN_DP:PL	0/0:59:94:59:0,94,2181
 20	10008990	.	C	<NON_REF>	.	.	END=10009226	GT:DP:GQ:MIN_DP:PL	0/0:61:99:38:0,102,1530
-20	10009227	.	A	G,<NON_REF>	1369.77	.	AS_RAW_BaseQRankSum=|-2.3,1|NaN;AS_RAW_MQ=70061.00|132527.00|0.00;AS_RAW_MQRankSum=|1.4,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=16,7|19,20|0,0;BaseQRankSum=-2.220;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.428;RAW_MQ=202588.00;ReadPosRankSum=-1.159	GT:AD:DP:GQ:PL:SB	0/1:23,39,0:62:99:1398,0,740,1468,857,2325:16,7,19,20
+20	10009227	.	A	G,<NON_REF>	1369.77	.	AS_RAW_BaseQRankSum=|-2.3,1|NaN;AS_RAW_MQ=70061.00|132527.00|0.00;AS_RAW_MQRankSum=|1.4,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=16,7|19,20|0,0;BaseQRankSum=-2.220;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.428;RAW_MQandDP=202588,62;ReadPosRankSum=-1.159	GT:AD:DP:GQ:PL:SB	0/1:23,39,0:62:99:1398,0,740,1468,857,2325:16,7,19,20
 20	10009228	.	G	<NON_REF>	.	.	END=10009245	GT:DP:GQ:MIN_DP:PL	0/0:62:99:59:0,120,1800
-20	10009246	.	A	G,<NON_REF>	3002.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|242208.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|42,35|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=242208.00	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:3031,231,0,3031,231,3031:0,0,42,35
+20	10009246	.	A	G,<NON_REF>	3002.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|242208.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|42,35|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=242208,77	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:3031,231,0,3031,231,3031:0,0,42,35
 20	10009247	.	A	<NON_REF>	.	.	END=10009399	GT:DP:GQ:MIN_DP:PL	0/0:86:99:68:0,120,1800
-20	10009400	.	T	A,<NON_REF>	2998.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|266400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|39,35|0,0;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=266400.00	GT:AD:DP:GQ:PL:SB	1/1:0,74,0:74:99:3027,223,0,3027,223,3027:0,0,39,35
+20	10009400	.	T	A,<NON_REF>	2998.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|266400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|39,35|0,0;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=266400,74	GT:AD:DP:GQ:PL:SB	1/1:0,74,0:74:99:3027,223,0,3027,223,3027:0,0,39,35
 20	10009401	.	A	<NON_REF>	.	.	END=10009511	GT:DP:GQ:MIN_DP:PL	0/0:78:99:72:0,120,1800
-20	10009512	.	C	G,<NON_REF>	3039.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|263240.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,47|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=263240.00	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:3068,231,0,3068,231,3068:0,0,30,47
+20	10009512	.	C	G,<NON_REF>	3039.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|263240.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,47|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=263240,77	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:3068,231,0,3068,231,3068:0,0,30,47
 20	10009513	.	A	<NON_REF>	.	.	END=10009718	GT:DP:GQ:MIN_DP:PL	0/0:81:99:63:0,120,1800
-20	10009719	.	A	G,<NON_REF>	1895.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|207410.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|26,33|0,0;DP=59;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=207410.00	GT:AD:DP:GQ:PL:SB	1/1:0,59,0:59:99:1924,175,0,1924,175,1924:0,0,26,33
+20	10009719	.	A	G,<NON_REF>	1895.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|207410.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|26,33|0,0;DP=59;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=207410,59	GT:AD:DP:GQ:PL:SB	1/1:0,59,0:59:99:1924,175,0,1924,175,1924:0,0,26,33
 20	10009720	.	T	<NON_REF>	.	.	END=10009794	GT:DP:GQ:MIN_DP:PL	0/0:54:99:47:0,120,1800
-20	10009795	.	A	G,<NON_REF>	1880.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|166969.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|16,31|0,0;DP=47;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=166969.00	GT:AD:DP:GQ:PL:SB	1/1:0,47,0:47:99:1909,141,0,1909,141,1909:0,0,16,31
+20	10009795	.	A	G,<NON_REF>	1880.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|166969.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|16,31|0,0;DP=47;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=166969,47	GT:AD:DP:GQ:PL:SB	1/1:0,47,0:47:99:1909,141,0,1909,141,1909:0,0,16,31
 20	10009796	.	C	<NON_REF>	.	.	END=10009832	GT:DP:GQ:MIN_DP:PL	0/0:49:99:44:0,99,1485
 20	10009833	.	A	<NON_REF>	.	.	END=10009840	GT:DP:GQ:MIN_DP:PL	0/0:53:66:51:0,66,990
 20	10009841	.	A	<NON_REF>	.	.	END=10009841	GT:DP:GQ:MIN_DP:PL	0/0:51:39:51:0,39,585
-20	10009842	.	G	GAA,<NON_REF>	532.73	.	AS_RAW_BaseQRankSum=|0.8,1|NaN;AS_RAW_MQ=51846.00|37046.00|0.00;AS_RAW_MQRankSum=|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|1.7,1|NaN;AS_SB_TABLE=9,10|8,7|0,0;BaseQRankSum=0.872;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.603;RAW_MQ=150092.00;ReadPosRankSum=1.720	GT:AD:DP:GQ:PL:SB	0/1:19,15,0:34:99:570,0,690,629,738,1367:9,10,8,7
+20	10009842	.	G	GAA,<NON_REF>	532.73	.	AS_RAW_BaseQRankSum=|0.8,1|NaN;AS_RAW_MQ=51846.00|37046.00|0.00;AS_RAW_MQRankSum=|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|1.7,1|NaN;AS_SB_TABLE=9,10|8,7|0,0;BaseQRankSum=0.872;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.603;RAW_MQandDP=150092,51;ReadPosRankSum=1.720	GT:AD:DP:GQ:PL:SB	0/1:19,15,0:34:99:570,0,690,629,738,1367:9,10,8,7
 20	10009843	.	A	<NON_REF>	.	.	END=10009843	GT:DP:GQ:MIN_DP:PL	0/0:51:36:51:0,36,540
-20	10009844	.	G	A,<NON_REF>	661.77	.	AS_RAW_BaseQRankSum=|1.0,1|NaN;AS_RAW_MQ=37722.00|51846.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=8,8|9,10|0,0;BaseQRankSum=1.048;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQ=147168.00;ReadPosRankSum=-1.555	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:8,8,9,10
+20	10009844	.	G	A,<NON_REF>	661.77	.	AS_RAW_BaseQRankSum=|1.0,1|NaN;AS_RAW_MQ=37722.00|51846.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=8,8|9,10|0,0;BaseQRankSum=1.048;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQandDP=147168,51;ReadPosRankSum=-1.555	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:8,8,9,10
 20	10009845	.	A	<NON_REF>	.	.	END=10009847	GT:DP:GQ:MIN_DP:PL	0/0:51:42:51:0,42,630
 20	10009848	.	G	<NON_REF>	.	.	END=10009848	GT:DP:GQ:MIN_DP:PL	0/0:54:51:54:0,51,765
 20	10009849	.	A	<NON_REF>	.	.	END=10009850	GT:DP:GQ:MIN_DP:PL	0/0:55:57:54:0,57,855
@@ -310,13 +310,13 @@
 20	10009861	.	A	<NON_REF>	.	.	END=10009864	GT:DP:GQ:MIN_DP:PL	0/0:58:84:56:0,84,1260
 20	10009865	.	A	<NON_REF>	.	.	END=10009869	GT:DP:GQ:MIN_DP:PL	0/0:57:90:56:0,90,1350
 20	10009870	.	G	<NON_REF>	.	.	END=10009870	GT:DP:GQ:MIN_DP:PL	0/0:57:99:57:0,99,1485
-20	10009871	.	A	G,<NON_REF>	658.77	.	AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=35804.00|51846.00|0.00;AS_RAW_MQRankSum=|1.4,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=10,7|9,10|0,0;BaseQRankSum=-0.803;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.495;RAW_MQ=154737.00;ReadPosRankSum=1.539	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:17,19,0:36:99:0|1:10009844_G_A:687,0,594,739,652,1391:10,7,9,10
+20	10009871	.	A	G,<NON_REF>	658.77	.	AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=35804.00|51846.00|0.00;AS_RAW_MQRankSum=|1.4,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=10,7|9,10|0,0;BaseQRankSum=-0.803;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.495;RAW_MQandDP=154737,60;ReadPosRankSum=1.539	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:17,19,0:36:99:0|1:10009844_G_A:687,0,594,739,652,1391:10,7,9,10
 20	10009872	.	G	<NON_REF>	.	.	END=10009874	GT:DP:GQ:MIN_DP:PL	0/0:57:99:55:0,108,1620
-20	10009875	.	A	G,AGGGAGG,<NON_REF>	2369.73	.	AS_RAW_BaseQRankSum=|1.3,1|-0.7,1|NaN;AS_RAW_MQ=1682.00|40205.00|26922.00|0.00;AS_RAW_MQRankSum=|1.8,1|0.8,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|0.5,1|NaN;AS_SB_TABLE=2,0|6,9|6,7|0,0;BaseQRankSum=0.378;DP=57;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.361;RAW_MQ=143937.00;ReadPosRankSum=1.040	GT:AD:DP:GQ:PL:SB	1/2:2,15,13,0:30:99:2407,645,533,697,0,574,1881,655,700,1805:2,0,12,16
+20	10009875	.	A	G,AGGGAGG,<NON_REF>	2369.73	.	AS_RAW_BaseQRankSum=|1.3,1|-0.7,1|NaN;AS_RAW_MQ=1682.00|40205.00|26922.00|0.00;AS_RAW_MQRankSum=|1.8,1|0.8,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|0.5,1|NaN;AS_SB_TABLE=2,0|6,9|6,7|0,0;BaseQRankSum=0.378;DP=57;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.361;RAW_MQandDP=143937,57;ReadPosRankSum=1.040	GT:AD:DP:GQ:PL:SB	1/2:2,15,13,0:30:99:2407,645,533,697,0,574,1881,655,700,1805:2,0,12,16
 20	10009876	.	G	<NON_REF>	.	.	END=10009878	GT:DP:GQ:MIN_DP:PL	0/0:52:99:51:0,114,1710
-20	10009879	.	A	G,<NON_REF>	2244.77	.	AS_RAW_BaseQRankSum=|1.5,1|NaN;AS_RAW_MQ=1682.00|118979.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=2,0|15,32|0,0;BaseQRankSum=1.534;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.570;RAW_MQ=120661.00;ReadPosRankSum=1.113	GT:AD:DP:GQ:PL:SB	1/1:2,47,0:49:99:2273,150,0,2276,154,2279:2,0,15,32
+20	10009879	.	A	G,<NON_REF>	2244.77	.	AS_RAW_BaseQRankSum=|1.5,1|NaN;AS_RAW_MQ=1682.00|118979.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=2,0|15,32|0,0;BaseQRankSum=1.534;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.570;RAW_MQandDP=120661,49;ReadPosRankSum=1.113	GT:AD:DP:GQ:PL:SB	1/1:2,47,0:49:99:2273,150,0,2276,154,2279:2,0,15,32
 20	10009880	.	G	<NON_REF>	.	.	END=10009882	GT:DP:GQ:MIN_DP:PL	0/0:49:99:48:0,120,1800
-20	10009883	.	A	G,<NON_REF>	2151.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|127656.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|15,32|0,0;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=129338.00	GT:AD:DP:GQ:PL:SB	1/1:0,47,0:47:99:2180,147,0,2180,147,2181:0,0,15,32
+20	10009883	.	A	G,<NON_REF>	2151.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|127656.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|15,32|0,0;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=129338,49	GT:AD:DP:GQ:PL:SB	1/1:0,47,0:47:99:2180,147,0,2180,147,2181:0,0,15,32
 20	10009884	.	G	<NON_REF>	.	.	END=10009884	GT:DP:GQ:MIN_DP:PL	0/0:53:99:53:0,120,1800
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 20	10009886	.	A	<NON_REF>	.	.	END=10009886	GT:DP:GQ:MIN_DP:PL	0/0:53:0:53:0,0,1567
@@ -327,25 +327,25 @@
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 20	10009895	.	G	<NON_REF>	.	.	END=10010392	GT:DP:GQ:MIN_DP:PL	0/0:70:99:45:0,111,1665
-20	10010393	.	T	G,<NON_REF>	1464.77	.	AS_RAW_BaseQRankSum=|-3.4,1|NaN;AS_RAW_MQ=129600.00|149282.00|0.00;AS_RAW_MQRankSum=|-1.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.8,1|NaN;AS_SB_TABLE=24,12|19,24|0,0;BaseQRankSum=-3.351;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.284;RAW_MQ=278882.00;ReadPosRankSum=-1.738	GT:AD:DP:GQ:PL:SB	0/1:36,43,0:79:99:1493,0,1230,1601,1359,2961:24,12,19,24
+20	10010393	.	T	G,<NON_REF>	1464.77	.	AS_RAW_BaseQRankSum=|-3.4,1|NaN;AS_RAW_MQ=129600.00|149282.00|0.00;AS_RAW_MQRankSum=|-1.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.8,1|NaN;AS_SB_TABLE=24,12|19,24|0,0;BaseQRankSum=-3.351;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.284;RAW_MQandDP=278882,79;ReadPosRankSum=-1.738	GT:AD:DP:GQ:PL:SB	0/1:36,43,0:79:99:1493,0,1230,1601,1359,2961:24,12,19,24
 20	10010394	.	T	<NON_REF>	.	.	END=10010535	GT:DP:GQ:MIN_DP:PL	0/0:83:99:67:0,120,1800
-20	10010536	.	G	GA,<NON_REF>	2462.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|301300.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|36,43|0,0;DP=85;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=322900.00	GT:AD:DP:GQ:PL:SB	1/1:0,79,0:79:99:2500,243,0,2500,244,2500:0,0,36,43
+20	10010536	.	G	GA,<NON_REF>	2462.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|301300.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|36,43|0,0;DP=85;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=322900,85	GT:AD:DP:GQ:PL:SB	1/1:0,79,0:79:99:2500,243,0,2500,244,2500:0,0,36,43
 20	10010537	.	A	<NON_REF>	.	.	END=10010765	GT:DP:GQ:MIN_DP:PL	0/0:79:99:68:0,120,1800
-20	10010766	.	T	G,<NON_REF>	2411.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|237600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,31|0,0;DP=67;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=241200.00	GT:AD:DP:GQ:PL:SB	1/1:0,66,0:66:99:2440,199,0,2440,199,2440:0,0,35,31
+20	10010766	.	T	G,<NON_REF>	2411.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|237600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,31|0,0;DP=67;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=241200,67	GT:AD:DP:GQ:PL:SB	1/1:0,66,0:66:99:2440,199,0,2440,199,2440:0,0,35,31
 20	10010767	.	G	<NON_REF>	.	.	END=10010831	GT:DP:GQ:MIN_DP:PL	0/0:74:99:61:0,120,1800
-20	10010832	.	T	C,<NON_REF>	2951.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|265538.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|31,44|0,0;DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=265538.00	GT:AD:DP:GQ:PL:SB	1/1:0,75,0:75:99:2980,226,0,2980,226,2980:0,0,31,44
+20	10010832	.	T	C,<NON_REF>	2951.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|265538.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|31,44|0,0;DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=265538,75	GT:AD:DP:GQ:PL:SB	1/1:0,75,0:75:99:2980,226,0,2980,226,2980:0,0,31,44
 20	10010833	.	A	<NON_REF>	.	.	END=10011074	GT:DP:GQ:MIN_DP:PL	0/0:89:99:73:0,120,1800
-20	10011075	.	C	T,<NON_REF>	1325.77	.	AS_RAW_BaseQRankSum=|5.3,1|NaN;AS_RAW_MQ=158400.00|140400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=22,22|22,17|0,0;BaseQRankSum=5.364;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=298800.00;ReadPosRankSum=-1.036	GT:AD:DP:GQ:PL:SB	0/1:44,39,0:83:99:1354,0,1333,1485,1450,2935:22,22,22,17
+20	10011075	.	C	T,<NON_REF>	1325.77	.	AS_RAW_BaseQRankSum=|5.3,1|NaN;AS_RAW_MQ=158400.00|140400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=22,22|22,17|0,0;BaseQRankSum=5.364;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=298800,83;ReadPosRankSum=-1.036	GT:AD:DP:GQ:PL:SB	0/1:44,39,0:83:99:1354,0,1333,1485,1450,2935:22,22,22,17
 20	10011076	.	G	<NON_REF>	.	.	END=10011308	GT:DP:GQ:MIN_DP:PL	0/0:74:99:52:0,120,1800
-20	10011309	.	T	C,<NON_REF>	2692.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|277200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,47|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=277200.00	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:2721,231,0,2721,231,2721:0,0,30,47
+20	10011309	.	T	C,<NON_REF>	2692.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|277200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,47|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=277200,77	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:2721,231,0,2721,231,2721:0,0,30,47
 20	10011310	.	G	<NON_REF>	.	.	END=10011516	GT:DP:GQ:MIN_DP:PL	0/0:80:99:70:0,120,1800
-20	10011517	.	GAA	G,GA,GAAA,<NON_REF>	490.73	.	AS_RAW_BaseQRankSum=|-0.9,1|0.9,1|0.2,1|NaN;AS_RAW_MQ=133200.00|7200.00|104700.00|21600.00|0.00;AS_RAW_MQRankSum=|0.0,1|2.0,1|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|0.6,1|-1.0,1|NaN;AS_SB_TABLE=23,14|0,2|15,13|4,2|0,0;BaseQRankSum=0.690;DP=91;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=1.797;RAW_MQ=326510.00;ReadPosRankSum=0.315	GT:AD:DP:GQ:PL:SB	0/2:37,2,28,6,0:73:99:528,611,2120,0,1042,875,604,1499,722,1648,667,1700,966,1470,1638:23,14,19,17
+20	10011517	.	GAA	G,GA,GAAA,<NON_REF>	490.73	.	AS_RAW_BaseQRankSum=|-0.9,1|0.9,1|0.2,1|NaN;AS_RAW_MQ=133200.00|7200.00|104700.00|21600.00|0.00;AS_RAW_MQRankSum=|0.0,1|2.0,1|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|0.6,1|-1.0,1|NaN;AS_SB_TABLE=23,14|0,2|15,13|4,2|0,0;BaseQRankSum=0.690;DP=91;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=1.797;RAW_MQandDP=326510,91;ReadPosRankSum=0.315	GT:AD:DP:GQ:PL:SB	0/2:37,2,28,6,0:73:99:528,611,2120,0,1042,875,604,1499,722,1648,667,1700,966,1470,1638:23,14,19,17
 20	10011520	.	A	<NON_REF>	.	.	END=10011665	GT:DP:GQ:MIN_DP:PL	0/0:68:99:62:0,120,1800
-20	10011666	.	C	T,<NON_REF>	2961.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|254523.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,30|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=254523.00	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2990,220,0,2990,220,2990:0,0,43,30
+20	10011666	.	C	T,<NON_REF>	2961.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|254523.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,30|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=254523,73	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2990,220,0,2990,220,2990:0,0,43,30
 20	10011667	.	A	<NON_REF>	.	.	END=10011938	GT:DP:GQ:MIN_DP:PL	0/0:87:99:64:0,111,1665
-20	10011939	.	C	T,<NON_REF>	2469.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|193043.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|23,38|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=193043.00	GT:AD:DP:GQ:PL:SB	1/1:0,61,0:61:99:2498,184,0,2498,184,2498:0,0,23,38
+20	10011939	.	C	T,<NON_REF>	2469.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|193043.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|23,38|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=193043,61	GT:AD:DP:GQ:PL:SB	1/1:0,61,0:61:99:2498,184,0,2498,184,2498:0,0,23,38
 20	10011940	.	G	<NON_REF>	.	.	END=10012020	GT:DP:GQ:MIN_DP:PL	0/0:56:99:42:0,101,1575
-20	10012021	.	CA	C,<NON_REF>	1975.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|215907.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|26,40|0,0;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=228076.00	GT:AD:DP:GQ:PL:SB	1/1:0,66,0:66:99:2013,198,0,2013,198,2013:0,0,26,40
+20	10012021	.	CA	C,<NON_REF>	1975.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|215907.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|26,40|0,0;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=228076,70	GT:AD:DP:GQ:PL:SB	1/1:0,66,0:66:99:2013,198,0,2013,198,2013:0,0,26,40
 20	10012023	.	A	<NON_REF>	.	.	END=10012147	GT:DP:GQ:MIN_DP:PL	0/0:70:99:38:0,99,1485
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 20	10012158	.	A	<NON_REF>	.	.	END=10012159	GT:DP:GQ:MIN_DP:PL	0/0:35:84:34:0,84,1260
@@ -397,7 +397,7 @@
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 20	10012361	.	C	<NON_REF>	.	.	END=10012361	GT:DP:GQ:MIN_DP:PL	0/0:23:48:23:0,48,720
-20	10012362	.	G	T,<NON_REF>	835.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|66527.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|2,21|0,0;DP=23;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=66527.00	GT:AD:DP:GQ:PL:SB	1/1:0,23,0:23:69:864,69,0,864,69,864:0,0,2,21
+20	10012362	.	G	T,<NON_REF>	835.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|66527.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|2,21|0,0;DP=23;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=66527,23	GT:AD:DP:GQ:PL:SB	1/1:0,23,0:23:69:864,69,0,864,69,864:0,0,2,21
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@@ -406,9 +406,9 @@
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-20	10012384	.	T	C,<NON_REF>	229.77	.	AS_RAW_BaseQRankSum=|-1.8,1|NaN;AS_RAW_MQ=30586.00|20700.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=0,10|2,6|0,0;BaseQRankSum=-1.773;DP=18;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.811;RAW_MQ=51286.00;ReadPosRankSum=0.800	GT:AD:DP:GQ:PL:SB	0/1:10,8,0:18:99:258,0,355,288,379,667:0,10,2,6
+20	10012384	.	T	C,<NON_REF>	229.77	.	AS_RAW_BaseQRankSum=|-1.8,1|NaN;AS_RAW_MQ=30586.00|20700.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=0,10|2,6|0,0;BaseQRankSum=-1.773;DP=18;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.811;RAW_MQandDP=51286,18;ReadPosRankSum=0.800	GT:AD:DP:GQ:PL:SB	0/1:10,8,0:18:99:258,0,355,288,379,667:0,10,2,6
 20	10012385	.	T	<NON_REF>	.	.	END=10012386	GT:DP:GQ:MIN_DP:PL	0/0:18:39:17:0,39,585
-20	10012387	.	T	C,<NON_REF>	533.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|44086.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|2,14|0,0;DP=16;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=44086.00	GT:AD:DP:GQ:PL:SB	1/1:0,16,0:16:50:562,50,0,562,50,562:0,0,2,14
+20	10012387	.	T	C,<NON_REF>	533.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|44086.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|2,14|0,0;DP=16;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=44086,16	GT:AD:DP:GQ:PL:SB	1/1:0,16,0:16:50:562,50,0,562,50,562:0,0,2,14
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@@ -448,22 +448,22 @@
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-20	10012479	.	A	G,<NON_REF>	592.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|45990.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|9,8|0,0;DP=17;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=45990.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,17,0:17:50:0|1:10012479_A_G:621,50,0,621,50,621:0,0,9,8
+20	10012479	.	A	G,<NON_REF>	592.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|45990.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|9,8|0,0;DP=17;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=45990,17	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,17,0:17:50:0|1:10012479_A_G:621,50,0,621,50,621:0,0,9,8
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-20	10012498	.	C	G,<NON_REF>	466.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|22302.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|4,7|0,0;DP=11;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=22302.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,11,0:11:33:0|1:10012479_A_G:495,33,0,495,33,495:0,0,4,7
+20	10012498	.	C	G,<NON_REF>	466.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|22302.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|4,7|0,0;DP=11;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=22302,11	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,11,0:11:33:0|1:10012479_A_G:495,33,0,495,33,495:0,0,4,7
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-20	10012518	.	T	C,<NON_REF>	406.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|15102.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|4,5|0,0;DP=9;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=15102.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,9,0:9:30:0|1:10012479_A_G:435,30,0,435,30,435:0,0,4,5
+20	10012518	.	T	C,<NON_REF>	406.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|15102.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|4,5|0,0;DP=9;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=15102,9	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,9,0:9:30:0|1:10012479_A_G:435,30,0,435,30,435:0,0,4,5
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-20	10012521	.	C	T,<NON_REF>	46.77	.	AS_RAW_BaseQRankSum=|2.3,1|NaN;AS_RAW_MQ=13910.00|5282.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|1.9,1|NaN;AS_SB_TABLE=4,4|2,1|0,0;BaseQRankSum=2.362;DP=11;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.038;RAW_MQ=19192.00;ReadPosRankSum=1.973	GT:AD:DP:GQ:PL:SB	0/1:8,3,0:11:75:75,0,224,99,233,332:4,4,2,1
+20	10012521	.	C	T,<NON_REF>	46.77	.	AS_RAW_BaseQRankSum=|2.3,1|NaN;AS_RAW_MQ=13910.00|5282.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|1.9,1|NaN;AS_SB_TABLE=4,4|2,1|0,0;BaseQRankSum=2.362;DP=11;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.038;RAW_MQandDP=19192,11;ReadPosRankSum=1.973	GT:AD:DP:GQ:PL:SB	0/1:8,3,0:11:75:75,0,224,99,233,332:4,4,2,1
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@@ -474,9 +474,9 @@
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-20	10012570	.	G	GCA,<NON_REF>	457.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|12736.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|8,1|0,0;DP=9;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=12736.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,9,0:9:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,8,1
+20	10012570	.	G	GCA,<NON_REF>	457.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|12736.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|8,1|0,0;DP=9;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=12736,9	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,9,0:9:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,8,1
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-20	10012572	.	GT	G,<NON_REF>	457.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|17177.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|10,1|0,0;DP=11;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=17177.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,11,0:11:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,10,1
+20	10012572	.	GT	G,<NON_REF>	457.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|17177.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|10,1|0,0;DP=11;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=17177,11	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,11,0:11:33:0|1:10012570_G_GCA:495,33,0,495,33,495:0,0,10,1
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@@ -496,11 +496,11 @@
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-20	10012631	.	C	CG,<NON_REF>	484.73	.	AS_RAW_BaseQRankSum=|-1.1,1|NaN;AS_RAW_MQ=23282.00|25783.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=8,0|9,4|0,0;BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.670;RAW_MQ=49065.00;ReadPosRankSum=-1.813	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:8,0,9,4
+20	10012631	.	C	CG,<NON_REF>	484.73	.	AS_RAW_BaseQRankSum=|-1.1,1|NaN;AS_RAW_MQ=23282.00|25783.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=8,0|9,4|0,0;BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.670;RAW_MQandDP=49065,21;ReadPosRankSum=-1.813	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:8,0,9,4
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-20	10012636	.	G	C,<NON_REF>	527.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=23282.00|29383.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-2.0,1|NaN;AS_SB_TABLE=8,0|10,4|0,0;BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.513;RAW_MQ=52665.00;ReadPosRankSum=-1.915	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:8,0,10,4
+20	10012636	.	G	C,<NON_REF>	527.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=23282.00|29383.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-2.0,1|NaN;AS_SB_TABLE=8,0|10,4|0,0;BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.513;RAW_MQandDP=52665,22;ReadPosRankSum=-1.915	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:8,0,10,4
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@@ -518,7 +518,7 @@
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-20	10012714	.	G	C,<NON_REF>	1300.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|98462.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|29,6|0,0;DP=35;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=98462.00	GT:AD:DP:GQ:PL:SB	1/1:0,35,0:35:99:1329,105,0,1329,105,1329:0,0,29,6
+20	10012714	.	G	C,<NON_REF>	1300.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|98462.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|29,6|0,0;DP=35;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=98462,35	GT:AD:DP:GQ:PL:SB	1/1:0,35,0:35:99:1329,105,0,1329,105,1329:0,0,29,6
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@@ -532,7 +532,7 @@
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-20	10012751	.	T	C,<NON_REF>	937.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|78546.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|17,13|0,0;DP=30;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=78546.00	GT:AD:DP:GQ:PL:SB	1/1:0,30,0:30:89:966,89,0,966,89,966:0,0,17,13
+20	10012751	.	T	C,<NON_REF>	937.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|78546.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|17,13|0,0;DP=30;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=78546,30	GT:AD:DP:GQ:PL:SB	1/1:0,30,0:30:89:966,89,0,966,89,966:0,0,17,13
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@@ -569,13 +569,13 @@
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-20	10013119	.	C	T,<NON_REF>	1011.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=81510.00|74871.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=19,10|17,13|0,0;BaseQRankSum=2.724;DP=59;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.089;RAW_MQ=156381.00;ReadPosRankSum=0.159	GT:AD:DP:GQ:PL:SB	0/1:29,30,0:59:99:1040,0,936,1127,1026,2153:19,10,17,13
+20	10013119	.	C	T,<NON_REF>	1011.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=81510.00|74871.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=19,10|17,13|0,0;BaseQRankSum=2.724;DP=59;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.089;RAW_MQandDP=156381,59;ReadPosRankSum=0.159	GT:AD:DP:GQ:PL:SB	0/1:29,30,0:59:99:1040,0,936,1127,1026,2153:19,10,17,13
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-20	10013574	.	G	A,<NON_REF>	1050.77	.	AS_RAW_BaseQRankSum=|3.4,1|NaN;AS_RAW_MQ=128479.00|104119.00|0.00;AS_RAW_MQRankSum=|-0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=15,23|7,24|0,0;BaseQRankSum=3.469;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.271;RAW_MQ=232598.00;ReadPosRankSum=0.706	GT:AD:DP:GQ:PL:SB	0/1:38,31,0:69:99:1079,0,1301,1194,1394,2588:15,23,7,24
+20	10013574	.	G	A,<NON_REF>	1050.77	.	AS_RAW_BaseQRankSum=|3.4,1|NaN;AS_RAW_MQ=128479.00|104119.00|0.00;AS_RAW_MQRankSum=|-0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=15,23|7,24|0,0;BaseQRankSum=3.469;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.271;RAW_MQandDP=232598,69;ReadPosRankSum=0.706	GT:AD:DP:GQ:PL:SB	0/1:38,31,0:69:99:1079,0,1301,1194,1394,2588:15,23,7,24
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-20	10014990	.	C	CAT,<NON_REF>	1237.73	.	AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=134569.00|147200.00|0.00;AS_RAW_MQRankSum=|3.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=28,10|25,13|0,0;BaseQRankSum=1.930;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.107;RAW_MQ=321369.00;ReadPosRankSum=-0.437	GT:AD:DP:GQ:PL:SB	0/1:38,38,0:76:99:1275,0,1248,1389,1365,2755:28,10,25,13
+20	10014990	.	C	CAT,<NON_REF>	1237.73	.	AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=134569.00|147200.00|0.00;AS_RAW_MQRankSum=|3.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=28,10|25,13|0,0;BaseQRankSum=1.930;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.107;RAW_MQandDP=321369,87;ReadPosRankSum=-0.437	GT:AD:DP:GQ:PL:SB	0/1:38,38,0:76:99:1275,0,1248,1389,1365,2755:28,10,25,13
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@@ -638,7 +638,7 @@
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-20	10015679	.	C	T,<NON_REF>	140.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=18000.00|18000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=5,0|5,0|0,0;BaseQRankSum=0.200;DP=10;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=36000.00;ReadPosRankSum=0.497	GT:AD:DP:GQ:PL:SB	0/1:5,5,0:10:99:169,0,166,184,181,365:5,0,5,0
+20	10015679	.	C	T,<NON_REF>	140.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=18000.00|18000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=5,0|5,0|0,0;BaseQRankSum=0.200;DP=10;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=36000,10;ReadPosRankSum=0.497	GT:AD:DP:GQ:PL:SB	0/1:5,5,0:10:99:169,0,166,184,181,365:5,0,5,0
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@@ -661,7 +661,7 @@
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-20	10015761	.	T	C,<NON_REF>	344.77	.	AS_RAW_BaseQRankSum=|-2.0,1|NaN;AS_RAW_MQ=29641.00|46800.00|0.00;AS_RAW_MQRankSum=|1.2,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=9,0|12,1|0,0;BaseQRankSum=-1.982;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.294;RAW_MQ=76441.00;ReadPosRankSum=1.805	GT:AD:DP:GQ:PL:SB	0/1:9,13,0:22:99:373,0,284,400,323,723:9,0,12,1
+20	10015761	.	T	C,<NON_REF>	344.77	.	AS_RAW_BaseQRankSum=|-2.0,1|NaN;AS_RAW_MQ=29641.00|46800.00|0.00;AS_RAW_MQRankSum=|1.2,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=9,0|12,1|0,0;BaseQRankSum=-1.982;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.294;RAW_MQandDP=76441,22;ReadPosRankSum=1.805	GT:AD:DP:GQ:PL:SB	0/1:9,13,0:22:99:373,0,284,400,323,723:9,0,12,1
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@@ -685,21 +685,21 @@
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+20	10018158	.	G	C,<NON_REF>	1639.77	.	AS_RAW_BaseQRankSum=|5.2,1|NaN;AS_RAW_MQ=141769.00|172800.00|0.00;AS_RAW_MQRankSum=|1.1,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=18,22|20,28|0,0;BaseQRankSum=5.213;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.118;RAW_MQandDP=318169,89;ReadPosRankSum=1.179	GT:AD:DP:GQ:PL:SB	0/1:40,48,0:88:99:1668,0,1165,1787,1309,3096:18,22,20,28
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-20	10023689	.	G	A,<NON_REF>	1852.77	.	AS_RAW_BaseQRankSum=|2.1,1|NaN;AS_RAW_MQ=102169.00|183600.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=16,13|26,25|0,0;BaseQRankSum=2.144;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.352;RAW_MQ=285769.00;ReadPosRankSum=1.162	GT:AD:DP:GQ:PL:SB	0/1:29,51,0:80:99:1881,0,946,1968,1099,3067:16,13,26,25
+20	10023689	.	G	A,<NON_REF>	1852.77	.	AS_RAW_BaseQRankSum=|2.1,1|NaN;AS_RAW_MQ=102169.00|183600.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=16,13|26,25|0,0;BaseQRankSum=2.144;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.352;RAW_MQandDP=285769,80;ReadPosRankSum=1.162	GT:AD:DP:GQ:PL:SB	0/1:29,51,0:80:99:1881,0,946,1968,1099,3067:16,13,26,25
 20	10023690	.	G	<NON_REF>	.	.	END=10024106	GT:DP:GQ:MIN_DP:PL	0/0:70:99:57:0,120,1800
-20	10024107	.	C	T,<NON_REF>	1694.77	.	AS_RAW_BaseQRankSum=|5.7,1|NaN;AS_RAW_MQ=136800.00|166763.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=21,17|28,20|0,0;BaseQRankSum=5.770;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.546;RAW_MQ=303563.00;ReadPosRankSum=0.148	GT:AD:DP:GQ:PL:SB	0/1:38,48,0:86:99:1723,0,1086,1837,1230,3068:21,17,28,20
+20	10024107	.	C	T,<NON_REF>	1694.77	.	AS_RAW_BaseQRankSum=|5.7,1|NaN;AS_RAW_MQ=136800.00|166763.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=21,17|28,20|0,0;BaseQRankSum=5.770;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.546;RAW_MQandDP=303563,86;ReadPosRankSum=0.148	GT:AD:DP:GQ:PL:SB	0/1:38,48,0:86:99:1723,0,1086,1837,1230,3068:21,17,28,20
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 20	10024284	.	T	<NON_REF>	.	.	END=10024287	GT:DP:GQ:MIN_DP:PL	0/0:71:99:65:0,120,1800
@@ -710,7 +710,7 @@
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 20	10024298	.	T	<NON_REF>	.	.	END=10024298	GT:DP:GQ:MIN_DP:PL	0/0:66:59:66:0,59,2080
 20	10024299	.	C	<NON_REF>	.	.	END=10024299	GT:DP:GQ:MIN_DP:PL	0/0:62:0:62:0,0,1480
-20	10024300	.	CTT	C,CT,CTTTT,<NON_REF>	87.76	.	AS_RAW_BaseQRankSum=|1.7,1|1.4,1|2.3,1|NaN;AS_RAW_MQ=8041.00|5858.00|5282.00|20523.00|0.00;AS_RAW_MQRankSum=|-1.1,1|-0.6,1|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.9,1|-2.0,1|-0.5,1|NaN;AS_SB_TABLE=1,2|3,1|2,1|6,2|0,0;BaseQRankSum=2.446;DP=50;ExcessHet=3.0103;MLEAC=1,0,1,0;MLEAF=0.500,0.00,0.500,0.00;MQRankSum=-0.600;RAW_MQ=134695.00;ReadPosRankSum=-1.073	GT:AD:DP:GQ:PL:SB	1/3:3,4,3,8,0:18:1:122,67,400,91,215,231,19,0,1,156,161,279,257,107,347:1,2,11,4
+20	10024300	.	CTT	C,CT,CTTTT,<NON_REF>	87.76	.	AS_RAW_BaseQRankSum=|1.7,1|1.4,1|2.3,1|NaN;AS_RAW_MQ=8041.00|5858.00|5282.00|20523.00|0.00;AS_RAW_MQRankSum=|-1.1,1|-0.6,1|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.9,1|-2.0,1|-0.5,1|NaN;AS_SB_TABLE=1,2|3,1|2,1|6,2|0,0;BaseQRankSum=2.446;DP=50;ExcessHet=3.0103;MLEAC=1,0,1,0;MLEAF=0.500,0.00,0.500,0.00;MQRankSum=-0.600;RAW_MQandDP=134695,50;ReadPosRankSum=-1.073	GT:AD:DP:GQ:PL:SB	1/3:3,4,3,8,0:18:1:122,67,400,91,215,231,19,0,1,156,161,279,257,107,347:1,2,11,4
 20	10024303	.	T	<NON_REF>	.	.	END=10024303	GT:DP:GQ:MIN_DP:PL	0/0:67:57:67:0,57,855
 20	10024304	.	T	<NON_REF>	.	.	END=10024307	GT:DP:GQ:MIN_DP:PL	0/0:69:63:68:0,63,945
 20	10024308	.	T	<NON_REF>	.	.	END=10024310	GT:DP:GQ:MIN_DP:PL	0/0:70:78:70:0,78,1170
@@ -725,41 +725,41 @@
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 20	10024326	.	A	<NON_REF>	.	.	END=10024326	GT:DP:GQ:MIN_DP:PL	0/0:44:58:44:0,58,1605
 20	10024327	.	G	<NON_REF>	.	.	END=10026356	GT:DP:GQ:MIN_DP:PL	0/0:79:99:39:0,105,1509
-20	10026357	.	T	C,<NON_REF>	1166.77	.	AS_RAW_BaseQRankSum=|-1.7,1|NaN;AS_RAW_MQ=95810.00|119307.00|0.00;AS_RAW_MQRankSum=|-0.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=10,18|20,15|0,0;BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.148;RAW_MQ=215117.00;ReadPosRankSum=-0.076	GT:AD:DP:GQ:PL:SB	0/1:28,35,0:63:99:1195,0,932,1279,1037,2316:10,18,20,15
+20	10026357	.	T	C,<NON_REF>	1166.77	.	AS_RAW_BaseQRankSum=|-1.7,1|NaN;AS_RAW_MQ=95810.00|119307.00|0.00;AS_RAW_MQRankSum=|-0.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=10,18|20,15|0,0;BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.148;RAW_MQandDP=215117,63;ReadPosRankSum=-0.076	GT:AD:DP:GQ:PL:SB	0/1:28,35,0:63:99:1195,0,932,1279,1037,2316:10,18,20,15
 20	10026358	.	A	<NON_REF>	.	.	END=10026793	GT:DP:GQ:MIN_DP:PL	0/0:72:99:41:0,102,1530
-20	10026794	.	C	T,<NON_REF>	1084.77	.	AS_RAW_BaseQRankSum=|2.8,1|NaN;AS_RAW_MQ=68400.00|116041.00|0.00;AS_RAW_MQRankSum=|-0.8,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=7,12|15,18|0,0;BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQ=184441.00;ReadPosRankSum=-0.533	GT:AD:DP:GQ:PL:SB	0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18
+20	10026794	.	C	T,<NON_REF>	1084.77	.	AS_RAW_BaseQRankSum=|2.8,1|NaN;AS_RAW_MQ=68400.00|116041.00|0.00;AS_RAW_MQRankSum=|-0.8,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=7,12|15,18|0,0;BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQandDP=184441,52;ReadPosRankSum=-0.533	GT:AD:DP:GQ:PL:SB	0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18
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-20	10027234	.	A	ATTAG,<NON_REF>	1320.73	.	AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=119641.00|106210.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=18,16|15,20|0,0;BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQ=236651.00;ReadPosRankSum=-0.979	GT:AD:DP:GQ:PL:SB	0/1:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20
+20	10027234	.	A	ATTAG,<NON_REF>	1320.73	.	AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=119641.00|106210.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=18,16|15,20|0,0;BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=236651,72;ReadPosRankSum=-0.979	GT:AD:DP:GQ:PL:SB	0/1:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20
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-20	10027868	.	A	G,<NON_REF>	1739.77	.	AS_RAW_BaseQRankSum=|-5.8,1|NaN;AS_RAW_MQ=155641.00|159241.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=19,25|26,19|0,0;BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQ=314882.00;ReadPosRankSum=1.872	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:19,25,26,19
+20	10027868	.	A	G,<NON_REF>	1739.77	.	AS_RAW_BaseQRankSum=|-5.8,1|NaN;AS_RAW_MQ=155641.00|159241.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=19,25|26,19|0,0;BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQandDP=314882,89;ReadPosRankSum=1.872	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:19,25,26,19
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-20	10027872	.	A	G,<NON_REF>	1724.77	.	AS_RAW_BaseQRankSum=|-5.5,1|NaN;AS_RAW_MQ=141241.00|159241.00|0.00;AS_RAW_MQRankSum=|0.1,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=16,24|26,19|0,0;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQ=300482.00;ReadPosRankSum=1.053	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:16,24,26,19
+20	10027872	.	A	G,<NON_REF>	1724.77	.	AS_RAW_BaseQRankSum=|-5.5,1|NaN;AS_RAW_MQ=141241.00|159241.00|0.00;AS_RAW_MQRankSum=|0.1,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=16,24|26,19|0,0;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQandDP=300482,85;ReadPosRankSum=1.053	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:16,24,26,19
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-20	10028867	.	A	ATG,<NON_REF>	1106.73	.	AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=115200.00|150800.00|0.00;AS_RAW_MQRankSum=|2.7,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=11,21|18,21|0,0;BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQ=338841.00;ReadPosRankSum=0.364	GT:AD:DP:GQ:PL:SB	0/1:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21
+20	10028867	.	A	ATG,<NON_REF>	1106.73	.	AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=115200.00|150800.00|0.00;AS_RAW_MQRankSum=|2.7,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=11,21|18,21|0,0;BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQandDP=338841,92;ReadPosRankSum=0.364	GT:AD:DP:GQ:PL:SB	0/1:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21
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-20	10030188	.	T	A,<NON_REF>	1372.77	.	AS_RAW_BaseQRankSum=|0.7,1|NaN;AS_RAW_MQ=151200.00|137641.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=24,18|15,24|0,0;BaseQRankSum=0.711;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.013;RAW_MQ=288841.00;ReadPosRankSum=-0.553	GT:AD:DP:GQ:PL:SB	0/1:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24
+20	10030188	.	T	A,<NON_REF>	1372.77	.	AS_RAW_BaseQRankSum=|0.7,1|NaN;AS_RAW_MQ=151200.00|137641.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=24,18|15,24|0,0;BaseQRankSum=0.711;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.013;RAW_MQandDP=288841,81;ReadPosRankSum=-0.553	GT:AD:DP:GQ:PL:SB	0/1:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24
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-20	10031254	.	A	AT,<NON_REF>	1463.73	.	AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=136800.00|168269.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=27,11|25,22|0,0;BaseQRankSum=-0.091;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQ=309510.00;ReadPosRankSum=0.495	GT:AD:DP:GQ:PL:SB	0/1:38,47,0:85:99:1501,0,1159,1616,1300,2916:27,11,25,22
+20	10031254	.	A	AT,<NON_REF>	1463.73	.	AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=136800.00|168269.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=27,11|25,22|0,0;BaseQRankSum=-0.091;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQandDP=309510,87;ReadPosRankSum=0.495	GT:AD:DP:GQ:PL:SB	0/1:38,47,0:85:99:1501,0,1159,1616,1300,2916:27,11,25,22
 20	10031255	.	T	<NON_REF>	.	.	END=10031341	GT:DP:GQ:MIN_DP:PL	0/0:95:99:86:0,120,1800
-20	10031342	.	G	A,<NON_REF>	1834.77	.	AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=147600.00|184441.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=22,19|31,21|0,0;BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQ=332041.00;ReadPosRankSum=-0.012	GT:AD:DP:GQ:PL:SB	0/1:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21
+20	10031342	.	G	A,<NON_REF>	1834.77	.	AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=147600.00|184441.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=22,19|31,21|0,0;BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQandDP=332041,93;ReadPosRankSum=-0.012	GT:AD:DP:GQ:PL:SB	0/1:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21
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-20	10031798	.	G	A,<NON_REF>	4296.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|369410.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|57,47|0,0;DP=104;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=369410.00	GT:AD:DP:GQ:PL:SB	1/1:0,104,0:104:99:4325,313,0,4325,313,4325:0,0,57,47
+20	10031798	.	G	A,<NON_REF>	4296.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|369410.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|57,47|0,0;DP=104;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=369410,104	GT:AD:DP:GQ:PL:SB	1/1:0,104,0:104:99:4325,313,0,4325,313,4325:0,0,57,47
 20	10031799	.	T	<NON_REF>	.	.	END=10031826	GT:DP:GQ:MIN_DP:PL	0/0:105:99:101:0,120,1800
-20	10031827	.	C	T,<NON_REF>	2004.77	.	AS_RAW_BaseQRankSum=|3.5,1|NaN;AS_RAW_MQ=187200.00|199369.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=32,20|29,27|0,0;BaseQRankSum=3.552;DP=108;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.945;RAW_MQ=386569.00;ReadPosRankSum=-1.396	GT:AD:DP:GQ:PL:SB	0/1:52,56,0:108:99:2033,0,1798,2189,1966,4155:32,20,29,27
+20	10031827	.	C	T,<NON_REF>	2004.77	.	AS_RAW_BaseQRankSum=|3.5,1|NaN;AS_RAW_MQ=187200.00|199369.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=32,20|29,27|0,0;BaseQRankSum=3.552;DP=108;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.945;RAW_MQandDP=386569,108;ReadPosRankSum=-1.396	GT:AD:DP:GQ:PL:SB	0/1:52,56,0:108:99:2033,0,1798,2189,1966,4155:32,20,29,27
 20	10031828	.	T	<NON_REF>	.	.	END=10032093	GT:DP:GQ:MIN_DP:PL	0/0:102:99:83:0,120,1800
-20	10032094	.	G	A,<NON_REF>	1220.77	.	AS_RAW_BaseQRankSum=|5.4,1|NaN;AS_RAW_MQ=169200.00|129600.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=14,33|16,20|0,0;BaseQRankSum=5.488;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=298800.00;ReadPosRankSum=-0.579	GT:AD:DP:GQ:PL:SB	0/1:47,36,0:83:99:1249,0,1497,1390,1605,2995:14,33,16,20
+20	10032094	.	G	A,<NON_REF>	1220.77	.	AS_RAW_BaseQRankSum=|5.4,1|NaN;AS_RAW_MQ=169200.00|129600.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=14,33|16,20|0,0;BaseQRankSum=5.488;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=298800,83;ReadPosRankSum=-0.579	GT:AD:DP:GQ:PL:SB	0/1:47,36,0:83:99:1249,0,1497,1390,1605,2995:14,33,16,20
 20	10032095	.	T	<NON_REF>	.	.	END=10032412	GT:DP:GQ:MIN_DP:PL	0/0:84:99:64:0,120,1800
-20	10032413	.	T	G,<NON_REF>	869.77	.	AS_RAW_BaseQRankSum=|-6.2,1|NaN;AS_RAW_MQ=123769.00|109369.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=15,20|20,11|0,0;BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.065;RAW_MQ=233138.00;ReadPosRankSum=-1.003	GT:AD:DP:GQ:PL:SB	0/1:35,31,0:66:99:898,0,1277,1003,1371,2374:15,20,20,11
+20	10032413	.	T	G,<NON_REF>	869.77	.	AS_RAW_BaseQRankSum=|-6.2,1|NaN;AS_RAW_MQ=123769.00|109369.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=15,20|20,11|0,0;BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.065;RAW_MQandDP=233138,66;ReadPosRankSum=-1.003	GT:AD:DP:GQ:PL:SB	0/1:35,31,0:66:99:898,0,1277,1003,1371,2374:15,20,20,11
 20	10032414	.	T	<NON_REF>	.	.	END=10032881	GT:DP:GQ:MIN_DP:PL	0/0:70:99:55:0,120,1800
-20	10032882	.	A	T,<NON_REF>	1202.77	.	AS_RAW_BaseQRankSum=|-3.7,1|NaN;AS_RAW_MQ=140400.00|126841.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=28,11|22,14|0,0;BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQ=267241.00;ReadPosRankSum=0.626	GT:AD:DP:GQ:PL:SB	0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14
+20	10032882	.	A	T,<NON_REF>	1202.77	.	AS_RAW_BaseQRankSum=|-3.7,1|NaN;AS_RAW_MQ=140400.00|126841.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=28,11|22,14|0,0;BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQandDP=267241,75;ReadPosRankSum=0.626	GT:AD:DP:GQ:PL:SB	0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14
 20	10032883	.	A	<NON_REF>	.	.	END=10032971	GT:DP:GQ:MIN_DP:PL	0/0:67:99:61:0,120,1800
-20	10032972	.	C	CAT,<NON_REF>	1122.73	.	AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=118800.00|105241.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=17,16|11,19|0,0;BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQ=231241.00;ReadPosRankSum=-1.232	GT:AD:DP:GQ:PL:SB	0/1:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19
+20	10032972	.	C	CAT,<NON_REF>	1122.73	.	AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=118800.00|105241.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=17,16|11,19|0,0;BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=231241,65;ReadPosRankSum=-1.232	GT:AD:DP:GQ:PL:SB	0/1:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19
 20	10032973	.	T	<NON_REF>	.	.	END=10033636	GT:DP:GQ:MIN_DP:PL	0/0:78:99:50:0,120,1800
 20	10033637	.	C	<NON_REF>	.	.	END=10033637	GT:DP:GQ:MIN_DP:PL	0/0:58:97:58:0,97,2210
 20	10033638	.	C	<NON_REF>	.	.	END=10034305	GT:DP:GQ:MIN_DP:PL	0/0:85:99:53:0,120,1800
-20	10034306	.	T	C,<NON_REF>	782.77	.	AS_RAW_BaseQRankSum=|-3.7,1|NaN;AS_RAW_MQ=160610.00|104400.00|0.00;AS_RAW_MQRankSum=|1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=24,22|14,15|0,0;BaseQRankSum=-3.661;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.150;RAW_MQ=268610.00;ReadPosRankSum=0.539	GT:AD:DP:GQ:PL:SB	0/1:46,29,0:75:99:811,0,1593,950,1680,2630:24,22,14,15
+20	10034306	.	T	C,<NON_REF>	782.77	.	AS_RAW_BaseQRankSum=|-3.7,1|NaN;AS_RAW_MQ=160610.00|104400.00|0.00;AS_RAW_MQRankSum=|1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=24,22|14,15|0,0;BaseQRankSum=-3.661;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.150;RAW_MQandDP=268610,76;ReadPosRankSum=0.539	GT:AD:DP:GQ:PL:SB	0/1:46,29,0:75:99:811,0,1593,950,1680,2630:24,22,14,15
 20	10034307	.	T	<NON_REF>	.	.	END=10036106	GT:DP:GQ:MIN_DP:PL	0/0:79:99:55:0,120,1800
 20	10036107	.	T	<NON_REF>	.	.	END=10036107	GT:DP:GQ:MIN_DP:PL	0/0:67:1:67:0,1,1807
 20	10036108	.	C	<NON_REF>	.	.	END=10036140	GT:DP:GQ:MIN_DP:PL	0/0:53:99:41:0,102,1504
@@ -773,7 +773,7 @@
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 20	10036161	.	T	<NON_REF>	.	.	END=10036161	GT:DP:GQ:MIN_DP:PL	0/0:42:82:42:0,82,1514
 20	10036162	.	G	<NON_REF>	.	.	END=10036929	GT:DP:GQ:MIN_DP:PL	0/0:76:99:43:0,113,1513
-20	10036930	.	CGATAGCCCTAGCCCTAGATA	C,<NON_REF>	1036.73	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=140400.00|58242.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=11,28|15,14|0,0;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQ=274847.00;ReadPosRankSum=0.460	GT:AD:DP:GQ:PL:SB	0/1:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14
+20	10036930	.	CGATAGCCCTAGCCCTAGATA	C,<NON_REF>	1036.73	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=140400.00|58242.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=11,28|15,14|0,0;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQandDP=274847,93;ReadPosRankSum=0.460	GT:AD:DP:GQ:PL:SB	0/1:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14
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 20	10036957	.	C	<NON_REF>	.	.	END=10036957	GT:DP:GQ:MIN_DP:PL	0/0:70:37:70:0,37,2472
 20	10036958	.	C	<NON_REF>	.	.	END=10036958	GT:DP:GQ:MIN_DP:PL	0/0:70:40:70:0,40,2490
@@ -788,11 +788,11 @@
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 20	10036969	.	T	<NON_REF>	.	.	END=10037036	GT:DP:GQ:MIN_DP:PL	0/0:87:99:72:0,107,1800
-20	10037037	.	C	T,<NON_REF>	1436.77	.	AS_RAW_BaseQRankSum=|3.5,1|NaN;AS_RAW_MQ=143521.00|149741.00|0.00;AS_RAW_MQRankSum=|-1.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.7,1|NaN;AS_SB_TABLE=28,11|28,14|0,0;BaseQRankSum=3.504;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.193;RAW_MQ=293262.00;ReadPosRankSum=-1.609	GT:AD:DP:GQ:PL:SB	0/1:39,42,0:81:99:1465,0,1124,1580,1251,2831:28,11,28,14
+20	10037037	.	C	T,<NON_REF>	1436.77	.	AS_RAW_BaseQRankSum=|3.5,1|NaN;AS_RAW_MQ=143521.00|149741.00|0.00;AS_RAW_MQRankSum=|-1.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.7,1|NaN;AS_SB_TABLE=28,11|28,14|0,0;BaseQRankSum=3.504;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.193;RAW_MQandDP=293262,81;ReadPosRankSum=-1.609	GT:AD:DP:GQ:PL:SB	0/1:39,42,0:81:99:1465,0,1124,1580,1251,2831:28,11,28,14
 20	10037038	.	G	<NON_REF>	.	.	END=10037109	GT:DP:GQ:MIN_DP:PL	0/0:88:99:75:0,120,1800
-20	10037110	.	T	TGATA,<NON_REF>	2780.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|193419.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,26|0,0;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=240219.00	GT:AD:DP:GQ:PL:SB	1/1:0,61,0:61:99:2818,189,0,2819,190,2820:0,0,35,26
+20	10037110	.	T	TGATA,<NON_REF>	2780.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|193419.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|35,26|0,0;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=240219,74	GT:AD:DP:GQ:PL:SB	1/1:0,61,0:61:99:2818,189,0,2819,190,2820:0,0,35,26
 20	10037111	.	G	<NON_REF>	.	.	END=10037143	GT:DP:GQ:MIN_DP:PL	0/0:77:99:68:0,120,1800
-20	10037144	.	T	TGATAGATA,<NON_REF>	1823.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|57470.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|15,21|0,0;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=187352.00	GT:AD:DP:GQ:PL:SB	1/1:0,36,0:36:99:1861,127,0,1864,129,1866:0,0,15,21
+20	10037144	.	T	TGATAGATA,<NON_REF>	1823.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|57470.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|15,21|0,0;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=187352,70	GT:AD:DP:GQ:PL:SB	1/1:0,36,0:36:99:1861,127,0,1864,129,1866:0,0,15,21
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@@ -803,40 +803,40 @@
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-20	10037709	.	A	T,<NON_REF>	1003.77	.	AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=137641.00|115200.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=24,15|19,13|0,0;BaseQRankSum=-2.367;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.934;RAW_MQ=252841.00;ReadPosRankSum=0.040	GT:AD:DP:GQ:PL:SB	0/1:39,32,0:71:99:1032,0,1354,1150,1450,2600:24,15,19,13
+20	10037709	.	A	T,<NON_REF>	1003.77	.	AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=137641.00|115200.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=24,15|19,13|0,0;BaseQRankSum=-2.367;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.934;RAW_MQandDP=252841,71;ReadPosRankSum=0.040	GT:AD:DP:GQ:PL:SB	0/1:39,32,0:71:99:1032,0,1354,1150,1450,2600:24,15,19,13
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 20	10038583	.	C	<NON_REF>	.	.	END=10038583	GT:DP:GQ:MIN_DP:PL	0/0:55:91:55:0,91,1806
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-20	10039371	.	T	G,<NON_REF>	1324.77	.	AS_RAW_BaseQRankSum=|-3.3,1|NaN;AS_RAW_MQ=122400.00|144000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=15,19|24,16|0,0;BaseQRankSum=-3.260;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=266400.00;ReadPosRankSum=0.391	GT:AD:DP:GQ:PL:SB	0/1:34,40,0:74:99:1353,0,1194,1455,1315,2770:15,19,24,16
+20	10039371	.	T	G,<NON_REF>	1324.77	.	AS_RAW_BaseQRankSum=|-3.3,1|NaN;AS_RAW_MQ=122400.00|144000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=15,19|24,16|0,0;BaseQRankSum=-3.260;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=266400,74;ReadPosRankSum=0.391	GT:AD:DP:GQ:PL:SB	0/1:34,40,0:74:99:1353,0,1194,1455,1315,2770:15,19,24,16
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-20	10040772	.	C	CT,<NON_REF>	1995.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|178648.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|37,33|0,0;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=211048.00	GT:AD:DP:GQ:PL:SB	1/1:0,70,0:70:99:2033,210,0,2034,210,2034:0,0,37,33
+20	10040772	.	C	CT,<NON_REF>	1995.73	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|178648.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|37,33|0,0;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=211048,79	GT:AD:DP:GQ:PL:SB	1/1:0,70,0:70:99:2033,210,0,2034,210,2034:0,0,37,33
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@@ -858,7 +858,7 @@
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@@ -866,15 +866,15 @@
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-20	10050828	.	T	C,<NON_REF>	1227.77	.	AS_RAW_BaseQRankSum=|-2.8,1|NaN;AS_RAW_MQ=173641.00|133200.00|0.00;AS_RAW_MQRankSum=|0.8,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=28,21|18,19|0,0;BaseQRankSum=-2.704;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.892;RAW_MQ=306841.00;ReadPosRankSum=-0.140	GT:AD:DP:GQ:PL:SB	0/1:49,37,0:86:99:1256,0,1768,1403,1879,3282:28,21,18,19
+20	10050828	.	T	C,<NON_REF>	1227.77	.	AS_RAW_BaseQRankSum=|-2.8,1|NaN;AS_RAW_MQ=173641.00|133200.00|0.00;AS_RAW_MQRankSum=|0.8,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=28,21|18,19|0,0;BaseQRankSum=-2.704;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.892;RAW_MQandDP=306841,86;ReadPosRankSum=-0.140	GT:AD:DP:GQ:PL:SB	0/1:49,37,0:86:99:1256,0,1768,1403,1879,3282:28,21,18,19
 20	10050829	.	T	<NON_REF>	.	.	END=10051447	GT:DP:GQ:MIN_DP:PL	0/0:68:99:40:0,99,1485
-20	10051448	.	T	C,<NON_REF>	1134.77	.	AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=126000.00|121010.00|0.00;AS_RAW_MQRankSum=|-1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=27,8|23,12|0,0;BaseQRankSum=-0.501;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.404;RAW_MQ=247010.00;ReadPosRankSum=-0.705	GT:AD:DP:GQ:PL:SB	0/1:35,35,0:70:99:1163,0,1150,1268,1255,2522:27,8,23,12
+20	10051448	.	T	C,<NON_REF>	1134.77	.	AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=126000.00|121010.00|0.00;AS_RAW_MQRankSum=|-1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=27,8|23,12|0,0;BaseQRankSum=-0.501;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.404;RAW_MQandDP=247010,70;ReadPosRankSum=-0.705	GT:AD:DP:GQ:PL:SB	0/1:35,35,0:70:99:1163,0,1150,1268,1255,2522:27,8,23,12
 20	10051449	.	T	<NON_REF>	.	.	END=10052687	GT:DP:GQ:MIN_DP:PL	0/0:82:99:55:0,114,1800
-20	10052688	.	C	A,<NON_REF>	1062.77	.	AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=159769.00|115200.00|0.00;AS_RAW_MQRankSum=|0.8,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=27,18|16,16|0,0;BaseQRankSum=0.180;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.870;RAW_MQ=274969.00;ReadPosRankSum=1.443	GT:AD:DP:GQ:PL:SB	0/1:45,32,0:77:99:1091,0,1645,1226,1741,2967:27,18,16,16
+20	10052688	.	C	A,<NON_REF>	1062.77	.	AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=159769.00|115200.00|0.00;AS_RAW_MQRankSum=|0.8,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=27,18|16,16|0,0;BaseQRankSum=0.180;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.870;RAW_MQandDP=274969,77;ReadPosRankSum=1.443	GT:AD:DP:GQ:PL:SB	0/1:45,32,0:77:99:1091,0,1645,1226,1741,2967:27,18,16,16
 20	10052689	.	A	<NON_REF>	.	.	END=10058021	GT:DP:GQ:MIN_DP:PL	0/0:74:99:36:0,99,1485
-20	10058022	.	T	C,<NON_REF>	975.77	.	AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=125138.00|112441.00|0.00;AS_RAW_MQRankSum=|0.4,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=16,20|13,19|0,0;BaseQRankSum=-2.346;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.466;RAW_MQ=237579.00;ReadPosRankSum=0.018	GT:AD:DP:GQ:PL:SB	0/1:36,32,0:68:99:1004,0,1261,1112,1357,2469:16,20,13,19
+20	10058022	.	T	C,<NON_REF>	975.77	.	AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=125138.00|112441.00|0.00;AS_RAW_MQRankSum=|0.4,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=16,20|13,19|0,0;BaseQRankSum=-2.346;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.466;RAW_MQandDP=237579,68;ReadPosRankSum=0.018	GT:AD:DP:GQ:PL:SB	0/1:36,32,0:68:99:1004,0,1261,1112,1357,2469:16,20,13,19
 20	10058023	.	A	<NON_REF>	.	.	END=10062934	GT:DP:GQ:MIN_DP:PL	0/0:76:99:46:0,105,1575
-20	10062935	.	CAAA	C,CA,CAA,CAAAA,<NON_REF>	92.84	.	AS_RAW_BaseQRankSum=|0.3,1|0.0,1|1.4,1|1.3,1|NaN;AS_RAW_MQ=18000.00|4441.00|7200.00|12169.00|24907.00|0.00;AS_RAW_MQRankSum=|-1.1,1|0.0,1|-0.8,1|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|-0.4,1|-0.3,1|-1.2,1|NaN;AS_SB_TABLE=2,3|1,1|1,1|3,1|4,6|0,0;BaseQRankSum=1.336;DP=79;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=-1.405;RAW_MQ=232368.00;ReadPosRankSum=-0.986	GT:AD:DP:GQ:PL:SB	0/4:5,2,2,4,10,0:23:16:130,219,1823,163,1171,1044,115,628,576,505,0,158,82,16,101,243,986,887,608,171,888:2,3,9,9
+20	10062935	.	CAAA	C,CA,CAA,CAAAA,<NON_REF>	92.84	.	AS_RAW_BaseQRankSum=|0.3,1|0.0,1|1.4,1|1.3,1|NaN;AS_RAW_MQ=18000.00|4441.00|7200.00|12169.00|24907.00|0.00;AS_RAW_MQRankSum=|-1.1,1|0.0,1|-0.8,1|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|-0.4,1|-0.3,1|-1.2,1|NaN;AS_SB_TABLE=2,3|1,1|1,1|3,1|4,6|0,0;BaseQRankSum=1.336;DP=79;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=-1.405;RAW_MQandDP=232368,79;ReadPosRankSum=-0.986	GT:AD:DP:GQ:PL:SB	0/4:5,2,2,4,10,0:23:16:130,219,1823,163,1171,1044,115,628,576,505,0,158,82,16,101,243,986,887,608,171,888:2,3,9,9
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@@ -888,15 +888,15 @@
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-20	10067049	.	TAAAAAAAAA	T,TA,TAA,<NON_REF>	613.73	.	AS_RAW_BaseQRankSum=|0.0,1|1.0,1|-0.5,1|NaN;AS_RAW_MQ=4441.00|8882.00|14164.00|13087.00|0.00;AS_RAW_MQRankSum=|0.0,1|-0.2,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|-0.7,1|-1.7,1|NaN;AS_SB_TABLE=1,1|3,1|5,2|4,5|0,0;BaseQRankSum=0.177;DP=69;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.342;RAW_MQ=204256.00;ReadPosRankSum=-1.322	GT:AD:DP:GQ:PL:SB	2/3:2,4,7,9,0:22:99:651,365,925,164,381,340,135,101,0,106,443,591,394,170,627:1,1,12,8
+20	10067049	.	TAAAAAAAAA	T,TA,TAA,<NON_REF>	613.73	.	AS_RAW_BaseQRankSum=|0.0,1|1.0,1|-0.5,1|NaN;AS_RAW_MQ=4441.00|8882.00|14164.00|13087.00|0.00;AS_RAW_MQRankSum=|0.0,1|-0.2,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|-0.7,1|-1.7,1|NaN;AS_SB_TABLE=1,1|3,1|5,2|4,5|0,0;BaseQRankSum=0.177;DP=69;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.342;RAW_MQandDP=204256,69;ReadPosRankSum=-1.322	GT:AD:DP:GQ:PL:SB	2/3:2,4,7,9,0:22:99:651,365,925,164,381,340,135,101,0,106,443,591,394,170,627:1,1,12,8
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-20	10067090	.	C	A,<NON_REF>	2004.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|165948.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,28|0,0;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=165948.00	GT:AD:DP:GQ:PL:SB	1/1:0,55,0:55:99:2033,164,0,2033,164,2033:0,0,27,28
+20	10067090	.	C	A,<NON_REF>	2004.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|165948.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,28|0,0;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=165948,55	GT:AD:DP:GQ:PL:SB	1/1:0,55,0:55:99:2033,164,0,2033,164,2033:0,0,27,28
 20	10067091	.	T	<NON_REF>	.	.	END=10067263	GT:DP:GQ:MIN_DP:PL	0/0:76:99:50:0,120,1800
-20	10067264	.	G	A,<NON_REF>	2922.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|257282.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,35|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=257282.00	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2951,219,0,2951,219,2951:0,0,38,35
+20	10067264	.	G	A,<NON_REF>	2922.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|257282.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,35|0,0;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=257282,73	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2951,219,0,2951,219,2951:0,0,38,35
 20	10067265	.	C	<NON_REF>	.	.	END=10067721	GT:DP:GQ:MIN_DP:PL	0/0:73:99:52:0,117,1800
-20	10067722	.	A	C,<NON_REF>	2146.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|194400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|25,29|0,0;DP=54;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=194400.00	GT:AD:DP:GQ:PL:SB	1/1:0,54,0:54:99:2175,163,0,2175,163,2175:0,0,25,29
+20	10067722	.	A	C,<NON_REF>	2146.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|194400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|25,29|0,0;DP=54;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=194400,54	GT:AD:DP:GQ:PL:SB	1/1:0,54,0:54:99:2175,163,0,2175,163,2175:0,0,25,29
 20	10067723	.	C	<NON_REF>	.	.	END=10068009	GT:DP:GQ:MIN_DP:PL	0/0:57:99:39:0,99,1485
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@@ -914,8 +914,8 @@
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-20	10068158	.	GTGTATATATATA	G,<NON_REF>	66.73	.	AS_RAW_BaseQRankSum=|-0.7,1|NaN;AS_RAW_MQ=5282.00|8882.00|0.00;AS_RAW_MQRankSum=|0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=0,3|2,2|0,0;BaseQRankSum=-0.652;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.328;RAW_MQ=93364.00;ReadPosRankSum=0.524	GT:AD:DP:GQ:PL:SB	0/1:3,4,0:7:57:104,0,57,114,69,183:0,3,2,2
-20	10068160	.	GTATATATATATGTA	G,*,<NON_REF>	697.73	.	AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|1682.00|8882.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|0,2|2,2|0,0;DP=28;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQ=87005.00	GT:AD:DP:GQ:PL:SB	1/2:0,2,4,0:6:53:735,162,131,102,0,53,507,174,108,472:0,0,2,4
+20	10068158	.	GTGTATATATATA	G,<NON_REF>	66.73	.	AS_RAW_BaseQRankSum=|-0.7,1|NaN;AS_RAW_MQ=5282.00|8882.00|0.00;AS_RAW_MQRankSum=|0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=0,3|2,2|0,0;BaseQRankSum=-0.652;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.328;RAW_MQandDP=93364,29;ReadPosRankSum=0.524	GT:AD:DP:GQ:PL:SB	0/1:3,4,0:7:57:104,0,57,114,69,183:0,3,2,2
+20	10068160	.	GTATATATATATGTA	G,*,<NON_REF>	697.73	.	AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|1682.00|8882.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|0,2|2,2|0,0;DP=28;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=87005,28	GT:AD:DP:GQ:PL:SB	1/2:0,2,4,0:6:53:735,162,131,102,0,53,507,174,108,472:0,0,2,4
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@@ -960,67 +960,67 @@
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-20	10068981	.	G	A,<NON_REF>	2503.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|219600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,34|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=219600.00	GT:AD:DP:GQ:PL:SB	1/1:0,61,0:61:99:2532,184,0,2532,184,2532:0,0,27,34
+20	10068981	.	G	A,<NON_REF>	2503.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|219600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|27,34|0,0;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=219600,61	GT:AD:DP:GQ:PL:SB	1/1:0,61,0:61:99:2532,184,0,2532,184,2532:0,0,27,34
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-20	10070602	.	T	C,<NON_REF>	2691.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|248164.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|37,35|0,0;DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=248164.00	GT:AD:DP:GQ:PL:SB	1/1:0,72,0:72:99:2720,216,0,2720,216,2720:0,0,37,35
+20	10070602	.	T	C,<NON_REF>	2691.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|248164.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|37,35|0,0;DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=248164,72	GT:AD:DP:GQ:PL:SB	1/1:0,72,0:72:99:2720,216,0,2720,216,2720:0,0,37,35
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+20	10076989	.	CAA	C,CA,CAAA,<NON_REF>	214.73	.	AS_RAW_BaseQRankSum=|-0.4,1|-1.0,1|0.1,1|NaN;AS_RAW_MQ=25200.00|10800.00|46800.00|22441.00|0.00;AS_RAW_MQRankSum=|0.0,1|0.0,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|-0.8,1|-0.4,1|NaN;AS_SB_TABLE=4,3|1,2|6,7|5,2|0,0;BaseQRankSum=-0.625;DP=75;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.473;RAW_MQandDP=253446,75;ReadPosRankSum=-0.918	GT:AD:DP:GQ:PL:SB	2/3:7,3,13,7,0:30:41:252,271,1146,41,448,376,147,276,0,361,322,712,423,318,705:4,3,12,11
 20	10076992	.	A	<NON_REF>	.	.	END=10077007	GT:DP:GQ:MIN_DP:PL	0/0:69:99:59:0,120,1800
-20	10077008	.	T	A,<NON_REF>	0	.	AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=160082.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=18,28|4,0|0,0;BaseQRankSum=-1.806;DP=51;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.608;RAW_MQ=175323.00;ReadPosRankSum=0.805	GT:AD:DP:GQ:PGT:PID:PL:SB	0/0:46,4,0:50:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,28,4,0
+20	10077008	.	T	A,<NON_REF>	0	.	AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=160082.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=18,28|4,0|0,0;BaseQRankSum=-1.806;DP=51;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.608;RAW_MQandDP=175323,51;ReadPosRankSum=0.805	GT:AD:DP:GQ:PGT:PID:PL:SB	0/0:46,4,0:50:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,28,4,0
 20	10077009	.	A	<NON_REF>	.	.	END=10077009	GT:DP:GQ:MIN_DP:PL	0/0:52:99:52:0,120,1800
-20	10077010	.	G	A,<NON_REF>	0	.	AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=167282.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=18,30|4,0|0,0;BaseQRankSum=-1.841;DP=53;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.658;RAW_MQ=182523.00;ReadPosRankSum=0.911	GT:AD:DP:GQ:PGT:PID:PL:SB	0/0:48,4,0:52:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,30,4,0
+20	10077010	.	G	A,<NON_REF>	0	.	AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=167282.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=18,30|4,0|0,0;BaseQRankSum=-1.841;DP=53;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.658;RAW_MQandDP=182523,53;ReadPosRankSum=0.911	GT:AD:DP:GQ:PGT:PID:PL:SB	0/0:48,4,0:52:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:18,30,4,0
 20	10077011	.	A	<NON_REF>	.	.	END=10077751	GT:DP:GQ:MIN_DP:PL	0/0:69:99:44:0,102,1654
-20	10077752	.	T	C,<NON_REF>	1345.77	.	AS_RAW_BaseQRankSum=|-6.6,1|NaN;AS_RAW_MQ=122400.00|162000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.4,1|NaN;AS_SB_TABLE=16,18|16,29|0,0;BaseQRankSum=-6.503;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=284400.00;ReadPosRankSum=-0.352	GT:AD:DP:GQ:PL:SB	0/1:34,45,0:79:99:1374,0,1187,1477,1322,2799:16,18,16,29
+20	10077752	.	T	C,<NON_REF>	1345.77	.	AS_RAW_BaseQRankSum=|-6.6,1|NaN;AS_RAW_MQ=122400.00|162000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.4,1|NaN;AS_SB_TABLE=16,18|16,29|0,0;BaseQRankSum=-6.503;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=284400,79;ReadPosRankSum=-0.352	GT:AD:DP:GQ:PL:SB	0/1:34,45,0:79:99:1374,0,1187,1477,1322,2799:16,18,16,29
 20	10077753	.	G	<NON_REF>	.	.	END=10079475	GT:DP:GQ:MIN_DP:PL	0/0:70:99:46:0,108,1620
-20	10079476	.	T	G,<NON_REF>	11.12	.	AS_RAW_BaseQRankSum=|-4.6,1|NaN;AS_RAW_MQ=116569.00|36841.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=6,27|11,0|0,0;BaseQRankSum=-4.570;DP=44;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.826;RAW_MQ=153410.00;ReadPosRankSum=1.533	GT:AD:DP:GQ:PL:SB	0/1:33,11,0:44:39:39,0,1137,137,1166,1304:6,27,11,0
+20	10079476	.	T	G,<NON_REF>	11.12	.	AS_RAW_BaseQRankSum=|-4.6,1|NaN;AS_RAW_MQ=116569.00|36841.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=6,27|11,0|0,0;BaseQRankSum=-4.570;DP=44;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.826;RAW_MQandDP=153410,44;ReadPosRankSum=1.533	GT:AD:DP:GQ:PL:SB	0/1:33,11,0:44:39:39,0,1137,137,1166,1304:6,27,11,0
 20	10079477	.	A	<NON_REF>	.	.	END=10079488	GT:DP:GQ:MIN_DP:PL	0/0:49:99:43:0,99,1485
 20	10079489	.	A	<NON_REF>	.	.	END=10079489	GT:DP:GQ:MIN_DP:PL	0/0:47:84:47:0,84,1672
 20	10079490	.	A	<NON_REF>	.	.	END=10081749	GT:DP:GQ:MIN_DP:PL	0/0:73:99:40:0,105,1571
-20	10081750	.	C	A,<NON_REF>	1353.77	.	AS_RAW_BaseQRankSum=|2.6,1|NaN;AS_RAW_MQ=158400.00|140400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=23,21|19,20|0,0;BaseQRankSum=2.670;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=298800.00;ReadPosRankSum=-0.406	GT:AD:DP:GQ:PL:SB	0/1:44,39,0:83:99:1382,0,1525,1514,1643,3157:23,21,19,20
+20	10081750	.	C	A,<NON_REF>	1353.77	.	AS_RAW_BaseQRankSum=|2.6,1|NaN;AS_RAW_MQ=158400.00|140400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=23,21|19,20|0,0;BaseQRankSum=2.670;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=298800,83;ReadPosRankSum=-0.406	GT:AD:DP:GQ:PL:SB	0/1:44,39,0:83:99:1382,0,1525,1514,1643,3157:23,21,19,20
 20	10081751	.	T	<NON_REF>	.	.	END=10081799	GT:DP:GQ:MIN_DP:PL	0/0:77:99:68:0,120,1800
-20	10081800	.	C	T,<NON_REF>	1109.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=126000.00|118800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-2.7,1|NaN;AS_SB_TABLE=26,9|17,16|0,0;BaseQRankSum=0.241;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=244800.00;ReadPosRankSum=-2.622	GT:AD:DP:GQ:PL:SB	0/1:35,33,0:68:99:1138,0,1222,1244,1322,2565:26,9,17,16
+20	10081800	.	C	T,<NON_REF>	1109.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=126000.00|118800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-2.7,1|NaN;AS_SB_TABLE=26,9|17,16|0,0;BaseQRankSum=0.241;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=244800,68;ReadPosRankSum=-2.622	GT:AD:DP:GQ:PL:SB	0/1:35,33,0:68:99:1138,0,1222,1244,1322,2565:26,9,17,16
 20	10081801	.	A	<NON_REF>	.	.	END=10082884	GT:DP:GQ:MIN_DP:PL	0/0:76:99:43:0,111,1665
 20	10082885	.	A	<NON_REF>	.	.	END=10082885	GT:DP:GQ:MIN_DP:PL	0/0:43:83:43:0,83,1521
 20	10082886	.	C	<NON_REF>	.	.	END=10082891	GT:DP:GQ:MIN_DP:PL	0/0:43:99:42:0,99,1485
-20	10082892	.	C	T,<NON_REF>	1712.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|155641.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|20,24|0,0;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=155641.00	GT:AD:DP:GQ:PL:SB	1/1:0,44,0:44:99:1741,132,0,1741,132,1741:0,0,20,24
+20	10082892	.	C	T,<NON_REF>	1712.77	.	AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|155641.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|20,24|0,0;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=155641,44	GT:AD:DP:GQ:PL:SB	1/1:0,44,0:44:99:1741,132,0,1741,132,1741:0,0,20,24
 20	10082893	.	C	<NON_REF>	.	.	END=10082901	GT:DP:GQ:MIN_DP:PL	0/0:41:99:38:0,99,1485
 20	10082902	.	C	<NON_REF>	.	.	END=10082903	GT:DP:GQ:MIN_DP:PL	0/0:38:96:38:0,96,1440
 20	10082904	.	C	<NON_REF>	.	.	END=10082905	GT:DP:GQ:MIN_DP:PL	0/0:40:99:39:0,102,1530
@@ -1033,43 +1033,43 @@
 20	10082926	.	C	<NON_REF>	.	.	END=10082930	GT:DP:GQ:MIN_DP:PL	0/0:37:90:36:0,90,1350
 20	10082931	.	T	<NON_REF>	.	.	END=10082931	GT:DP:GQ:MIN_DP:PL	0/0:38:75:38:0,75,1443
 20	10082932	.	C	<NON_REF>	.	.	END=10085210	GT:DP:GQ:MIN_DP:PL	0/0:77:99:38:0,102,1530
-20	10085211	.	A	T,<NON_REF>	1210.77	.	AS_RAW_BaseQRankSum=|-1.5,1|NaN;AS_RAW_MQ=144000.00|126841.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|NaN;AS_SB_TABLE=21,19|17,19|0,0;BaseQRankSum=-1.501;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.028;RAW_MQ=270841.00;ReadPosRankSum=-1.405	GT:AD:DP:GQ:PL:SB	0/1:40,36,0:76:99:1239,0,1443,1360,1551,2911:21,19,17,19
+20	10085211	.	A	T,<NON_REF>	1210.77	.	AS_RAW_BaseQRankSum=|-1.5,1|NaN;AS_RAW_MQ=144000.00|126841.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|NaN;AS_SB_TABLE=21,19|17,19|0,0;BaseQRankSum=-1.501;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.028;RAW_MQandDP=270841,76;ReadPosRankSum=-1.405	GT:AD:DP:GQ:PL:SB	0/1:40,36,0:76:99:1239,0,1443,1360,1551,2911:21,19,17,19
 20	10085212	.	G	<NON_REF>	.	.	END=10086109	GT:DP:GQ:MIN_DP:PL	0/0:77:99:54:0,120,1800
-20	10086110	.	G	A,<NON_REF>	1274.77	.	AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=152041.00|131282.00|0.00;AS_RAW_MQRankSum=|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=24,19|19,19|0,0;BaseQRankSum=-0.343;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.680;RAW_MQ=283323.00;ReadPosRankSum=0.170	GT:AD:DP:GQ:PL:SB	0/1:43,38,0:81:99:1303,0,1506,1432,1621,3053:24,19,19,19
+20	10086110	.	G	A,<NON_REF>	1274.77	.	AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=152041.00|131282.00|0.00;AS_RAW_MQRankSum=|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=24,19|19,19|0,0;BaseQRankSum=-0.343;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.680;RAW_MQandDP=283323,81;ReadPosRankSum=0.170	GT:AD:DP:GQ:PL:SB	0/1:43,38,0:81:99:1303,0,1506,1432,1621,3053:24,19,19,19
 20	10086111	.	C	<NON_REF>	.	.	END=10086282	GT:DP:GQ:MIN_DP:PL	0/0:75:99:55:0,120,1800
-20	10086283	.	G	T,<NON_REF>	1025.77	.	AS_RAW_BaseQRankSum=|2.3,1|NaN;AS_RAW_MQ=187200.00|115200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=30,22|17,15|0,0;BaseQRankSum=2.304;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=302400.00;ReadPosRankSum=1.889	GT:AD:DP:GQ:PL:SB	0/1:52,32,0:84:99:1054,0,1771,1210,1867,3077:30,22,17,15
+20	10086283	.	G	T,<NON_REF>	1025.77	.	AS_RAW_BaseQRankSum=|2.3,1|NaN;AS_RAW_MQ=187200.00|115200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=30,22|17,15|0,0;BaseQRankSum=2.304;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=302400,84;ReadPosRankSum=1.889	GT:AD:DP:GQ:PL:SB	0/1:52,32,0:84:99:1054,0,1771,1210,1867,3077:30,22,17,15
 20	10086284	.	G	<NON_REF>	.	.	END=10086618	GT:DP:GQ:MIN_DP:PL	0/0:80:99:51:0,120,1800
-20	10086619	.	T	A,<NON_REF>	796.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=162000.00|87241.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=18,27|9,16|0,0;BaseQRankSum=0.256;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.312;RAW_MQ=249241.00;ReadPosRankSum=-0.760	GT:AD:DP:GQ:PL:SB	0/1:45,25,0:70:99:825,0,1603,961,1679,2639:18,27,9,16
+20	10086619	.	T	A,<NON_REF>	796.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=162000.00|87241.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=18,27|9,16|0,0;BaseQRankSum=0.256;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.312;RAW_MQandDP=249241,70;ReadPosRankSum=-0.760	GT:AD:DP:GQ:PL:SB	0/1:45,25,0:70:99:825,0,1603,961,1679,2639:18,27,9,16
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-20	10086853	.	G	A,<NON_REF>	1002.77	.	AS_RAW_BaseQRankSum=|3.9,1|NaN;AS_RAW_MQ=145369.00|112441.00|0.00;AS_RAW_MQRankSum=|-0.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=21,20|17,15|0,0;BaseQRankSum=3.915;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.177;RAW_MQ=257810.00;ReadPosRankSum=-0.100	GT:AD:DP:GQ:PL:SB	0/1:41,32,0:73:99:1031,0,1280,1154,1376,2530:21,20,17,15
+20	10086853	.	G	A,<NON_REF>	1002.77	.	AS_RAW_BaseQRankSum=|3.9,1|NaN;AS_RAW_MQ=145369.00|112441.00|0.00;AS_RAW_MQRankSum=|-0.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=21,20|17,15|0,0;BaseQRankSum=3.915;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.177;RAW_MQandDP=257810,73;ReadPosRankSum=-0.100	GT:AD:DP:GQ:PL:SB	0/1:41,32,0:73:99:1031,0,1280,1154,1376,2530:21,20,17,15
 20	10086854	.	T	<NON_REF>	.	.	END=10086953	GT:DP:GQ:MIN_DP:PL	0/0:67:99:60:0,120,1800
-20	10086954	.	G	A,<NON_REF>	1095.77	.	AS_RAW_BaseQRankSum=|2.6,1|NaN;AS_RAW_MQ=122400.00|122400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=16,18|21,13|0,0;BaseQRankSum=2.606;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=244800.00;ReadPosRankSum=-0.534	GT:AD:DP:GQ:PL:SB	0/1:34,34,0:68:99:1124,0,1051,1226,1153,2380:16,18,21,13
+20	10086954	.	G	A,<NON_REF>	1095.77	.	AS_RAW_BaseQRankSum=|2.6,1|NaN;AS_RAW_MQ=122400.00|122400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=16,18|21,13|0,0;BaseQRankSum=2.606;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=244800,68;ReadPosRankSum=-0.534	GT:AD:DP:GQ:PL:SB	0/1:34,34,0:68:99:1124,0,1051,1226,1153,2380:16,18,21,13
 20	10086955	.	C	<NON_REF>	.	.	END=10087229	GT:DP:GQ:MIN_DP:PL	0/0:70:99:55:0,120,1800
-20	10087230	.	A	G,<NON_REF>	1842.77	.	AS_RAW_BaseQRankSum=|-2.5,1|NaN;AS_RAW_MQ=140692.00|192169.00|0.00;AS_RAW_MQRankSum=|1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=22,20|23,31|0,0;BaseQRankSum=-2.407;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.707;RAW_MQ=332861.00;ReadPosRankSum=0.307	GT:AD:DP:GQ:PL:SB	0/1:42,54,0:96:99:1871,0,1428,1998,1590,3588:22,20,23,31
+20	10087230	.	A	G,<NON_REF>	1842.77	.	AS_RAW_BaseQRankSum=|-2.5,1|NaN;AS_RAW_MQ=140692.00|192169.00|0.00;AS_RAW_MQRankSum=|1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=22,20|23,31|0,0;BaseQRankSum=-2.407;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.707;RAW_MQandDP=332861,96;ReadPosRankSum=0.307	GT:AD:DP:GQ:PL:SB	0/1:42,54,0:96:99:1871,0,1428,1998,1590,3588:22,20,23,31
 20	10087231	.	C	<NON_REF>	.	.	END=10087393	GT:DP:GQ:MIN_DP:PL	0/0:101:99:84:0,120,1800
-20	10087394	.	T	G,<NON_REF>	1688.77	.	AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=123241.00|176400.00|0.00;AS_RAW_MQRankSum=|1.2,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=21,14|24,25|0,0;BaseQRankSum=-2.340;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.207;RAW_MQ=299641.00;ReadPosRankSum=0.885	GT:AD:DP:GQ:PL:SB	0/1:35,49,0:84:99:1717,0,1186,1823,1334,3156:21,14,24,25
+20	10087394	.	T	G,<NON_REF>	1688.77	.	AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=123241.00|176400.00|0.00;AS_RAW_MQRankSum=|1.2,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=21,14|24,25|0,0;BaseQRankSum=-2.340;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.207;RAW_MQandDP=299641,84;ReadPosRankSum=0.885	GT:AD:DP:GQ:PL:SB	0/1:35,49,0:84:99:1717,0,1186,1823,1334,3156:21,14,24,25
 20	10087395	.	T	<NON_REF>	.	.	END=10087753	GT:DP:GQ:MIN_DP:PL	0/0:83:99:61:0,120,1800
-20	10087754	.	T	G,<NON_REF>	1347.77	.	AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=133200.00|154100.00|0.00;AS_RAW_MQRankSum=|2.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=23,14|24,17|0,0;BaseQRankSum=0.355;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.193;RAW_MQ=288141.00;ReadPosRankSum=-0.551	GT:AD:DP:GQ:PL:SB	0/1:37,41,0:78:99:1376,0,1239,1488,1362,2849:23,14,24,17
+20	10087754	.	T	G,<NON_REF>	1347.77	.	AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=133200.00|154100.00|0.00;AS_RAW_MQRankSum=|2.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=23,14|24,17|0,0;BaseQRankSum=0.355;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.193;RAW_MQandDP=288141,79;ReadPosRankSum=-0.551	GT:AD:DP:GQ:PL:SB	0/1:37,41,0:78:99:1376,0,1239,1488,1362,2849:23,14,24,17
 20	10087755	.	G	<NON_REF>	.	.	END=10087803	GT:DP:GQ:MIN_DP:PL	0/0:100:99:81:0,120,1800
-20	10087804	.	C	T,<NON_REF>	1619.77	.	AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=178541.00|190769.00|0.00;AS_RAW_MQRankSum=|2.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=33,17|28,22|0,0;BaseQRankSum=1.940;DP=100;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.618;RAW_MQ=369310.00;ReadPosRankSum=0.341	GT:AD:DP:GQ:PL:SB	0/1:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22
+20	10087804	.	C	T,<NON_REF>	1619.77	.	AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=178541.00|190769.00|0.00;AS_RAW_MQRankSum=|2.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=33,17|28,22|0,0;BaseQRankSum=1.940;DP=100;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.618;RAW_MQandDP=369310,100;ReadPosRankSum=0.341	GT:AD:DP:GQ:PL:SB	0/1:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22
 20	10087805	.	G	<NON_REF>	.	.	END=10087819	GT:DP:GQ:MIN_DP:PL	0/0:101:99:96:0,120,1800
-20	10087820	.	CAG	C,CAGAG,<NON_REF>	428.73	.	AS_RAW_BaseQRankSum=|NaN|-2.0,1|NaN;AS_RAW_MQ=123769.00|0.00|63869.00|0.00;AS_RAW_MQRankSum=|NaN|0.4,1|NaN;AS_RAW_ReadPosRankSum=|NaN|-0.4,1|NaN;AS_SB_TABLE=17,18|0,0|8,10|0,0;BaseQRankSum=-1.974;DP=99;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQ=362700.00;ReadPosRankSum=-0.357	GT:AD:DP:GQ:PL:SB	0/2:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:17,18,8,10
+20	10087820	.	CAG	C,CAGAG,<NON_REF>	428.73	.	AS_RAW_BaseQRankSum=|NaN|-2.0,1|NaN;AS_RAW_MQ=123769.00|0.00|63869.00|0.00;AS_RAW_MQRankSum=|NaN|0.4,1|NaN;AS_RAW_ReadPosRankSum=|NaN|-0.4,1|NaN;AS_SB_TABLE=17,18|0,0|8,10|0,0;BaseQRankSum=-1.974;DP=99;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQandDP=362700,99;ReadPosRankSum=-0.357	GT:AD:DP:GQ:PL:SB	0/2:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:17,18,8,10
 20	10087823	.	A	<NON_REF>	.	.	END=10087841	GT:DP:GQ:MIN_DP:PL	0/0:86:99:83:0,120,1800
 20	10087842	.	A	<NON_REF>	.	.	END=10087842	GT:DP:GQ:MIN_DP:PL	0/0:82:0:82:0,0,2206
 20	10087843	.	A	<NON_REF>	.	.	END=10087843	GT:DP:GQ:MIN_DP:PL	0/0:82:73:82:0,73,2973
 20	10087844	.	G	<NON_REF>	.	.	END=10087844	GT:DP:GQ:MIN_DP:PL	0/0:80:0:80:0,0,2190
 20	10087845	.	A	<NON_REF>	.	.	END=10088062	GT:DP:GQ:MIN_DP:PL	0/0:95:99:71:0,120,1800
-20	10088063	.	C	T,<NON_REF>	1417.77	.	AS_RAW_BaseQRankSum=|3.4,1|NaN;AS_RAW_MQ=171410.00|156169.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=24,25|18,26|0,0;BaseQRankSum=3.405;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.515;RAW_MQ=327579.00;ReadPosRankSum=0.285	GT:AD:DP:GQ:PL:SB	0/1:49,44,0:93:99:1446,0,1403,1592,1535,3128:24,25,18,26
+20	10088063	.	C	T,<NON_REF>	1417.77	.	AS_RAW_BaseQRankSum=|3.4,1|NaN;AS_RAW_MQ=171410.00|156169.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=24,25|18,26|0,0;BaseQRankSum=3.405;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.515;RAW_MQandDP=327579,93;ReadPosRankSum=0.285	GT:AD:DP:GQ:PL:SB	0/1:49,44,0:93:99:1446,0,1403,1592,1535,3128:24,25,18,26
 20	10088064	.	G	<NON_REF>	.	.	END=10088698	GT:DP:GQ:MIN_DP:PL	0/0:87:99:60:0,120,1800
-20	10088699	.	C	T,<NON_REF>	776.77	.	AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=127369.00|71528.00|0.00;AS_RAW_MQRankSum=|-3.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|NaN;AS_SB_TABLE=15,21|19,7|0,0;BaseQRankSum=3.803;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.140;RAW_MQ=199738.00;ReadPosRankSum=-1.456	GT:AD:DP:GQ:PL:SB	0/1:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7
+20	10088699	.	C	T,<NON_REF>	776.77	.	AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=127369.00|71528.00|0.00;AS_RAW_MQRankSum=|-3.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|NaN;AS_SB_TABLE=15,21|19,7|0,0;BaseQRankSum=3.803;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.140;RAW_MQandDP=199738,63;ReadPosRankSum=-1.456	GT:AD:DP:GQ:PL:SB	0/1:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7
 20	10088700	.	G	<NON_REF>	.	.	END=10088729	GT:DP:GQ:MIN_DP:PL	0/0:53:99:51:0,120,1800
-20	10088730	.	G	A,<NON_REF>	972.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=104400.00|43958.00|0.00;AS_RAW_MQRankSum=|-4.9,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=11,18|16,7|0,0;BaseQRankSum=0.224;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.839;RAW_MQ=148358.00;ReadPosRankSum=0.581	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:29,23,0:52:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:11,18,16,7
+20	10088730	.	G	A,<NON_REF>	972.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=104400.00|43958.00|0.00;AS_RAW_MQRankSum=|-4.9,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=11,18|16,7|0,0;BaseQRankSum=0.224;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.839;RAW_MQandDP=148358,52;ReadPosRankSum=0.581	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:29,23,0:52:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:11,18,16,7
 20	10088731	.	G	<NON_REF>	.	.	END=10088735	GT:DP:GQ:MIN_DP:PL	0/0:55:99:55:0,120,1800
-20	10088736	.	A	C,<NON_REF>	1081.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=100800.00|48882.00|0.00;AS_RAW_MQRankSum=|-5.2,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=10,18|16,11|0,0;BaseQRankSum=0.282;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.169;RAW_MQ=149682.00;ReadPosRankSum=0.573	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:28,27,0:55:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10,18,16,11
+20	10088736	.	A	C,<NON_REF>	1081.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=100800.00|48882.00|0.00;AS_RAW_MQRankSum=|-5.2,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=10,18|16,11|0,0;BaseQRankSum=0.282;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.169;RAW_MQandDP=149682,55;ReadPosRankSum=0.573	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:28,27,0:55:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10,18,16,11
 20	10088737	.	C	<NON_REF>	.	.	END=10088746	GT:DP:GQ:MIN_DP:PL	0/0:56:99:53:0,120,1800
-20	10088747	.	A	G,<NON_REF>	1111.77	.	AS_RAW_BaseQRankSum=|-3.9,1|NaN;AS_RAW_MQ=90000.00|55398.00|0.00;AS_RAW_MQRankSum=|-5.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=10,15|18,11|0,0;BaseQRankSum=-3.877;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.907;RAW_MQ=146239.00;ReadPosRankSum=0.009	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10,15,18,11
+20	10088747	.	A	G,<NON_REF>	1111.77	.	AS_RAW_BaseQRankSum=|-3.9,1|NaN;AS_RAW_MQ=90000.00|55398.00|0.00;AS_RAW_MQRankSum=|-5.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=10,15|18,11|0,0;BaseQRankSum=-3.877;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.907;RAW_MQandDP=146239,55;ReadPosRankSum=0.009	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10,15,18,11
 20	10088748	.	G	<NON_REF>	.	.	END=10088798	GT:DP:GQ:MIN_DP:PL	0/0:49:99:46:0,114,1710
-20	10088799	.	G	A,<NON_REF>	1018.77	.	AS_RAW_BaseQRankSum=|5.5,1|NaN;AS_RAW_MQ=74903.00|75137.00|0.00;AS_RAW_MQRankSum=|-2.5,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=14,8|12,19|0,0;BaseQRankSum=5.503;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.498;RAW_MQ=150040.00;ReadPosRankSum=1.075	GT:AD:DP:GQ:PL:SB	0/1:22,31,0:53:99:1047,0,617,1114,711,1824:14,8,12,19
+20	10088799	.	G	A,<NON_REF>	1018.77	.	AS_RAW_BaseQRankSum=|5.5,1|NaN;AS_RAW_MQ=74903.00|75137.00|0.00;AS_RAW_MQRankSum=|-2.5,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=14,8|12,19|0,0;BaseQRankSum=5.503;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.498;RAW_MQandDP=150040,53;ReadPosRankSum=1.075	GT:AD:DP:GQ:PL:SB	0/1:22,31,0:53:99:1047,0,617,1114,711,1824:14,8,12,19
 20	10088800	.	T	<NON_REF>	.	.	END=10088831	GT:DP:GQ:MIN_DP:PL	0/0:54:99:50:0,113,1800
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 20	10088843	.	C	<NON_REF>	.	.	END=10088843	GT:DP:GQ:MIN_DP:PL	0/0:25:16:25:0,16,759
@@ -1088,13 +1088,13 @@
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 20	10088867	.	A	<NON_REF>	.	.	END=10088870	GT:DP:GQ:MIN_DP:PL	0/0:32:90:32:0,90,1350
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-20	10088895	.	C	T,<NON_REF>	532.77	.	AS_RAW_BaseQRankSum=|2.4,1|NaN;AS_RAW_MQ=74073.00|60377.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|1.3,1|NaN;AS_SB_TABLE=10,13|8,10|0,0;BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.577;RAW_MQ=134450.00;ReadPosRankSum=1.301	GT:AD:DP:GQ:PL:SB	0/1:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10
+20	10088895	.	C	T,<NON_REF>	532.77	.	AS_RAW_BaseQRankSum=|2.4,1|NaN;AS_RAW_MQ=74073.00|60377.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|1.3,1|NaN;AS_SB_TABLE=10,13|8,10|0,0;BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.577;RAW_MQandDP=134450,41;ReadPosRankSum=1.301	GT:AD:DP:GQ:PL:SB	0/1:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10
 20	10088896	.	G	<NON_REF>	.	.	END=10088967	GT:DP:GQ:MIN_DP:PL	0/0:49:99:42:0,110,1709
-20	10088968	.	C	CAAA,<NON_REF>	1175.73	.	AS_RAW_BaseQRankSum=|0.5,1|NaN;AS_RAW_MQ=105241.00|42471.00|0.00;AS_RAW_MQRankSum=|-4.8,1|NaN;AS_RAW_ReadPosRankSum=|2.4,1|NaN;AS_SB_TABLE=16,14|14,9|0,0;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQ=177808.00;ReadPosRankSum=2.416	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:16,14,14,9
+20	10088968	.	C	CAAA,<NON_REF>	1175.73	.	AS_RAW_BaseQRankSum=|0.5,1|NaN;AS_RAW_MQ=105241.00|42471.00|0.00;AS_RAW_MQRankSum=|-4.8,1|NaN;AS_RAW_ReadPosRankSum=|2.4,1|NaN;AS_SB_TABLE=16,14|14,9|0,0;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQandDP=177808,62;ReadPosRankSum=2.416	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:16,14,14,9
 20	10088969	.	A	<NON_REF>	.	.	END=10088979	GT:DP:GQ:MIN_DP:PL	0/0:71:99:70:0,120,1800
-20	10088980	.	T	C,<NON_REF>	1247.77	.	AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=124923.00|51430.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=19,18|15,16|0,0;BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQ=176353.00;ReadPosRankSum=1.288	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:19,18,15,16
+20	10088980	.	T	C,<NON_REF>	1247.77	.	AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=124923.00|51430.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=19,18|15,16|0,0;BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQandDP=176353,68;ReadPosRankSum=1.288	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:19,18,15,16
 20	10088981	.	A	<NON_REF>	.	.	END=10088984	GT:DP:GQ:MIN_DP:PL	0/0:71:99:69:0,120,1800
-20	10088985	.	T	C,<NON_REF>	1178.77	.	AS_RAW_BaseQRankSum=|-0.2,1|NaN;AS_RAW_MQ=138965.00|52799.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=22,20|15,17|0,0;BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQ=191764.00;ReadPosRankSum=1.228	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:22,20,15,17
+20	10088985	.	T	C,<NON_REF>	1178.77	.	AS_RAW_BaseQRankSum=|-0.2,1|NaN;AS_RAW_MQ=138965.00|52799.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=22,20|15,17|0,0;BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQandDP=191764,74;ReadPosRankSum=1.228	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:22,20,15,17
 20	10088986	.	A	<NON_REF>	.	.	END=10088989	GT:DP:GQ:MIN_DP:PL	0/0:82:99:81:0,120,1800
 20	10088990	.	A	<NON_REF>	.	.	END=10088990	GT:DP:GQ:MIN_DP:PL	0/0:84:7:84:0,7,2771
 20	10088991	.	C	<NON_REF>	.	.	END=10088991	GT:DP:GQ:MIN_DP:PL	0/0:81:95:81:0,95,2703
@@ -1108,69 +1108,69 @@
 20	10089038	.	A	<NON_REF>	.	.	END=10089042	GT:DP:GQ:MIN_DP:PL	0/0:83:99:81:0,120,1800
 20	10089043	.	T	<NON_REF>	.	.	END=10089043	GT:DP:GQ:MIN_DP:PL	0/0:76:79:76:0,79,2231
 20	10089044	.	G	<NON_REF>	.	.	END=10089440	GT:DP:GQ:MIN_DP:PL	0/0:82:99:74:0,120,1800
-20	10089441	.	A	G,<NON_REF>	1179.77	.	AS_RAW_BaseQRankSum=|-4.9,1|NaN;AS_RAW_MQ=133200.00|137641.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=19,18|14,25|0,0;BaseQRankSum=-4.885;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.948;RAW_MQ=270841.00;ReadPosRankSum=-0.156	GT:AD:DP:GQ:PL:SB	0/1:37,39,0:76:99:1208,0,1313,1319,1430,2749:19,18,14,25
+20	10089441	.	A	G,<NON_REF>	1179.77	.	AS_RAW_BaseQRankSum=|-4.9,1|NaN;AS_RAW_MQ=133200.00|137641.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=19,18|14,25|0,0;BaseQRankSum=-4.885;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.948;RAW_MQandDP=270841,76;ReadPosRankSum=-0.156	GT:AD:DP:GQ:PL:SB	0/1:37,39,0:76:99:1208,0,1313,1319,1430,2749:19,18,14,25
 20	10089442	.	G	<NON_REF>	.	.	END=10089524	GT:DP:GQ:MIN_DP:PL	0/0:81:99:74:0,120,1800
-20	10089525	.	C	T,<NON_REF>	1548.77	.	AS_RAW_BaseQRankSum=|5.8,1|NaN;AS_RAW_MQ=131810.00|154800.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=22,16|20,23|0,0;BaseQRankSum=5.859;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.531;RAW_MQ=286610.00;ReadPosRankSum=0.862	GT:AD:DP:GQ:PL:SB	0/1:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23
+20	10089525	.	C	T,<NON_REF>	1548.77	.	AS_RAW_BaseQRankSum=|5.8,1|NaN;AS_RAW_MQ=131810.00|154800.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=22,16|20,23|0,0;BaseQRankSum=5.859;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.531;RAW_MQandDP=286610,81;ReadPosRankSum=0.862	GT:AD:DP:GQ:PL:SB	0/1:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23
 20	10089526	.	G	<NON_REF>	.	.	END=10090288	GT:DP:GQ:MIN_DP:PL	0/0:72:99:55:0,111,1800
-20	10090289	.	CAA	C,CA,<NON_REF>	384.73	.	AS_RAW_BaseQRankSum=|0.6,1|0.3,1|NaN;AS_RAW_MQ=50400.00|14400.00|75900.00|0.00;AS_RAW_MQRankSum=|0.0,1|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|0.5,1|NaN;AS_SB_TABLE=7,7|3,1|8,12|0,0;BaseQRankSum=0.441;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.393;RAW_MQ=287682.00;ReadPosRankSum=0.048	GT:AD:DP:GQ:PL:SB	0/2:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:7,7,11,13
+20	10090289	.	CAA	C,CA,<NON_REF>	384.73	.	AS_RAW_BaseQRankSum=|0.6,1|0.3,1|NaN;AS_RAW_MQ=50400.00|14400.00|75900.00|0.00;AS_RAW_MQRankSum=|0.0,1|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|0.5,1|NaN;AS_SB_TABLE=7,7|3,1|8,12|0,0;BaseQRankSum=0.441;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.393;RAW_MQandDP=287682,80;ReadPosRankSum=0.048	GT:AD:DP:GQ:PL:SB	0/2:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:7,7,11,13
 20	10090292	.	A	<NON_REF>	.	.	END=10090763	GT:DP:GQ:MIN_DP:PL	0/0:75:99:61:0,120,1800
-20	10090764	.	A	G,<NON_REF>	840.77	.	AS_RAW_BaseQRankSum=|-2.7,1|NaN;AS_RAW_MQ=122400.00|104400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=12,22|14,15|0,0;BaseQRankSum=-2.659;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=226800.00;ReadPosRankSum=1.207	GT:AD:DP:GQ:PL:SB	0/1:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15
+20	10090764	.	A	G,<NON_REF>	840.77	.	AS_RAW_BaseQRankSum=|-2.7,1|NaN;AS_RAW_MQ=122400.00|104400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=12,22|14,15|0,0;BaseQRankSum=-2.659;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=226800,63;ReadPosRankSum=1.207	GT:AD:DP:GQ:PL:SB	0/1:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15
 20	10090765	.	A	<NON_REF>	.	.	END=10090969	GT:DP:GQ:MIN_DP:PL	0/0:75:99:65:0,120,1800
-20	10090970	.	T	C,<NON_REF>	1257.77	.	AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=114338.00|129600.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=20,13|20,16|0,0;BaseQRankSum=-0.484;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.509;RAW_MQ=243938.00;ReadPosRankSum=-0.072	GT:AD:DP:GQ:PL:SB	0/1:33,36,0:69:99:1286,0,1092,1384,1201,2585:20,13,20,16
+20	10090970	.	T	C,<NON_REF>	1257.77	.	AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=114338.00|129600.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=20,13|20,16|0,0;BaseQRankSum=-0.484;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.509;RAW_MQandDP=243938,69;ReadPosRankSum=-0.072	GT:AD:DP:GQ:PL:SB	0/1:33,36,0:69:99:1286,0,1092,1384,1201,2585:20,13,20,16
 20	10090971	.	C	<NON_REF>	.	.	END=10091213	GT:DP:GQ:MIN_DP:PL	0/0:61:99:49:0,120,1800
-20	10091214	.	C	T,<NON_REF>	1249.77	.	AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=118800.00|130969.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=11,22|13,24|0,0;BaseQRankSum=0.361;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.916;RAW_MQ=249769.00;ReadPosRankSum=-0.035	GT:AD:DP:GQ:PL:SB	0/1:33,37,0:70:99:1278,0,1110,1377,1222,2599:11,22,13,24
+20	10091214	.	C	T,<NON_REF>	1249.77	.	AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=118800.00|130969.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=11,22|13,24|0,0;BaseQRankSum=0.361;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.916;RAW_MQandDP=249769,70;ReadPosRankSum=-0.035	GT:AD:DP:GQ:PL:SB	0/1:33,37,0:70:99:1278,0,1110,1377,1222,2599:11,22,13,24
 20	10091215	.	C	<NON_REF>	.	.	END=10092414	GT:DP:GQ:MIN_DP:PL	0/0:69:99:46:0,120,1800
-20	10092415	.	A	G,<NON_REF>	1635.77	.	AS_RAW_BaseQRankSum=|-6.8,1|NaN;AS_RAW_MQ=187200.00|176400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=27,25|24,25|0,0;BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=363600.00;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	0/1:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25
+20	10092415	.	A	G,<NON_REF>	1635.77	.	AS_RAW_BaseQRankSum=|-6.8,1|NaN;AS_RAW_MQ=187200.00|176400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=27,25|24,25|0,0;BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=363600,101;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	0/1:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25
 20	10092416	.	G	<NON_REF>	.	.	END=10092926	GT:DP:GQ:MIN_DP:PL	0/0:80:99:60:0,120,1800
-20	10092927	.	G	T,<NON_REF>	106.77	.	AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=212400.00|41282.00|0.00;AS_RAW_MQRankSum=|-3.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=43,16|0,13|0,0;BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.009;RAW_MQ=257282.00;ReadPosRankSum=-0.220	GT:AD:DP:GQ:PL:SB	0/1:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13
+20	10092927	.	G	T,<NON_REF>	106.77	.	AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=212400.00|41282.00|0.00;AS_RAW_MQRankSum=|-3.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=43,16|0,13|0,0;BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.009;RAW_MQandDP=257282,73;ReadPosRankSum=-0.220	GT:AD:DP:GQ:PL:SB	0/1:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13
 20	10092928	.	T	<NON_REF>	.	.	END=10093567	GT:DP:GQ:MIN_DP:PL	0/0:79:99:57:0,120,1800
-20	10093568	.	GTT	G,GT,GTTT,<NON_REF>	326.73	.	AS_RAW_BaseQRankSum=|-1.7,1|1.1,1|0.2,1|NaN;AS_RAW_MQ=61200.00|11641.00|62869.00|14400.00|0.00;AS_RAW_MQRankSum=|-2.0,1|1.0,1|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.6,1|0.6,1|1.1,1|NaN;AS_SB_TABLE=7,10|2,2|7,10|1,3|0,0;BaseQRankSum=0.426;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=0.410;RAW_MQ=203561.00;ReadPosRankSum=1.257	GT:AD:DP:GQ:PL:SB	0/2:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:7,10,10,15
+20	10093568	.	GTT	G,GT,GTTT,<NON_REF>	326.73	.	AS_RAW_BaseQRankSum=|-1.7,1|1.1,1|0.2,1|NaN;AS_RAW_MQ=61200.00|11641.00|62869.00|14400.00|0.00;AS_RAW_MQRankSum=|-2.0,1|1.0,1|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.6,1|0.6,1|1.1,1|NaN;AS_SB_TABLE=7,10|2,2|7,10|1,3|0,0;BaseQRankSum=0.426;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=0.410;RAW_MQandDP=203561,59;ReadPosRankSum=1.257	GT:AD:DP:GQ:PL:SB	0/2:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:7,10,10,15
 20	10093571	.	T	<NON_REF>	.	.	END=10093922	GT:DP:GQ:MIN_DP:PL	0/0:62:99:51:0,99,1485
-20	10093923	.	T	A,<NON_REF>	1075.77	.	AS_RAW_BaseQRankSum=|-0.7,1|NaN;AS_RAW_MQ=122419.00|112285.00|0.00;AS_RAW_MQRankSum=|0.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=18,17|15,17|0,0;BaseQRankSum=-0.667;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.358;RAW_MQ=234704.00;ReadPosRankSum=-1.583	GT:AD:DP:GQ:PL:SB	0/1:35,32,0:67:99:1104,0,1257,1209,1353,2563:18,17,15,17
+20	10093923	.	T	A,<NON_REF>	1075.77	.	AS_RAW_BaseQRankSum=|-0.7,1|NaN;AS_RAW_MQ=122419.00|112285.00|0.00;AS_RAW_MQRankSum=|0.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=18,17|15,17|0,0;BaseQRankSum=-0.667;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.358;RAW_MQandDP=234704,67;ReadPosRankSum=-1.583	GT:AD:DP:GQ:PL:SB	0/1:35,32,0:67:99:1104,0,1257,1209,1353,2563:18,17,15,17
 20	10093924	.	G	<NON_REF>	.	.	END=10094250	GT:DP:GQ:MIN_DP:PL	0/0:66:99:53:0,120,1800
-20	10094251	.	T	A,<NON_REF>	1270.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=93600.00|129600.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=10,16|23,13|0,0;BaseQRankSum=0.251;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=223200.00;ReadPosRankSum=1.806	GT:AD:DP:GQ:PL:SB	0/1:26,36,0:62:99:1299,0,781,1376,889,2265:10,16,23,13
+20	10094251	.	T	A,<NON_REF>	1270.77	.	AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=93600.00|129600.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=10,16|23,13|0,0;BaseQRankSum=0.251;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=223200,62;ReadPosRankSum=1.806	GT:AD:DP:GQ:PL:SB	0/1:26,36,0:62:99:1299,0,781,1376,889,2265:10,16,23,13
 20	10094252	.	C	<NON_REF>	.	.	END=10094581	GT:DP:GQ:MIN_DP:PL	0/0:68:99:46:0,117,1755
-20	10094582	.	A	G,<NON_REF>	923.77	.	AS_RAW_BaseQRankSum=|-1.4,1|NaN;AS_RAW_MQ=135410.00|108000.00|0.00;AS_RAW_MQRankSum=|1.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=20,19|16,14|0,0;BaseQRankSum=-1.388;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.270;RAW_MQ=243410.00;ReadPosRankSum=-0.018	GT:AD:DP:GQ:PL:SB	0/1:39,30,0:69:99:952,0,1350,1070,1440,2510:20,19,16,14
+20	10094582	.	A	G,<NON_REF>	923.77	.	AS_RAW_BaseQRankSum=|-1.4,1|NaN;AS_RAW_MQ=135410.00|108000.00|0.00;AS_RAW_MQRankSum=|1.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=20,19|16,14|0,0;BaseQRankSum=-1.388;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.270;RAW_MQandDP=243410,69;ReadPosRankSum=-0.018	GT:AD:DP:GQ:PL:SB	0/1:39,30,0:69:99:952,0,1350,1070,1440,2510:20,19,16,14
 20	10094583	.	T	<NON_REF>	.	.	END=10094773	GT:DP:GQ:MIN_DP:PL	0/0:78:99:67:0,120,1800
-20	10094774	.	C	T,<NON_REF>	1036.77	.	AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=141241.00|126000.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=24,16|21,14|0,0;BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQ=267241.00;ReadPosRankSum=0.197	GT:AD:DP:GQ:PL:SB	0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14
+20	10094774	.	C	T,<NON_REF>	1036.77	.	AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=141241.00|126000.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=24,16|21,14|0,0;BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQandDP=267241,75;ReadPosRankSum=0.197	GT:AD:DP:GQ:PL:SB	0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14
 20	10094775	.	A	<NON_REF>	.	.	END=10095431	GT:DP:GQ:MIN_DP:PL	0/0:77:99:63:0,120,1800
-20	10095432	.	GTGATGATGA	G,<NON_REF>	839.73	.	AS_RAW_BaseQRankSum=|1.2,1|NaN;AS_RAW_MQ=97200.00|35579.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,11|12,11|0,0;BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQ=227748.00;ReadPosRankSum=0.396	GT:AD:DP:GQ:PL:SB	0/1:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11
+20	10095432	.	GTGATGATGA	G,<NON_REF>	839.73	.	AS_RAW_BaseQRankSum=|1.2,1|NaN;AS_RAW_MQ=97200.00|35579.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,11|12,11|0,0;BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQandDP=227748,77;ReadPosRankSum=0.396	GT:AD:DP:GQ:PL:SB	0/1:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11
 20	10095442	.	T	<NON_REF>	.	.	END=10095740	GT:DP:GQ:MIN_DP:PL	0/0:80:99:64:0,120,1800
-20	10095741	.	A	G,<NON_REF>	1075.77	.	AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=126841.00|103087.00|0.00;AS_RAW_MQRankSum=|-2.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=14,22|18,16|0,0;BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQ=233528.00;ReadPosRankSum=-0.500	GT:AD:DP:GQ:PL:SB	0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16
+20	10095741	.	A	G,<NON_REF>	1075.77	.	AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=126841.00|103087.00|0.00;AS_RAW_MQRankSum=|-2.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=14,22|18,16|0,0;BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQandDP=233528,71;ReadPosRankSum=-0.500	GT:AD:DP:GQ:PL:SB	0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16
 20	10095742	.	G	<NON_REF>	.	.	END=10096292	GT:DP:GQ:MIN_DP:PL	0/0:73:99:63:0,120,1800
-20	10096293	.	C	T,<NON_REF>	1355.77	.	AS_RAW_BaseQRankSum=|4.6,1|NaN;AS_RAW_MQ=123220.00|134041.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=21,16|21,17|0,0;BaseQRankSum=4.664;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.397;RAW_MQ=257261.00;ReadPosRankSum=-1.135	GT:AD:DP:GQ:PL:SB	0/1:37,38,0:75:99:1384,0,1258,1495,1372,2867:21,16,21,17
+20	10096293	.	C	T,<NON_REF>	1355.77	.	AS_RAW_BaseQRankSum=|4.6,1|NaN;AS_RAW_MQ=123220.00|134041.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=21,16|21,17|0,0;BaseQRankSum=4.664;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.397;RAW_MQandDP=257261,75;ReadPosRankSum=-1.135	GT:AD:DP:GQ:PL:SB	0/1:37,38,0:75:99:1384,0,1258,1495,1372,2867:21,16,21,17
 20	10096294	.	T	<NON_REF>	.	.	END=10096595	GT:DP:GQ:MIN_DP:PL	0/0:68:99:57:0,120,1800
-20	10096596	.	C	T,<NON_REF>	1562.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=136779.00|163682.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=19,21|23,24|0,0;BaseQRankSum=2.728;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.612;RAW_MQ=300461.00;ReadPosRankSum=-0.170	GT:AD:DP:GQ:PL:SB	0/1:40,47,0:87:99:1591,0,1273,1711,1414,3125:19,21,23,24
+20	10096596	.	C	T,<NON_REF>	1562.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=136779.00|163682.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=19,21|23,24|0,0;BaseQRankSum=2.728;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.612;RAW_MQandDP=300461,87;ReadPosRankSum=-0.170	GT:AD:DP:GQ:PL:SB	0/1:40,47,0:87:99:1591,0,1273,1711,1414,3125:19,21,23,24
 20	10096597	.	T	<NON_REF>	.	.	END=10096767	GT:DP:GQ:MIN_DP:PL	0/0:90:99:75:0,120,1800
-20	10096768	.	A	C,<NON_REF>	1682.77	.	AS_RAW_BaseQRankSum=|-2.8,1|NaN;AS_RAW_MQ=151200.00|168123.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=25,17|24,25|0,0;BaseQRankSum=-2.764;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.609;RAW_MQ=319323.00;ReadPosRankSum=0.613	GT:AD:DP:GQ:PL:SB	0/1:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25
+20	10096768	.	A	C,<NON_REF>	1682.77	.	AS_RAW_BaseQRankSum=|-2.8,1|NaN;AS_RAW_MQ=151200.00|168123.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=25,17|24,25|0,0;BaseQRankSum=-2.764;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.609;RAW_MQandDP=319323,91;ReadPosRankSum=0.613	GT:AD:DP:GQ:PL:SB	0/1:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25
 20	10096769	.	A	<NON_REF>	.	.	END=10096898	GT:DP:GQ:MIN_DP:PL	0/0:78:99:65:0,120,1800
-20	10096899	.	G	T,<NON_REF>	1614.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=140400.00|139538.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=19,20|12,28|0,0;BaseQRankSum=2.755;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.387;RAW_MQ=279938.00;ReadPosRankSum=0.422	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:19,20,12,28
+20	10096899	.	G	T,<NON_REF>	1614.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=140400.00|139538.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=19,20|12,28|0,0;BaseQRankSum=2.755;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.387;RAW_MQandDP=279938,79;ReadPosRankSum=0.422	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:19,20,12,28
 20	10096900	.	G	<NON_REF>	.	.	END=10096904	GT:DP:GQ:MIN_DP:PL	0/0:82:99:78:0,120,1800
-20	10096905	.	TA	T,<NON_REF>	1600.73	.	AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=144000.00|147579.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=20,20|13,30|0,0;BaseQRankSum=-0.755;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQ=291579.00;ReadPosRankSum=0.461	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30
+20	10096905	.	TA	T,<NON_REF>	1600.73	.	AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=144000.00|147579.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=20,20|13,30|0,0;BaseQRankSum=-0.755;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQandDP=291579,83;ReadPosRankSum=0.461	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30
 20	10096907	.	A	<NON_REF>	.	.	END=10096932	GT:DP:GQ:MIN_DP:PL	0/0:84:99:82:0,120,1800
-20	10096933	.	G	C,<NON_REF>	1511.77	.	AS_RAW_BaseQRankSum=|-2.0,1|NaN;AS_RAW_MQ=158400.00|140379.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=28,16|13,28|0,0;BaseQRankSum=-1.914;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.802;RAW_MQ=298779.00;ReadPosRankSum=0.334	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:28,16,13,28
+20	10096933	.	G	C,<NON_REF>	1511.77	.	AS_RAW_BaseQRankSum=|-2.0,1|NaN;AS_RAW_MQ=158400.00|140379.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=28,16|13,28|0,0;BaseQRankSum=-1.914;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.802;RAW_MQandDP=298779,85;ReadPosRankSum=0.334	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:28,16,13,28
 20	10096934	.	T	<NON_REF>	.	.	END=10096957	GT:DP:GQ:MIN_DP:PL	0/0:90:99:86:0,120,1800
-20	10096958	.	G	A,<NON_REF>	1766.77	.	AS_RAW_BaseQRankSum=|2.8,1|NaN;AS_RAW_MQ=162000.00|161979.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=27,18|16,31|0,0;BaseQRankSum=2.839;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.701;RAW_MQ=323979.00;ReadPosRankSum=-1.833	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:27,18,16,31
+20	10096958	.	G	A,<NON_REF>	1766.77	.	AS_RAW_BaseQRankSum=|2.8,1|NaN;AS_RAW_MQ=162000.00|161979.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=27,18|16,31|0,0;BaseQRankSum=2.839;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.701;RAW_MQandDP=323979,92;ReadPosRankSum=-1.833	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:27,18,16,31
 20	10096959	.	G	<NON_REF>	.	.	END=10097074	GT:DP:GQ:MIN_DP:PL	0/0:92:99:84:0,120,1800
-20	10097075	.	T	G,<NON_REF>	1445.77	.	AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=159700.00|155928.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=18,26|26,22|0,0;BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQ=315628.00;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22
+20	10097075	.	T	G,<NON_REF>	1445.77	.	AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=159700.00|155928.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=18,26|26,22|0,0;BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQandDP=315628,92;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22
 20	10097076	.	A	<NON_REF>	.	.	END=10097100	GT:DP:GQ:MIN_DP:PL	0/0:91:99:77:0,120,1800
-20	10097101	.	C	CTTT,CTTTT,<NON_REF>	1091.73	.	AS_RAW_BaseQRankSum=|-0.9,1|-1.2,1|NaN;AS_RAW_MQ=121504.00|76887.00|6803.00|0.00;AS_RAW_MQRankSum=|-1.8,1|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|2.7,1|-1.4,1|NaN;AS_SB_TABLE=22,12|12,14|3,1|0,0;BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQ=252294.00;ReadPosRankSum=2.086	GT:AD:DP:GQ:PL:SB	0/1:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15
+20	10097101	.	C	CTTT,CTTTT,<NON_REF>	1091.73	.	AS_RAW_BaseQRankSum=|-0.9,1|-1.2,1|NaN;AS_RAW_MQ=121504.00|76887.00|6803.00|0.00;AS_RAW_MQRankSum=|-1.8,1|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|2.7,1|-1.4,1|NaN;AS_SB_TABLE=22,12|12,14|3,1|0,0;BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQandDP=252294,76;ReadPosRankSum=2.086	GT:AD:DP:GQ:PL:SB	0/1:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15
 20	10097102	.	T	<NON_REF>	.	.	END=10097435	GT:DP:GQ:MIN_DP:PL	0/0:70:99:60:0,120,1800
-20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C,<NON_REF>	1054.73	.	AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=204882.00|57261.00|0.00;AS_RAW_MQRankSum=|-6.5,1|NaN;AS_RAW_ReadPosRankSum=|-3.1,1|NaN;AS_SB_TABLE=23,34|11,21|0,0;BaseQRankSum=1.820;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQ=262143.00;ReadPosRankSum=-3.097	GT:AD:DP:GQ:PL:SB	0/1:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21
-20	10097437	.	TTTTC	*,T,<NON_REF>	2089.73	.	AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|57261.00|84469.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|11,21|5,18|0,0;DP=76;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQ=217330.00	GT:AD:DP:GQ:PL:SB	1/2:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642:0,0,16,39
+20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C,<NON_REF>	1054.73	.	AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=204882.00|57261.00|0.00;AS_RAW_MQRankSum=|-6.5,1|NaN;AS_RAW_ReadPosRankSum=|-3.1,1|NaN;AS_SB_TABLE=23,34|11,21|0,0;BaseQRankSum=1.820;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQandDP=262143,89;ReadPosRankSum=-3.097	GT:AD:DP:GQ:PL:SB	0/1:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21
+20	10097437	.	TTTTC	*,T,<NON_REF>	2089.73	.	AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|57261.00|84469.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|11,21|5,18|0,0;DP=76;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=217330,76	GT:AD:DP:GQ:PL:SB	1/2:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642:0,0,16,39
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-20	10097626	.	C	A,<NON_REF>	626.77	.	AS_RAW_BaseQRankSum=|1.0,1|NaN;AS_RAW_MQ=98041.00|64779.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=8,20|8,12|0,0;BaseQRankSum=1.085;DP=48;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.331;RAW_MQ=162820.00;ReadPosRankSum=1.015	GT:AD:DP:GQ:PL:SB	0/1:28,20,0:48:99:655,0,957,739,1017,1757:8,20,8,12
+20	10097626	.	C	A,<NON_REF>	626.77	.	AS_RAW_BaseQRankSum=|1.0,1|NaN;AS_RAW_MQ=98041.00|64779.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=8,20|8,12|0,0;BaseQRankSum=1.085;DP=48;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.331;RAW_MQandDP=162820,48;ReadPosRankSum=1.015	GT:AD:DP:GQ:PL:SB	0/1:28,20,0:48:99:655,0,957,739,1017,1757:8,20,8,12
 20	10097627	.	T	<NON_REF>	.	.	END=10097788	GT:DP:GQ:MIN_DP:PL	0/0:60:99:49:0,120,1800
-20	10097789	.	T	C,<NON_REF>	688.77	.	AS_RAW_BaseQRankSum=|-1.2,1|NaN;AS_RAW_MQ=122400.00|69005.00|0.00;AS_RAW_MQRankSum=|-2.9,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=14,20|13,10|0,0;BaseQRankSum=-1.157;DP=57;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.805;RAW_MQ=191405.00;ReadPosRankSum=0.220	GT:AD:DP:GQ:PL:SB	0/1:34,23,0:57:99:717,0,1190,820,1260,2079:14,20,13,10
+20	10097789	.	T	C,<NON_REF>	688.77	.	AS_RAW_BaseQRankSum=|-1.2,1|NaN;AS_RAW_MQ=122400.00|69005.00|0.00;AS_RAW_MQRankSum=|-2.9,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=14,20|13,10|0,0;BaseQRankSum=-1.157;DP=57;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.805;RAW_MQandDP=191405,57;ReadPosRankSum=0.220	GT:AD:DP:GQ:PL:SB	0/1:34,23,0:57:99:717,0,1190,820,1260,2079:14,20,13,10
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-20	10097928	.	G	A,<NON_REF>	570.77	.	AS_RAW_BaseQRankSum=|-1.3,1|NaN;AS_RAW_MQ=61200.00|60123.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=9,8|8,11|0,0;BaseQRankSum=-1.203;DP=36;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.654;RAW_MQ=121323.00;ReadPosRankSum=-0.079	GT:AD:DP:GQ:PL:SB	0/1:17,19,0:36:99:599,0,586,650,643,1293:9,8,8,11
+20	10097928	.	G	A,<NON_REF>	570.77	.	AS_RAW_BaseQRankSum=|-1.3,1|NaN;AS_RAW_MQ=61200.00|60123.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=9,8|8,11|0,0;BaseQRankSum=-1.203;DP=36;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.654;RAW_MQandDP=121323,36;ReadPosRankSum=-0.079	GT:AD:DP:GQ:PL:SB	0/1:17,19,0:36:99:599,0,586,650,643,1293:9,8,8,11
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@@ -1197,7 +1197,7 @@
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-20	10098110	.	G	C,<NON_REF>	586.77	.	AS_RAW_BaseQRankSum=|2.5,1|NaN;AS_RAW_MQ=68400.00|55682.00|0.00;AS_RAW_MQRankSum=|-1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=0,19|2,15|0,0;BaseQRankSum=2.510;DP=36;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.477;RAW_MQ=124082.00;ReadPosRankSum=-0.730	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:19,17,0:36:99:0|1:10098110_G_C:615,0,727,672,779,1451:0,19,2,15
+20	10098110	.	G	C,<NON_REF>	586.77	.	AS_RAW_BaseQRankSum=|2.5,1|NaN;AS_RAW_MQ=68400.00|55682.00|0.00;AS_RAW_MQRankSum=|-1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=0,19|2,15|0,0;BaseQRankSum=2.510;DP=36;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.477;RAW_MQandDP=124082,36;ReadPosRankSum=-0.730	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:19,17,0:36:99:0|1:10098110_G_C:615,0,727,672,779,1451:0,19,2,15
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@@ -1205,7 +1205,7 @@
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-20	10098135	.	C	A,<NON_REF>	471.77	.	AS_RAW_BaseQRankSum=|-1.2,1|NaN;AS_RAW_MQ=83641.00|51541.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=0,24|1,13|0,0;BaseQRankSum=-1.155;DP=38;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.546;RAW_MQ=135182.00;ReadPosRankSum=-0.591	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:24,14,0:38:99:0|1:10098110_G_C:500,0,964,575,1006,1581:0,24,1,13
+20	10098135	.	C	A,<NON_REF>	471.77	.	AS_RAW_BaseQRankSum=|-1.2,1|NaN;AS_RAW_MQ=83641.00|51541.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=0,24|1,13|0,0;BaseQRankSum=-1.155;DP=38;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.546;RAW_MQandDP=135182,38;ReadPosRankSum=-0.591	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:24,14,0:38:99:0|1:10098110_G_C:500,0,964,575,1006,1581:0,24,1,13
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@@ -1215,21 +1215,21 @@
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-20	10098219	.	TATATATA	T,<NON_REF>	295.73	.	AS_RAW_BaseQRankSum=|3.1,1|NaN;AS_RAW_MQ=40441.00|25264.00|0.00;AS_RAW_MQRankSum=|-0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=0,12|0,9|0,0;BaseQRankSum=3.147;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.205;RAW_MQ=65705.00;ReadPosRankSum=0.427	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9
+20	10098219	.	TATATATA	T,<NON_REF>	295.73	.	AS_RAW_BaseQRankSum=|3.1,1|NaN;AS_RAW_MQ=40441.00|25264.00|0.00;AS_RAW_MQRankSum=|-0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=0,12|0,9|0,0;BaseQRankSum=3.147;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.205;RAW_MQandDP=65705,21;ReadPosRankSum=0.427	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:0,12,0,9
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-20	10098237	.	A	T,<NON_REF>	244.77	.	AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=21600.00|15464.00|0.00;AS_RAW_MQRankSum=|-1.8,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=0,6|0,7|0,0;BaseQRankSum=0.006;DP=13;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.742;RAW_MQ=37064.00;ReadPosRankSum=0.277	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:6,7,0:13:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:0,6,0,7
+20	10098237	.	A	T,<NON_REF>	244.77	.	AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=21600.00|15464.00|0.00;AS_RAW_MQRankSum=|-1.8,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=0,6|0,7|0,0;BaseQRankSum=0.006;DP=13;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.742;RAW_MQandDP=37064,13;ReadPosRankSum=0.277	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:6,7,0:13:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:0,6,0,7
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-20	10098265	.	T	C,<NON_REF>	133.77	.	AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=7200.00|3364.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=0,2|0,4|0,0;BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.834;RAW_MQ=10564.00;ReadPosRankSum=0.000	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:2,4,0:6:59:0|1:10098219_TATATATA_T:162,0,59,168,71,239:0,2,0,4
+20	10098265	.	T	C,<NON_REF>	133.77	.	AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=7200.00|3364.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=0,2|0,4|0,0;BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.834;RAW_MQandDP=10564,6;ReadPosRankSum=0.000	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:2,4,0:6:59:0|1:10098219_TATATATA_T:162,0,59,168,71,239:0,2,0,4
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-20	10098308	.	AAT	A,<NON_REF>	0	.	AS_RAW_BaseQRankSum=|NaN|NaN;AS_RAW_MQ=7200.00|0.00|0.00;AS_RAW_MQRankSum=|NaN|NaN;AS_RAW_ReadPosRankSum=|NaN|NaN;AS_SB_TABLE=0,0|0,0|0,0;DP=2;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;RAW_MQ=7200.00	GT:AD:DP:GQ:PL:SB	0/0:2,0,0:2:6:0,6,81,6,81,81:0,2,0,0
+20	10098308	.	AAT	A,<NON_REF>	0	.	AS_RAW_BaseQRankSum=|NaN|NaN;AS_RAW_MQ=7200.00|0.00|0.00;AS_RAW_MQRankSum=|NaN|NaN;AS_RAW_ReadPosRankSum=|NaN|NaN;AS_SB_TABLE=0,0|0,0|0,0;DP=2;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;RAW_MQandDP=7200,2	GT:AD:DP:GQ:PL:SB	0/0:2,0,0:2:6:0,6,81,6,81,81:0,2,0,0
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@@ -1299,7 +1299,7 @@
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-20	10098885	.	C	CA,<NON_REF>	433.73	.	AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=58969.00|18188.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=16,1|13,1|0,0;BaseQRankSum=0.165;DP=31;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.449;RAW_MQ=77157.00;ReadPosRankSum=-1.073	GT:AD:DP:GQ:PL:SB	0/1:17,14,0:31:99:471,0,572,523,614,1137:16,1,13,1
+20	10098885	.	C	CA,<NON_REF>	433.73	.	AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=58969.00|18188.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=16,1|13,1|0,0;BaseQRankSum=0.165;DP=31;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.449;RAW_MQandDP=77157,31;ReadPosRankSum=-1.073	GT:AD:DP:GQ:PL:SB	0/1:17,14,0:31:99:471,0,572,523,614,1137:16,1,13,1
 20	10098886	.	C	<NON_REF>	.	.	END=10098890	GT:DP:GQ:MIN_DP:PL	0/0:31:84:29:0,84,1260
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@@ -1316,7 +1316,7 @@
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-20	10098945	.	T	C,<NON_REF>	452.77	.	AS_RAW_BaseQRankSum=|1.4,1|NaN;AS_RAW_MQ=32049.00|25504.00|0.00;AS_RAW_MQRankSum=|-2.6,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=8,1|13,0|0,0;BaseQRankSum=1.475;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.504;RAW_MQ=57553.00;ReadPosRankSum=1.038	GT:AD:DP:GQ:PL:SB	0/1:9,13,0:22:99:481,0,248,508,288,795:8,1,13,0
+20	10098945	.	T	C,<NON_REF>	452.77	.	AS_RAW_BaseQRankSum=|1.4,1|NaN;AS_RAW_MQ=32049.00|25504.00|0.00;AS_RAW_MQRankSum=|-2.6,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=8,1|13,0|0,0;BaseQRankSum=1.475;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.504;RAW_MQandDP=57553,22;ReadPosRankSum=1.038	GT:AD:DP:GQ:PL:SB	0/1:9,13,0:22:99:481,0,248,508,288,795:8,1,13,0
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@@ -1324,7 +1324,7 @@
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-20	10098987	.	C	T,<NON_REF>	379.77	.	AS_RAW_BaseQRankSum=|3.1,1|NaN;AS_RAW_MQ=39249.00|25337.00|0.00;AS_RAW_MQRankSum=|-2.8,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=9,2|13,0|0,0;BaseQRankSum=3.127;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.734;RAW_MQ=64586.00;ReadPosRankSum=0.436	GT:AD:DP:GQ:PL:SB	0/1:11,13,0:24:99:408,0,350,441,389,830:9,2,13,0
+20	10098987	.	C	T,<NON_REF>	379.77	.	AS_RAW_BaseQRankSum=|3.1,1|NaN;AS_RAW_MQ=39249.00|25337.00|0.00;AS_RAW_MQRankSum=|-2.8,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=9,2|13,0|0,0;BaseQRankSum=3.127;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.734;RAW_MQandDP=64586,24;ReadPosRankSum=0.436	GT:AD:DP:GQ:PL:SB	0/1:11,13,0:24:99:408,0,350,441,389,830:9,2,13,0
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@@ -1332,26 +1332,26 @@
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-20	10099029	.	T	C,<NON_REF>	334.77	.	AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=62569.00|17048.00|0.00;AS_RAW_MQRankSum=|-3.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=14,4|9,1|0,0;BaseQRankSum=-1.809;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;RAW_MQ=79617.00;ReadPosRankSum=-1.224	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:14,4,9,1
+20	10099029	.	T	C,<NON_REF>	334.77	.	AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=62569.00|17048.00|0.00;AS_RAW_MQRankSum=|-3.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=14,4|9,1|0,0;BaseQRankSum=-1.809;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;RAW_MQandDP=79617,28;ReadPosRankSum=-1.224	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:14,4,9,1
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-20	10099034	.	C	A,<NON_REF>	334.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=62569.00|17048.00|0.00;AS_RAW_MQRankSum=|-3.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=13,5|9,1|0,0;BaseQRankSum=2.757;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;RAW_MQ=79617.00;ReadPosRankSum=-1.850	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:13,5,9,1
+20	10099034	.	C	A,<NON_REF>	334.77	.	AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=62569.00|17048.00|0.00;AS_RAW_MQRankSum=|-3.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=13,5|9,1|0,0;BaseQRankSum=2.757;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;RAW_MQandDP=79617,28;ReadPosRankSum=-1.850	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:13,5,9,1
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-20	10099044	.	A	C,<NON_REF>	334.77	.	AS_RAW_BaseQRankSum=|-1.2,1|NaN;AS_RAW_MQ=51769.00|8082.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-2.3,1|NaN;AS_SB_TABLE=12,3|7,2|0,0;BaseQRankSum=-1.148;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQ=59851.00;ReadPosRankSum=-2.207	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:12,3,7,2
+20	10099044	.	A	C,<NON_REF>	334.77	.	AS_RAW_BaseQRankSum=|-1.2,1|NaN;AS_RAW_MQ=51769.00|8082.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-2.3,1|NaN;AS_SB_TABLE=12,3|7,2|0,0;BaseQRankSum=-1.148;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQandDP=59851,24;ReadPosRankSum=-2.207	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:12,3,7,2
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-20	10099046	.	T	C,<NON_REF>	304.77	.	AS_RAW_BaseQRankSum=|-2.2,1|NaN;AS_RAW_MQ=51769.00|8082.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-2.3,1|NaN;AS_SB_TABLE=12,3|7,2|0,0;BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQ=59851.00;ReadPosRankSum=-2.297	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:12,3,7,2
+20	10099046	.	T	C,<NON_REF>	304.77	.	AS_RAW_BaseQRankSum=|-2.2,1|NaN;AS_RAW_MQ=51769.00|8082.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-2.3,1|NaN;AS_SB_TABLE=12,3|7,2|0,0;BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQandDP=59851,24;ReadPosRankSum=-2.297	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:12,3,7,2
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-20	10099055	.	T	C,<NON_REF>	256.77	.	AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=51769.00|6786.00|0.00;AS_RAW_MQRankSum=|-4.4,1|NaN;AS_RAW_ReadPosRankSum=|-2.0,1|NaN;AS_SB_TABLE=11,4|6,2|0,0;BaseQRankSum=-1.554;DP=23;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.316;RAW_MQ=58555.00;ReadPosRankSum=-1.970	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:11,4,6,2
+20	10099055	.	T	C,<NON_REF>	256.77	.	AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=51769.00|6786.00|0.00;AS_RAW_MQRankSum=|-4.4,1|NaN;AS_RAW_ReadPosRankSum=|-2.0,1|NaN;AS_SB_TABLE=11,4|6,2|0,0;BaseQRankSum=-1.554;DP=23;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.316;RAW_MQandDP=58555,23;ReadPosRankSum=-1.970	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:11,4,6,2
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-20	10099079	.	C	T,<NON_REF>	116.77	.	AS_RAW_BaseQRankSum=|1.4,1|NaN;AS_RAW_MQ=70213.00|8485.00|0.00;AS_RAW_MQRankSum=|-2.9,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=11,12|4,2|0,0;BaseQRankSum=1.434;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.821;RAW_MQ=78698.00;ReadPosRankSum=0.969	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:11,12,4,2
+20	10099079	.	C	T,<NON_REF>	116.77	.	AS_RAW_BaseQRankSum=|1.4,1|NaN;AS_RAW_MQ=70213.00|8485.00|0.00;AS_RAW_MQRankSum=|-2.9,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=11,12|4,2|0,0;BaseQRankSum=1.434;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.821;RAW_MQandDP=78698,29;ReadPosRankSum=0.969	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:11,12,4,2
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@@ -1359,13 +1359,13 @@
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-20	10099111	.	T	TTTTGTTTG,<NON_REF>	656.73	.	AS_RAW_BaseQRankSum=|-1.3,1|NaN;AS_RAW_MQ=68844.00|15693.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=13,9|7,6|0,0;BaseQRankSum=-1.207;DP=42;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.071;RAW_MQ=109737.00;ReadPosRankSum=-0.273	GT:AD:DP:GQ:PL:SB	0/1:22,13,0:35:99:694,0,802,763,859,1622:13,9,7,6
+20	10099111	.	T	TTTTGTTTG,<NON_REF>	656.73	.	AS_RAW_BaseQRankSum=|-1.3,1|NaN;AS_RAW_MQ=68844.00|15693.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=13,9|7,6|0,0;BaseQRankSum=-1.207;DP=42;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.071;RAW_MQandDP=109737,42;ReadPosRankSum=-0.273	GT:AD:DP:GQ:PL:SB	0/1:22,13,0:35:99:694,0,802,763,859,1622:13,9,7,6
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-20	10099140	.	G	T,<NON_REF>	1005.77	.	AS_RAW_BaseQRankSum=|-0.2,1|NaN;AS_RAW_MQ=108000.00|84512.00|0.00;AS_RAW_MQRankSum=|-2.5,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=18,12|22,10|0,0;BaseQRankSum=-0.114;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.469;RAW_MQ=192512.00;ReadPosRankSum=0.338	GT:AD:DP:GQ:PL:SB	0/1:30,32,0:62:99:1034,0,931,1122,1028,2150:18,12,22,10
+20	10099140	.	G	T,<NON_REF>	1005.77	.	AS_RAW_BaseQRankSum=|-0.2,1|NaN;AS_RAW_MQ=108000.00|84512.00|0.00;AS_RAW_MQRankSum=|-2.5,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=18,12|22,10|0,0;BaseQRankSum=-0.114;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.469;RAW_MQandDP=192512,62;ReadPosRankSum=0.338	GT:AD:DP:GQ:PL:SB	0/1:30,32,0:62:99:1034,0,931,1122,1028,2150:18,12,22,10
 20	10099141	.	G	<NON_REF>	.	.	END=10099189	GT:DP:GQ:MIN_DP:PL	0/0:67:99:64:0,120,1800
-20	10099190	.	G	T,<NON_REF>	1034.77	.	AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=118800.00|96551.00|0.00;AS_RAW_MQRankSum=|-1.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=21,12|21,11|0,0;BaseQRankSum=-0.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.711;RAW_MQ=215351.00;ReadPosRankSum=-1.260	GT:AD:DP:GQ:PL:SB	0/1:33,32,0:65:99:1063,0,1154,1162,1251,2413:21,12,21,11
+20	10099190	.	G	T,<NON_REF>	1034.77	.	AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=118800.00|96551.00|0.00;AS_RAW_MQRankSum=|-1.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=21,12|21,11|0,0;BaseQRankSum=-0.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.711;RAW_MQandDP=215351,65;ReadPosRankSum=-1.260	GT:AD:DP:GQ:PL:SB	0/1:33,32,0:65:99:1063,0,1154,1162,1251,2413:21,12,21,11
 20	10099191	.	C	<NON_REF>	.	.	END=10099219	GT:DP:GQ:MIN_DP:PL	0/0:58:99:46:0,111,1665
-20	10099220	.	A	G,<NON_REF>	577.77	.	AS_RAW_BaseQRankSum=|-1.7,1|NaN;AS_RAW_MQ=90000.00|59477.00|0.00;AS_RAW_MQRankSum=|-2.6,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=15,10|11,9|0,0;BaseQRankSum=-1.664;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.596;RAW_MQ=149477.00;ReadPosRankSum=0.629	GT:AD:DP:GQ:PL:SB	0/1:25,20,0:45:99:606,0,873,681,933,1614:15,10,11,9
+20	10099220	.	A	G,<NON_REF>	577.77	.	AS_RAW_BaseQRankSum=|-1.7,1|NaN;AS_RAW_MQ=90000.00|59477.00|0.00;AS_RAW_MQRankSum=|-2.6,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=15,10|11,9|0,0;BaseQRankSum=-1.664;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.596;RAW_MQandDP=149477,45;ReadPosRankSum=0.629	GT:AD:DP:GQ:PL:SB	0/1:25,20,0:45:99:606,0,873,681,933,1614:15,10,11,9
 20	10099221	.	T	<NON_REF>	.	.	END=10099229	GT:DP:GQ:MIN_DP:PL	0/0:44:99:42:0,102,1530
 20	10099230	.	T	<NON_REF>	.	.	END=10099233	GT:DP:GQ:MIN_DP:PL	0/0:41:90:41:0,90,1350
 20	10099234	.	T	<NON_REF>	.	.	END=10099235	GT:DP:GQ:MIN_DP:PL	0/0:44:87:44:0,87,1305
@@ -1373,16 +1373,16 @@
 20	10099239	.	C	<NON_REF>	.	.	END=10099246	GT:DP:GQ:MIN_DP:PL	0/0:36:84:35:0,84,1260
 20	10099247	.	C	<NON_REF>	.	.	END=10099248	GT:DP:GQ:MIN_DP:PL	0/0:37:93:36:0,93,1395
 20	10099249	.	C	<NON_REF>	.	.	END=10099249	GT:DP:GQ:MIN_DP:PL	0/0:36:87:36:0,87,1305
-20	10099250	.	G	A,<NON_REF>	699.77	.	AS_RAW_BaseQRankSum=|3.1,1|NaN;AS_RAW_MQ=57600.00|61406.00|0.00;AS_RAW_MQRankSum=|-2.3,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=12,4|11,10|0,0;BaseQRankSum=3.170;DP=37;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.272;RAW_MQ=119006.00;ReadPosRankSum=0.583	GT:AD:DP:GQ:PL:SB	0/1:16,21,0:37:99:728,0,424,776,487,1263:12,4,11,10
+20	10099250	.	G	A,<NON_REF>	699.77	.	AS_RAW_BaseQRankSum=|3.1,1|NaN;AS_RAW_MQ=57600.00|61406.00|0.00;AS_RAW_MQRankSum=|-2.3,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=12,4|11,10|0,0;BaseQRankSum=3.170;DP=37;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.272;RAW_MQandDP=119006,37;ReadPosRankSum=0.583	GT:AD:DP:GQ:PL:SB	0/1:16,21,0:37:99:728,0,424,776,487,1263:12,4,11,10
 20	10099251	.	A	<NON_REF>	.	.	END=10099269	GT:DP:GQ:MIN_DP:PL	0/0:30:81:28:0,81,1132
-20	10099270	.	A	C,<NON_REF>	0	.	AS_RAW_BaseQRankSum=|-2.9,1|NaN;AS_RAW_MQ=92210.00|6058.00|0.00;AS_RAW_MQRankSum=|-2.7,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=19,8|0,3|0,0;BaseQRankSum=-2.866;DP=30;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-2.691;RAW_MQ=98268.00;ReadPosRankSum=-0.138	GT:AD:DP:GQ:PL:SB	0/0:27,3,0:30:60:0,60,1084,81,1092,1113:19,8,0,3
+20	10099270	.	A	C,<NON_REF>	0	.	AS_RAW_BaseQRankSum=|-2.9,1|NaN;AS_RAW_MQ=92210.00|6058.00|0.00;AS_RAW_MQRankSum=|-2.7,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=19,8|0,3|0,0;BaseQRankSum=-2.866;DP=30;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-2.691;RAW_MQandDP=98268,30;ReadPosRankSum=-0.138	GT:AD:DP:GQ:PL:SB	0/0:27,3,0:30:60:0,60,1084,81,1092,1113:19,8,0,3
 20	10099271	.	C	<NON_REF>	.	.	END=10099271	GT:DP:GQ:MIN_DP:PL	0/0:31:84:31:0,84,1260
 20	10099272	.	C	<NON_REF>	.	.	END=10099534	GT:DP:GQ:MIN_DP:PL	0/0:57:99:36:0,99,1485
-20	10099535	.	G	A,<NON_REF>	1335.77	.	AS_RAW_BaseQRankSum=|5.0,1|NaN;AS_RAW_MQ=93600.00|132651.00|0.00;AS_RAW_MQRankSum=|-1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=17,9|22,17|0,0;BaseQRankSum=5.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.418;RAW_MQ=226251.00;ReadPosRankSum=-0.777	GT:AD:DP:GQ:PL:SB	0/1:26,39,0:65:99:1364,0,686,1442,803,2245:17,9,22,17
+20	10099535	.	G	A,<NON_REF>	1335.77	.	AS_RAW_BaseQRankSum=|5.0,1|NaN;AS_RAW_MQ=93600.00|132651.00|0.00;AS_RAW_MQRankSum=|-1.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=17,9|22,17|0,0;BaseQRankSum=5.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.418;RAW_MQandDP=226251,65;ReadPosRankSum=-0.777	GT:AD:DP:GQ:PL:SB	0/1:26,39,0:65:99:1364,0,686,1442,803,2245:17,9,22,17
 20	10099536	.	T	<NON_REF>	.	.	END=10099564	GT:DP:GQ:MIN_DP:PL	0/0:67:99:63:0,120,1800
-20	10099565	.	C	T,<NON_REF>	1346.77	.	AS_RAW_BaseQRankSum=|4.5,1|NaN;AS_RAW_MQ=111600.00|131810.00|0.00;AS_RAW_MQRankSum=|-1.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=23,8|21,17|0,0;BaseQRankSum=4.595;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.266;RAW_MQ=243410.00;ReadPosRankSum=1.225	GT:AD:DP:GQ:PL:SB	0/1:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17
+20	10099565	.	C	T,<NON_REF>	1346.77	.	AS_RAW_BaseQRankSum=|4.5,1|NaN;AS_RAW_MQ=111600.00|131810.00|0.00;AS_RAW_MQRankSum=|-1.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=23,8|21,17|0,0;BaseQRankSum=4.595;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.266;RAW_MQandDP=243410,69;ReadPosRankSum=1.225	GT:AD:DP:GQ:PL:SB	0/1:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17
 20	10099566	.	T	<NON_REF>	.	.	END=10099754	GT:DP:GQ:MIN_DP:PL	0/0:77:99:66:0,120,1800
-20	10099755	.	C	T,<NON_REF>	1098.77	.	AS_RAW_BaseQRankSum=|1.5,1|NaN;AS_RAW_MQ=116569.00|112441.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=20,13|17,15|0,0;BaseQRankSum=1.550;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.022;RAW_MQ=229010.00;ReadPosRankSum=-0.230	GT:AD:DP:GQ:PL:SB	0/1:33,32,0:65:99:1127,0,1148,1226,1245,2470:20,13,17,15
+20	10099755	.	C	T,<NON_REF>	1098.77	.	AS_RAW_BaseQRankSum=|1.5,1|NaN;AS_RAW_MQ=116569.00|112441.00|0.00;AS_RAW_MQRankSum=|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=20,13|17,15|0,0;BaseQRankSum=1.550;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.022;RAW_MQandDP=229010,65;ReadPosRankSum=-0.230	GT:AD:DP:GQ:PL:SB	0/1:33,32,0:65:99:1127,0,1148,1226,1245,2470:20,13,17,15
 20	10099756	.	C	<NON_REF>	.	.	END=10099831	GT:DP:GQ:MIN_DP:PL	0/0:63:99:58:0,120,1800
-20	10099832	.	A	G,<NON_REF>	1073.77	.	AS_RAW_BaseQRankSum=|-4.6,1|NaN;AS_RAW_MQ=133707.00|116569.00|0.00;AS_RAW_MQRankSum=|0.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=22,17|14,19|0,0;BaseQRankSum=-4.563;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.869;RAW_MQ=250276.00;ReadPosRankSum=-1.023	GT:AD:DP:GQ:PL:SB	0/1:39,33,0:72:99:1102,0,1430,1220,1530,2749:22,17,14,19
+20	10099832	.	A	G,<NON_REF>	1073.77	.	AS_RAW_BaseQRankSum=|-4.6,1|NaN;AS_RAW_MQ=133707.00|116569.00|0.00;AS_RAW_MQRankSum=|0.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=22,17|14,19|0,0;BaseQRankSum=-4.563;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.869;RAW_MQandDP=250276,72;ReadPosRankSum=-1.023	GT:AD:DP:GQ:PL:SB	0/1:39,33,0:72:99:1102,0,1430,1220,1530,2749:22,17,14,19
 20	10099833	.	T	<NON_REF>	.	.	END=10100000	GT:DP:GQ:MIN_DP:PL	0/0:85:99:73:0,120,1800
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx
new file mode 100644
index 00000000000..c777c8154ae
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf
index 864c8e90d8e..9a02870ebe3 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf
@@ -84,29 +84,29 @@
 ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
 ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
 ##contig=<ID=20,length=63025520>
 ##contig=<ID=21,length=48129895>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 20	10000000	.	T	<NON_REF>	.	.	END=10000116	GT:DP:GQ:MIN_DP:PL	0/0:84:99:64:0,120,1800
-20	10000117	.	C	T,<NON_REF>	905.77	.	BaseQRankSum=2.136;DP=64;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.913;RAW_MQ=228169.00;ReadPosRankSum=-0.223	GT:AD:DP:GQ:PL:SB	0/1:36,28,0:64:99:934,0,1248,1042,1332,2374:16,20,19,9
+20	10000117	.	C	T,<NON_REF>	905.77	.	BaseQRankSum=2.136;DP=64;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.913;RAW_MQandDP=228169,64;ReadPosRankSum=-0.223	GT:AD:DP:GQ:PL:SB	0/1:36,28,0:64:99:934,0,1248,1042,1332,2374:16,20,19,9
 20	10000118	.	T	<NON_REF>	.	.	END=10000210	GT:DP:GQ:MIN_DP:PL	0/0:52:99:44:0,108,1620
-20	10000211	.	C	T,<NON_REF>	941.77	.	BaseQRankSum=1.867;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.057;RAW_MQ=188569.00;ReadPosRankSum=0.703	GT:AD:DP:GQ:PL:SB	0/1:26,27,0:53:99:970,0,906,1049,988,2036:15,11,11,16
+20	10000211	.	C	T,<NON_REF>	941.77	.	BaseQRankSum=1.867;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.057;RAW_MQandDP=188569,53;ReadPosRankSum=0.703	GT:AD:DP:GQ:PL:SB	0/1:26,27,0:53:99:970,0,906,1049,988,2036:15,11,11,16
 20	10000212	.	A	<NON_REF>	.	.	END=10000438	GT:DP:GQ:MIN_DP:PL	0/0:79:99:55:0,120,1800
-20	10000439	.	T	G,<NON_REF>	2804.77	.	DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=279076.00	GT:AD:DP:GQ:PL:SB	1/1:0,80,0:80:99:2833,240,0,2833,240,2833:0,0,49,31
+20	10000439	.	T	G,<NON_REF>	2804.77	.	DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=279076,80	GT:AD:DP:GQ:PL:SB	1/1:0,80,0:80:99:2833,240,0,2833,240,2833:0,0,49,31
 20	10000440	.	T	<NON_REF>	.	.	END=10000585	GT:DP:GQ:MIN_DP:PL	0/0:55:99:41:0,102,1530
 20	10000586	.	C	<NON_REF>	.	.	END=10000586	GT:DP:GQ:MIN_DP:PL	0/0:44:93:44:0,93,1503
 20	10000587	.	G	<NON_REF>	.	.	END=10000597	GT:DP:GQ:MIN_DP:PL	0/0:46:99:42:0,108,1620
-20	10000598	.	T	A,<NON_REF>	1941.77	.	DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=149628.00	GT:AD:DP:GQ:PL:SB	1/1:0,49,0:49:99:1970,147,0,1970,147,1970:0,0,19,30
+20	10000598	.	T	A,<NON_REF>	1941.77	.	DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=149628,49	GT:AD:DP:GQ:PL:SB	1/1:0,49,0:49:99:1970,147,0,1970,147,1970:0,0,19,30
 20	10000599	.	T	<NON_REF>	.	.	END=10000693	GT:DP:GQ:MIN_DP:PL	0/0:72:99:48:0,120,1800
-20	10000694	.	G	A,<NON_REF>	1008.77	.	BaseQRankSum=3.599;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.114;RAW_MQ=194196.00;ReadPosRankSum=0.657	GT:AD:DP:GQ:PL:SB	0/1:45,37,0:82:99:1037,0,1601,1173,1712,2885:25,20,18,19
+20	10000694	.	G	A,<NON_REF>	1008.77	.	BaseQRankSum=3.599;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.114;RAW_MQandDP=194196,82;ReadPosRankSum=0.657	GT:AD:DP:GQ:PL:SB	0/1:45,37,0:82:99:1037,0,1601,1173,1712,2885:25,20,18,19
 20	10000695	.	G	<NON_REF>	.	.	END=10000757	GT:DP:GQ:MIN_DP:PL	0/0:89:99:79:0,120,1800
-20	10000758	.	T	A,<NON_REF>	3838.77	.	DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=270581.00	GT:AD:DP:GQ:PL:SB	1/1:0,95,0:95:99:3867,286,0,3867,286,3867:0,0,45,50
+20	10000758	.	T	A,<NON_REF>	3838.77	.	DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=270581,95	GT:AD:DP:GQ:PL:SB	1/1:0,95,0:95:99:3867,286,0,3867,286,3867:0,0,45,50
 20	10000759	.	A	<NON_REF>	.	.	END=10001018	GT:DP:GQ:MIN_DP:PL	0/0:66:99:52:0,120,1800
-20	10001019	.	T	G,<NON_REF>	650.77	.	BaseQRankSum=-2.541;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-7.498;RAW_MQ=159195.00;ReadPosRankSum=-0.925	GT:AD:DP:GQ:PL:SB	0/1:39,26,0:65:99:679,0,1426,796,1504,2300:17,22,14,12
+20	10001019	.	T	G,<NON_REF>	650.77	.	BaseQRankSum=-2.541;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-7.498;RAW_MQandDP=159195,65;ReadPosRankSum=-0.925	GT:AD:DP:GQ:PL:SB	0/1:39,26,0:65:99:679,0,1426,796,1504,2300:17,22,14,12
 20	10001020	.	C	<NON_REF>	.	.	END=10001297	GT:DP:GQ:MIN_DP:PL	0/0:68:99:46:0,117,1755
-20	10001298	.	T	A,<NON_REF>	2917.77	.	DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=218493.00	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2946,220,0,2946,220,2946:0,0,41,32
+20	10001298	.	T	A,<NON_REF>	2917.77	.	DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=218493,74	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2946,220,0,2946,220,2946:0,0,41,32
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@@ -142,13 +142,13 @@
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@@ -177,9 +177,9 @@
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@@ -187,114 +187,114 @@
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-20	10004193	.	G	T,<NON_REF>	918.77	.	BaseQRankSum=-0.504;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.421;RAW_MQ=182869.00;ReadPosRankSum=1.512	GT:AD:DP:GQ:PL:SB	0/1:23,29,0:52:99:947,0,775,1016,860,1876:12,11,12,17
+20	10004193	.	G	T,<NON_REF>	918.77	.	BaseQRankSum=-0.504;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.421;RAW_MQandDP=182869,52;ReadPosRankSum=1.512	GT:AD:DP:GQ:PL:SB	0/1:23,29,0:52:99:947,0,775,1016,860,1876:12,11,12,17
 20	10004194	.	C	<NON_REF>	.	.	END=10004221	GT:DP:GQ:MIN_DP:PL	0/0:50:99:46:0,105,1575
-20	10004222	.	C	CA,<NON_REF>	12.96	.	BaseQRankSum=0.335;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.042;RAW_MQ=194729.00;ReadPosRankSum=1.271	GT:AD:DP:GQ:PL:SB	0/1:31,8,0:39:50:50,0,923,153,952,1105:18,13,4,4
-20	10004223	.	A	AG,<NON_REF>	47.73	.	BaseQRankSum=-0.480;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.886;RAW_MQ=210769.00;ReadPosRankSum=0.339	GT:AD:DP:GQ:PL:SB	0/1:36,11,0:47:85:85,0,982,193,1017,1210:16,20,5,6
+20	10004222	.	C	CA,<NON_REF>	12.96	.	BaseQRankSum=0.335;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.042;RAW_MQandDP=194729,54;ReadPosRankSum=1.271	GT:AD:DP:GQ:PL:SB	0/1:31,8,0:39:50:50,0,923,153,952,1105:18,13,4,4
+20	10004223	.	A	AG,<NON_REF>	47.73	.	BaseQRankSum=-0.480;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.886;RAW_MQandDP=210769,62;ReadPosRankSum=0.339	GT:AD:DP:GQ:PL:SB	0/1:36,11,0:47:85:85,0,982,193,1017,1210:16,20,5,6
 20	10004224	.	A	<NON_REF>	.	.	END=10004224	GT:DP:GQ:MIN_DP:PL	0/0:66:0:66:0,0,1403
 20	10004225	.	A	<NON_REF>	.	.	END=10004240	GT:DP:GQ:MIN_DP:PL	0/0:70:99:65:0,117,1755
 20	10004241	.	G	<NON_REF>	.	.	END=10004241	GT:DP:GQ:MIN_DP:PL	0/0:66:0:66:0,0,1965
 20	10004242	.	A	<NON_REF>	.	.	END=10004350	GT:DP:GQ:MIN_DP:PL	0/0:73:99:58:0,120,1800
-20	10004351	.	C	G,<NON_REF>	2755.77	.	DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=243987.00	GT:AD:DP:GQ:PL:SB	1/1:0,70,0:70:99:2784,211,0,2784,211,2784:0,0,38,32
+20	10004351	.	C	G,<NON_REF>	2755.77	.	DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=243987,70	GT:AD:DP:GQ:PL:SB	1/1:0,70,0:70:99:2784,211,0,2784,211,2784:0,0,38,32
 20	10004352	.	A	<NON_REF>	.	.	END=10004388	GT:DP:GQ:MIN_DP:PL	0/0:65:99:62:0,120,1800
-20	10004389	.	T	G,<NON_REF>	2494.77	.	DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=199570.00	GT:AD:DP:GQ:PL:SB	1/1:0,62,0:62:99:2523,187,0,2523,187,2523:0,0,25,37
+20	10004389	.	T	G,<NON_REF>	2494.77	.	DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=199570,62	GT:AD:DP:GQ:PL:SB	1/1:0,62,0:62:99:2523,187,0,2523,187,2523:0,0,25,37
 20	10004390	.	G	<NON_REF>	.	.	END=10004609	GT:DP:GQ:MIN_DP:PL	0/0:73:99:58:0,120,1800
-20	10004610	.	A	C,<NON_REF>	3625.77	.	DP=89;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=306605.00	GT:AD:DP:GQ:PL:SB	1/1:0,89,0:89:99:3654,267,0,3654,267,3654:0,0,46,43
+20	10004610	.	A	C,<NON_REF>	3625.77	.	DP=89;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=306605,89	GT:AD:DP:GQ:PL:SB	1/1:0,89,0:89:99:3654,267,0,3654,267,3654:0,0,46,43
 20	10004611	.	C	<NON_REF>	.	.	END=10004724	GT:DP:GQ:MIN_DP:PL	0/0:75:99:64:0,120,1800
-20	10004725	.	A	G,<NON_REF>	951.77	.	BaseQRankSum=-2.154;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.008;RAW_MQ=198562.00;ReadPosRankSum=2.087	GT:AD:DP:GQ:PL:SB	0/1:35,30,0:65:99:980,0,1168,1085,1258,2343:10,25,17,13
+20	10004725	.	A	G,<NON_REF>	951.77	.	BaseQRankSum=-2.154;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.008;RAW_MQandDP=198562,65;ReadPosRankSum=2.087	GT:AD:DP:GQ:PL:SB	0/1:35,30,0:65:99:980,0,1168,1085,1258,2343:10,25,17,13
 20	10004726	.	T	<NON_REF>	.	.	END=10004768	GT:DP:GQ:MIN_DP:PL	0/0:66:99:62:0,120,1800
-20	10004769	.	TAAAACTATGC	T,<NON_REF>	981.73	.	BaseQRankSum=1.603;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.625;RAW_MQ=216626.00;ReadPosRankSum=1.879	GT:AD:DP:GQ:PL:SB	0/1:37,27,0:64:99:1019,0,1471,1130,1554,2684:14,23,7,20
+20	10004769	.	TAAAACTATGC	T,<NON_REF>	981.73	.	BaseQRankSum=1.603;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.625;RAW_MQandDP=216626,79;ReadPosRankSum=1.879	GT:AD:DP:GQ:PL:SB	0/1:37,27,0:64:99:1019,0,1471,1130,1554,2684:14,23,7,20
 20	10004780	.	A	<NON_REF>	.	.	END=10004873	GT:DP:GQ:MIN_DP:PL	0/0:77:99:69:0,120,1800
-20	10004874	.	A	C,<NON_REF>	3602.77	.	DP=87;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=306223.00	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:0,0,54,33
+20	10004874	.	A	C,<NON_REF>	3602.77	.	DP=87;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=306223,87	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:0,0,54,33
 20	10004875	.	T	<NON_REF>	.	.	END=10004886	GT:DP:GQ:MIN_DP:PL	0/0:86:99:85:0,120,1800
-20	10004887	.	A	G,<NON_REF>	1323.77	.	BaseQRankSum=0.356;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.067;RAW_MQ=300482.00;ReadPosRankSum=-1.114	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:45,40,0:85:99:0|1:10004874_A_C:1352,0,1542,1487,1662,3149:24,21,24,16
+20	10004887	.	A	G,<NON_REF>	1323.77	.	BaseQRankSum=0.356;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.067;RAW_MQandDP=300482,85;ReadPosRankSum=-1.114	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:45,40,0:85:99:0|1:10004874_A_C:1352,0,1542,1487,1662,3149:24,21,24,16
 20	10004888	.	A	<NON_REF>	.	.	END=10005009	GT:DP:GQ:MIN_DP:PL	0/0:81:99:65:0,120,1800
-20	10005010	.	C	T,<NON_REF>	2934.77	.	DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=256441.00	GT:AD:DP:GQ:PL:SB	1/1:0,72,0:72:99:2963,217,0,2963,217,2963:0,0,44,28
+20	10005010	.	C	T,<NON_REF>	2934.77	.	DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=256441,72	GT:AD:DP:GQ:PL:SB	1/1:0,72,0:72:99:2963,217,0,2963,217,2963:0,0,44,28
 20	10005011	.	G	<NON_REF>	.	.	END=10005426	GT:DP:GQ:MIN_DP:PL	0/0:72:99:51:0,120,1800
-20	10005427	.	C	T,<NON_REF>	2214.77	.	DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=195241.00	GT:AD:DP:GQ:PL:SB	1/1:0,55,0:55:99:2243,165,0,2243,165,2243:0,0,27,28
+20	10005427	.	C	T,<NON_REF>	2214.77	.	DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=195241,55	GT:AD:DP:GQ:PL:SB	1/1:0,55,0:55:99:2243,165,0,2243,165,2243:0,0,27,28
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-20	10005499	.	A	G,<NON_REF>	3053.77	.	DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=273600.00	GT:AD:DP:GQ:PL:SB	1/1:0,76,0:76:99:3082,229,0,3082,229,3082:0,0,45,31
+20	10005499	.	A	G,<NON_REF>	3053.77	.	DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=273600,76	GT:AD:DP:GQ:PL:SB	1/1:0,76,0:76:99:3082,229,0,3082,229,3082:0,0,45,31
 20	10005500	.	T	<NON_REF>	.	.	END=10005586	GT:DP:GQ:MIN_DP:PL	0/0:71:99:66:0,120,1800
-20	10005587	.	A	G,<NON_REF>	1229.77	.	BaseQRankSum=-0.834;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.972;RAW_MQ=256969.00;ReadPosRankSum=0.248	GT:AD:DP:GQ:PL:SB	0/1:36,36,0:72:99:1258,0,1236,1366,1345,2710:19,17,16,20
+20	10005587	.	A	G,<NON_REF>	1229.77	.	BaseQRankSum=-0.834;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.972;RAW_MQandDP=256969,72;ReadPosRankSum=0.248	GT:AD:DP:GQ:PL:SB	0/1:36,36,0:72:99:1258,0,1236,1366,1345,2710:19,17,16,20
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-20	10005723	.	A	G,<NON_REF>	3062.77	.	DP=86;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=307369.00	GT:AD:DP:GQ:PL:SB	1/1:0,86,0:86:99:3091,258,0,3091,258,3091:0,0,48,38
+20	10005723	.	A	G,<NON_REF>	3062.77	.	DP=86;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=307369,86	GT:AD:DP:GQ:PL:SB	1/1:0,86,0:86:99:3091,258,0,3091,258,3091:0,0,48,38
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-20	10006291	.	G	A,<NON_REF>	978.77	.	BaseQRankSum=0.311;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.081;RAW_MQ=295179.00;ReadPosRankSum=-1.447	GT:AD:DP:GQ:PL:SB	0/1:53,31,0:84:99:1007,0,1905,1167,1998,3165:25,28,16,15
+20	10006291	.	G	A,<NON_REF>	978.77	.	BaseQRankSum=0.311;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.081;RAW_MQandDP=295179,84;ReadPosRankSum=-1.447	GT:AD:DP:GQ:PL:SB	0/1:53,31,0:84:99:1007,0,1905,1167,1998,3165:25,28,16,15
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-20	10006404	.	A	C,<NON_REF>	2928.77	.	DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=269451.00	GT:AD:DP:GQ:PL:SB	1/1:0,76,0:76:99:2957,228,0,2957,228,2957:0,0,27,49
+20	10006404	.	A	C,<NON_REF>	2928.77	.	DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=269451,77	GT:AD:DP:GQ:PL:SB	1/1:0,76,0:76:99:2957,228,0,2957,228,2957:0,0,27,49
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-20	10006682	.	T	A,<NON_REF>	2874.77	.	DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=257810.00	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2903,219,0,2903,219,2903:0,0,44,29
+20	10006682	.	T	A,<NON_REF>	2874.77	.	DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=257810,73	GT:AD:DP:GQ:PL:SB	1/1:0,73,0:73:99:2903,219,0,2903,219,2903:0,0,44,29
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-20	10006819	.	AAAAC	A,<NON_REF>	2531.73	.	DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=284000.00	GT:AD:DP:GQ:PL:SB	1/1:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28
+20	10006819	.	AAAAC	A,<NON_REF>	2531.73	.	DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=284000,76	GT:AD:DP:GQ:PL:SB	1/1:0,58,0:58:99:2569,176,0,2569,176,2569:0,0,30,28
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-20	10007150	.	G	C,<NON_REF>	669.77	.	BaseQRankSum=-4.476;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=226800.00;ReadPosRankSum=-0.077	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:38,25,0:63:99:0|1:10007150_G_C:698,0,1479,813,1554,2366:16,22,14,11
+20	10007150	.	G	C,<NON_REF>	669.77	.	BaseQRankSum=-4.476;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=226800,63;ReadPosRankSum=-0.077	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:38,25,0:63:99:0|1:10007150_G_C:698,0,1479,813,1554,2366:16,22,14,11
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-20	10007175	.	C	T,<NON_REF>	1350.77	.	BaseQRankSum=2.249;DP=61;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.319;RAW_MQ=216841.00;ReadPosRankSum=-1.213	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:23,38,0:61:99:1|0:10007150_G_C:1379,0,780,1448,894,2343:9,14,18,20
+20	10007175	.	C	T,<NON_REF>	1350.77	.	BaseQRankSum=2.249;DP=61;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.319;RAW_MQandDP=216841,61;ReadPosRankSum=-1.213	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:23,38,0:61:99:1|0:10007150_G_C:1379,0,780,1448,894,2343:9,14,18,20
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-20	10007352	.	C	T,<NON_REF>	2764.77	.	DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=245641.00	GT:AD:DP:GQ:PL:SB	1/1:0,69,0:69:99:2793,208,0,2793,208,2793:0,0,29,40
+20	10007352	.	C	T,<NON_REF>	2764.77	.	DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=245641,69	GT:AD:DP:GQ:PL:SB	1/1:0,69,0:69:99:2793,208,0,2793,208,2793:0,0,29,40
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-20	10007531	.	A	G,<NON_REF>	2920.77	.	DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=256969.00	GT:AD:DP:GQ:PL:SB	1/1:0,72,0:72:99:2949,217,0,2949,217,2949:0,0,48,24
+20	10007531	.	A	G,<NON_REF>	2920.77	.	DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=256969,72	GT:AD:DP:GQ:PL:SB	1/1:0,72,0:72:99:2949,217,0,2949,217,2949:0,0,48,24
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-20	10007980	.	A	C,<NON_REF>	3524.77	.	DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=331800.00	GT:AD:DP:GQ:PL:SB	1/1:0,90,0:90:99:3553,270,0,3553,270,3553:0,0,39,51
+20	10007980	.	A	C,<NON_REF>	3524.77	.	DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=331800,90	GT:AD:DP:GQ:PL:SB	1/1:0,90,0:90:99:3553,270,0,3553,270,3553:0,0,39,51
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-20	10008029	.	T	TA,<NON_REF>	1986.73	.	BaseQRankSum=0.409;DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.576;RAW_MQ=327251.00;ReadPosRankSum=-1.326	GT:AD:DP:GQ:PL:SB	1/1:3,72,0:75:99:2024,145,0,2033,222,2110:1,2,27,45
+20	10008029	.	T	TA,<NON_REF>	1986.73	.	BaseQRankSum=0.409;DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.576;RAW_MQandDP=327251,88;ReadPosRankSum=-1.326	GT:AD:DP:GQ:PL:SB	1/1:3,72,0:75:99:2024,145,0,2033,222,2110:1,2,27,45
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-20	10008146	.	TA	T,<NON_REF>	2141.73	.	DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=268000.00	GT:AD:DP:GQ:PL:SB	1/1:0,70,0:70:99:2179,211,0,2179,211,2179:0,0,38,32
+20	10008146	.	TA	T,<NON_REF>	2141.73	.	DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=268000,73	GT:AD:DP:GQ:PL:SB	1/1:0,70,0:70:99:2179,211,0,2179,211,2179:0,0,38,32
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-20	10008221	.	T	C,<NON_REF>	3224.77	.	DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=289669.00	GT:AD:DP:GQ:PL:SB	1/1:0,80,0:80:99:3253,240,0,3253,240,3253:0,0,43,37
+20	10008221	.	T	C,<NON_REF>	3224.77	.	DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=289669,80	GT:AD:DP:GQ:PL:SB	1/1:0,80,0:80:99:3253,240,0,3253,240,3253:0,0,43,37
 20	10008222	.	T	<NON_REF>	.	.	END=10008457	GT:DP:GQ:MIN_DP:PL	0/0:64:99:45:0,108,1620
-20	10008458	.	T	G,<NON_REF>	2654.77	.	DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=191842.00	GT:AD:DP:GQ:PL:SB	1/1:0,69,0:69:99:2683,207,0,2683,207,2683:0,0,30,39
+20	10008458	.	T	G,<NON_REF>	2654.77	.	DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=191842,69	GT:AD:DP:GQ:PL:SB	1/1:0,69,0:69:99:2683,207,0,2683,207,2683:0,0,30,39
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-20	10008742	.	G	T,<NON_REF>	715.77	.	BaseQRankSum=3.893;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQ=67874.00;ReadPosRankSum=0.190	GT:AD:DP:GQ:PL:SB	0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15
+20	10008742	.	G	T,<NON_REF>	715.77	.	BaseQRankSum=3.893;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQandDP=67874,49;ReadPosRankSum=0.190	GT:AD:DP:GQ:PL:SB	0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15
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-20	10008758	.	C	CA,<NON_REF>	684.14	.	BaseQRankSum=0.130;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-1.168;RAW_MQ=54656.00;ReadPosRankSum=-0.052	GT:AD:DP:GQ:PL:SB	1/1:4,31,0:35:10:721,10,0,733,102,825:3,1,16,15
+20	10008758	.	C	CA,<NON_REF>	684.14	.	BaseQRankSum=0.130;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-1.168;RAW_MQandDP=54656,44;ReadPosRankSum=-0.052	GT:AD:DP:GQ:PL:SB	1/1:4,31,0:35:10:721,10,0,733,102,825:3,1,16,15
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-20	10008921	.	C	CA,<NON_REF>	253.73	.	BaseQRankSum=0.610;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.906;RAW_MQ=155512.00;ReadPosRankSum=0.173	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:10,8,8,8
+20	10008921	.	C	CA,<NON_REF>	253.73	.	BaseQRankSum=0.610;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.906;RAW_MQandDP=155512,49;ReadPosRankSum=0.173	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:10,8,8,8
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-20	10008948	.	TA	T,<NON_REF>	2057.73	.	BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQ=138622.00;ReadPosRankSum=0.884	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15
+20	10008948	.	TA	T,<NON_REF>	2057.73	.	BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQandDP=138622,52;ReadPosRankSum=0.884	GT:AD:DP:GQ:PGT:PID:PL:SB	1/1:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15
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-20	10008952	.	CACACACACACACA	C,CCA,CCACACACACA,CCACACACACACA,<NON_REF>	1666.73	.	BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQ=154068.00;ReadPosRankSum=0.716	GT:AD:DP:GQ:PL:SB	2/4:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8
+20	10008952	.	CACACACACACACA	C,CCA,CCACACACACA,CCACACACACACA,<NON_REF>	1666.73	.	BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=154068,59;ReadPosRankSum=0.716	GT:AD:DP:GQ:PL:SB	2/4:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8
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-20	10009227	.	A	G,<NON_REF>	1369.77	.	BaseQRankSum=-2.220;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.428;RAW_MQ=202588.00;ReadPosRankSum=-1.159	GT:AD:DP:GQ:PL:SB	0/1:23,39,0:62:99:1398,0,740,1468,857,2325:16,7,19,20
+20	10009227	.	A	G,<NON_REF>	1369.77	.	BaseQRankSum=-2.220;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.428;RAW_MQandDP=202588,62;ReadPosRankSum=-1.159	GT:AD:DP:GQ:PL:SB	0/1:23,39,0:62:99:1398,0,740,1468,857,2325:16,7,19,20
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-20	10009246	.	A	G,<NON_REF>	3002.77	.	DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=242208.00	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:3031,231,0,3031,231,3031:0,0,42,35
+20	10009246	.	A	G,<NON_REF>	3002.77	.	DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=242208,77	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:3031,231,0,3031,231,3031:0,0,42,35
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-20	10009400	.	T	A,<NON_REF>	2998.77	.	DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=266400.00	GT:AD:DP:GQ:PL:SB	1/1:0,74,0:74:99:3027,223,0,3027,223,3027:0,0,39,35
+20	10009400	.	T	A,<NON_REF>	2998.77	.	DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=266400,74	GT:AD:DP:GQ:PL:SB	1/1:0,74,0:74:99:3027,223,0,3027,223,3027:0,0,39,35
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-20	10009512	.	C	G,<NON_REF>	3039.77	.	DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=263240.00	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:3068,231,0,3068,231,3068:0,0,30,47
+20	10009512	.	C	G,<NON_REF>	3039.77	.	DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=263240,77	GT:AD:DP:GQ:PL:SB	1/1:0,77,0:77:99:3068,231,0,3068,231,3068:0,0,30,47
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-20	10009719	.	A	G,<NON_REF>	1895.77	.	DP=59;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=207410.00	GT:AD:DP:GQ:PL:SB	1/1:0,59,0:59:99:1924,175,0,1924,175,1924:0,0,26,33
+20	10009719	.	A	G,<NON_REF>	1895.77	.	DP=59;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=207410,59	GT:AD:DP:GQ:PL:SB	1/1:0,59,0:59:99:1924,175,0,1924,175,1924:0,0,26,33
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-20	10009795	.	A	G,<NON_REF>	1880.77	.	DP=47;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=166969.00	GT:AD:DP:GQ:PL:SB	1/1:0,47,0:47:99:1909,141,0,1909,141,1909:0,0,16,31
+20	10009795	.	A	G,<NON_REF>	1880.77	.	DP=47;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=166969,47	GT:AD:DP:GQ:PL:SB	1/1:0,47,0:47:99:1909,141,0,1909,141,1909:0,0,16,31
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-20	10009842	.	G	GAA,<NON_REF>	532.73	.	BaseQRankSum=0.872;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.603;RAW_MQ=150092.00;ReadPosRankSum=1.720	GT:AD:DP:GQ:PL:SB	0/1:19,15,0:34:99:570,0,690,629,738,1367:9,10,8,7
+20	10009842	.	G	GAA,<NON_REF>	532.73	.	BaseQRankSum=0.872;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.603;RAW_MQandDP=150092,51;ReadPosRankSum=1.720	GT:AD:DP:GQ:PL:SB	0/1:19,15,0:34:99:570,0,690,629,738,1367:9,10,8,7
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-20	10009844	.	G	A,<NON_REF>	661.77	.	BaseQRankSum=1.048;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQ=147168.00;ReadPosRankSum=-1.555	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:8,8,9,10
+20	10009844	.	G	A,<NON_REF>	661.77	.	BaseQRankSum=1.048;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQandDP=147168,51;ReadPosRankSum=-1.555	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:8,8,9,10
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@@ -303,13 +303,13 @@
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+20	10009871	.	A	G,<NON_REF>	658.77	.	BaseQRankSum=-0.803;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.495;RAW_MQandDP=154737,60;ReadPosRankSum=1.539	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:17,19,0:36:99:0|1:10009844_G_A:687,0,594,739,652,1391:10,7,9,10
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+20	10009875	.	A	G,AGGGAGG,<NON_REF>	2369.73	.	BaseQRankSum=0.378;DP=57;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.361;RAW_MQandDP=143937,57;ReadPosRankSum=1.040	GT:AD:DP:GQ:PL:SB	1/2:2,15,13,0:30:99:2407,645,533,697,0,574,1881,655,700,1805:2,0,12,16
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@@ -390,7 +390,7 @@
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@@ -399,9 +399,9 @@
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@@ -441,22 +441,22 @@
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@@ -467,9 +467,9 @@
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@@ -489,11 +489,11 @@
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@@ -511,7 +511,7 @@
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@@ -525,7 +525,7 @@
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@@ -562,13 +562,13 @@
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+20	10013119	.	C	T,<NON_REF>	1011.77	.	BaseQRankSum=2.724;DP=59;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.089;RAW_MQandDP=156381,59;ReadPosRankSum=0.159	GT:AD:DP:GQ:PL:SB	0/1:29,30,0:59:99:1040,0,936,1127,1026,2153:19,10,17,13
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+20	10014990	.	C	CAT,<NON_REF>	1237.73	.	BaseQRankSum=1.930;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.107;RAW_MQandDP=321369,87;ReadPosRankSum=-0.437	GT:AD:DP:GQ:PL:SB	0/1:38,38,0:76:99:1275,0,1248,1389,1365,2755:28,10,25,13
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@@ -631,7 +631,7 @@
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+20	10015679	.	C	T,<NON_REF>	140.77	.	BaseQRankSum=0.200;DP=10;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=36000,10;ReadPosRankSum=0.497	GT:AD:DP:GQ:PL:SB	0/1:5,5,0:10:99:169,0,166,184,181,365:5,0,5,0
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@@ -654,7 +654,7 @@
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+20	10015761	.	T	C,<NON_REF>	344.77	.	BaseQRankSum=-1.982;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.294;RAW_MQandDP=76441,22;ReadPosRankSum=1.805	GT:AD:DP:GQ:PL:SB	0/1:9,13,0:22:99:373,0,284,400,323,723:9,0,12,1
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@@ -678,21 +678,21 @@
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-20	10024107	.	C	T,<NON_REF>	1694.77	.	BaseQRankSum=5.770;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.546;RAW_MQ=303563.00;ReadPosRankSum=0.148	GT:AD:DP:GQ:PL:SB	0/1:38,48,0:86:99:1723,0,1086,1837,1230,3068:21,17,28,20
+20	10024107	.	C	T,<NON_REF>	1694.77	.	BaseQRankSum=5.770;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.546;RAW_MQandDP=303563,86;ReadPosRankSum=0.148	GT:AD:DP:GQ:PL:SB	0/1:38,48,0:86:99:1723,0,1086,1837,1230,3068:21,17,28,20
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@@ -703,7 +703,7 @@
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-20	10024300	.	CTT	C,CT,CTTTT,<NON_REF>	87.76	.	BaseQRankSum=2.446;DP=50;ExcessHet=3.0103;MLEAC=1,0,1,0;MLEAF=0.500,0.00,0.500,0.00;MQRankSum=-0.600;RAW_MQ=134695.00;ReadPosRankSum=-1.073	GT:AD:DP:GQ:PL:SB	1/3:3,4,3,8,0:18:1:122,67,400,91,215,231,19,0,1,156,161,279,257,107,347:1,2,11,4
+20	10024300	.	CTT	C,CT,CTTTT,<NON_REF>	87.76	.	BaseQRankSum=2.446;DP=50;ExcessHet=3.0103;MLEAC=1,0,1,0;MLEAF=0.500,0.00,0.500,0.00;MQRankSum=-0.600;RAW_MQandDP=134695,50;ReadPosRankSum=-1.073	GT:AD:DP:GQ:PL:SB	1/3:3,4,3,8,0:18:1:122,67,400,91,215,231,19,0,1,156,161,279,257,107,347:1,2,11,4
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@@ -718,41 +718,41 @@
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-20	10026357	.	T	C,<NON_REF>	1166.77	.	BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.148;RAW_MQ=215117.00;ReadPosRankSum=-0.076	GT:AD:DP:GQ:PL:SB	0/1:28,35,0:63:99:1195,0,932,1279,1037,2316:10,18,20,15
+20	10026357	.	T	C,<NON_REF>	1166.77	.	BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.148;RAW_MQandDP=215117,63;ReadPosRankSum=-0.076	GT:AD:DP:GQ:PL:SB	0/1:28,35,0:63:99:1195,0,932,1279,1037,2316:10,18,20,15
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-20	10026794	.	C	T,<NON_REF>	1084.77	.	BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQ=184441.00;ReadPosRankSum=-0.533	GT:AD:DP:GQ:PL:SB	0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18
+20	10026794	.	C	T,<NON_REF>	1084.77	.	BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQandDP=184441,52;ReadPosRankSum=-0.533	GT:AD:DP:GQ:PL:SB	0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18
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-20	10027234	.	A	ATTAG,<NON_REF>	1320.73	.	BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQ=236651.00;ReadPosRankSum=-0.979	GT:AD:DP:GQ:PL:SB	0/1:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20
+20	10027234	.	A	ATTAG,<NON_REF>	1320.73	.	BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=236651,72;ReadPosRankSum=-0.979	GT:AD:DP:GQ:PL:SB	0/1:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20
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-20	10027868	.	A	G,<NON_REF>	1739.77	.	BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQ=314882.00;ReadPosRankSum=1.872	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:19,25,26,19
+20	10027868	.	A	G,<NON_REF>	1739.77	.	BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQandDP=314882,89;ReadPosRankSum=1.872	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:19,25,26,19
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-20	10027872	.	A	G,<NON_REF>	1724.77	.	BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQ=300482.00;ReadPosRankSum=1.053	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:16,24,26,19
+20	10027872	.	A	G,<NON_REF>	1724.77	.	BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQandDP=300482,85;ReadPosRankSum=1.053	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:16,24,26,19
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-20	10028867	.	A	ATG,<NON_REF>	1106.73	.	BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQ=338841.00;ReadPosRankSum=0.364	GT:AD:DP:GQ:PL:SB	0/1:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21
+20	10028867	.	A	ATG,<NON_REF>	1106.73	.	BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQandDP=338841,92;ReadPosRankSum=0.364	GT:AD:DP:GQ:PL:SB	0/1:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21
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-20	10030188	.	T	A,<NON_REF>	1372.77	.	BaseQRankSum=0.711;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.013;RAW_MQ=288841.00;ReadPosRankSum=-0.553	GT:AD:DP:GQ:PL:SB	0/1:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24
+20	10030188	.	T	A,<NON_REF>	1372.77	.	BaseQRankSum=0.711;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.013;RAW_MQandDP=288841,81;ReadPosRankSum=-0.553	GT:AD:DP:GQ:PL:SB	0/1:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24
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-20	10031254	.	A	AT,<NON_REF>	1463.73	.	BaseQRankSum=-0.091;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQ=309510.00;ReadPosRankSum=0.495	GT:AD:DP:GQ:PL:SB	0/1:38,47,0:85:99:1501,0,1159,1616,1300,2916:27,11,25,22
+20	10031254	.	A	AT,<NON_REF>	1463.73	.	BaseQRankSum=-0.091;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQandDP=309510,87;ReadPosRankSum=0.495	GT:AD:DP:GQ:PL:SB	0/1:38,47,0:85:99:1501,0,1159,1616,1300,2916:27,11,25,22
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-20	10031342	.	G	A,<NON_REF>	1834.77	.	BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQ=332041.00;ReadPosRankSum=-0.012	GT:AD:DP:GQ:PL:SB	0/1:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21
+20	10031342	.	G	A,<NON_REF>	1834.77	.	BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQandDP=332041,93;ReadPosRankSum=-0.012	GT:AD:DP:GQ:PL:SB	0/1:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21
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-20	10031798	.	G	A,<NON_REF>	4296.77	.	DP=104;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=369410.00	GT:AD:DP:GQ:PL:SB	1/1:0,104,0:104:99:4325,313,0,4325,313,4325:0,0,57,47
+20	10031798	.	G	A,<NON_REF>	4296.77	.	DP=104;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=369410,104	GT:AD:DP:GQ:PL:SB	1/1:0,104,0:104:99:4325,313,0,4325,313,4325:0,0,57,47
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-20	10031827	.	C	T,<NON_REF>	2004.77	.	BaseQRankSum=3.552;DP=108;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.945;RAW_MQ=386569.00;ReadPosRankSum=-1.396	GT:AD:DP:GQ:PL:SB	0/1:52,56,0:108:99:2033,0,1798,2189,1966,4155:32,20,29,27
+20	10031827	.	C	T,<NON_REF>	2004.77	.	BaseQRankSum=3.552;DP=108;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.945;RAW_MQandDP=386569,108;ReadPosRankSum=-1.396	GT:AD:DP:GQ:PL:SB	0/1:52,56,0:108:99:2033,0,1798,2189,1966,4155:32,20,29,27
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-20	10032094	.	G	A,<NON_REF>	1220.77	.	BaseQRankSum=5.488;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=298800.00;ReadPosRankSum=-0.579	GT:AD:DP:GQ:PL:SB	0/1:47,36,0:83:99:1249,0,1497,1390,1605,2995:14,33,16,20
+20	10032094	.	G	A,<NON_REF>	1220.77	.	BaseQRankSum=5.488;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=298800,83;ReadPosRankSum=-0.579	GT:AD:DP:GQ:PL:SB	0/1:47,36,0:83:99:1249,0,1497,1390,1605,2995:14,33,16,20
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-20	10032413	.	T	G,<NON_REF>	869.77	.	BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.065;RAW_MQ=233138.00;ReadPosRankSum=-1.003	GT:AD:DP:GQ:PL:SB	0/1:35,31,0:66:99:898,0,1277,1003,1371,2374:15,20,20,11
+20	10032413	.	T	G,<NON_REF>	869.77	.	BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.065;RAW_MQandDP=233138,66;ReadPosRankSum=-1.003	GT:AD:DP:GQ:PL:SB	0/1:35,31,0:66:99:898,0,1277,1003,1371,2374:15,20,20,11
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-20	10032882	.	A	T,<NON_REF>	1202.77	.	BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQ=267241.00;ReadPosRankSum=0.626	GT:AD:DP:GQ:PL:SB	0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14
+20	10032882	.	A	T,<NON_REF>	1202.77	.	BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQandDP=267241,75;ReadPosRankSum=0.626	GT:AD:DP:GQ:PL:SB	0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14
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-20	10032972	.	C	CAT,<NON_REF>	1122.73	.	BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQ=231241.00;ReadPosRankSum=-1.232	GT:AD:DP:GQ:PL:SB	0/1:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19
+20	10032972	.	C	CAT,<NON_REF>	1122.73	.	BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=231241,65;ReadPosRankSum=-1.232	GT:AD:DP:GQ:PL:SB	0/1:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19
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+20	10034306	.	T	C,<NON_REF>	782.77	.	BaseQRankSum=-3.661;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.150;RAW_MQandDP=268610,76;ReadPosRankSum=0.539	GT:AD:DP:GQ:PL:SB	0/1:46,29,0:75:99:811,0,1593,950,1680,2630:24,22,14,15
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@@ -766,7 +766,7 @@
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@@ -1026,43 +1026,43 @@
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-20	10086954	.	G	A,<NON_REF>	1095.77	.	BaseQRankSum=2.606;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=244800.00;ReadPosRankSum=-0.534	GT:AD:DP:GQ:PL:SB	0/1:34,34,0:68:99:1124,0,1051,1226,1153,2380:16,18,21,13
+20	10086954	.	G	A,<NON_REF>	1095.77	.	BaseQRankSum=2.606;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=244800,68;ReadPosRankSum=-0.534	GT:AD:DP:GQ:PL:SB	0/1:34,34,0:68:99:1124,0,1051,1226,1153,2380:16,18,21,13
 20	10086955	.	C	<NON_REF>	.	.	END=10087229	GT:DP:GQ:MIN_DP:PL	0/0:70:99:55:0,120,1800
-20	10087230	.	A	G,<NON_REF>	1842.77	.	BaseQRankSum=-2.407;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.707;RAW_MQ=332861.00;ReadPosRankSum=0.307	GT:AD:DP:GQ:PL:SB	0/1:42,54,0:96:99:1871,0,1428,1998,1590,3588:22,20,23,31
+20	10087230	.	A	G,<NON_REF>	1842.77	.	BaseQRankSum=-2.407;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.707;RAW_MQandDP=332861,96;ReadPosRankSum=0.307	GT:AD:DP:GQ:PL:SB	0/1:42,54,0:96:99:1871,0,1428,1998,1590,3588:22,20,23,31
 20	10087231	.	C	<NON_REF>	.	.	END=10087393	GT:DP:GQ:MIN_DP:PL	0/0:101:99:84:0,120,1800
-20	10087394	.	T	G,<NON_REF>	1688.77	.	BaseQRankSum=-2.340;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.207;RAW_MQ=299641.00;ReadPosRankSum=0.885	GT:AD:DP:GQ:PL:SB	0/1:35,49,0:84:99:1717,0,1186,1823,1334,3156:21,14,24,25
+20	10087394	.	T	G,<NON_REF>	1688.77	.	BaseQRankSum=-2.340;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.207;RAW_MQandDP=299641,84;ReadPosRankSum=0.885	GT:AD:DP:GQ:PL:SB	0/1:35,49,0:84:99:1717,0,1186,1823,1334,3156:21,14,24,25
 20	10087395	.	T	<NON_REF>	.	.	END=10087753	GT:DP:GQ:MIN_DP:PL	0/0:83:99:61:0,120,1800
-20	10087754	.	T	G,<NON_REF>	1347.77	.	BaseQRankSum=0.355;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.193;RAW_MQ=288141.00;ReadPosRankSum=-0.551	GT:AD:DP:GQ:PL:SB	0/1:37,41,0:78:99:1376,0,1239,1488,1362,2849:23,14,24,17
+20	10087754	.	T	G,<NON_REF>	1347.77	.	BaseQRankSum=0.355;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.193;RAW_MQandDP=288141,79;ReadPosRankSum=-0.551	GT:AD:DP:GQ:PL:SB	0/1:37,41,0:78:99:1376,0,1239,1488,1362,2849:23,14,24,17
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-20	10087804	.	C	T,<NON_REF>	1619.77	.	BaseQRankSum=1.940;DP=100;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.618;RAW_MQ=369310.00;ReadPosRankSum=0.341	GT:AD:DP:GQ:PL:SB	0/1:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22
+20	10087804	.	C	T,<NON_REF>	1619.77	.	BaseQRankSum=1.940;DP=100;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.618;RAW_MQandDP=369310,100;ReadPosRankSum=0.341	GT:AD:DP:GQ:PL:SB	0/1:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22
 20	10087805	.	G	<NON_REF>	.	.	END=10087819	GT:DP:GQ:MIN_DP:PL	0/0:101:99:96:0,120,1800
-20	10087820	.	CAG	C,CAGAG,<NON_REF>	428.73	.	BaseQRankSum=-1.974;DP=99;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQ=362700.00;ReadPosRankSum=-0.357	GT:AD:DP:GQ:PL:SB	0/2:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:17,18,8,10
+20	10087820	.	CAG	C,CAGAG,<NON_REF>	428.73	.	BaseQRankSum=-1.974;DP=99;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQandDP=362700,99;ReadPosRankSum=-0.357	GT:AD:DP:GQ:PL:SB	0/2:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:17,18,8,10
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-20	10088063	.	C	T,<NON_REF>	1417.77	.	BaseQRankSum=3.405;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.515;RAW_MQ=327579.00;ReadPosRankSum=0.285	GT:AD:DP:GQ:PL:SB	0/1:49,44,0:93:99:1446,0,1403,1592,1535,3128:24,25,18,26
+20	10088063	.	C	T,<NON_REF>	1417.77	.	BaseQRankSum=3.405;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.515;RAW_MQandDP=327579,93;ReadPosRankSum=0.285	GT:AD:DP:GQ:PL:SB	0/1:49,44,0:93:99:1446,0,1403,1592,1535,3128:24,25,18,26
 20	10088064	.	G	<NON_REF>	.	.	END=10088698	GT:DP:GQ:MIN_DP:PL	0/0:87:99:60:0,120,1800
-20	10088699	.	C	T,<NON_REF>	776.77	.	BaseQRankSum=3.803;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.140;RAW_MQ=199738.00;ReadPosRankSum=-1.456	GT:AD:DP:GQ:PL:SB	0/1:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7
+20	10088699	.	C	T,<NON_REF>	776.77	.	BaseQRankSum=3.803;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.140;RAW_MQandDP=199738,63;ReadPosRankSum=-1.456	GT:AD:DP:GQ:PL:SB	0/1:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7
 20	10088700	.	G	<NON_REF>	.	.	END=10088729	GT:DP:GQ:MIN_DP:PL	0/0:53:99:51:0,120,1800
-20	10088730	.	G	A,<NON_REF>	972.77	.	BaseQRankSum=0.224;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.839;RAW_MQ=148358.00;ReadPosRankSum=0.581	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:29,23,0:52:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:11,18,16,7
+20	10088730	.	G	A,<NON_REF>	972.77	.	BaseQRankSum=0.224;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.839;RAW_MQandDP=148358,52;ReadPosRankSum=0.581	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:29,23,0:52:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:11,18,16,7
 20	10088731	.	G	<NON_REF>	.	.	END=10088735	GT:DP:GQ:MIN_DP:PL	0/0:55:99:55:0,120,1800
-20	10088736	.	A	C,<NON_REF>	1081.77	.	BaseQRankSum=0.282;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.169;RAW_MQ=149682.00;ReadPosRankSum=0.573	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:28,27,0:55:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10,18,16,11
+20	10088736	.	A	C,<NON_REF>	1081.77	.	BaseQRankSum=0.282;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.169;RAW_MQandDP=149682,55;ReadPosRankSum=0.573	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:28,27,0:55:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10,18,16,11
 20	10088737	.	C	<NON_REF>	.	.	END=10088746	GT:DP:GQ:MIN_DP:PL	0/0:56:99:53:0,120,1800
-20	10088747	.	A	G,<NON_REF>	1111.77	.	BaseQRankSum=-3.877;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.907;RAW_MQ=146239.00;ReadPosRankSum=0.009	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10,15,18,11
+20	10088747	.	A	G,<NON_REF>	1111.77	.	BaseQRankSum=-3.877;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.907;RAW_MQandDP=146239,55;ReadPosRankSum=0.009	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10,15,18,11
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-20	10088799	.	G	A,<NON_REF>	1018.77	.	BaseQRankSum=5.503;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.498;RAW_MQ=150040.00;ReadPosRankSum=1.075	GT:AD:DP:GQ:PL:SB	0/1:22,31,0:53:99:1047,0,617,1114,711,1824:14,8,12,19
+20	10088799	.	G	A,<NON_REF>	1018.77	.	BaseQRankSum=5.503;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.498;RAW_MQandDP=150040,53;ReadPosRankSum=1.075	GT:AD:DP:GQ:PL:SB	0/1:22,31,0:53:99:1047,0,617,1114,711,1824:14,8,12,19
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 20	10088843	.	C	<NON_REF>	.	.	END=10088843	GT:DP:GQ:MIN_DP:PL	0/0:25:16:25:0,16,759
@@ -1081,13 +1081,13 @@
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-20	10088895	.	C	T,<NON_REF>	532.77	.	BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.577;RAW_MQ=134450.00;ReadPosRankSum=1.301	GT:AD:DP:GQ:PL:SB	0/1:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10
+20	10088895	.	C	T,<NON_REF>	532.77	.	BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.577;RAW_MQandDP=134450,41;ReadPosRankSum=1.301	GT:AD:DP:GQ:PL:SB	0/1:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10
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-20	10088968	.	C	CAAA,<NON_REF>	1175.73	.	BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQ=177808.00;ReadPosRankSum=2.416	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:16,14,14,9
+20	10088968	.	C	CAAA,<NON_REF>	1175.73	.	BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQandDP=177808,62;ReadPosRankSum=2.416	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:16,14,14,9
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-20	10088980	.	T	C,<NON_REF>	1247.77	.	BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQ=176353.00;ReadPosRankSum=1.288	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:19,18,15,16
+20	10088980	.	T	C,<NON_REF>	1247.77	.	BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQandDP=176353,68;ReadPosRankSum=1.288	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:19,18,15,16
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-20	10088985	.	T	C,<NON_REF>	1178.77	.	BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQ=191764.00;ReadPosRankSum=1.228	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:22,20,15,17
+20	10088985	.	T	C,<NON_REF>	1178.77	.	BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQandDP=191764,74;ReadPosRankSum=1.228	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:22,20,15,17
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@@ -1101,69 +1101,69 @@
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-20	10089441	.	A	G,<NON_REF>	1179.77	.	BaseQRankSum=-4.885;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.948;RAW_MQ=270841.00;ReadPosRankSum=-0.156	GT:AD:DP:GQ:PL:SB	0/1:37,39,0:76:99:1208,0,1313,1319,1430,2749:19,18,14,25
+20	10089441	.	A	G,<NON_REF>	1179.77	.	BaseQRankSum=-4.885;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.948;RAW_MQandDP=270841,76;ReadPosRankSum=-0.156	GT:AD:DP:GQ:PL:SB	0/1:37,39,0:76:99:1208,0,1313,1319,1430,2749:19,18,14,25
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-20	10089525	.	C	T,<NON_REF>	1548.77	.	BaseQRankSum=5.859;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.531;RAW_MQ=286610.00;ReadPosRankSum=0.862	GT:AD:DP:GQ:PL:SB	0/1:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23
+20	10089525	.	C	T,<NON_REF>	1548.77	.	BaseQRankSum=5.859;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.531;RAW_MQandDP=286610,81;ReadPosRankSum=0.862	GT:AD:DP:GQ:PL:SB	0/1:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23
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-20	10090289	.	CAA	C,CA,<NON_REF>	384.73	.	BaseQRankSum=0.441;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.393;RAW_MQ=287682.00;ReadPosRankSum=0.048	GT:AD:DP:GQ:PL:SB	0/2:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:7,7,11,13
+20	10090289	.	CAA	C,CA,<NON_REF>	384.73	.	BaseQRankSum=0.441;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.393;RAW_MQandDP=287682,80;ReadPosRankSum=0.048	GT:AD:DP:GQ:PL:SB	0/2:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:7,7,11,13
 20	10090292	.	A	<NON_REF>	.	.	END=10090763	GT:DP:GQ:MIN_DP:PL	0/0:75:99:61:0,120,1800
-20	10090764	.	A	G,<NON_REF>	840.77	.	BaseQRankSum=-2.659;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=226800.00;ReadPosRankSum=1.207	GT:AD:DP:GQ:PL:SB	0/1:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15
+20	10090764	.	A	G,<NON_REF>	840.77	.	BaseQRankSum=-2.659;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=226800,63;ReadPosRankSum=1.207	GT:AD:DP:GQ:PL:SB	0/1:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15
 20	10090765	.	A	<NON_REF>	.	.	END=10090969	GT:DP:GQ:MIN_DP:PL	0/0:75:99:65:0,120,1800
-20	10090970	.	T	C,<NON_REF>	1257.77	.	BaseQRankSum=-0.484;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.509;RAW_MQ=243938.00;ReadPosRankSum=-0.072	GT:AD:DP:GQ:PL:SB	0/1:33,36,0:69:99:1286,0,1092,1384,1201,2585:20,13,20,16
+20	10090970	.	T	C,<NON_REF>	1257.77	.	BaseQRankSum=-0.484;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.509;RAW_MQandDP=243938,69;ReadPosRankSum=-0.072	GT:AD:DP:GQ:PL:SB	0/1:33,36,0:69:99:1286,0,1092,1384,1201,2585:20,13,20,16
 20	10090971	.	C	<NON_REF>	.	.	END=10091213	GT:DP:GQ:MIN_DP:PL	0/0:61:99:49:0,120,1800
-20	10091214	.	C	T,<NON_REF>	1249.77	.	BaseQRankSum=0.361;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.916;RAW_MQ=249769.00;ReadPosRankSum=-0.035	GT:AD:DP:GQ:PL:SB	0/1:33,37,0:70:99:1278,0,1110,1377,1222,2599:11,22,13,24
+20	10091214	.	C	T,<NON_REF>	1249.77	.	BaseQRankSum=0.361;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.916;RAW_MQandDP=249769,70;ReadPosRankSum=-0.035	GT:AD:DP:GQ:PL:SB	0/1:33,37,0:70:99:1278,0,1110,1377,1222,2599:11,22,13,24
 20	10091215	.	C	<NON_REF>	.	.	END=10092414	GT:DP:GQ:MIN_DP:PL	0/0:69:99:46:0,120,1800
-20	10092415	.	A	G,<NON_REF>	1635.77	.	BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=363600.00;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	0/1:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25
+20	10092415	.	A	G,<NON_REF>	1635.77	.	BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=363600,101;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	0/1:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25
 20	10092416	.	G	<NON_REF>	.	.	END=10092926	GT:DP:GQ:MIN_DP:PL	0/0:80:99:60:0,120,1800
-20	10092927	.	G	T,<NON_REF>	106.77	.	BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.009;RAW_MQ=257282.00;ReadPosRankSum=-0.220	GT:AD:DP:GQ:PL:SB	0/1:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13
+20	10092927	.	G	T,<NON_REF>	106.77	.	BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.009;RAW_MQandDP=257282,73;ReadPosRankSum=-0.220	GT:AD:DP:GQ:PL:SB	0/1:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13
 20	10092928	.	T	<NON_REF>	.	.	END=10093567	GT:DP:GQ:MIN_DP:PL	0/0:79:99:57:0,120,1800
-20	10093568	.	GTT	G,GT,GTTT,<NON_REF>	326.73	.	BaseQRankSum=0.426;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=0.410;RAW_MQ=203561.00;ReadPosRankSum=1.257	GT:AD:DP:GQ:PL:SB	0/2:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:7,10,10,15
+20	10093568	.	GTT	G,GT,GTTT,<NON_REF>	326.73	.	BaseQRankSum=0.426;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=0.410;RAW_MQandDP=203561,59;ReadPosRankSum=1.257	GT:AD:DP:GQ:PL:SB	0/2:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:7,10,10,15
 20	10093571	.	T	<NON_REF>	.	.	END=10093922	GT:DP:GQ:MIN_DP:PL	0/0:62:99:51:0,99,1485
-20	10093923	.	T	A,<NON_REF>	1075.77	.	BaseQRankSum=-0.667;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.358;RAW_MQ=234704.00;ReadPosRankSum=-1.583	GT:AD:DP:GQ:PL:SB	0/1:35,32,0:67:99:1104,0,1257,1209,1353,2563:18,17,15,17
+20	10093923	.	T	A,<NON_REF>	1075.77	.	BaseQRankSum=-0.667;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.358;RAW_MQandDP=234704,67;ReadPosRankSum=-1.583	GT:AD:DP:GQ:PL:SB	0/1:35,32,0:67:99:1104,0,1257,1209,1353,2563:18,17,15,17
 20	10093924	.	G	<NON_REF>	.	.	END=10094250	GT:DP:GQ:MIN_DP:PL	0/0:66:99:53:0,120,1800
-20	10094251	.	T	A,<NON_REF>	1270.77	.	BaseQRankSum=0.251;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=223200.00;ReadPosRankSum=1.806	GT:AD:DP:GQ:PL:SB	0/1:26,36,0:62:99:1299,0,781,1376,889,2265:10,16,23,13
+20	10094251	.	T	A,<NON_REF>	1270.77	.	BaseQRankSum=0.251;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=223200,62;ReadPosRankSum=1.806	GT:AD:DP:GQ:PL:SB	0/1:26,36,0:62:99:1299,0,781,1376,889,2265:10,16,23,13
 20	10094252	.	C	<NON_REF>	.	.	END=10094581	GT:DP:GQ:MIN_DP:PL	0/0:68:99:46:0,117,1755
-20	10094582	.	A	G,<NON_REF>	923.77	.	BaseQRankSum=-1.388;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.270;RAW_MQ=243410.00;ReadPosRankSum=-0.018	GT:AD:DP:GQ:PL:SB	0/1:39,30,0:69:99:952,0,1350,1070,1440,2510:20,19,16,14
+20	10094582	.	A	G,<NON_REF>	923.77	.	BaseQRankSum=-1.388;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.270;RAW_MQandDP=243410,69;ReadPosRankSum=-0.018	GT:AD:DP:GQ:PL:SB	0/1:39,30,0:69:99:952,0,1350,1070,1440,2510:20,19,16,14
 20	10094583	.	T	<NON_REF>	.	.	END=10094773	GT:DP:GQ:MIN_DP:PL	0/0:78:99:67:0,120,1800
-20	10094774	.	C	T,<NON_REF>	1036.77	.	BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQ=267241.00;ReadPosRankSum=0.197	GT:AD:DP:GQ:PL:SB	0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14
+20	10094774	.	C	T,<NON_REF>	1036.77	.	BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQandDP=267241,75;ReadPosRankSum=0.197	GT:AD:DP:GQ:PL:SB	0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14
 20	10094775	.	A	<NON_REF>	.	.	END=10095431	GT:DP:GQ:MIN_DP:PL	0/0:77:99:63:0,120,1800
-20	10095432	.	GTGATGATGA	G,<NON_REF>	839.73	.	BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQ=227748.00;ReadPosRankSum=0.396	GT:AD:DP:GQ:PL:SB	0/1:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11
+20	10095432	.	GTGATGATGA	G,<NON_REF>	839.73	.	BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQandDP=227748,77;ReadPosRankSum=0.396	GT:AD:DP:GQ:PL:SB	0/1:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11
 20	10095442	.	T	<NON_REF>	.	.	END=10095740	GT:DP:GQ:MIN_DP:PL	0/0:80:99:64:0,120,1800
-20	10095741	.	A	G,<NON_REF>	1075.77	.	BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQ=233528.00;ReadPosRankSum=-0.500	GT:AD:DP:GQ:PL:SB	0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16
+20	10095741	.	A	G,<NON_REF>	1075.77	.	BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQandDP=233528,71;ReadPosRankSum=-0.500	GT:AD:DP:GQ:PL:SB	0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16
 20	10095742	.	G	<NON_REF>	.	.	END=10096292	GT:DP:GQ:MIN_DP:PL	0/0:73:99:63:0,120,1800
-20	10096293	.	C	T,<NON_REF>	1355.77	.	BaseQRankSum=4.664;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.397;RAW_MQ=257261.00;ReadPosRankSum=-1.135	GT:AD:DP:GQ:PL:SB	0/1:37,38,0:75:99:1384,0,1258,1495,1372,2867:21,16,21,17
+20	10096293	.	C	T,<NON_REF>	1355.77	.	BaseQRankSum=4.664;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.397;RAW_MQandDP=257261,75;ReadPosRankSum=-1.135	GT:AD:DP:GQ:PL:SB	0/1:37,38,0:75:99:1384,0,1258,1495,1372,2867:21,16,21,17
 20	10096294	.	T	<NON_REF>	.	.	END=10096595	GT:DP:GQ:MIN_DP:PL	0/0:68:99:57:0,120,1800
-20	10096596	.	C	T,<NON_REF>	1562.77	.	BaseQRankSum=2.728;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.612;RAW_MQ=300461.00;ReadPosRankSum=-0.170	GT:AD:DP:GQ:PL:SB	0/1:40,47,0:87:99:1591,0,1273,1711,1414,3125:19,21,23,24
+20	10096596	.	C	T,<NON_REF>	1562.77	.	BaseQRankSum=2.728;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.612;RAW_MQandDP=300461,87;ReadPosRankSum=-0.170	GT:AD:DP:GQ:PL:SB	0/1:40,47,0:87:99:1591,0,1273,1711,1414,3125:19,21,23,24
 20	10096597	.	T	<NON_REF>	.	.	END=10096767	GT:DP:GQ:MIN_DP:PL	0/0:90:99:75:0,120,1800
-20	10096768	.	A	C,<NON_REF>	1682.77	.	BaseQRankSum=-2.764;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.609;RAW_MQ=319323.00;ReadPosRankSum=0.613	GT:AD:DP:GQ:PL:SB	0/1:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25
+20	10096768	.	A	C,<NON_REF>	1682.77	.	BaseQRankSum=-2.764;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.609;RAW_MQandDP=319323,91;ReadPosRankSum=0.613	GT:AD:DP:GQ:PL:SB	0/1:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25
 20	10096769	.	A	<NON_REF>	.	.	END=10096898	GT:DP:GQ:MIN_DP:PL	0/0:78:99:65:0,120,1800
-20	10096899	.	G	T,<NON_REF>	1614.77	.	BaseQRankSum=2.755;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.387;RAW_MQ=279938.00;ReadPosRankSum=0.422	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:19,20,12,28
+20	10096899	.	G	T,<NON_REF>	1614.77	.	BaseQRankSum=2.755;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.387;RAW_MQandDP=279938,79;ReadPosRankSum=0.422	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:19,20,12,28
 20	10096900	.	G	<NON_REF>	.	.	END=10096904	GT:DP:GQ:MIN_DP:PL	0/0:82:99:78:0,120,1800
-20	10096905	.	TA	T,<NON_REF>	1600.73	.	BaseQRankSum=-0.755;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQ=291579.00;ReadPosRankSum=0.461	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30
+20	10096905	.	TA	T,<NON_REF>	1600.73	.	BaseQRankSum=-0.755;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQandDP=291579,83;ReadPosRankSum=0.461	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30
 20	10096907	.	A	<NON_REF>	.	.	END=10096932	GT:DP:GQ:MIN_DP:PL	0/0:84:99:82:0,120,1800
-20	10096933	.	G	C,<NON_REF>	1511.77	.	BaseQRankSum=-1.914;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.802;RAW_MQ=298779.00;ReadPosRankSum=0.334	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:28,16,13,28
+20	10096933	.	G	C,<NON_REF>	1511.77	.	BaseQRankSum=-1.914;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.802;RAW_MQandDP=298779,85;ReadPosRankSum=0.334	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:28,16,13,28
 20	10096934	.	T	<NON_REF>	.	.	END=10096957	GT:DP:GQ:MIN_DP:PL	0/0:90:99:86:0,120,1800
-20	10096958	.	G	A,<NON_REF>	1766.77	.	BaseQRankSum=2.839;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.701;RAW_MQ=323979.00;ReadPosRankSum=-1.833	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:27,18,16,31
+20	10096958	.	G	A,<NON_REF>	1766.77	.	BaseQRankSum=2.839;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.701;RAW_MQandDP=323979,92;ReadPosRankSum=-1.833	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:27,18,16,31
 20	10096959	.	G	<NON_REF>	.	.	END=10097074	GT:DP:GQ:MIN_DP:PL	0/0:92:99:84:0,120,1800
-20	10097075	.	T	G,<NON_REF>	1445.77	.	BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQ=315628.00;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22
+20	10097075	.	T	G,<NON_REF>	1445.77	.	BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQandDP=315628,92;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22
 20	10097076	.	A	<NON_REF>	.	.	END=10097100	GT:DP:GQ:MIN_DP:PL	0/0:91:99:77:0,120,1800
-20	10097101	.	C	CTTT,CTTTT,<NON_REF>	1091.73	.	BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQ=252294.00;ReadPosRankSum=2.086	GT:AD:DP:GQ:PL:SB	0/1:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15
+20	10097101	.	C	CTTT,CTTTT,<NON_REF>	1091.73	.	BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQandDP=252294,76;ReadPosRankSum=2.086	GT:AD:DP:GQ:PL:SB	0/1:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15
 20	10097102	.	T	<NON_REF>	.	.	END=10097435	GT:DP:GQ:MIN_DP:PL	0/0:70:99:60:0,120,1800
-20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C,<NON_REF>	1054.73	.	BaseQRankSum=1.820;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQ=262143.00;ReadPosRankSum=-3.097	GT:AD:DP:GQ:PL:SB	0/1:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21
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-20	10099029	.	T	C,<NON_REF>	334.77	.	BaseQRankSum=-1.809;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;RAW_MQ=79617.00;ReadPosRankSum=-1.224	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:14,4,9,1
+20	10099029	.	T	C,<NON_REF>	334.77	.	BaseQRankSum=-1.809;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;RAW_MQandDP=79617,28;ReadPosRankSum=-1.224	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:14,4,9,1
 20	10099030	.	C	<NON_REF>	.	.	END=10099031	GT:DP:GQ:MIN_DP:PL	0/0:29:72:28:0,72,1080
 20	10099032	.	T	<NON_REF>	.	.	END=10099033	GT:DP:GQ:MIN_DP:PL	0/0:28:63:28:0,63,945
-20	10099034	.	C	A,<NON_REF>	334.77	.	BaseQRankSum=2.757;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;RAW_MQ=79617.00;ReadPosRankSum=-1.850	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:13,5,9,1
+20	10099034	.	C	A,<NON_REF>	334.77	.	BaseQRankSum=2.757;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;RAW_MQandDP=79617,28;ReadPosRankSum=-1.850	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:13,5,9,1
 20	10099035	.	G	<NON_REF>	.	.	END=10099039	GT:DP:GQ:MIN_DP:PL	0/0:29:60:26:0,60,900
 20	10099040	.	T	<NON_REF>	.	.	END=10099040	GT:DP:GQ:MIN_DP:PL	0/0:26:51:26:0,51,765
 20	10099041	.	C	<NON_REF>	.	.	END=10099041	GT:DP:GQ:MIN_DP:PL	0/0:27:54:27:0,54,810
 20	10099042	.	T	<NON_REF>	.	.	END=10099043	GT:DP:GQ:MIN_DP:PL	0/0:26:57:24:0,57,855
-20	10099044	.	A	C,<NON_REF>	334.77	.	BaseQRankSum=-1.148;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQ=59851.00;ReadPosRankSum=-2.207	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:12,3,7,2
+20	10099044	.	A	C,<NON_REF>	334.77	.	BaseQRankSum=-1.148;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQandDP=59851,24;ReadPosRankSum=-2.207	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:12,3,7,2
 20	10099045	.	C	<NON_REF>	.	.	END=10099045	GT:DP:GQ:MIN_DP:PL	0/0:24:60:24:0,60,900
-20	10099046	.	T	C,<NON_REF>	304.77	.	BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQ=59851.00;ReadPosRankSum=-2.297	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:12,3,7,2
+20	10099046	.	T	C,<NON_REF>	304.77	.	BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQandDP=59851,24;ReadPosRankSum=-2.297	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:12,3,7,2
 20	10099047	.	G	<NON_REF>	.	.	END=10099052	GT:DP:GQ:MIN_DP:PL	0/0:24:57:23:0,57,855
 20	10099053	.	G	<NON_REF>	.	.	END=10099054	GT:DP:GQ:MIN_DP:PL	0/0:23:54:23:0,54,810
-20	10099055	.	T	C,<NON_REF>	256.77	.	BaseQRankSum=-1.554;DP=23;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.316;RAW_MQ=58555.00;ReadPosRankSum=-1.970	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:11,4,6,2
+20	10099055	.	T	C,<NON_REF>	256.77	.	BaseQRankSum=-1.554;DP=23;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.316;RAW_MQandDP=58555,23;ReadPosRankSum=-1.970	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:11,4,6,2
 20	10099056	.	T	<NON_REF>	.	.	END=10099061	GT:DP:GQ:MIN_DP:PL	0/0:24:60:23:0,60,900
 20	10099062	.	A	<NON_REF>	.	.	END=10099067	GT:DP:GQ:MIN_DP:PL	0/0:25:72:24:0,72,921
 20	10099068	.	G	<NON_REF>	.	.	END=10099072	GT:DP:GQ:MIN_DP:PL	0/0:27:81:27:0,81,1042
 20	10099073	.	T	<NON_REF>	.	.	END=10099077	GT:DP:GQ:MIN_DP:PL	0/0:27:78:27:0,78,1170
 20	10099078	.	G	<NON_REF>	.	.	END=10099078	GT:DP:GQ:MIN_DP:PL	0/0:28:81:28:0,81,1215
-20	10099079	.	C	T,<NON_REF>	116.77	.	BaseQRankSum=1.434;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.821;RAW_MQ=78698.00;ReadPosRankSum=0.969	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:11,12,4,2
+20	10099079	.	C	T,<NON_REF>	116.77	.	BaseQRankSum=1.434;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.821;RAW_MQandDP=78698,29;ReadPosRankSum=0.969	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:11,12,4,2
 20	10099080	.	G	<NON_REF>	.	.	END=10099089	GT:DP:GQ:MIN_DP:PL	0/0:30:81:29:0,81,1215
 20	10099090	.	A	<NON_REF>	.	.	END=10099095	GT:DP:GQ:MIN_DP:PL	0/0:34:90:31:0,90,1350
 20	10099096	.	A	<NON_REF>	.	.	END=10099096	GT:DP:GQ:MIN_DP:PL	0/0:35:74:35:0,74,1310
@@ -1352,13 +1352,13 @@
 20	10099101	.	G	<NON_REF>	.	.	END=10099105	GT:DP:GQ:MIN_DP:PL	0/0:37:99:36:0,99,1485
 20	10099106	.	T	<NON_REF>	.	.	END=10099106	GT:DP:GQ:MIN_DP:PL	0/0:36:96:36:0,96,1440
 20	10099107	.	T	<NON_REF>	.	.	END=10099110	GT:DP:GQ:MIN_DP:PL	0/0:41:99:39:0,99,1485
-20	10099111	.	T	TTTTGTTTG,<NON_REF>	656.73	.	BaseQRankSum=-1.207;DP=42;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.071;RAW_MQ=109737.00;ReadPosRankSum=-0.273	GT:AD:DP:GQ:PL:SB	0/1:22,13,0:35:99:694,0,802,763,859,1622:13,9,7,6
+20	10099111	.	T	TTTTGTTTG,<NON_REF>	656.73	.	BaseQRankSum=-1.207;DP=42;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.071;RAW_MQandDP=109737,42;ReadPosRankSum=-0.273	GT:AD:DP:GQ:PL:SB	0/1:22,13,0:35:99:694,0,802,763,859,1622:13,9,7,6
 20	10099112	.	T	<NON_REF>	.	.	END=10099139	GT:DP:GQ:MIN_DP:PL	0/0:57:99:49:0,114,1710
-20	10099140	.	G	T,<NON_REF>	1005.77	.	BaseQRankSum=-0.114;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.469;RAW_MQ=192512.00;ReadPosRankSum=0.338	GT:AD:DP:GQ:PL:SB	0/1:30,32,0:62:99:1034,0,931,1122,1028,2150:18,12,22,10
+20	10099140	.	G	T,<NON_REF>	1005.77	.	BaseQRankSum=-0.114;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.469;RAW_MQandDP=192512,62;ReadPosRankSum=0.338	GT:AD:DP:GQ:PL:SB	0/1:30,32,0:62:99:1034,0,931,1122,1028,2150:18,12,22,10
 20	10099141	.	G	<NON_REF>	.	.	END=10099189	GT:DP:GQ:MIN_DP:PL	0/0:67:99:64:0,120,1800
-20	10099190	.	G	T,<NON_REF>	1034.77	.	BaseQRankSum=-0.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.711;RAW_MQ=215351.00;ReadPosRankSum=-1.260	GT:AD:DP:GQ:PL:SB	0/1:33,32,0:65:99:1063,0,1154,1162,1251,2413:21,12,21,11
+20	10099190	.	G	T,<NON_REF>	1034.77	.	BaseQRankSum=-0.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.711;RAW_MQandDP=215351,65;ReadPosRankSum=-1.260	GT:AD:DP:GQ:PL:SB	0/1:33,32,0:65:99:1063,0,1154,1162,1251,2413:21,12,21,11
 20	10099191	.	C	<NON_REF>	.	.	END=10099219	GT:DP:GQ:MIN_DP:PL	0/0:58:99:46:0,111,1665
-20	10099220	.	A	G,<NON_REF>	577.77	.	BaseQRankSum=-1.664;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.596;RAW_MQ=149477.00;ReadPosRankSum=0.629	GT:AD:DP:GQ:PL:SB	0/1:25,20,0:45:99:606,0,873,681,933,1614:15,10,11,9
+20	10099220	.	A	G,<NON_REF>	577.77	.	BaseQRankSum=-1.664;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.596;RAW_MQandDP=149477,45;ReadPosRankSum=0.629	GT:AD:DP:GQ:PL:SB	0/1:25,20,0:45:99:606,0,873,681,933,1614:15,10,11,9
 20	10099221	.	T	<NON_REF>	.	.	END=10099229	GT:DP:GQ:MIN_DP:PL	0/0:44:99:42:0,102,1530
 20	10099230	.	T	<NON_REF>	.	.	END=10099233	GT:DP:GQ:MIN_DP:PL	0/0:41:90:41:0,90,1350
 20	10099234	.	T	<NON_REF>	.	.	END=10099235	GT:DP:GQ:MIN_DP:PL	0/0:44:87:44:0,87,1305
@@ -1366,16 +1366,16 @@
 20	10099239	.	C	<NON_REF>	.	.	END=10099246	GT:DP:GQ:MIN_DP:PL	0/0:36:84:35:0,84,1260
 20	10099247	.	C	<NON_REF>	.	.	END=10099248	GT:DP:GQ:MIN_DP:PL	0/0:37:93:36:0,93,1395
 20	10099249	.	C	<NON_REF>	.	.	END=10099249	GT:DP:GQ:MIN_DP:PL	0/0:36:87:36:0,87,1305
-20	10099250	.	G	A,<NON_REF>	699.77	.	BaseQRankSum=3.170;DP=37;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.272;RAW_MQ=119006.00;ReadPosRankSum=0.583	GT:AD:DP:GQ:PL:SB	0/1:16,21,0:37:99:728,0,424,776,487,1263:12,4,11,10
+20	10099250	.	G	A,<NON_REF>	699.77	.	BaseQRankSum=3.170;DP=37;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.272;RAW_MQandDP=119006,37;ReadPosRankSum=0.583	GT:AD:DP:GQ:PL:SB	0/1:16,21,0:37:99:728,0,424,776,487,1263:12,4,11,10
 20	10099251	.	A	<NON_REF>	.	.	END=10099269	GT:DP:GQ:MIN_DP:PL	0/0:30:81:28:0,81,1132
-20	10099270	.	A	C,<NON_REF>	0	.	BaseQRankSum=-2.866;DP=30;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-2.691;RAW_MQ=98268.00;ReadPosRankSum=-0.138	GT:AD:DP:GQ:PL:SB	0/0:27,3,0:30:60:0,60,1084,81,1092,1113:19,8,0,3
+20	10099270	.	A	C,<NON_REF>	0	.	BaseQRankSum=-2.866;DP=30;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-2.691;RAW_MQandDP=98268,30;ReadPosRankSum=-0.138	GT:AD:DP:GQ:PL:SB	0/0:27,3,0:30:60:0,60,1084,81,1092,1113:19,8,0,3
 20	10099271	.	C	<NON_REF>	.	.	END=10099271	GT:DP:GQ:MIN_DP:PL	0/0:31:84:31:0,84,1260
 20	10099272	.	C	<NON_REF>	.	.	END=10099534	GT:DP:GQ:MIN_DP:PL	0/0:57:99:36:0,99,1485
-20	10099535	.	G	A,<NON_REF>	1335.77	.	BaseQRankSum=5.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.418;RAW_MQ=226251.00;ReadPosRankSum=-0.777	GT:AD:DP:GQ:PL:SB	0/1:26,39,0:65:99:1364,0,686,1442,803,2245:17,9,22,17
+20	10099535	.	G	A,<NON_REF>	1335.77	.	BaseQRankSum=5.034;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.418;RAW_MQandDP=226251,65;ReadPosRankSum=-0.777	GT:AD:DP:GQ:PL:SB	0/1:26,39,0:65:99:1364,0,686,1442,803,2245:17,9,22,17
 20	10099536	.	T	<NON_REF>	.	.	END=10099564	GT:DP:GQ:MIN_DP:PL	0/0:67:99:63:0,120,1800
-20	10099565	.	C	T,<NON_REF>	1346.77	.	BaseQRankSum=4.595;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.266;RAW_MQ=243410.00;ReadPosRankSum=1.225	GT:AD:DP:GQ:PL:SB	0/1:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17
+20	10099565	.	C	T,<NON_REF>	1346.77	.	BaseQRankSum=4.595;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.266;RAW_MQandDP=243410,69;ReadPosRankSum=1.225	GT:AD:DP:GQ:PL:SB	0/1:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17
 20	10099566	.	T	<NON_REF>	.	.	END=10099754	GT:DP:GQ:MIN_DP:PL	0/0:77:99:66:0,120,1800
-20	10099755	.	C	T,<NON_REF>	1098.77	.	BaseQRankSum=1.550;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.022;RAW_MQ=229010.00;ReadPosRankSum=-0.230	GT:AD:DP:GQ:PL:SB	0/1:33,32,0:65:99:1127,0,1148,1226,1245,2470:20,13,17,15
+20	10099755	.	C	T,<NON_REF>	1098.77	.	BaseQRankSum=1.550;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.022;RAW_MQandDP=229010,65;ReadPosRankSum=-0.230	GT:AD:DP:GQ:PL:SB	0/1:33,32,0:65:99:1127,0,1148,1226,1245,2470:20,13,17,15
 20	10099756	.	C	<NON_REF>	.	.	END=10099831	GT:DP:GQ:MIN_DP:PL	0/0:63:99:58:0,120,1800
-20	10099832	.	A	G,<NON_REF>	1073.77	.	BaseQRankSum=-4.563;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.869;RAW_MQ=250276.00;ReadPosRankSum=-1.023	GT:AD:DP:GQ:PL:SB	0/1:39,33,0:72:99:1102,0,1430,1220,1530,2749:22,17,14,19
+20	10099832	.	A	G,<NON_REF>	1073.77	.	BaseQRankSum=-4.563;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.869;RAW_MQandDP=250276,72;ReadPosRankSum=-1.023	GT:AD:DP:GQ:PL:SB	0/1:39,33,0:72:99:1102,0,1430,1220,1530,2749:22,17,14,19
 20	10099833	.	T	<NON_REF>	.	.	END=10100000	GT:DP:GQ:MIN_DP:PL	0/0:85:99:73:0,120,1800
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx
index e63f7ce8701..fa5d9fb4b4e 100644
Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGenotypeGivenAllelesMode.gatk4.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGenotypeGivenAllelesMode.gatk4.vcf.idx
index 4f3cb8b5598..45b7719fc3e 100644
Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGenotypeGivenAllelesMode.gatk4.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGenotypeGivenAllelesMode.gatk4.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf
new file mode 100644
index 00000000000..16f02662637
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf
@@ -0,0 +1,10858 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf.idx
new file mode 100644
index 00000000000..032ca554d28
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf
new file mode 100644
index 00000000000..045a076f3aa
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf
@@ -0,0 +1,11696 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=CombineGVCFs,CommandLine="CombineGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/combinegvcfs7653474452446360719.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --convert-to-base-pair-resolution false --break-bands-at-multiples-of 0 --ignore-variants-starting-outside-interval false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="September 18, 2018 1:42:13 PM EDT">
+##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller  --emit-ref-confidence GVCF --output YRIoffspring.chr20snippet.g.vcf --intervals 20:10000000-10100000 --input /seq/picard_aggregation/G96830/NA19240/v1/NA19240.bam --reference /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta  --annotation-group StandardAnnotation --annotation-group StandardHCAnnotation --disable-tool-default-annotations false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20",Version=4.0.4.0-52-g41c08ad-SNAPSHOT,Date="June 12, 2018 9:01:56 AM EDT">
+##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
+##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
+##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
+##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
+##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
+##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)
+##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)
+##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
+##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)
+##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
+##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
+##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
+##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
+##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
+##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
+##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)
+##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
+##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
+##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
+##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
+##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
+##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
+##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
+##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
+##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
+##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
+##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
+##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)
+##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)
+##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
+##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)
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+##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
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+##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)
+##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)
+##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)
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+##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)
+##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)
+##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)
+##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)
+##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
+##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
+##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
+##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)
+##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)
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+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
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+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
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+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
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+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA19240
+20	10000000	.	T	<NON_REF>	.	.	END=10000068	GT:DP:GQ:MIN_DP:PL	./.:84:99:64:0,120,1800	./.:47:99:42:0,117,1341
+20	10000069	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:84:99:64:0,120,1800	./.:43:96:43:0,96,1270
+20	10000070	.	A	<NON_REF>	.	.	END=10000116	GT:DP:GQ:MIN_DP:PL	./.:84:99:64:0,120,1800	./.:46:99:43:0,109,1311
+20	10000117	.	C	T,<NON_REF>	.	.	BaseQRankSum=2.14;DP=107;ExcessHet=3.01;MQRankSum=0.913;RAW_MQandDP=228169,64;ReadPosRankSum=-2.230e-01	GT:AD:DP:GQ:MIN_DP:PL:SB	./.:36,28,0:64:99:.:934,0,1248,1042,1332,2374:16,20,19,9	./.:.:46:99:43:0,109,1311,109,1311,1311
+20	10000118	.	T	<NON_REF>	.	.	END=10000130	GT:DP:GQ:MIN_DP:PL	./.:52:99:44:0,108,1620	./.:46:99:43:0,109,1311
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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf.idx
new file mode 100644
index 00000000000..58d0ea4acd7
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf
new file mode 100644
index 00000000000..d0f8b7155ab
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf
@@ -0,0 +1,11613 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport  --genomicsdb-workspace-path /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsdb-tests-2160631194140750294/workspace --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools//haplotypecaller/expected.testGVCFMode.gatk4.g.vcf --variant src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf --batch-size 0 --reader-threads 1 --intervals 20:1-11000000 --verbosity ERROR  --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --consolidate false --validate-sample-name-map false --max-num-intervals-to-import-in-parallel 1 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version=Unavailable,Date="September 18, 2018 1:44:33 PM EDT">
+##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants  --output src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf --variant gendb:///var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsdb-tests-2160631194140750294/workspace --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta  --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version=4.0.8.1-42-g21f16d5-SNAPSHOT,Date="September 18, 2018 1:45:39 PM EDT">
+##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
+##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
+##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
+##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
+##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
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+##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
+##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)
+##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
+##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
+##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
+##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
+##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
+##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
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+##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
+##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
+##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
+##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
+##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
+##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
+##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
+##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
+##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
+##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
+##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
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+##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
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+##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)
+##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)
+##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)
+##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
+##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)
+##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)
+##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)
+##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)
+##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)
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+##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
+##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
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+##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)
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+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf.idx
new file mode 100644
index 00000000000..b916553c260
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.g.vcf
new file mode 100644
index 00000000000..f35c7856e72
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.g.vcf
@@ -0,0 +1,11806 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=CombineGVCFs,CommandLine="CombineGVCFs  --output fixMQ.combined.g.vcf --variant YRIoffspring.chr20snippet.g.vcf --variant expected.testGVCFMode.gatk4.g.vcf --intervals 20:10000000-10100000 --reference /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta  --annotation-group StandardAnnotation --disable-tool-default-annotations false --convert-to-base-pair-resolution false --break-bands-at-multiples-of 0 --ignore-variants-starting-outside-interval false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.4.0-52-g41c08ad-SNAPSHOT,Date="June 12, 2018 9:10:07 AM EDT">
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+20	10000211	.	C	T,<NON_REF>	.	.	BaseQRankSum=1.87;ClippingRankSum=0.00;DP=100;ExcessHet=3.01;MQRankSum=1.06;RAW_MQandDP=192169,54;ReadPosRankSum=1.07	GT:AD:DP:GQ:MIN_DP:PL:SB	./.:26,27,0:53:99:.:970,0,906,1049,988,2036:15,11,11,16	./.:.:52:99:46:0,115,1456,115,1456,1456
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+20	10000333	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.:46:88:46:0,88,1303
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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.g.vcf.idx
new file mode 100644
index 00000000000..fe57e3888c1
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.g.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf
new file mode 100644
index 00000000000..21600933933
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf
@@ -0,0 +1,475 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=CombineGVCFs,CommandLine="CombineGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/combinegvcfs6343110786387644439.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --convert-to-base-pair-resolution false --break-bands-at-multiples-of 0 --ignore-variants-starting-outside-interval false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="September 17, 2018 4:22:41 PM EDT">
+##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genotypegvcf298518204847218079.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="September 17, 2018 4:25:45 PM EDT">
+##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller  --emit-ref-confidence GVCF --output YRIoffspring.chr20snippet.g.vcf --intervals 20:10000000-10100000 --input /seq/picard_aggregation/G96830/NA19240/v1/NA19240.bam --reference /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta  --annotation-group StandardAnnotation --annotation-group StandardHCAnnotation --disable-tool-default-annotations false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20",Version=4.0.4.0-52-g41c08ad-SNAPSHOT,Date="June 12, 2018 9:01:56 AM EDT">
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+##INFO=<ID=AF,Number=A,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=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
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+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
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+##source=CombineGVCFs
+##source=GenotypeGVCFs
+##source=HaplotypeCaller
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA19240
+20	10000117	.	C	T	904.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.14;DP=107;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.250;MQ=59.71;MQRankSum=0.913;QD=14.13;ReadPosRankSum=-2.230e-01;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248	0/0:43,0:43:99:0,109,1311
+20	10000211	.	C	T	940.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.87;DP=99;ExcessHet=3.0103;FS=5.587;MLEAC=1;MLEAF=0.250;MQ=59.65;MQRankSum=1.06;QD=17.74;ReadPosRankSum=0.703;SOR=0.944	GT:AD:DP:GQ:PL	0/1:26,27:53:99:970,0,906	0/0:46,0:46:99:0,115,1456
+20	10000439	.	T	G	3522.20	.	AC=4;AF=1.00;AN=4;DP=107;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.30;QD=32.92;SOR=1.380	GT:AD:DP:GQ:PL	1/1:0,80:80:99:2833,240,0	1/1:0,27:27:80:716,80,0
+20	10000534	.	T	C	306.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.640e+00;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=1.309;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=8.75;ReadPosRankSum=-3.830e-01;SOR=0.446	GT:AD:DP:GQ:PL	0/0:41,0:41:99:0,102,1530	0/1:19,16:35:99:336,0,521
+20	10000598	.	T	A	2935.20	.	AC=4;AF=1.00;AN=4;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.14;QD=25.36;SOR=1.096	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1970,147,0	1/1:0,31:31:93:992,93,0
+20	10000694	.	G	A	1007.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=3.60;DP=119;ExcessHet=3.0103;FS=1.822;MLEAC=1;MLEAF=0.250;MQ=48.66;MQRankSum=-5.114e+00;QD=12.28;ReadPosRankSum=0.657;SOR=0.566	GT:AD:DP:GQ:PL	0/1:45,37:82:99:1037,0,1601	0/0:37,0:37:99:0,99,1125
+20	10000758	.	T	A	5255.20	.	AC=4;AF=1.00;AN=4;DP=143;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=55.68;QD=28.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3867,286,0	1/1:0,47:47:99:1415,140,0
+20	10001019	.	T	G	649.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.541e+00;DP=97;ExcessHet=3.0103;FS=3.406;MLEAC=1;MLEAF=0.250;MQ=49.49;MQRankSum=-7.498e+00;QD=9.99;ReadPosRankSum=-9.250e-01;SOR=0.665	GT:AD:DP:GQ:PL	0/1:39,26:65:99:679,0,1426	0/0:32,0:32:81:0,81,1215
+20	10001298	.	T	A	3837.20	.	AC=4;AF=1.00;AN=4;DP=105;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.07;QD=30.97;SOR=0.925	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2946,220,0	1/1:0,30:30:90:918,90,0
+20	10001436	.	A	AAGGCT	3923.16	.	AC=4;AF=1.00;AN=4;DP=94;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=49.80;QD=27.24;SOR=1.995	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2339,156,0	1/1:0,36:36:99:1620,108,0
+20	10001474	.	C	T	3876.20	.	AC=4;AF=1.00;AN=4;DP=112;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=50.09;QD=34.61;SOR=1.262	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2669,219,0	1/1:0,39:39:99:1234,117,0
+20	10001617	.	C	A	1730.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.26;DP=136;ExcessHet=3.0103;FS=13.163;MLEAC=1;MLEAF=0.250;MQ=59.00;MQRankSum=1.37;QD=16.80;ReadPosRankSum=-2.800e-01;SOR=1.346	GT:AD:DP:GQ:PL	0/1:52,51:103:99:1760,0,1781	0/0:33,0:33:90:0,90,1044
+20	10001628	.	G	A	5019.20	.	AC=4;AF=1.00;AN=4;DP=133;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.40;QD=28.20;SOR=1.038	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3927,285,0	1/1:0,37:37:99:1119,110,0
+20	10001661	.	T	C	5161.20	.	AC=4;AF=1.00;AN=4;DP=117;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=58.85;QD=25.00;SOR=0.877	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3635,249,0	1/1:0,35:35:99:1|1:10001661_T_C:1553,105,0
+20	10001670	.	T	G	5258.20	.	AC=4;AF=1.00;AN=4;DP=118;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=58.26;QD=29.56;SOR=0.781	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3702,253,0	1/1:0,36:36:99:1|1:10001661_T_C:1583,108,0
+20	10002058	.	T	G	4142.20	.	AC=4;AF=1.00;AN=4;BaseQRankSum=1.93;DP=111;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=58.50;MQRankSum=3.07;QD=30.62;ReadPosRankSum=0.624;SOR=0.749	GT:AD:DP:GQ:PL	1/1:1,74:75:99:2992,216,0	1/1:0,36:36:99:1177,108,0
+20	10002099	.	C	T	1504.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-2.820e-01;ClippingRankSum=0.00;DP=101;ExcessHet=4.7712;FS=0.786;MLEAC=2;MLEAF=0.500;MQ=57.64;MQRankSum=0.00;QD=14.90;ReadPosRankSum=0.173;SOR=0.544	GT:AD:DP:GQ:PL	0/1:27,38:65:99:1223,0,844	0/1:22,14:36:99:310,0,563
+20	10002138	.	C	G	4087.20	.	AC=4;AF=1.00;AN=4;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.89;QD=28.17;SOR=1.166	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,53:53:99:1|1:10002138_C_G:2472,169,0	1/1:0,37:37:99:1|1:10002138_C_G:1642,111,0
+20	10002142	.	G	C	4082.20	.	AC=4;AF=1.00;AN=4;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.87;QD=26.80;SOR=1.022	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,52:52:99:1|1:10002138_C_G:2436,166,0	1/1:0,37:37:99:1|1:10002138_C_G:1673,114,0
+20	10002458	.	G	GTT,GTTT	3294.16	.	AC=1,3;AF=0.250,0.750;AN=4;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1,2;MLEAF=0.250,0.500;MQ=55.02;QD=26.00;SOR=1.609	GT:AD:DP:GQ:PL	2/2:0,0,6:16:86:2090,794,648,167,86,0	1/2:0,8,4:12:78:1157,165,78,207,0,120
+20	10002470	.	C	T	3780.20	.	AC=4;AF=1.00;AN=4;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=52.65;QD=30.02;SOR=0.959	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2551,189,0	1/1:0,30:30:93:1256,93,0
+20	10002625	.	G	T	3696.20	.	AC=4;AF=1.00;AN=4;DP=96;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.37;QD=31.98;SOR=0.919	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2694,193,0	1/1:0,32:32:96:1029,96,0
+20	10003021	.	C	T	3213.20	.	AC=4;AF=1.00;AN=4;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.30;QD=27.51;SOR=1.005	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2412,181,0	1/1:0,26:26:78:828,78,0
+20	10003358	.	A	C	1453.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=4.000e-03;DP=119;ExcessHet=3.0103;FS=0.844;MLEAC=1;MLEAF=0.250;MQ=59.79;MQRankSum=1.01;QD=16.33;ReadPosRankSum=-1.355e+00;SOR=0.572	GT:AD:DP:GQ:PL	0/1:45,44:89:99:1483,0,1477	0/0:30,0:30:87:0,87,1305
+20	10003446	.	G	T	205.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-8.520e-01;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=7.60;ReadPosRankSum=-1.061e+00;SOR=0.970	GT:AD:DP:GQ:PL	0/0:50,0:50:99:0,120,1800	0/1:16,11:27:99:235,0,418
+20	10003651	.	T	C	4553.20	.	AC=4;AF=1.00;AN=4;DP=123;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.39;QD=29.11;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,93:93:99:3649,279,0	1/1:0,30:30:90:931,90,0
+20	10003692	.	A	G	3520.20	.	AC=4;AF=1.00;AN=4;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.62;QD=28.08;SOR=1.014	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2638,205,0	1/1:0,30:30:90:909,90,0
+20	10003832	.	G	A	3978.20	.	AC=4;AF=1.00;AN=4;DP=107;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=58.25;QD=23.23;SOR=1.211	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2734,199,0	1/1:0,41:41:99:1271,123,0
+20	10004094	.	A	C	3282.20	.	AC=4;AF=1.00;AN=4;DP=100;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.28;QD=32.82;SOR=1.167	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1854,157,0	1/1:0,47:47:99:1455,140,0
+20	10004147	.	A	G	2814.20	.	AC=4;AF=1.00;AN=4;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.06;QD=32.35;SOR=1.030	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1866,156,0	1/1:0,35:35:99:975,103,0
+20	10004193	.	G	T	917.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-5.040e-01;DP=88;ExcessHet=3.0103;FS=2.391;MLEAC=1;MLEAF=0.250;MQ=59.30;MQRankSum=3.42;QD=17.64;ReadPosRankSum=1.51;SOR=1.019	GT:AD:DP:GQ:PL	0/1:23,29:52:99:947,0,775	0/0:36,0:36:99:0,102,1152
+20	10004222	.	C	CA	14.97	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.335;DP=92;ExcessHet=3.9794;FS=1.494;MLEAC=2;MLEAF=0.500;MQ=60.05;MQRankSum=-2.042e+00;QD=0.38;ReadPosRankSum=1.27;SOR=0.434	GT:AD:DP:GQ:PL	0/1:31,8:39:50:50,0,923	0/0:38,0:38:0:0,0,689
+20	10004223	.	A	AG	172.40	.	AC=2;AF=0.500;AN=4;BaseQRankSum=0.803;ClippingRankSum=0.00;DP=90;ExcessHet=4.7712;FS=2.297;MLEAC=2;MLEAF=0.500;MQ=58.51;MQRankSum=1.89;QD=2.54;ReadPosRankSum=1.09;SOR=0.580	GT:AD:DP:GQ:PL	0/1:36,11:47:85:85,0,982	0/1:13,8:21:99:125,0,211
+20	10004224	.	A	G	124.87	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-5.440e-01;ClippingRankSum=0.00;DP=94;ExcessHet=3.9794;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=58.95;MQRankSum=0.069;QD=5.95;ReadPosRankSum=0.459;SOR=0.551	GT:AD:DP:GQ:PL	0/0:66,0:66:0:0,0,1403	0/1:11,10:21:99:151,0,199
+20	10004351	.	C	G	4278.20	.	AC=4;AF=1.00;AN=4;DP=125;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.46;QD=34.78;SOR=0.924	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2784,211,0	1/1:0,53:53:99:1521,157,0
+20	10004389	.	T	G	3853.20	.	AC=4;AF=1.00;AN=4;BaseQRankSum=1.77;ClippingRankSum=0.00;DP=113;ExcessHet=3.0103;FS=3.502;MLEAC=4;MLEAF=1.00;MQ=58.23;MQRankSum=0.00;QD=34.40;ReadPosRankSum=1.41;SOR=0.608	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2523,187,0	1/1:1,49:50:99:1357,138,0
+20	10004610	.	A	C	4964.20	.	AC=4;AF=1.00;AN=4;DP=134;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.14;QD=29.03;SOR=0.818	GT:AD:DP:GQ:PL	1/1:0,89:89:99:3654,267,0	1/1:0,45:45:99:1337,134,0
+20	10004725	.	A	G	950.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.154e+00;DP=107;ExcessHet=3.0103;FS=15.830;MLEAC=1;MLEAF=0.250;MQ=55.27;MQRankSum=3.01;QD=14.62;ReadPosRankSum=2.09;SOR=0.605	GT:AD:DP:GQ:PL	0/1:35,30:65:99:980,0,1168	0/0:42,0:42:93:0,93,1395
+20	10004769	.	TAAAACTATGC	T	1516.40	.	AC=2;AF=0.500;AN=4;BaseQRankSum=1.60;ClippingRankSum=0.00;DP=117;ExcessHet=4.7712;FS=2.783;MLEAC=2;MLEAF=0.500;MQ=54.96;MQRankSum=0.00;QD=15.80;ReadPosRankSum=1.88;SOR=1.045	GT:AD:DP:GQ:PL	0/1:37,27:64:99:1019,0,1471	0/1:18,14:32:99:535,0,1946
+20	10004874	.	A	C	5348.20	.	AC=4;AF=1.00;AN=4;DP=134;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.56;QD=30.67;SOR=0.994	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,87:87:99:1|1:10004874_A_C:3631,261,0	1/1:0,47:47:99:1|1:10004874_A_C:1744,141,0
+20	10004887	.	A	G	1834.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=0.356;ClippingRankSum=0.00;DP=133;ExcessHet=4.7712;FS=2.181;MLEAC=2;MLEAF=0.500;MQ=59.65;MQRankSum=0.00;QD=13.79;ReadPosRankSum=2.05;SOR=0.889	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,40:85:99:0|1:10004874_A_C:1352,0,1542	0/1:27,21:48:99:0|1:10004874_A_C:511,0,709
+20	10005010	.	C	T	4302.20	.	AC=4;AF=1.00;AN=4;DP=117;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.80;QD=26.61;SOR=0.984	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2963,217,0	1/1:0,43:43:99:1366,129,0
+20	10005427	.	C	T	3709.20	.	AC=4;AF=1.00;AN=4;BaseQRankSum=1.77;ClippingRankSum=0.00;DP=105;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.78;MQRankSum=0.00;QD=29.20;ReadPosRankSum=-7.250e-01;SOR=0.254	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2243,165,0	1/1:1,48:49:99:1493,136,0
+20	10005499	.	A	G	4700.20	.	AC=4;AF=1.00;AN=4;DP=129;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=28.55;SOR=0.933	GT:AD:DP:GQ:PL	1/1:0,76:76:99:3082,229,0	1/1:0,52:52:99:1645,155,0
+20	10005587	.	A	G	1228.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-8.340e-01;DP=114;ExcessHet=3.0103;FS=1.955;MLEAC=1;MLEAF=0.250;MQ=59.74;MQRankSum=-9.720e-01;QD=17.06;ReadPosRankSum=0.248;SOR=0.848	GT:AD:DP:GQ:PL	0/1:36,36:72:99:1258,0,1236	0/0:42,0:42:99:0,109,1334
+20	10005723	.	A	G	4501.20	.	AC=4;AF=1.00;AN=4;DP=137;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.86;QD=32.86;SOR=0.969	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3091,258,0	1/1:0,51:51:99:1437,152,0
+20	10006291	.	G	A	977.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.311;DP=121;ExcessHet=3.0103;FS=0.853;MLEAC=1;MLEAF=0.250;MQ=59.28;MQRankSum=-1.081e+00;QD=11.63;ReadPosRankSum=-1.447e+00;SOR=0.659	GT:AD:DP:GQ:PL	0/1:53,31:84:99:1007,0,1905	0/0:37,0:37:99:0,99,1162
+20	10006404	.	A	C	3991.20	.	AC=4;AF=1.00;AN=4;BaseQRankSum=1.72;ClippingRankSum=0.00;DP=114;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.43;MQRankSum=0.00;QD=34.42;ReadPosRankSum=-5.390e-01;SOR=0.520	GT:AD:DP:GQ:PL	1/1:0,76:76:99:2957,228,0	1/1:1,36:37:99:1061,100,0
+20	10006682	.	T	A	4275.20	.	AC=4;AF=1.00;AN=4;DP=120;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.60;QD=28.53;SOR=1.104	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2903,219,0	1/1:0,46:46:99:1399,137,0
+20	10006819	.	AAAAC	A	3791.16	.	AC=4;AF=1.00;AN=4;DP=115;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.84;QD=27.23;SOR=0.863	GT:AD:DP:GQ:PL	1/1:0,58:58:99:2569,176,0	1/1:0,29:29:88:1258,88,0
+20	10007043	.	G	A	722.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.41;ClippingRankSum=0.00;DP=101;ExcessHet=3.0103;FS=2.906;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=17.61;ReadPosRankSum=0.482;SOR=1.302	GT:AD:DP:GQ:PL	0/0:59,0:59:99:0,120,1800	0/1:14,27:41:99:752,0,298
+20	10007150	.	G	C	868.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-2.939e+00;ClippingRankSum=0.00;DP=104;ExcessHet=4.7712;FS=1.683;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.43;ReadPosRankSum=-7.700e-02;SOR=0.951	GT:AD:DP:GQ:PGT:PID:PL	0/1:38,25:63:99:0|1:10007150_G_C:698,0,1479	0/1:29,11:40:99:.:.:199,0,798
+20	10007175	.	C	T	1349.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.25;DP=98;ExcessHet=3.0103;FS=2.211;MLEAC=1;MLEAF=0.250;MQ=59.62;MQRankSum=1.32;QD=22.12;ReadPosRankSum=-1.213e+00;SOR=0.434	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,38:61:99:1|0:10007150_G_C:1379,0,780	0/0:37,0:37:89:.:.:0,89,1076
+20	10007352	.	C	T	3916.20	.	AC=4;AF=1.00;AN=4;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.78;QD=29.52;SOR=1.358	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2793,208,0	1/1:0,37:37:99:1150,110,0
+20	10007420	.	T	C	382.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-3.784e+00;ClippingRankSum=0.00;DP=95;ExcessHet=3.0103;FS=12.992;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=10.33;ReadPosRankSum=1.03;SOR=1.456	GT:AD:DP:GQ:PL	0/0:58,0:58:99:0,120,1800	0/1:18,19:37:99:412,0,447
+20	10007531	.	A	G	4150.20	.	AC=4;AF=1.00;AN=4;DP=115;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.84;QD=33.47;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2949,217,0	1/1:0,43:43:99:1228,127,0
+20	10007575	.	C	T	470.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.490e-01;ClippingRankSum=0.00;DP=102;ExcessHet=3.0103;FS=1.317;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.71;ReadPosRankSum=-8.910e-01;SOR=0.399	GT:AD:DP:GQ:PL	0/0:65,0:65:99:0,120,1800	0/1:17,20:37:99:500,0,413
+20	10007835	.	T	C	509.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-4.583e+00;ClippingRankSum=0.00;DP=105;ExcessHet=3.0103;FS=13.142;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=13.06;ReadPosRankSum=0.073;SOR=0.376	GT:AD:DP:GQ:PL	0/0:65,0:65:99:0,120,1800	0/1:15,24:39:99:539,0,382
+20	10007980	.	A	C	4833.20	.	AC=4;AF=1.00;AN=4;DP=133;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.49;QD=32.91;SOR=0.978	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3553,270,0	1/1:0,43:43:99:1307,128,0
+20	10008029	.	T	TA,TAA	3232.16	.	AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.409;DP=130;ExcessHet=3.0103;FS=0.000;MLEAC=3,1;MLEAF=0.750,0.250;MQ=60.67;MQRankSum=0.576;QD=28.35;ReadPosRankSum=-1.326e+00;SOR=0.701	GT:AD:DP:GQ:PL	1/1:3,72,0:75:99:2024,145,0,2033,222,2110	1/2:0,17,22:39:99:1244,629,524,416,0,337
+20	10008146	.	TA	T	3511.16	.	AC=4;AF=1.00;AN=4;DP=121;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.45;QD=30.80;SOR=0.841	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2179,211,0	1/1:0,44:44:99:1368,132,0
+20	10008221	.	T	C	4265.20	.	AC=4;AF=1.00;AN=4;DP=116;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.21;QD=31.31;SOR=0.877	GT:AD:DP:GQ:PL	1/1:0,80:80:99:3253,240,0	1/1:0,36:36:99:1039,106,0
+20	10008389	.	A	G	644.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-3.469e+00;ClippingRankSum=0.00;DP=102;ExcessHet=3.0103;FS=5.563;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=11.71;ReadPosRankSum=0.498;SOR=0.369	GT:AD:DP:GQ:PL	0/0:45,0:45:99:0,108,1620	0/1:26,29:55:99:674,0,697
+20	10008458	.	T	G	4054.20	.	AC=4;AF=1.00;AN=4;DP=117;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=55.83;QD=31.45;SOR=0.820	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2683,207,0	1/1:0,46:46:99:1398,138,0
+20	10008742	.	G	T	1257.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=3.89;ClippingRankSum=0.00;DP=84;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=47.37;MQRankSum=-1.113e+00;QD=15.33;ReadPosRankSum=0.221;SOR=0.757	GT:AD:DP:GQ:PL	0/1:23,26:49:99:744,0,580	0/1:13,20:33:99:542,0,265
+20	10008758	.	C	CA,CAA	1489.37	.	AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.130;DP=81;ExcessHet=3.0103;FS=2.124;MLEAC=3,1;MLEAF=0.750,0.250;MQ=47.46;MQRankSum=-1.168e+00;QD=22.57;ReadPosRankSum=-5.200e-02;SOR=0.324	GT:AD:DP:GQ:PL	1/1:4,31,0:35:10:721,10,0,733,102,825	1/2:0,20,11:31:99:804,284,194,434,0,396
+20	10008921	.	C	CA	253.40	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.610;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=56.34;MQRankSum=-1.906e+00;QD=7.45;ReadPosRankSum=0.173;SOR=0.512	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,16:34:99:0|1:10008921_C_CA:291,0,366	0/0:31,0:31:6:.:.:0,6,658
+20	10008948	.	TA	T	3465.16	.	AC=4;AF=1.00;AN=4;BaseQRankSum=0.994;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=54.92;MQRankSum=2.05;QD=33.27;ReadPosRankSum=0.884;SOR=0.446	GT:AD:DP:GQ:PGT:PID:PL	1/1:1,50:51:99:1|1:10008921_C_CA:2095,107,0	1/1:0,33:33:99:.:.:1406,99,0
+20	10008952	.	CACACACACACA	C,CCACACACA,CCACACACACA,CCA	2983.16	.	AC=1,1,1,1;AF=0.250,0.250,0.250,0.250;AN=4;BaseQRankSum=0.941;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,1,1;MLEAF=0.250,0.250,0.250,0.250;MQ=54.55;MQRankSum=1.84;QD=31.26;ReadPosRankSum=0.716;SOR=0.487	GT:AD:DP:GQ:PL	1/3:1,14,5,11,0:34:99:1704,525,845,726,173,703,582,0,443,530,1135,744,779,607,1321	2/4:0,0,15,0,12:27:99:1315,1243,1282,505,512,439,1243,1282,512,1282,648,714,0,714,719
+20	10009227	.	A	G	2009.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-1.130e-01;ClippingRankSum=0.00;DP=103;ExcessHet=4.7712;FS=1.650;MLEAC=2;MLEAF=0.500;MQ=58.31;MQRankSum=1.43;QD=19.70;ReadPosRankSum=-1.119e+00;SOR=0.502	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,39:62:99:.:.:1398,0,740	0/1:16,24:40:99:0|1:10009227_A_G:640,0,377
+20	10009246	.	A	G	4316.20	.	AC=4;AF=1.00;AN=4;BaseQRankSum=1.56;ClippingRankSum=0.00;DP=114;ExcessHet=3.0103;FS=3.371;MLEAC=4;MLEAF=1.00;MQ=57.39;MQRankSum=0.00;QD=27.76;ReadPosRankSum=1.72;SOR=0.514	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,77:77:99:.:.:3031,231,0	1/1:1,35:36:99:1|1:10009227_A_G:1312,101,0
+20	10009400	.	T	A	4856.20	.	AC=4;AF=1.00;AN=4;DP=132;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=29.09;SOR=0.820	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3027,223,0	1/1:0,58:58:99:1856,174,0
+20	10009512	.	C	G	4619.20	.	AC=4;AF=1.00;AN=4;DP=131;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.11;QD=26.08;SOR=0.856	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3068,231,0	1/1:0,53:53:99:1578,158,0
+20	10009719	.	A	G	2611.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-3.827e+00;ClippingRankSum=0.00;DP=115;ExcessHet=3.0103;FS=7.708;MLEAC=3;MLEAF=0.750;MQ=59.64;MQRankSum=0.00;QD=22.71;ReadPosRankSum=-1.459e+00;SOR=0.281	GT:AD:DP:GQ:PL	1/1:0,59:59:99:1924,175,0	0/1:24,32:56:99:717,0,596
+20	10009795	.	A	G	3311.20	.	AC=4;AF=1.00;AN=4;DP=92;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.80;QD=33.85;SOR=1.071	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1909,141,0	1/1:0,44:44:99:1429,132,0
+20	10009842	.	G	GAA	531.15	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.872;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=54.25;MQRankSum=-6.030e-01;QD=15.62;ReadPosRankSum=1.72;SOR=0.738	GT:AD:DP:GQ:PL	0/1:19,15:34:99:570,0,690	0/0:34,0:34:54:0,54,810
+20	10009844	.	G	A	1954.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=1.05;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=56.22;MQRankSum=0.975;QD=29.61;ReadPosRankSum=-1.555e+00;SOR=0.773	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,19:35:99:0|1:10009844_G_A:690,0,586	1/1:0,31:31:93:1|1:10009844_G_A:1294,93,0
+20	10009871	.	A	G	2322.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-8.030e-01;DP=98;ExcessHet=3.0103;FS=5.548;MLEAC=3;MLEAF=0.750;MQ=54.54;MQRankSum=1.50;QD=31.81;ReadPosRankSum=1.54;SOR=0.820	GT:AD:DP:GQ:PGT:PID:PL	0/1:17,19:36:99:0|1:10009844_G_A:687,0,594	1/1:0,37:37:99:1|1:10009844_G_A:1665,111,0
+20	10009875	.	A	G,AGGGAGG	4045.20	.	AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.378;DP=95;ExcessHet=3.0103;FS=7.361;MLEAC=3,1;MLEAF=0.750,0.250;MQ=54.36;MQRankSum=1.36;QD=27.08;ReadPosRankSum=1.04;SOR=0.718	GT:AD:DP:GQ:PGT:PID:PL	1/2:2,15,13:30:99:.:.:2407,645,533,697,0,574	1/1:0,37,0:37:99:1|1:10009844_G_A:1665,111,0,1665,111,1665
+20	10009879	.	A	G	3821.20	.	AC=4;AF=1.00;AN=4;BaseQRankSum=1.53;DP=85;ExcessHet=3.0103;FS=8.468;MLEAC=4;MLEAF=1.00;MQ=54.26;MQRankSum=1.57;QD=25.42;ReadPosRankSum=1.11;SOR=1.110	GT:AD:DP:GQ:PGT:PID:PL	1/1:2,47:49:99:.:.:2273,150,0	1/1:0,35:35:99:1|1:10009844_G_A:1575,105,0
+20	10009883	.	A	G	3638.20	.	AC=4;AF=1.00;AN=4;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=55.07;QD=27.65;SOR=1.468	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,47:47:99:.:.:2180,147,0	1/1:0,33:33:99:1|1:10009844_G_A:1485,99,0
+20	10010393	.	T	G	1994.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-1.738e+00;ClippingRankSum=0.00;DP=118;ExcessHet=4.7712;FS=8.582;MLEAC=2;MLEAF=0.500;MQ=59.61;MQRankSum=0.00;QD=16.90;ReadPosRankSum=-3.900e-01;SOR=0.398	GT:AD:DP:GQ:PL	0/1:36,43:79:99:1493,0,1230	0/1:18,21:39:99:530,0,466
+20	10010536	.	G	GA	3973.16	.	AC=4;AF=1.00;AN=4;DP=140;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=61.15;QD=31.04;SOR=0.971	GT:AD:DP:GQ:PL	1/1:0,79:79:99:2500,243,0	1/1:0,49:49:99:1509,147,0
+20	10010766	.	T	G	3478.20	.	AC=4;AF=1.00;AN=4;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=33.44;SOR=0.732	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2440,199,0	1/1:0,38:38:99:1065,112,0
+20	10010832	.	T	C	4276.20	.	AC=4;AF=1.00;AN=4;DP=118;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.68;QD=29.48;SOR=1.040	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2980,226,0	1/1:0,43:43:99:1323,128,0
+20	10011075	.	C	T	1324.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=5.36;DP=117;ExcessHet=3.0103;FS=1.800;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=15.95;ReadPosRankSum=-1.036e+00;SOR=0.968	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1354,0,1333	0/0:34,0:34:99:0,99,932
+20	10011309	.	T	C	4152.20	.	AC=4;AF=1.00;AN=4;DP=129;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=32.19;SOR=0.740	GT:AD:DP:GQ:PL	1/1:0,77:77:99:2721,231,0	1/1:0,52:52:99:1458,154,0
+20	10011517	.	GA	G	1431.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=0.690;ClippingRankSum=0.00;DP=135;ExcessHet=3.0103;FS=3.769;MLEAC=3;MLEAF=0.750;MQ=60.01;MQRankSum=1.80;QD=13.89;ReadPosRankSum=0.315;SOR=0.385	GT:AD:DP:GQ:PL	0/1:37,28:73:99:528,0,875	1/1:1,37:38:88:942,88,0
+20	10011666	.	C	T	4103.20	.	AC=4;AF=1.00;AN=4;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.36;QD=30.56;SOR=0.892	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2990,220,0	1/1:0,35:35:99:1140,105,0
+20	10011939	.	C	T	3775.20	.	AC=4;AF=1.00;AN=4;DP=103;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.81;QD=33.63;SOR=0.973	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2498,184,0	1/1:0,42:42:99:1304,126,0
+20	10012021	.	CA	C	3352.16	.	AC=4;AF=1.00;AN=4;DP=119;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=58.30;QD=30.20;SOR=1.138	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2013,198,0	1/1:0,45:45:99:1375,135,0
+20	10012362	.	G	T,A	2483.20	.	AC=3,1;AF=0.750,0.250;AN=4;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=3,1;MLEAF=0.750,0.250;MQ=57.74;QD=29.21;SOR=1.375	GT:AD:DP:GQ:PL	1/1:0,23,0:23:69:864,69,0,864,69,864	1/2:0,23,39:62:99:1646,970,901,677,0,562
+20	10012384	.	T	C	228.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.773e+00;DP=73;ExcessHet=3.0103;FS=7.375;MLEAC=1;MLEAF=0.250;MQ=53.38;MQRankSum=-8.110e-01;QD=12.68;ReadPosRankSum=0.800;SOR=0.044	GT:AD:DP:GQ:PL	0/1:10,8:18:99:258,0,355	0/0:55,0:55:99:0,120,1800
+20	10012387	.	T	C	2022.20	.	AC=4;AF=1.00;AN=4;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=58.34;QD=28.09;SOR=1.308	GT:AD:DP:GQ:PL	1/1:0,16:16:50:562,50,0	1/1:0,56:56:99:1487,165,0
+20	10012479	.	A	G	2978.20	.	AC=4;AF=1.00;AN=4;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.26;QD=30.55;SOR=0.904	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,17:17:50:1|1:10012479_A_G:621,50,0	1/1:0,54:54:99:1|1:10012479_A_G:2384,168,0
+20	10012498	.	C	G	3012.20	.	AC=4;AF=1.00;AN=4;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=55.17;QD=32.62;SOR=0.784	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012479_A_G:495,33,0	1/1:0,56:56:99:1|1:10012479_A_G:2544,172,0
+20	10012518	.	T	C	2705.20	.	AC=4;AF=1.00;AN=4;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=54.11;QD=29.33;SOR=0.725	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:30:1|1:10012479_A_G:435,30,0	1/1:0,52:52:99:1|1:10012479_A_G:2297,157,0
+20	10012521	.	C	T	45.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.36;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=41.77;MQRankSum=-3.800e-02;QD=4.11;ReadPosRankSum=1.97;SOR=1.179	GT:AD:DP:GQ:PL	0/1:8,3:11:75:75,0,224	0/0:54,0:54:99:0,99,1485
+20	10012570	.	G	GCA	2627.16	.	AC=4;AF=1.00;AN=4;DP=58;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=51.38;QD=35.36;SOR=0.884	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:33:1|1:10012570_G_GCA:495,33,0	1/1:0,46:46:99:1|1:10012570_G_GCA:2168,147,0
+20	10012572	.	GT	G	2627.16	.	AC=4;AF=1.00;AN=4;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=51.24;QD=34.30;SOR=1.034	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012570_G_GCA:495,33,0	1/1:0,48:48:99:1|1:10012570_G_GCA:2168,147,0
+20	10012631	.	C	CG	2416.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.030e+00;DP=65;ExcessHet=3.0103;FS=17.786;MLEAC=3;MLEAF=0.750;MQ=54.04;MQRankSum=-1.670e+00;QD=27.00;ReadPosRankSum=-1.813e+00;SOR=0.014	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,13:21:99:0|1:10012631_C_CG:522,0,297	1/1:0,43:43:99:1|1:10012631_C_CG:1933,132,0
+20	10012636	.	G	C	2458.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=2.71;DP=64;ExcessHet=3.0103;FS=17.784;MLEAC=3;MLEAF=0.750;MQ=54.13;MQRankSum=-1.513e+00;QD=30.82;ReadPosRankSum=-1.915e+00;SOR=0.015	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,14:22:99:0|1:10012631_C_CG:556,0,294	1/1:0,41:41:99:1|1:10012631_C_CG:1932,132,0
+20	10012714	.	G	C	2643.20	.	AC=4;AF=1.00;AN=4;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.10;QD=33.46;SOR=1.358	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1329,105,0	1/1:0,44:44:99:1341,132,0
+20	10012751	.	T	C	2237.20	.	AC=4;AF=1.00;AN=4;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.58;QD=31.07;SOR=0.807	GT:AD:DP:GQ:PL	1/1:0,30:30:89:966,89,0	1/1:0,42:42:99:1298,125,0
+20	10012969	.	G	A	613.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-3.050e-01;ClippingRankSum=0.00;DP=81;ExcessHet=3.0103;FS=1.174;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.26;ReadPosRankSum=0.498;SOR=0.941	GT:AD:DP:GQ:PL	0/0:38,0:38:99:0,99,1485	0/1:18,25:43:99:643,0,410
+20	10012997	.	C	T	618.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.991;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.05;ReadPosRankSum=0.206;SOR=0.631	GT:AD:DP:GQ:PL	0/0:38,0:38:99:0,99,1485	0/1:19,25:44:99:648,0,454
+20	10013119	.	C	T	1465.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=2.72;ClippingRankSum=0.00;DP=92;ExcessHet=4.7712;FS=6.668;MLEAC=2;MLEAF=0.500;MQ=54.57;MQRankSum=0.131;QD=15.93;ReadPosRankSum=0.159;SOR=0.462	GT:AD:DP:GQ:PL	0/1:29,30:59:99:1040,0,936	0/1:15,18:33:99:454,0,354
+20	10013574	.	G	A	1049.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=3.47;DP=104;ExcessHet=3.0103;FS=7.109;MLEAC=1;MLEAF=0.250;MQ=58.06;MQRankSum=-2.710e-01;QD=15.21;ReadPosRankSum=0.706;SOR=1.675	GT:AD:DP:GQ:PL	0/1:38,31:69:99:1079,0,1301	0/0:35,0:35:99:0,105,1074
+20	10014990	.	C	CAT	1972.40	.	AC=2;AF=0.500;AN=4;BaseQRankSum=1.93;ClippingRankSum=0.00;DP=123;ExcessHet=4.7712;FS=0.730;MLEAC=2;MLEAF=0.500;MQ=60.64;MQRankSum=3.11;QD=17.93;ReadPosRankSum=0.144;SOR=0.559	GT:AD:DP:GQ:PL	0/1:38,38:76:99:1275,0,1248	0/1:12,22:34:99:735,0,363
+20	10015547	.	GGGCGGAGGCGGAGGCGGA	G	154.17	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-6.510e-01;ClippingRankSum=0.00;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.69;MQRankSum=-8.130e-01;QD=7.01;ReadPosRankSum=-4.540e-01;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	0/0:15,0:15:24:.:.:0,24,360	0/1:16,6:22:99:0|1:10015547_GGGCGGAGGCGGAGGCGGA_G:193,0,619
+20	10015558	.	GA	G	545.16	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.93;ClippingRankSum=0.00;DP=35;ExcessHet=3.0103;FS=1.441;MLEAC=1;MLEAF=0.500;MQ=60.74;MQRankSum=1.30;QD=19.47;ReadPosRankSum=1.42;SOR=0.446	GT:AD:DP:GQ:PGT:PID:PL	./.:6,0:6:.:.:.:0,0,0	0/1:12,16:28:99:1|0:10015547_GGGCGGAGGCGGAGGCGGA_G:581,0,362
+20	10015560	.	GGCGGAGGCGGA	G	542.16	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.91;ClippingRankSum=0.00;DP=36;ExcessHet=3.0103;FS=1.483;MLEAC=1;MLEAF=0.500;MQ=60.72;MQRankSum=1.35;QD=18.70;ReadPosRankSum=1.70;SOR=0.368	GT:AD:DP:GQ:PGT:PID:PL	./.:6,0:6:.:.:.:0,0,0	0/1:13,16:29:99:1|0:10015547_GGGCGGAGGCGGAGGCGGA_G:578,0,383
+20	10015679	.	C	T	381.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=1.79;ClippingRankSum=0.00;DP=43;ExcessHet=4.7712;FS=7.294;MLEAC=2;MLEAF=0.500;MQ=60.50;MQRankSum=0.00;QD=8.87;ReadPosRankSum=0.497;SOR=1.961	GT:AD:DP:GQ:PL	0/1:5,5:10:99:169,0,166	0/1:22,11:33:99:241,0,808
+20	10015729	.	C	A	570.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.28;ClippingRankSum=0.00;DP=52;ExcessHet=3.0103;FS=10.401;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=15.41;ReadPosRankSum=-1.448e+00;SOR=0.401	GT:AD:DP:GQ:PL	0/0:15,0:15:42:0,42,630	0/1:13,24:37:99:600,0,373
+20	10015761	.	T	C	1738.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.982e+00;DP=61;ExcessHet=3.0103;FS=16.166;MLEAC=3;MLEAF=0.750;MQ=59.62;MQRankSum=1.29;QD=28.49;ReadPosRankSum=1.81;SOR=0.024	GT:AD:DP:GQ:PL	0/1:9,13:22:99:373,0,284	1/1:0,39:39:99:1395,117,0
+20	10016207	.	C	G	658.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.27;ClippingRankSum=0.00;DP=93;ExcessHet=3.0103;FS=5.364;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=11.35;ReadPosRankSum=-1.090e-01;SOR=0.510	GT:AD:DP:GQ:PL	0/0:35,0:35:99:0,99,1485	0/1:30,28:58:99:688,0,722
+20	10017776	.	A	G	411.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.641e+00;ClippingRankSum=0.00;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=11.11;ReadPosRankSum=0.038;SOR=0.610	GT:AD:DP:GQ:PL	0/0:45,0:45:99:0,114,1710	0/1:19,18:37:99:441,0,519
+20	10018158	.	G	C	3298.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=5.21;DP=142;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=59.87;MQRankSum=1.12;QD=23.39;ReadPosRankSum=1.18;SOR=0.640	GT:AD:DP:GQ:PL	0/1:40,48:88:99:1668,0,1165	1/1:0,53:53:99:1660,159,0
+20	10018555	.	G	A	2057.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=0.301;ClippingRankSum=0.00;DP=137;ExcessHet=4.7712;FS=5.185;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.24;ReadPosRankSum=0.815;SOR=0.561	GT:AD:DP:GQ:PL	0/1:35,45:80:99:1596,0,1211	0/1:33,22:55:99:490,0,809
+20	10018700	.	T	C	530.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.659e+00;ClippingRankSum=0.00;DP=117;ExcessHet=3.0103;FS=6.369;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=11.53;ReadPosRankSum=0.244;SOR=0.333	GT:AD:DP:GQ:PL	0/0:70,0:70:99:0,120,1800	0/1:23,23:46:99:560,0,626
+20	10019093	.	A	G	2575.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=1.71;ClippingRankSum=0.00;DP=118;ExcessHet=3.0103;FS=2.636;MLEAC=3;MLEAF=0.750;MQ=59.80;MQRankSum=1.07;QD=22.01;ReadPosRankSum=-2.520e-01;SOR=0.720	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1273,0,1104	1/1:2,46:48:93:1332,93,0
+20	10020229	.	G	A	1906.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=5.79;ClippingRankSum=0.00;DP=127;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=59.67;MQRankSum=0.104;QD=15.01;ReadPosRankSum=0.858;SOR=0.754	GT:AD:DP:GQ:PL	0/1:38,44:82:99:1567,0,1130	0/1:30,15:45:99:368,0,693
+20	10021946	.	T	A	636.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.906e+00;ClippingRankSum=0.00;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=13.54;ReadPosRankSum=2.22;SOR=0.751	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1721	0/1:21,26:47:99:666,0,522
+20	10023442	.	G	A	929.42	.	AC=2;AF=0.500;AN=4;BaseQRankSum=0.223;ClippingRankSum=0.00;DP=79;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=29.04;ReadPosRankSum=-5.460e-01;SOR=0.379	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1721	1/1:1,31:32:62:964,62,0
+20	10023689	.	G	A	1851.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.14;DP=119;ExcessHet=3.0103;FS=0.877;MLEAC=1;MLEAF=0.250;MQ=59.77;MQRankSum=1.35;QD=23.14;ReadPosRankSum=1.16;SOR=0.549	GT:AD:DP:GQ:PL	0/1:29,51:80:99:1881,0,946	0/0:39,0:39:99:0,102,1217
+20	10024107	.	C	T	1693.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=5.77;DP=138;ExcessHet=3.0103;FS=0.817;MLEAC=1;MLEAF=0.250;MQ=59.41;MQRankSum=-1.546e+00;QD=19.69;ReadPosRankSum=0.148;SOR=0.823	GT:AD:DP:GQ:PL	0/1:38,48:86:99:1723,0,1086	0/0:52,0:52:96:0,96,1322
+20	10024300	.	C	CTT	151.18	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.45;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=3.773;MLEAC=1;MLEAF=0.250;MQ=54.80;MQRankSum=0.00;QD=13.74;ReadPosRankSum=-1.073e+00;SOR=0.208	GT:AD:DP:GQ:PL	0/1:3,8:18:99:103,0,137	0/0:7,0:12:20:0,20,115
+20	10024388	.	C	T	321.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-9.240e-01;ClippingRankSum=0.00;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=11.90;ReadPosRankSum=0.267;SOR=0.527	GT:AD:DP:GQ:PL	0/0:39,0:39:99:0,105,1509	0/1:13,14:27:99:351,0,344
+20	10024950	.	G	T	920.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.081;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=7.110;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=22.44;ReadPosRankSum=0.132;SOR=1.770	GT:AD:DP:GQ:PGT:PID:PL	0/0:39,0:39:99:.:.:0,105,1509	0/1:17,24:41:99:0|1:10024950_G_T:950,0,913
+20	10024951	.	G	T	920.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.14;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=7.110;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=22.44;ReadPosRankSum=-8.000e-02;SOR=1.770	GT:AD:DP:GQ:PGT:PID:PL	0/0:39,0:39:99:.:.:0,105,1509	0/1:17,24:41:99:0|1:10024950_G_T:950,0,913
+20	10026357	.	T	C	1660.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-6.420e-01;ClippingRankSum=0.00;DP=102;ExcessHet=4.7712;FS=11.376;MLEAC=2;MLEAF=0.500;MQ=59.04;MQRankSum=0.00;QD=16.44;ReadPosRankSum=1.62;SOR=0.779	GT:AD:DP:GQ:PL	0/1:28,35:63:99:1195,0,932	0/1:19,19:38:99:494,0,521
+20	10026794	.	C	T	1685.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=2.83;ClippingRankSum=0.00;DP=104;ExcessHet=4.7712;FS=0.732;MLEAC=2;MLEAF=0.500;MQ=59.78;MQRankSum=0.00;QD=16.36;ReadPosRankSum=-5.330e-01;SOR=0.783	GT:AD:DP:GQ:PL	0/1:19,33:52:99:1113,0,529	0/1:27,24:51:99:601,0,657
+20	10027234	.	A	ATTAG	3086.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-4.060e-01;ClippingRankSum=0.00;DP=113;ExcessHet=3.0103;FS=1.661;MLEAC=3;MLEAF=0.750;MQ=58.61;MQRankSum=0.375;QD=28.06;ReadPosRankSum=0.211;SOR=0.849	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1358,0,1964	1/1:1,40:41:65:1767,65,0
+20	10027868	.	A	G	2666.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-4.141e+00;ClippingRankSum=0.00;DP=134;ExcessHet=4.7712;FS=6.535;MLEAC=2;MLEAF=0.500;MQ=59.66;MQRankSum=0.032;QD=20.20;ReadPosRankSum=1.87;SOR=0.956	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,45:89:99:0|1:10027868_A_G:1768,0,3201	0/1:19,24:43:99:0|1:10027868_A_G:927,0,1091
+20	10027872	.	A	G	2651.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-8.550e-01;ClippingRankSum=0.00;DP=129;ExcessHet=4.7712;FS=9.561;MLEAC=2;MLEAF=0.500;MQ=59.64;MQRankSum=0.101;QD=20.88;ReadPosRankSum=1.05;SOR=0.897	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,45:85:99:0|1:10027868_A_G:1753,0,3136	0/1:18,24:42:99:0|1:10027868_A_G:927,0,1091
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+20	10028316	.	C	T	591.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.911;ClippingRankSum=0.00;DP=98;ExcessHet=3.0103;FS=6.822;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.08;ReadPosRankSum=-7.190e-01;SOR=1.715	GT:AD:DP:GQ:PGT:PID:PL	0/0:55,0:55:99:.:.:0,120,1800	0/1:25,17:42:99:0|1:10028302_G_T:621,0,1379
+20	10028725	.	A	G	437.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.165e+00;ClippingRankSum=0.00;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.14;ReadPosRankSum=0.184;SOR=0.892	GT:AD:DP:GQ:PL	0/0:55,0:55:99:0,120,1800	0/1:17,19:36:99:467,0,436
+20	10028867	.	A	ATG	1690.40	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-6.100e-02;ClippingRankSum=0.00;DP=128;ExcessHet=4.7712;FS=3.716;MLEAC=2;MLEAF=0.500;MQ=60.66;MQRankSum=2.71;QD=16.41;ReadPosRankSum=0.364;SOR=0.408	GT:AD:DP:GQ:PL	0/1:32,39:71:99:1144,0,916	0/1:13,19:32:99:584,0,361
+20	10029104	.	G	A	1312.42	.	AC=2;AF=0.500;AN=4;DP=103;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=30.52;SOR=0.739	GT:AD:DP:GQ:PL	0/0:60,0:60:99:0,120,1800	1/1:0,43:43:99:1347,128,0
+20	10030188	.	T	A	1786.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=1.36;ClippingRankSum=0.00;DP=113;ExcessHet=4.7712;FS=4.632;MLEAC=2;MLEAF=0.500;MQ=59.80;MQRankSum=0.00;QD=15.95;ReadPosRankSum=0.917;SOR=0.650	GT:AD:DP:GQ:PL	0/1:42,39:81:99:1401,0,1524	0/1:16,15:31:99:414,0,398
+20	10030452	.	G	A	738.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.085e+00;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=2.968;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=18.45;ReadPosRankSum=-4.040e-01;SOR=0.339	GT:AD:DP:GQ:PL	0/0:41,0:41:99:0,103,1575	0/1:12,28:40:99:768,0,241
+20	10030931	.	C	A	541.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=3.73;ClippingRankSum=0.00;DP=95;ExcessHet=3.0103;FS=6.218;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=10.21;ReadPosRankSum=-2.630e-01;SOR=1.773	GT:AD:DP:GQ:PL	0/0:42,0:42:99:0,114,1710	0/1:31,22:53:99:571,0,659
+20	10031254	.	A	AT	2046.40	.	AC=2;AF=0.500;AN=4;BaseQRankSum=0.497;ClippingRankSum=0.00;DP=131;ExcessHet=4.7712;FS=8.195;MLEAC=2;MLEAF=0.500;MQ=59.85;MQRankSum=0.017;QD=16.11;ReadPosRankSum=0.495;SOR=0.286	GT:AD:DP:GQ:PL	0/1:38,47:85:99:1501,0,1159	0/1:23,19:42:99:583,0,725
+20	10031342	.	G	A	2454.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=3.43;ClippingRankSum=0.00;DP=138;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=59.83;MQRankSum=0.00;QD=17.79;ReadPosRankSum=0.857;SOR=0.722	GT:AD:DP:GQ:PL	0/1:41,52:93:99:1863,0,1375	0/1:22,23:45:99:620,0,534
+20	10031798	.	G	A	5354.20	.	AC=4;AF=1.00;AN=4;DP=138;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.70;QD=29.27;SOR=0.783	GT:AD:DP:GQ:PL	1/1:0,104:104:99:4325,313,0	1/1:0,34:34:99:1056,102,0
+20	10031827	.	C	T	2321.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=3.55;ClippingRankSum=0.00;DP=140;ExcessHet=4.7712;FS=5.086;MLEAC=2;MLEAF=0.500;MQ=59.87;MQRankSum=0.00;QD=16.70;ReadPosRankSum=-6.750e-01;SOR=0.563	GT:AD:DP:GQ:PL	0/1:52,56:108:99:2033,0,1798	0/1:18,13:31:99:317,0,456
+20	10032094	.	G	A	1897.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=5.49;ClippingRankSum=0.00;DP=132;ExcessHet=4.7712;FS=9.336;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.48;ReadPosRankSum=0.092;SOR=0.468	GT:AD:DP:GQ:PL	0/1:47,36:83:99:1249,0,1497	0/1:21,27:48:99:677,0,458
+20	10032413	.	T	G	1434.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-2.742e+00;ClippingRankSum=0.00;DP=116;ExcessHet=4.7712;FS=8.785;MLEAC=2;MLEAF=0.500;MQ=59.68;MQRankSum=0.00;QD=12.47;ReadPosRankSum=-1.110e-01;SOR=1.453	GT:AD:DP:GQ:PL	0/1:35,31:66:99:898,0,1277	0/1:23,26:49:99:565,0,554
+20	10032882	.	A	T	2507.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.280e-01;ClippingRankSum=0.00;DP=119;ExcessHet=3.0103;FS=9.634;MLEAC=3;MLEAF=0.750;MQ=59.81;MQRankSum=0.00;QD=21.43;ReadPosRankSum=0.626;SOR=0.225	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1231,0,1406	1/1:1,41:42:93:1306,93,0
+20	10032972	.	C	CAT	3065.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-3.540e-01;DP=109;ExcessHet=3.0103;FS=2.753;MLEAC=3;MLEAF=0.750;MQ=59.89;MQRankSum=-1.017e+00;QD=28.92;ReadPosRankSum=-1.232e+00;SOR=0.921	GT:AD:DP:GQ:PL	0/1:33,30:63:99:1160,0,1477	1/1:0,43:43:99:1944,132,0
+20	10034306	.	T	C	1268.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-2.200e-01;ClippingRankSum=0.00;DP=107;ExcessHet=4.7712;FS=2.552;MLEAC=2;MLEAF=0.500;MQ=59.61;MQRankSum=1.15;QD=12.08;ReadPosRankSum=0.885;SOR=1.023	GT:AD:DP:GQ:PL	0/1:46,29:75:99:811,0,1593	0/1:11,19:30:99:486,0,219
+20	10034425	.	C	T	530.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.76;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=5.760;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.57;ReadPosRankSum=-8.950e-01;SOR=0.499	GT:AD:DP:GQ:PL	0/0:55,0:55:99:0,120,1800	0/1:10,22:32:99:560,0,175
+20	10036930	.	CGATAGCCCTAGCCCTAGATA	C	1523.40	.	AC=2;AF=0.500;AN=4;BaseQRankSum=0.200;ClippingRankSum=0.00;DP=129;ExcessHet=4.7712;FS=10.062;MLEAC=2;MLEAF=0.500;MQ=55.99;MQRankSum=0.00;QD=15.08;ReadPosRankSum=0.460;SOR=0.213	GT:AD:DP:GQ:PL	0/1:39,29:68:99:1074,0,5571	0/1:20,13:33:99:487,0,3108
+20	10037037	.	C	T	1435.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=3.50;DP=116;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.250;MQ=60.17;MQRankSum=-1.193e+00;QD=17.72;ReadPosRankSum=-1.609e+00;SOR=0.495	GT:AD:DP:GQ:PL	0/1:39,42:81:99:1465,0,1124	0/0:35,0:35:99:0,102,1530
+20	10037110	.	T	TGATA	4473.16	.	AC=4;AF=1.00;AN=4;DP=111;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.85;QD=35.92;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2818,189,0	1/1:0,36:36:99:1691,114,0
+20	10037144	.	TGATA	T,TGATAGATA,TGATAGATAGATA	3043.16	.	AC=1,1,2;AF=0.250,0.250,0.500;AN=4;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,2;MLEAF=0.250,0.250,0.500;MQ=54.72;QD=29.63;SOR=1.000	GT:AD:DP:GQ:PL	3/3:0,0,0,36:36:99:1861,1864,1866,1864,1866,1866,127,129,129,0	1/2:0,18,11,0:29:99:1218,461,407,756,0,724,1218,462,757,1218
+20	10037709	.	A	T	1463.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=0.120;ClippingRankSum=0.00;DP=106;ExcessHet=4.7712;FS=2.521;MLEAC=2;MLEAF=0.500;MQ=59.78;MQRankSum=0.934;QD=13.81;ReadPosRankSum=1.15;SOR=0.751	GT:AD:DP:GQ:PL	0/1:39,32:71:99:1032,0,1354	0/1:17,18:35:99:460,0,435
+20	10038534	.	CTTGT	C	975.15	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.936e+00;ClippingRankSum=0.00;DP=113;ExcessHet=3.0103;FS=1.121;MLEAC=1;MLEAF=0.250;MQ=60.18;MQRankSum=0.962;QD=20.32;ReadPosRankSum=0.880;SOR=0.717	GT:AD:DP:GQ:PL	0/0:54,0:54:99:0,120,1800	0/1:22,26:48:99:1014,0,1079
+20	10038640	.	A	C	549.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.630e-01;ClippingRankSum=0.00;DP=99;ExcessHet=3.0103;FS=22.369;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.20;ReadPosRankSum=0.213;SOR=2.700	GT:AD:DP:GQ:PL	0/0:54,0:54:99:0,120,1800	0/1:23,22:45:99:579,0,582
+20	10038994	.	C	T	494.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.96;ClippingRankSum=0.00;DP=92;ExcessHet=3.0103;FS=7.360;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=13.00;ReadPosRankSum=-2.350e-01;SOR=0.315	GT:AD:DP:GQ:PL	0/0:54,0:54:99:0,120,1800	0/1:19,19:38:99:524,0,452
+20	10039371	.	T	G	1735.44	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-1.667e+00;ClippingRankSum=0.00;DP=119;ExcessHet=4.7712;FS=11.712;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.58;ReadPosRankSum=0.391;SOR=0.841	GT:AD:DP:GQ:PL	0/1:34,40:74:99:1353,0,1194	0/1:28,17:45:99:411,0,777
+20	10040772	.	C	CT,CTT	2634.15	.	AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=0.374;ClippingRankSum=0.00;DP=120;ExcessHet=3.0103;FS=3.572;MLEAC=2,1;MLEAF=0.500,0.250;MQ=54.67;MQRankSum=0.00;QD=24.62;ReadPosRankSum=-4.270e-01;SOR=0.542	GT:AD:DP:GQ:PL	1/1:0,70,0:70:99:2033,210,0,2034,210,2034	0/2:17,0,20:37:99:640,692,1318,0,626,563
+20	10040812	.	AT	A	2973.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=0.905;ClippingRankSum=0.00;DP=122;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=54.18;MQRankSum=0.00;QD=27.53;ReadPosRankSum=0.031;SOR=0.674	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2645,214,0	0/1:21,16:37:99:367,0,494
+20	10040821	.	T	A	1170.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.100e-02;ClippingRankSum=0.00;DP=119;ExcessHet=3.0103;FS=0.721;MLEAC=1;MLEAF=0.250;MQ=54.02;MQRankSum=0.00;QD=15.00;ReadPosRankSum=-3.470e-01;SOR=0.671	GT:AD:DP:GQ:PL	0/1:38,40:78:99:1200,0,1099	0/0:39,0:40:99:0,117,1322
+20	10041304	.	C	T	3155.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=3.22;ClippingRankSum=0.00;DP=102;ExcessHet=3.0103;FS=0.983;MLEAC=3;MLEAF=0.750;MQ=59.59;MQRankSum=0.00;QD=31.24;ReadPosRankSum=0.714;SOR=0.532	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2794,204,0	0/1:18,15:33:99:391,0,405
+20	10041701	.	A	ATATG	1694.40	.	AC=2;AF=0.500;AN=4;BaseQRankSum=0.848;ClippingRankSum=0.00;DP=103;ExcessHet=4.7712;FS=4.019;MLEAC=2;MLEAF=0.500;MQ=59.38;MQRankSum=0.959;QD=22.59;ReadPosRankSum=1.12;SOR=0.298	GT:AD:DP:GQ:PL	0/1:8,48:56:58:1441,0,58	0/1:8,11:19:99:291,0,568
+20	10042319	.	C	T	3220.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=1.66;ClippingRankSum=0.00;DP=108;ExcessHet=3.0103;FS=8.399;MLEAC=3;MLEAF=0.750;MQ=59.40;MQRankSum=0.00;QD=29.82;ReadPosRankSum=-8.950e-01;SOR=0.795	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2687,199,0	0/1:21,21:42:99:563,0,514
+20	10042761	.	A	G	4313.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-2.960e-01;ClippingRankSum=0.00;DP=143;ExcessHet=3.0103;FS=0.870;MLEAC=3;MLEAF=0.750;MQ=60.00;MQRankSum=0.00;QD=30.16;ReadPosRankSum=-7.100e-02;SOR=0.863	GT:AD:DP:GQ:PL	1/1:0,91:91:99:3582,272,0	0/1:23,29:52:99:761,0,602
+20	10042829	.	A	G	3834.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.650e-01;ClippingRankSum=0.00;DP=134;ExcessHet=3.0103;FS=0.852;MLEAC=3;MLEAF=0.750;MQ=59.86;MQRankSum=0.00;QD=28.83;ReadPosRankSum=-8.090e-01;SOR=0.556	GT:AD:DP:GQ:PL	1/1:0,78:78:99:3084,235,0	0/1:24,31:55:99:780,0,566
+20	10043002	.	A	T	1286.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=3.99;DP=126;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.96;ReadPosRankSum=-3.500e-02;SOR=0.434	GT:AD:DP:GQ:PL	0/1:48,38:86:99:1316,0,1659	0/0:40,0:40:99:0,109,1146
+20	10044650	.	A	G	622.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-5.504e+00;ClippingRankSum=0.00;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=11.52;ReadPosRankSum=0.426;SOR=0.636	GT:AD:DP:GQ:PL	0/0:44,0:44:99:0,104,1655	0/1:24,30:54:99:652,0,625
+20	10044849	.	A	G	2085.42	.	AC=2;AF=0.500;AN=4;DP=98;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=59.61;QD=28.76;SOR=1.316	GT:AD:DP:GQ:PL	1/1:0,59:59:99:2120,177,0	0/0:39,0:39:99:0,105,1212
+20	10045078	.	G	T	3265.42	.	AC=2;AF=0.500;AN=4;DP=120;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=58.73;QD=29.94;SOR=0.876	GT:AD:DP:GQ:PL	1/1:0,81:81:99:3300,244,0	0/0:39,0:39:99:0,105,1212
+20	10045642	.	G	C	3410.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-4.850e-01;ClippingRankSum=0.00;DP=112;ExcessHet=3.0103;FS=2.145;MLEAC=3;MLEAF=0.750;MQ=59.63;MQRankSum=0.00;QD=30.45;ReadPosRankSum=-3.380e-01;SOR=1.029	GT:AD:DP:GQ:PL	1/1:0,81:81:99:3136,243,0	0/1:18,13:31:99:304,0,478
+20	10046178	.	AAGAAAGAAAG	A	4025.16	.	AC=4;AF=1.00;AN=4;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=54.33;QD=31.54;SOR=0.829	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2197,152,0	1/1:0,42:42:99:1864,127,0
+20	10046537	.	A	G	818.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-3.909e+00;DP=92;ExcessHet=3.0103;FS=3.724;MLEAC=1;MLEAF=0.250;MQ=54.50;MQRankSum=0.395;QD=14.35;ReadPosRankSum=0.727;SOR=1.262	GT:AD:DP:GQ:PL	0/1:28,29:57:99:848,0,902	0/0:35,0:35:99:0,99,1485
+20	10046828	.	T	C	958.42	.	AC=2;AF=0.500;AN=4;DP=75;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=29.95;SOR=0.818	GT:AD:DP:GQ:PL	0/0:43,0:43:99:0,101,1614	1/1:0,32:32:96:993,96,0
+20	10047038	.	T	C	523.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.461e+00;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.88;ReadPosRankSum=0.254;SOR=0.929	GT:AD:DP:GQ:PL	0/0:43,0:43:99:0,101,1614	0/1:11,20:31:99:553,0,276
+20	10047435	.	G	A	499.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.75;ClippingRankSum=0.00;DP=85;ExcessHet=3.0103;FS=6.684;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.18;ReadPosRankSum=-5.400e-01;SOR=0.701	GT:AD:DP:GQ:PL	0/0:43,0:43:99:0,101,1614	0/1:20,21:41:99:529,0,417
+20	10048393	.	C	G	1574.42	.	AC=2;AF=0.500;AN=4;DP=87;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=28.86;SOR=0.836	GT:AD:DP:GQ:PGT:PID:PL	0/0:43,0:43:99:.:.:0,101,1614	1/1:0,43:43:99:1|1:10048393_C_G:1609,132,0
+20	10048400	.	C	T	437.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.20;ClippingRankSum=0.00;DP=92;ExcessHet=3.0103;FS=4.286;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=9.72;ReadPosRankSum=1.71;SOR=1.149	GT:AD:DP:GQ:PGT:PID:PL	0/0:43,0:43:99:.:.:0,101,1614	0/1:24,21:45:99:0|1:10048393_C_G:467,0,468
+20	10049120	.	A	G	537.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.571;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.28;ReadPosRankSum=-1.548e+00;SOR=0.569	GT:AD:DP:GQ:PL	0/0:43,0:43:99:0,101,1614	0/1:11,22:33:99:567,0,223
+20	10050667	.	C	T	1150.42	.	AC=2;AF=0.500;AN=4;DP=93;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=30.27;SOR=0.798	GT:AD:DP:GQ:PL	0/0:52,0:52:99:0,120,1800	1/1:0,38:38:99:1185,114,0
+20	10050828	.	T	C	2381.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-2.704e+00;DP=123;ExcessHet=3.0103;FS=3.363;MLEAC=3;MLEAF=0.750;MQ=59.81;MQRankSum=0.892;QD=19.52;ReadPosRankSum=-1.400e-01;SOR=0.489	GT:AD:DP:GQ:PL	0/1:49,37:86:99:1256,0,1768	1/1:0,36:36:99:1155,108,0
+20	10051376	.	A	G	484.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-3.580e-01;ClippingRankSum=0.00;DP=78;ExcessHet=3.0103;FS=2.909;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.74;ReadPosRankSum=-1.189e+00;SOR=1.402	GT:AD:DP:GQ:PL	0/0:40,0:40:99:0,99,1485	0/1:18,20:38:99:514,0,430
+20	10051448	.	T	C	2123.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-5.010e-01;DP=101;ExcessHet=3.0103;FS=7.325;MLEAC=3;MLEAF=0.750;MQ=59.59;MQRankSum=-1.404e+00;QD=21.02;ReadPosRankSum=-7.050e-01;SOR=0.267	GT:AD:DP:GQ:PL	0/1:35,35:70:99:1163,0,1150	1/1:0,31:31:93:990,93,0
+20	10051695	.	G	A	637.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=3.95;ClippingRankSum=0.00;DP=101;ExcessHet=3.0103;FS=5.972;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=13.85;ReadPosRankSum=-2.980e-01;SOR=0.681	GT:AD:DP:GQ:PL	0/0:55,0:55:99:0,114,1800	0/1:21,25:46:99:667,0,425
+20	10052688	.	C	A	1061.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.180;DP=116;ExcessHet=3.0103;FS=3.135;MLEAC=1;MLEAF=0.250;MQ=59.76;MQRankSum=0.870;QD=13.78;ReadPosRankSum=1.44;SOR=0.379	GT:AD:DP:GQ:PL	0/1:45,32:77:99:1091,0,1645	0/0:39,0:39:99:0,102,1246
+20	10053023	.	T	G	389.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.451e+00;ClippingRankSum=0.00;DP=64;ExcessHet=3.0103;FS=3.722;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.41;ReadPosRankSum=-1.276e+00;SOR=0.395	GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1485	0/1:10,17:27:99:419,0,247
+20	10053267	.	G	A	353.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.321;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=10.09;ReadPosRankSum=0.409;SOR=0.829	GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1485	0/1:19,16:35:99:383,0,480
+20	10053395	.	G	C	1534.42	.	AC=2;AF=0.500;AN=4;DP=95;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=26.92;SOR=0.800	GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1485	1/1:0,57:57:99:1569,169,0
+20	10053891	.	C	G	1398.42	.	AC=2;AF=0.500;AN=4;DP=83;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=29.75;SOR=1.022	GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1485	1/1:0,47:47:99:1433,140,0
+20	10055046	.	A	G	500.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-5.250e-01;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=6.884;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.83;ReadPosRankSum=1.50;SOR=1.052	GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1485	0/1:18,21:39:99:530,0,438
+20	10055829	.	T	C	316.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.257e+00;ClippingRankSum=0.00;DP=69;ExcessHet=3.0103;FS=3.192;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=9.88;ReadPosRankSum=0.424;SOR=0.944	GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1485	0/1:17,15:32:99:346,0,466
+20	10056026	.	C	G	434.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.78;ClippingRankSum=0.00;DP=74;ExcessHet=3.0103;FS=7.360;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=11.73;ReadPosRankSum=-7.530e-01;SOR=0.332	GT:AD:DP:GQ:PL	0/0:36,0:36:99:0,99,1485	0/1:18,19:37:99:464,0,405
+20	10056782	.	A	C	632.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.811e+00;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=6.477;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.70;ReadPosRankSum=2.51;SOR=0.837	GT:AD:DP:GQ:PGT:PID:PL	0/0:36,0:36:99:.:.:0,99,1485	0/1:26,17:43:99:0|1:10056782_A_C:662,0,1496
+20	10056784	.	A	C	632.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-9.100e-01;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=4.375;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.70;ReadPosRankSum=2.15;SOR=0.676	GT:AD:DP:GQ:PGT:PID:PL	0/0:36,0:36:99:.:.:0,99,1485	0/1:25,18:43:99:0|1:10056782_A_C:662,0,1496
+20	10058022	.	T	C	974.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.346e+00;DP=99;ExcessHet=3.0103;FS=0.920;MLEAC=1;MLEAF=0.250;MQ=59.11;MQRankSum=0.466;QD=14.33;ReadPosRankSum=0.018;SOR=0.849	GT:AD:DP:GQ:PL	0/1:36,32:68:99:1004,0,1261	0/0:31,0:31:90:0,90,1350
+20	10058248	.	G	A	863.42	.	AC=2;AF=0.500;AN=4;BaseQRankSum=1.77;ClippingRankSum=0.00;DP=77;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=27.85;ReadPosRankSum=-6.060e-01;SOR=0.223	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1575	1/1:1,30:31:82:898,82,0
+20	10061579	.	T	C	361.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.610;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=11.29;ReadPosRankSum=0.844;SOR=0.512	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1575	0/1:17,15:32:99:391,0,454
+20	10061632	.	C	T	1071.42	.	AC=2;AF=0.500;AN=4;DP=80;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=31.51;SOR=0.811	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1575	1/1:0,34:34:99:1106,102,0
+20	10062151	.	A	G	376.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.656e+00;ClippingRankSum=0.00;DP=105;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=6.60;ReadPosRankSum=-6.130e-01;SOR=0.688	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1575	0/1:38,19:57:99:406,0,1012
+20	10062329	.	T	C	590.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.037e+00;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=7.273;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.75;ReadPosRankSum=0.337;SOR=0.288	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1575	0/1:15,25:40:99:620,0,364
+20	10062531	.	A	G	283.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.520e-01;ClippingRankSum=0.00;DP=90;ExcessHet=3.0103;FS=2.923;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=6.44;ReadPosRankSum=0.447;SOR=1.387	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1575	0/1:29,15:44:99:313,0,725
+20	10062696	.	T	C	638.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.953;ClippingRankSum=0.00;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.18;ReadPosRankSum=-1.579e+00;SOR=0.638	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1575	0/1:18,27:45:99:668,0,404
+20	10062922	.	T	C	882.42	.	AC=2;AF=0.500;AN=4;DP=77;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=28.47;SOR=1.044	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,105,1575	1/1:0,31:31:92:917,92,0
+20	10062935	.	CA	C,CAA	230.48	.	AC=1,1;AF=0.250,0.250;AN=4;BaseQRankSum=1.34;ClippingRankSum=0.00;DP=111;ExcessHet=4.7712;FS=2.595;MLEAC=1,1;MLEAF=0.250,0.250;MQ=56.17;MQRankSum=1.71;QD=5.49;ReadPosRankSum=-8.900e-02;SOR=1.179	GT:AD:DP:GQ:PL	0/2:5,4,10:23:16:130,115,505,0,16,101	0/1:13,10,0:23:99:138,0,197,177,227,404
+20	10064261	.	T	G	542.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.993;ClippingRankSum=0.00;DP=90;ExcessHet=3.0103;FS=1.174;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.05;ReadPosRankSum=-1.260e+00;SOR=0.960	GT:AD:DP:GQ:PL	0/0:42,0:42:99:0,105,1575	0/1:22,23:45:99:572,0,499
+20	10064306	.	T	A	1476.42	.	AC=2;AF=0.500;AN=4;DP=90;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=30.76;SOR=0.963	GT:AD:DP:GQ:PL	0/0:42,0:42:99:0,105,1575	1/1:0,48:48:99:1511,144,0
+20	10064529	.	A	G	1014.42	.	AC=2;AF=0.500;AN=4;DP=83;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=26.01;SOR=0.968	GT:AD:DP:GQ:PL	0/0:42,0:42:99:0,105,1575	1/1:0,39:39:99:1049,115,0
+20	10065383	.	T	G	312.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-4.436e+00;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=10.07;ReadPosRankSum=-7.660e-01;SOR=0.569	GT:AD:DP:GQ:PL	0/0:42,0:42:99:0,105,1575	0/1:15,16:31:99:342,0,417
+20	10065517	.	T	C	243.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.690;ClippingRankSum=0.00;DP=73;ExcessHet=3.0103;FS=3.325;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=8.11;ReadPosRankSum=-1.828e+00;SOR=1.445	GT:AD:DP:GQ:PGT:PID:PL	0/0:42,0:42:99:.:.:0,105,1575	0/1:18,12:30:99:0|1:10065517_T_C:273,0,706
+20	10065525	.	G	A	451.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.814;ClippingRankSum=0.00;DP=70;ExcessHet=3.0103;FS=1.583;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.71;ReadPosRankSum=0.551;SOR=0.557	GT:AD:DP:GQ:PGT:PID:PL	0/0:42,0:42:99:.:.:0,105,1575	0/1:10,17:27:99:1|0:10065517_T_C:481,0,391
+20	10065779	.	G	GTT	651.82	.	AC=2;AF=0.500;AN=4;DP=78;ExcessHet=1.5490;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.32;QD=29.41;SOR=0.836	GT:AD:DP:GQ:PL	0/0:52,0:52:0:0,0,1441	1/1:0,7:13:81:637,81,0
+20	10067049	.	TAAAAAAA	T,TAAAA	1186.16	.	AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.177;ClippingRankSum=0.00;DP=99;ExcessHet=3.0103;FS=2.372;MLEAC=2,1;MLEAF=0.500,0.250;MQ=55.98;MQRankSum=0.00;QD=31.11;ReadPosRankSum=-1.322e+00;SOR=0.751	GT:AD:DP:GQ:PL	1/1:2,9,0:22:29:545,29,0,337,64,521	1/2:1,8,9:18:99:571,324,502,248,0,237
+20	10067090	.	C	A	2975.20	.	AC=4;AF=1.00;AN=4;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.77;QD=34.66;SOR=0.716	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2033,164,0	1/1:0,30:30:90:969,90,0
+20	10067264	.	G	A	3240.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=0.369;ClippingRankSum=0.00;DP=106;ExcessHet=3.0103;FS=3.400;MLEAC=3;MLEAF=0.750;MQ=59.56;MQRankSum=0.00;QD=30.57;ReadPosRankSum=-4.930e-01;SOR=0.518	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2951,219,0	0/1:20,13:33:99:319,0,534
+20	10067722	.	A	C	3333.20	.	AC=4;AF=1.00;AN=4;DP=92;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=29.40;SOR=0.782	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2175,163,0	1/1:0,38:38:99:1185,114,0
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+20	10068981	.	G	A	3350.20	.	AC=4;AF=1.00;AN=4;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=30.54;SOR=0.812	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2532,184,0	1/1:0,26:26:78:845,78,0
+20	10070602	.	T	C	3165.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-3.081e+00;ClippingRankSum=0.00;DP=112;ExcessHet=3.0103;FS=4.673;MLEAC=3;MLEAF=0.750;MQ=59.17;MQRankSum=0.00;QD=28.26;ReadPosRankSum=-6.890e-01;SOR=0.377	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0	0/1:21,19:40:99:475,0,592
+20	10070936	.	T	A	4355.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.071e+00;ClippingRankSum=0.00;DP=122;ExcessHet=3.0103;FS=1.991;MLEAC=3;MLEAF=0.750;MQ=59.18;MQRankSum=0.00;QD=21.53;ReadPosRankSum=0.014;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10070936_T_A:3660,247,0	0/1:21,19:40:99:0|1:10070936_T_A:725,0,1215
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+20	10071187	.	G	A	4028.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=2.97;ClippingRankSum=0.00;DP=128;ExcessHet=3.0103;FS=12.768;MLEAC=3;MLEAF=0.750;MQ=59.82;MQRankSum=0.00;QD=31.72;ReadPosRankSum=-2.080e-01;SOR=1.126	GT:AD:DP:GQ:PL	1/1:0,82:82:99:3439,246,0	0/1:21,24:45:99:619,0,444
+20	10071890	.	T	C	2461.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-4.435e+00;ClippingRankSum=0.00;DP=100;ExcessHet=3.0103;FS=0.935;MLEAC=3;MLEAF=0.750;MQ=59.81;MQRankSum=0.00;QD=24.61;ReadPosRankSum=0.584;SOR=0.850	GT:AD:DP:GQ:PL	1/1:0,57:57:99:2003,171,0	0/1:20,23:43:99:488,0,521
+20	10072505	.	A	G	2581.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.080e+00;ClippingRankSum=0.00;DP=104;ExcessHet=3.0103;FS=3.410;MLEAC=3;MLEAF=0.750;MQ=60.00;MQRankSum=0.00;QD=25.06;ReadPosRankSum=0.816;SOR=0.569	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2128,191,0	0/1:19,20:39:99:483,0,448
+20	10074187	.	A	G	3794.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-6.360e-01;ClippingRankSum=0.00;DP=123;ExcessHet=3.0103;FS=2.196;MLEAC=3;MLEAF=0.750;MQ=59.44;MQRankSum=0.00;QD=31.10;ReadPosRankSum=2.42;SOR=0.449	GT:AD:DP:GQ:PL	1/1:0,79:79:99:3130,238,0	0/1:17,26:43:99:694,0,403
+20	10074240	.	T	C	3998.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-3.298e+00;ClippingRankSum=0.00;DP=136;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=59.86;MQRankSum=0.00;QD=29.84;ReadPosRankSum=-1.192e+00;SOR=0.756	GT:AD:DP:GQ:PL	1/1:0,85:85:99:3435,255,0	0/1:24,25:49:99:593,0,646
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+20	10075043	.	T	C	3584.20	.	AC=4;AF=1.00;AN=4;DP=101;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.77;QD=34.17;SOR=1.225	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2434,184,0	1/1:0,39:39:99:1177,116,0
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+20	10075463	.	G	A	506.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.247;ClippingRankSum=0.00;DP=91;ExcessHet=3.0103;FS=4.566;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.05;ReadPosRankSum=-2.174e+00;SOR=1.383	GT:AD:DP:GQ:PL	0/0:49,0:49:99:0,119,1800	0/1:19,23:42:99:536,0,436
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+20	10076339	.	A	G	2905.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-6.900e-02;DP=127;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=59.82;MQRankSum=-8.660e-01;QD=22.88;ReadPosRankSum=1.02;SOR=0.697	GT:AD:DP:GQ:PL	0/1:32,40:72:99:1338,0,1035	1/1:0,55:55:99:1597,164,0
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+20	10076749	.	G	A	1232.42	.	AC=2;AF=0.500;AN=4;DP=90;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=32.43;SOR=1.329	GT:AD:DP:GQ:PL	0/0:51,0:51:99:0,120,1800	1/1:0,38:38:99:1267,114,0
+20	10076796	.	A	G	1129.42	.	AC=2;AF=0.500;AN=4;DP=88;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=30.52;SOR=0.984	GT:AD:DP:GQ:PL	0/0:51,0:51:99:0,120,1800	1/1:0,37:37:99:1164,111,0
+20	10076860	.	A	C	1192.42	.	AC=2;AF=0.500;AN=4;DP=94;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=27.73;SOR=0.941	GT:AD:DP:GQ:PL	0/0:51,0:51:99:0,120,1800	1/1:0,43:43:99:1227,129,0
+20	10076989	.	CA	CAAAAA,C	1180.16	.	AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-1.760e-01;ClippingRankSum=0.00;DP=102;ExcessHet=3.0103;FS=0.000;MLEAC=2,1;MLEAF=0.500,0.250;MQ=58.30;MQRankSum=-1.670e-01;QD=29.50;ReadPosRankSum=0.087;SOR=0.571	GT:AD:DP:GQ:PGT:PID:PL	0/2:7,0,13:30:99:.:.:211,281,664,0,382,335	1/1:1,19,0:20:62:1|1:10076989_C_CAAAA:964,62,0,967,69,975
+20	10077267	.	A	T	1681.42	.	AC=2;AF=0.500;AN=4;DP=85;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=33.11;SOR=0.968	GT:AD:DP:GQ:PGT:PID:PL	0/0:44,0:44:99:.:.:0,102,1654	1/1:0,39:39:99:1|1:10077267_A_T:1716,117,0
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+20	10077752	.	T	C	1344.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-6.503e+00;DP=123;ExcessHet=3.0103;FS=4.458;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=17.02;ReadPosRankSum=-3.520e-01;SOR=1.251	GT:AD:DP:GQ:PL	0/1:34,45:79:99:1374,0,1187	0/0:44,0:44:99:0,99,1170
+20	10077820	.	TC	T	1232.38	.	AC=2;AF=0.500;AN=4;DP=81;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=30.49;SOR=0.749	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,108,1620	1/1:0,35:35:99:1276,105,0
+20	10078505	.	G	A	1141.42	.	AC=2;AF=0.500;AN=4;DP=83;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=32.61;SOR=0.749	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,108,1620	1/1:0,35:35:99:1176,105,0
+20	10078897	.	T	TA	1175.38	.	AC=2;AF=0.500;AN=4;DP=88;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=29.38;SOR=0.793	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,108,1620	1/1:0,40:40:99:1219,129,0
+20	10079065	.	T	C	1087.42	.	AC=2;AF=0.500;AN=4;DP=87;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=27.88;SOR=0.850	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,108,1620	1/1:0,39:39:99:1122,116,0
+20	10079396	.	A	G	1398.42	.	AC=2;AF=0.500;AN=4;DP=97;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=27.97;SOR=0.773	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,108,1620	1/1:0,50:50:99:1433,150,0
+20	10079761	.	T	TAA	1820.38	.	AC=2;AF=0.500;AN=4;DP=81;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=31.67;SOR=0.843	GT:AD:DP:GQ:PL	0/0:40,0:40:99:0,105,1571	1/1:0,41:41:99:1864,126,0
+20	10079821	.	C	G	1124.42	.	AC=2;AF=0.500;AN=4;DP=76;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=31.23;SOR=0.804	GT:AD:DP:GQ:PL	0/0:40,0:40:99:0,105,1571	1/1:0,36:36:99:1159,108,0
+20	10081750	.	C	A	1352.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.67;DP=121;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.29;ReadPosRankSum=-4.060e-01;SOR=0.664	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1382,0,1525	0/0:38,0:38:95:0,95,1088
+20	10081800	.	C	T	1108.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.241;DP=105;ExcessHet=3.0103;FS=11.086;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.30;ReadPosRankSum=-2.622e+00;SOR=0.143	GT:AD:DP:GQ:PL	0/1:35,33:68:99:1138,0,1222	0/0:37,0:37:99:0,99,1143
+20	10082476	.	A	G	522.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.25;ClippingRankSum=0.00;DP=83;ExcessHet=3.0103;FS=1.252;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=13.05;ReadPosRankSum=-5.430e-01;SOR=1.099	GT:AD:DP:GQ:PL	0/0:43,0:43:99:0,111,1665	0/1:19,21:40:99:552,0,487
+20	10082892	.	C	T	2681.20	.	AC=4;AF=1.00;AN=4;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.69;QD=29.53;SOR=0.719	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1741,132,0	1/1:0,31:31:93:967,93,0
+20	10083191	.	A	T	482.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.131e+00;ClippingRankSum=0.00;DP=78;ExcessHet=3.0103;FS=2.742;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.69;ReadPosRankSum=-6.800e-01;SOR=0.368	GT:AD:DP:GQ:PL	0/0:38,0:38:99:0,102,1530	0/1:18,20:38:99:512,0,452
+20	10084121	.	C	T	1451.42	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-1.401e+00;ClippingRankSum=0.00;DP=85;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=30.88;ReadPosRankSum=-4.290e-01;SOR=0.527	GT:AD:DP:GQ:PL	0/0:38,0:38:99:0,102,1530	1/1:1,46:47:99:1486,107,0
+20	10085054	.	A	G	1201.42	.	AC=2;AF=0.500;AN=4;DP=79;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=29.30;SOR=0.843	GT:AD:DP:GQ:PL	0/0:38,0:38:99:0,102,1530	1/1:0,41:41:99:1236,123,0
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+20	10085320	.	C	T	1234.42	.	AC=2;AF=0.500;AN=4;DP=95;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=30.86;SOR=0.902	GT:AD:DP:GQ:PL	0/0:54,0:54:99:0,120,1800	1/1:0,40:40:99:1269,120,0
+20	10086110	.	G	A	2141.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-3.430e-01;DP=108;ExcessHet=3.0103;FS=1.581;MLEAC=3;MLEAF=0.750;MQ=59.36;MQRankSum=-6.800e-01;QD=19.83;ReadPosRankSum=0.170;SOR=0.518	GT:AD:DP:GQ:PL	0/1:43,38:81:99:1303,0,1506	1/1:0,27:27:81:868,81,0
+20	10086283	.	G	T	2120.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=2.30;ClippingRankSum=0.00;DP=123;ExcessHet=3.0103;FS=1.467;MLEAC=3;MLEAF=0.750;MQ=60.00;MQRankSum=0.00;QD=17.38;ReadPosRankSum=1.89;SOR=0.522	GT:AD:DP:GQ:PL	0/1:52,32:84:99:1054,0,1771	1/1:1,37:38:99:1096,104,0
+20	10086619	.	T	A	795.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.256;DP=106;ExcessHet=3.0103;FS=0.958;MLEAC=1;MLEAF=0.250;MQ=59.67;MQRankSum=-1.312e+00;QD=11.36;ReadPosRankSum=-7.600e-01;SOR=0.846	GT:AD:DP:GQ:PL	0/1:45,25:70:99:825,0,1603	0/0:36,0:36:99:0,99,1127
+20	10086853	.	G	A	2053.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=3.92;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=59.61;MQRankSum=-1.770e-01;QD=19.37;ReadPosRankSum=-1.000e-01;SOR=0.737	GT:AD:DP:GQ:PGT:PID:PL	0/1:41,32:73:99:.:.:1031,0,1280	1/1:0,33:33:99:1|1:10086847_G_T:1052,99,0
+20	10086954	.	G	A	2013.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=2.61;DP=101;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=60.00;MQRankSum=0.00;QD=20.34;ReadPosRankSum=-5.340e-01;SOR=0.672	GT:AD:DP:GQ:PL	0/1:34,34:68:99:1124,0,1051	1/1:0,31:31:92:919,92,0
+20	10087230	.	A	G	2798.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.427e+00;ClippingRankSum=0.00;DP=130;ExcessHet=3.0103;FS=3.379;MLEAC=3;MLEAF=0.750;MQ=59.18;MQRankSum=1.71;QD=21.52;ReadPosRankSum=0.307;SOR=0.759	GT:AD:DP:GQ:PL	0/1:42,54:96:99:1871,0,1428	1/1:1,33:34:66:957,66,0
+20	10087394	.	T	G	1687.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.340e+00;DP=122;ExcessHet=3.0103;FS=4.225;MLEAC=1;MLEAF=0.250;MQ=59.73;MQRankSum=1.21;QD=20.09;ReadPosRankSum=0.885;SOR=0.436	GT:AD:DP:GQ:PL	0/1:35,49:84:99:1717,0,1186	0/0:38,0:38:99:0,99,1150
+20	10087754	.	T	G	1346.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.355;DP=110;ExcessHet=3.0103;FS=0.869;MLEAC=1;MLEAF=0.250;MQ=60.39;MQRankSum=2.19;QD=17.26;ReadPosRankSum=-5.510e-01;SOR=0.562	GT:AD:DP:GQ:PL	0/1:37,41:78:99:1376,0,1239	0/0:31,0:31:90:0,90,1350
+20	10087804	.	C	T	2500.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=1.94;DP=132;ExcessHet=3.0103;FS=1.477;MLEAC=3;MLEAF=0.750;MQ=60.99;MQRankSum=2.62;QD=18.94;ReadPosRankSum=0.341;SOR=0.554	GT:AD:DP:GQ:PL	0/1:50,50:100:99:1648,0,1511	1/1:0,32:32:94:882,94,0
+20	10087820	.	C	CAGAG,CAG	1855.15	.	AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-1.974e+00;DP=133;ExcessHet=3.0103;FS=2.946;MLEAC=2,1;MLEAF=0.500,0.250;MQ=60.88;MQRankSum=0.422;QD=21.83;ReadPosRankSum=-3.570e-01;SOR=1.014	GT:AD:DP:GQ:PL	0/2:35,0,18:53:99:466,661,2189,0,1238,1168	1/1:0,32,0:32:96:1428,96,0,1428,96,1428
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+20	10088699	.	C	T	2180.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=3.80;DP=113;ExcessHet=3.0103;FS=11.595;MLEAC=3;MLEAF=0.750;MQ=57.87;MQRankSum=-3.140e+00;QD=20.38;ReadPosRankSum=-1.456e+00;SOR=1.041	GT:AD:DP:GQ:PL	0/1:36,26:62:99:805,0,1088	1/1:0,45:45:99:1405,135,0
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+20	10088968	.	C	CAAA	2955.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=0.552;DP=95;ExcessHet=3.0103;FS=1.907;MLEAC=3;MLEAF=0.750;MQ=55.48;MQRankSum=-4.750e+00;QD=32.63;ReadPosRankSum=2.42;SOR=1.012	GT:AD:DP:GQ:PGT:PID:PL	0/1:30,23:53:99:0|1:10088968_C_CAAA:1213,0,1367	1/1:0,30:30:99:1|1:10088968_C_CAAA:1781,128,0
+20	10088980	.	T	C	3105.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.585e+00;DP=113;ExcessHet=3.0103;FS=2.621;MLEAC=3;MLEAF=0.750;MQ=54.22;MQRankSum=-5.232e+00;QD=27.72;ReadPosRankSum=1.29;SOR=0.917	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,31:68:99:0|1:10088968_C_CAAA:1276,0,1627	1/1:0,44:44:99:1|1:10088968_C_CAAA:1859,135,0
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+20	10089525	.	C	T	2899.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=5.86;DP=124;ExcessHet=3.0103;FS=7.522;MLEAC=3;MLEAF=0.750;MQ=59.66;MQRankSum=1.53;QD=23.38;ReadPosRankSum=0.862;SOR=0.754	GT:AD:DP:GQ:PL	0/1:38,43:81:99:1577,0,1088	1/1:0,43:43:99:1352,128,0
+20	10090289	.	CAA	C,CA	1392.15	.	AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=0.441;ClippingRankSum=0.00;DP=118;ExcessHet=3.0103;FS=0.000;MLEAC=2,1;MLEAF=0.500,0.250;MQ=59.98;MQRankSum=1.39;QD=20.47;ReadPosRankSum=0.048;SOR=0.841	GT:AD:DP:GQ:PL	0/2:14,4,20:38:99:422,360,986,0,261,230	1/1:1,29,0:30:66:1009,66,0,1012,88,1033
+20	10090764	.	A	G	2026.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-2.659e+00;DP=109;ExcessHet=3.0103;FS=9.917;MLEAC=3;MLEAF=0.750;MQ=60.00;MQRankSum=0.00;QD=18.76;ReadPosRankSum=1.21;SOR=0.441	GT:AD:DP:GQ:PL	0/1:34,29:63:99:869,0,1207	1/1:0,45:45:99:1187,133,0
+20	10090886	.	G	A	1432.42	.	AC=2;AF=0.500;AN=4;BaseQRankSum=1.03;ClippingRankSum=0.00;DP=121;ExcessHet=0.7918;FS=1.777;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=25.58;ReadPosRankSum=1.80;SOR=0.597	GT:AD:DP:GQ:PL	0/0:65,0:65:99:0,120,1800	1/1:5,51:56:48:1467,48,0
+20	10090970	.	T	C	1256.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-4.840e-01;DP=113;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.250;MQ=59.46;MQRankSum=1.51;QD=18.21;ReadPosRankSum=-7.200e-02;SOR=0.518	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1286,0,1092	0/0:44,0:44:99:0,113,1448
+20	10091214	.	C	T	1248.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.361;DP=114;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.73;MQRankSum=-9.160e-01;QD=17.83;ReadPosRankSum=-3.500e-02;SOR=0.625	GT:AD:DP:GQ:PL	0/1:33,37:70:99:1278,0,1110	0/0:44,0:44:99:0,113,1448
+20	10091220	.	A	G	1200.42	.	AC=2;AF=0.500;AN=4;DP=91;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=27.28;SOR=0.883	GT:AD:DP:GQ:PL	0/0:46,0:46:99:0,120,1800	1/1:0,44:44:99:1235,130,0
+20	10092415	.	A	G	1634.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-6.731e+00;DP=140;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.18;ReadPosRankSum=0.082;SOR=0.665	GT:AD:DP:GQ:PL	0/1:52,49:101:99:1664,0,1902	0/0:39,0:39:99:0,108,1239
+20	10092642	.	T	C	1393.42	.	AC=2;AF=0.500;AN=4;DP=111;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=27.32;SOR=0.732	GT:AD:DP:GQ:PL	0/0:60,0:60:99:0,120,1800	1/1:0,51:51:99:1428,151,0
+20	10092927	.	G	T	105.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-2.507e+00;DP=113;ExcessHet=3.0103;FS=60.191;MLEAC=1;MLEAF=0.250;MQ=59.37;MQRankSum=-3.009e+00;QD=1.46;ReadPosRankSum=-2.200e-01;SOR=5.279	GT:AD:DP:GQ:PL	0/1:59,13:72:99:135,0,1864	0/0:40,0:40:99:0,108,1608
+20	10093568	.	GT	GTTT,G	1219.15	.	AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=0.426;DP=87;ExcessHet=3.0103;FS=1.087;MLEAC=2,1;MLEAF=0.500,0.250;MQ=59.27;MQRankSum=0.410;QD=21.02;ReadPosRankSum=1.26;SOR=0.452	GT:AD:DP:GQ:PGT:PID:PL	0/2:17,0,17:42:99:.:.:364,431,885,0,449,386	1/1:0,24,0:24:75:1|1:10093568_G_GTT:894,75,0,894,75,894
+20	10093923	.	T	A	1074.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-6.670e-01;DP=104;ExcessHet=3.0103;FS=0.924;MLEAC=1;MLEAF=0.250;MQ=59.19;MQRankSum=0.358;QD=16.03;ReadPosRankSum=-1.583e+00;SOR=0.772	GT:AD:DP:GQ:PL	0/1:35,32:67:99:1104,0,1257	0/0:37,0:37:91:0,91,1230
+20	10094251	.	T	A	1269.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=0.251;DP=99;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=20.47;ReadPosRankSum=1.81;SOR=1.211	GT:AD:DP:GQ:PL	0/1:26,36:62:99:1299,0,781	0/0:37,0:37:99:0,100,1165
+20	10094582	.	A	G	922.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-1.388e+00;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.39;MQRankSum=1.27;QD=13.37;ReadPosRankSum=-1.800e-02;SOR=0.772	GT:AD:DP:GQ:PL	0/1:39,30:69:99:952,0,1350	0/0:37,0:37:99:0,99,1130
+20	10094774	.	C	T	1035.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-7.840e-01;DP=124;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.69;MQRankSum=0.962;QD=13.80;ReadPosRankSum=0.197;SOR=0.690	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1065,0,1282	0/0:49,0:49:97:0,97,1393
+20	10095432	.	GTGATGATGA	GTGA,G	2055.15	.	AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=1.27;DP=112;ExcessHet=3.0103;FS=3.183;MLEAC=2,1;MLEAF=0.500,0.250;MQ=56.20;MQRankSum=-4.431e+00;QD=26.69;ReadPosRankSum=0.396;SOR=0.404	GT:AD:DP:GQ:PL	0/2:27,0,23:50:99:877,959,3140,0,2181,2108	1/1:0,27,0:27:82:1217,82,0,1217,82,1217
+20	10095741	.	A	G	1074.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-5.340e-01;DP=105;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.250;MQ=57.35;MQRankSum=-2.313e+00;QD=15.35;ReadPosRankSum=-5.000e-01;SOR=0.515	GT:AD:DP:GQ:PL	0/1:36,34:70:99:1104,0,1233	0/0:34,0:34:67:0,67,972
+20	10096293	.	C	T	1354.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=4.66;DP=115;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=58.57;MQRankSum=1.40;QD=18.06;ReadPosRankSum=-1.135e+00;SOR=0.638	GT:AD:DP:GQ:PL	0/1:37,38:75:99:1384,0,1258	0/0:40,0:40:99:0,108,1181
+20	10096357	.	A	G	1131.42	.	AC=2;AF=0.500;AN=4;BaseQRankSum=0.964;ClippingRankSum=0.00;DP=101;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=26.94;ReadPosRankSum=1.55;SOR=0.460	GT:AD:DP:GQ:PL	0/0:57,0:57:99:0,120,1800	1/1:1,41:42:94:1166,94,0
+20	10096596	.	C	T	1561.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.73;DP=130;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=58.77;MQRankSum=0.612;QD=17.94;ReadPosRankSum=-1.700e-01;SOR=0.640	GT:AD:DP:GQ:PL	0/1:40,47:87:99:1591,0,1273	0/0:43,0:43:99:0,99,1273
+20	10096733	.	C	T	1712.42	.	AC=2;AF=0.500;AN=4;BaseQRankSum=1.16;ClippingRankSum=0.00;DP=134;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=30.04;ReadPosRankSum=-9.330e-01;SOR=0.252	GT:AD:DP:GQ:PL	0/0:75,0:75:99:0,120,1800	1/1:1,56:57:99:1747,143,0
+20	10096768	.	A	C	3466.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-2.764e+00;DP=148;ExcessHet=3.0103;FS=6.852;MLEAC=3;MLEAF=0.750;MQ=59.61;MQRankSum=-1.609e+00;QD=23.58;ReadPosRankSum=0.613;SOR=0.522	GT:AD:DP:GQ:PL	0/1:42,49:91:99:1711,0,1452	1/1:0,56:56:99:1785,168,0
+20	10096899	.	G	T	3448.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=2.76;DP=120;ExcessHet=3.0103;FS=9.707;MLEAC=3;MLEAF=0.750;MQ=59.78;MQRankSum=-1.387e+00;QD=28.73;ReadPosRankSum=0.422;SOR=1.590	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,40:79:99:0|1:10096899_G_T:1643,0,1520	1/1:0,41:41:99:1|1:10096899_G_T:1835,123,0
+20	10096905	.	TA	T	3434.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-7.550e-01;DP=123;ExcessHet=3.0103;FS=13.029;MLEAC=3;MLEAF=0.750;MQ=59.60;MQRankSum=-1.677e+00;QD=27.92;ReadPosRankSum=0.461;SOR=1.725	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,43:83:99:0|1:10096899_G_T:1638,0,1623	1/1:0,40:40:99:1|1:10096899_G_T:1835,123,0
+20	10096925	.	T	C	334.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-4.687e+00;ClippingRankSum=0.00;DP=120;ExcessHet=3.0103;FS=1.342;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=8.79;ReadPosRankSum=-6.140e-01;SOR=0.399	GT:AD:DP:GQ:PL	0/0:82,0:82:99:0,120,1800	0/1:20,18:38:99:364,0,556
+20	10096933	.	G	C	3240.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.914e+00;DP=123;ExcessHet=3.0103;FS=28.941;MLEAC=3;MLEAF=0.750;MQ=59.51;MQRankSum=-1.802e+00;QD=26.34;ReadPosRankSum=0.334;SOR=1.469	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,41:85:99:0|1:10096933_G_C:1540,0,1770	1/1:0,38:38:99:1|1:10096933_G_C:1730,117,0
+20	10096958	.	G	A	3662.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=2.84;DP=139;ExcessHet=3.0103;FS=22.455;MLEAC=3;MLEAF=0.750;MQ=59.57;MQRankSum=-1.701e+00;QD=26.35;ReadPosRankSum=-1.833e+00;SOR=1.412	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,47:92:99:0|1:10096933_G_C:1795,0,1629	1/1:0,47:47:99:1|1:10096933_G_C:1897,141,0
+20	10097075	.	T	G	2500.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=1.82;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=5.781;MLEAC=3;MLEAF=0.750;MQ=58.96;MQRankSum=0.00;QD=19.84;ReadPosRankSum=1.53;SOR=0.480	GT:AD:DP:GQ:PL	0/1:44,48:92:99:1474,0,1482	1/1:1,33:34:92:1056,92,0
+20	10097101	.	C	CTTTT,CTTT	2098.15	.	AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-1.134e+00;DP=104;ExcessHet=3.0103;FS=4.258;MLEAC=2,1;MLEAF=0.500,0.250;MQ=58.27;MQRankSum=-2.428e+00;QD=24.40;ReadPosRankSum=2.09;SOR=0.358	GT:AD:DP:GQ:PL	0/2:34,4,26:64:99:1129,558,2012,0,1324,1306	1/1:0,22,0:22:71:1008,71,0,1008,71,1009
+20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C	1053.15	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.82;DP=119;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.250;MQ=54.27;MQRankSum=-6.464e+00;QD=11.83;ReadPosRankSum=-3.097e+00;SOR=0.948	GT:AD:DP:GQ:PL	0/1:57,32:89:99:1092,0,2241	0/0:30,0:30:66:0,66,990
+20	10097437	.	TTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC	*,TTTTCTTTCTTTCTTTCTTTCTTTCTTTC,T	3019.16	.	AC=1,1,2;AF=0.250,0.250,0.500;AN=4;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,2;MLEAF=0.250,0.250,0.500;MQ=55.40;QD=30.36;SOR=1.905	GT:AD:DP:GQ:PL	1/2:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642	3/3:0,0,0,21:21:67:928,928,928,928,928,928,67,67,67,0
+20	10097626	.	C	A	625.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.09;DP=77;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.250;MQ=58.24;MQRankSum=-1.331e+00;QD=13.02;ReadPosRankSum=1.02;SOR=0.324	GT:AD:DP:GQ:PL	0/1:28,20:48:99:655,0,957	0/0:29,0:29:81:0,81,1014
+20	10097751	.	T	C	959.42	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-3.680e-01;ClippingRankSum=0.00;DP=87;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=25.25;ReadPosRankSum=1.08;SOR=0.350	GT:AD:DP:GQ:PL	0/0:49,0:49:99:0,120,1800	1/1:1,37:38:82:994,82,0
+20	10097789	.	T	C	2017.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.157e+00;DP=100;ExcessHet=3.0103;FS=5.286;MLEAC=3;MLEAF=0.750;MQ=58.63;MQRankSum=-2.805e+00;QD=20.17;ReadPosRankSum=0.220;SOR=0.574	GT:AD:DP:GQ:PL	0/1:34,23:57:99:717,0,1190	1/1:0,43:43:99:1330,129,0
+20	10097928	.	G	A	1508.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.203e+00;DP=66;ExcessHet=3.0103;FS=1.106;MLEAC=3;MLEAF=0.750;MQ=58.95;MQRankSum=-1.654e+00;QD=23.20;ReadPosRankSum=-7.900e-02;SOR=1.038	GT:AD:DP:GQ:PL	0/1:17,19:36:99:599,0,586	1/1:0,29:29:87:939,87,0
+20	10098110	.	G	C	2478.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=2.51;DP=80;ExcessHet=3.0103;FS=26.615;MLEAC=3;MLEAF=0.750;MQ=59.42;MQRankSum=-1.477e+00;QD=30.98;ReadPosRankSum=-7.300e-01;SOR=0.010	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,17:36:99:0|1:10098110_G_C:615,0,727	1/1:0,44:44:99:1|1:10098110_G_C:1893,135,0
+20	10098135	.	C	A	2250.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.155e+00;DP=80;ExcessHet=3.0103;FS=40.921;MLEAC=3;MLEAF=0.750;MQ=59.83;MQRankSum=1.55;QD=28.48;ReadPosRankSum=-5.910e-01;SOR=0.003	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,14:38:99:0|1:10098110_G_C:500,0,964	1/1:0,41:41:99:1|1:10098110_G_C:1780,126,0
+20	10098219	.	TATATATA	T	1663.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=3.15;DP=54;ExcessHet=3.0103;FS=19.931;MLEAC=3;MLEAF=0.750;MQ=58.45;MQRankSum=-2.050e-01;QD=31.98;ReadPosRankSum=0.427;SOR=0.013	GT:AD:DP:GQ:PGT:PID:PL	0/1:12,9:21:99:0|1:10098219_TATATATA_T:333,0,461	1/1:0,31:31:96:1|1:10098219_TATATATA_T:1369,96,0
+20	10098237	.	A	T	1588.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=6.000e-03;DP=47;ExcessHet=3.0103;FS=11.066;MLEAC=3;MLEAF=0.750;MQ=58.16;MQRankSum=-1.742e+00;QD=34.53;ReadPosRankSum=0.277;SOR=0.043	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,7:13:99:0|1:10098219_TATATATA_T:273,0,273	1/1:0,33:33:98:1|1:10098219_TATATATA_T:1345,98,0
+20	10098265	.	T	C	132.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.83;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=41.96;MQRankSum=-1.834e+00;QD=22.03;ReadPosRankSum=0.00;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,4:6:59:0|1:10098219_TATATATA_T:162,0,59	0/0:44,0:44:90:.:.:0,90,1350
+20	10098644	.	ATT	A	189.29	.	AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.33;QD=28.13;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	./.:1,0:1:.:.:.:0,0,0	1/1:0,4:4:15:1|1:10098644_ATT_A:225,15,0
+20	10098660	.	G	A	284.47	.	AC=2;AF=0.500;AN=4;DP=11;ExcessHet=0.7918;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=41.04;QD=27.97;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/0:1,0:1:3:.:.:0,3,33	1/1:0,7:7:21:1|1:10098644_ATT_A:315,21,0
+20	10098668	.	A	AAT	365.38	.	AC=2;AF=0.500;AN=4;DP=12;ExcessHet=0.7918;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=43.11;QD=28.31;SOR=1.863	GT:AD:DP:GQ:PGT:PID:PL	0/0:1,0:1:3:.:.:0,3,33	1/1:0,8:8:27:1|1:10098644_ATT_A:405,27,0
+20	10098689	.	GTA	G	587.13	.	AC=2;AF=0.500;AN=4;DP=21;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=46.88;QD=35.21;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/0:4,0:4:12:.:.:0,12,150	1/1:0,13:13:42:1|1:10098644_ATT_A:630,42,0
+20	10098704	.	A	G	775.62	.	AC=2;AF=0.500;AN=4;DP=26;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=49.08;QD=35.18;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/0:6,0:6:18:.:.:0,18,231	1/1:0,16:16:54:1|1:10098644_ATT_A:810,54,0
+20	10098729	.	T	TATATA	811.43	.	AC=2;AF=0.500;AN=4;DP=32;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=51.87;QD=29.59;SOR=1.292	GT:AD:DP:GQ:PGT:PID:PL	0/0:9,0:9:24:.:.:0,24,360	1/1:0,19:19:57:1|1:10098644_ATT_A:855,57,0
+20	10098784	.	TAC	T	280.63	.	AC=2;AF=0.500;AN=4;DP=19;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=57.51;QD=32.25;SOR=0.693	GT:AD:DP:GQ:PL	0/0:9,0:9:18:0,18,270	1/1:0,8:8:24:324,24,0
+20	10098885	.	C	CA	1595.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=0.165;DP=61;ExcessHet=3.0103;FS=13.392;MLEAC=3;MLEAF=0.750;MQ=54.77;MQRankSum=-4.449e+00;QD=26.59;ReadPosRankSum=-1.073e+00;SOR=0.054	GT:AD:DP:GQ:PL	0/1:17,14:31:99:471,0,572	1/1:0,29:29:87:1163,87,0
+20	10098945	.	T	C	1244.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=1.48;DP=48;ExcessHet=3.0103;FS=3.874;MLEAC=3;MLEAF=0.750;MQ=55.63;MQRankSum=-2.504e+00;QD=26.47;ReadPosRankSum=1.04;SOR=0.193	GT:AD:DP:GQ:PL	0/1:9,13:22:99:481,0,248	1/1:0,25:25:75:793,75,0
+20	10098987	.	C	T	378.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=3.13;DP=55;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.250;MQ=51.88;MQRankSum=-2.734e+00;QD=15.76;ReadPosRankSum=0.436;SOR=2.925	GT:AD:DP:GQ:PL	0/1:11,13:24:99:408,0,350	0/0:31,0:31:90:0,90,977
+20	10099029	.	T	C	1610.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.809e+00;DP=57;ExcessHet=3.0103;FS=2.698;MLEAC=3;MLEAF=0.750;MQ=56.40;MQRankSum=-3.641e+00;QD=28.25;ReadPosRankSum=-1.224e+00;SOR=0.346	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768	1/1:0,29:29:87:1|1:10099029_T_C:1277,87,0
+20	10099034	.	C	A	1548.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=2.76;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=56.26;MQRankSum=-3.641e+00;QD=28.15;ReadPosRankSum=-1.850e+00;SOR=0.657	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768	1/1:0,27:27:81:1|1:10099029_T_C:1215,81,0
+20	10099044	.	A	C	1548.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.148e+00;DP=51;ExcessHet=3.0103;FS=2.900;MLEAC=3;MLEAF=0.750;MQ=54.53;MQRankSum=-4.418e+00;QD=30.36;ReadPosRankSum=-2.207e+00;SOR=0.368	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:363,0,768	1/1:0,27:27:81:1|1:10099029_T_C:1215,81,0
+20	10099046	.	T	C	1563.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-2.165e+00;DP=51;ExcessHet=3.0103;FS=2.900;MLEAC=3;MLEAF=0.750;MQ=54.53;MQRankSum=-4.418e+00;QD=30.65;ReadPosRankSum=-2.297e+00;SOR=0.368	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:333,0,603	1/1:0,27:27:84:1|1:10099029_T_C:1260,84,0
+20	10099055	.	T	C	1605.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.554e+00;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=55.24;MQRankSum=-4.316e+00;QD=30.29;ReadPosRankSum=-1.970e+00;SOR=0.559	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,8:23:99:0|1:10099029_T_C:285,0,673	1/1:0,30:30:90:1|1:10099029_T_C:1350,90,0
+20	10099079	.	C	T	1501.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=1.43;DP=61;ExcessHet=3.0103;FS=5.502;MLEAC=3;MLEAF=0.750;MQ=55.66;MQRankSum=-2.821e+00;QD=25.02;ReadPosRankSum=0.969;SOR=1.396	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,6:29:99:0|1:10099029_T_C:145,0,886	1/1:0,31:31:96:1|1:10099029_T_C:1386,96,0
+20	10099111	.	T	TTTTGTTTG	1696.15	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.207e+00;DP=70;ExcessHet=3.0103;FS=1.042;MLEAC=3;MLEAF=0.750;MQ=54.66;MQRankSum=-4.071e+00;QD=29.24;ReadPosRankSum=-2.730e-01;SOR=0.489	GT:AD:DP:GQ:PL	0/1:22,13:35:99:694,0,802	1/1:0,23:23:72:1041,72,0
+20	10099140	.	G	T	2034.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.140e-01;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=56.86;MQRankSum=-2.469e+00;QD=21.87;ReadPosRankSum=0.338;SOR=0.656	GT:AD:DP:GQ:PL	0/1:30,32:62:99:1034,0,931	1/1:0,31:31:93:1030,93,0
+20	10099190	.	G	T	2180.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-3.400e-02;DP=103;ExcessHet=3.0103;FS=1.732;MLEAC=3;MLEAF=0.750;MQ=58.24;MQRankSum=-1.711e+00;QD=21.59;ReadPosRankSum=-1.260e+00;SOR=0.529	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1063,0,1154	1/1:0,36:36:99:1147,108,0
+20	10099220	.	A	G	1500.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.664e+00;DP=76;ExcessHet=3.0103;FS=2.044;MLEAC=3;MLEAF=0.750;MQ=58.61;MQRankSum=-2.596e+00;QD=20.00;ReadPosRankSum=0.629;SOR=0.439	GT:AD:DP:GQ:PL	0/1:25,20:45:99:606,0,873	1/1:0,30:30:89:924,89,0
+20	10099250	.	G	A	698.19	.	AC=1;AF=0.250;AN=4;BaseQRankSum=3.17;DP=69;ExcessHet=3.0103;FS=7.195;MLEAC=1;MLEAF=0.250;MQ=56.71;MQRankSum=-2.272e+00;QD=18.87;ReadPosRankSum=0.583;SOR=0.162	GT:AD:DP:GQ:PL	0/1:16,21:37:99:728,0,424	0/0:32,0:32:90:0,90,1350
+20	10099535	.	G	A	2589.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=5.03;DP=104;ExcessHet=3.0103;FS=5.820;MLEAC=3;MLEAF=0.750;MQ=59.38;MQRankSum=-1.418e+00;QD=25.14;ReadPosRankSum=-7.770e-01;SOR=0.307	GT:AD:DP:GQ:PL	0/1:26,39:65:99:1364,0,686	1/1:0,38:38:99:1255,114,0
+20	10099565	.	C	T	2689.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=4.60;DP=113;ExcessHet=3.0103;FS=16.934;MLEAC=3;MLEAF=0.750;MQ=59.63;MQRankSum=-1.266e+00;QD=24.01;ReadPosRankSum=1.23;SOR=0.174	GT:AD:DP:GQ:PL	0/1:31,38:69:99:1375,0,994	1/1:0,43:43:99:1344,128,0
+20	10099755	.	C	T	2076.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=1.55;DP=99;ExcessHet=3.0103;FS=5.472;MLEAC=3;MLEAF=0.750;MQ=59.58;MQRankSum=-2.200e-02;QD=21.40;ReadPosRankSum=-2.300e-01;SOR=0.542	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1127,0,1148	1/1:0,32:32:95:979,95,0
+20	10099832	.	A	G	2184.19	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-4.563e+00;DP=108;ExcessHet=3.0103;FS=6.351;MLEAC=3;MLEAF=0.750;MQ=59.31;MQRankSum=0.869;QD=20.22;ReadPosRankSum=-1.023e+00;SOR=0.823	GT:AD:DP:GQ:PL	0/1:39,33:72:99:1102,0,1430	1/1:0,36:36:99:1112,108,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx
new file mode 100644
index 00000000000..a644c92b01e
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf
new file mode 100644
index 00000000000..f36c3f3fa52
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf
@@ -0,0 +1,289 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport  --genomicsdb-workspace-path /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsDBWorkspace9055268512336574401/workspace --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf --intervals 20:1-11000000 --verbosity ERROR  --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --batch-size 0 --consolidate false --validate-sample-name-map false --reader-threads 1 --max-num-intervals-to-import-in-parallel 1 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version=Unavailable,Date="September 14, 2018 10:43:26 AM EDT">
+##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output singleSampleWithNewMQ.vcf --variant gendb:///var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsDBWorkspace9055268512336574401/workspace --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta  --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.8.1-35-g6c8b010-SNAPSHOT,Date="September 14, 2018 10:44:08 AM EDT">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,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=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##contig=<ID=20,length=63025520>
+##contig=<ID=21,length=48129895>
+##source=GenomicsDBImport
+##source=GenotypeGVCFs
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+20	10000117	.	C	T	905.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;DP=64;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=0.913;QD=14.15;ReadPosRankSum=-2.230e-01;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248
+20	10000211	.	C	T	941.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;DP=53;ExcessHet=3.0103;FS=5.587;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=1.06;QD=17.77;ReadPosRankSum=0.703;SOR=0.944	GT:AD:DP:GQ:PL	0/1:26,27:53:99:970,0,906
+20	10000439	.	T	G	2804.77	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;QD=25.36;SOR=1.236	GT:AD:DP:GQ:PL	1/1:0,80:80:99:2833,240,0
+20	10000598	.	T	A	1941.77	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.26;QD=28.73;SOR=1.225	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1970,147,0
+20	10000694	.	G	A	1008.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.60;DP=82;ExcessHet=3.0103;FS=1.822;MLEAC=1;MLEAF=0.500;MQ=48.66;MQRankSum=-5.114e+00;QD=12.30;ReadPosRankSum=0.657;SOR=0.566	GT:AD:DP:GQ:PL	0/1:45,37:82:99:1037,0,1601
+20	10000758	.	T	A	3838.77	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.37;QD=30.97;SOR=0.802	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3867,286,0
+20	10001019	.	T	G	650.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.541e+00;DP=65;ExcessHet=3.0103;FS=3.406;MLEAC=1;MLEAF=0.500;MQ=49.49;MQRankSum=-7.498e+00;QD=10.01;ReadPosRankSum=-9.250e-01;SOR=0.665	GT:AD:DP:GQ:PL	0/1:39,26:65:99:679,0,1426
+20	10001298	.	T	A	2917.77	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.34;QD=27.24;SOR=0.963	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2946,220,0
+20	10001436	.	A	AAGGCT	2301.73	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.07;QD=28.20;SOR=3.442	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2339,156,0
+20	10001474	.	C	T	2640.77	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.89;QD=25.00;SOR=1.516	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2669,219,0
+20	10001617	.	C	A	1731.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.26;DP=103;ExcessHet=3.0103;FS=13.163;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=1.37;QD=16.81;ReadPosRankSum=-2.800e-01;SOR=1.346	GT:AD:DP:GQ:PL	0/1:52,51:103:99:1760,0,1781
+20	10001628	.	G	A	3898.77	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.17;QD=29.56;SOR=1.053	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3927,285,0
+20	10001661	.	T	C	3606.77	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;QD=30.62;SOR=1.193	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3635,249,0
+20	10001670	.	T	G	3673.77	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.45;QD=28.17;SOR=0.995	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3702,253,0
+20	10002058	.	T	G	2963.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.93;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.76;MQRankSum=3.07;QD=26.80;ReadPosRankSum=0.624;SOR=0.776	GT:AD:DP:GQ:PL	1/1:1,74:75:99:2992,216,0
+20	10002099	.	C	T	1194.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.820e-01;DP=65;ExcessHet=3.0103;FS=3.528;MLEAC=1;MLEAF=0.500;MQ=56.29;MQRankSum=-8.500e-01;QD=18.38;ReadPosRankSum=0.173;SOR=0.375	GT:AD:DP:GQ:PL	0/1:27,38:65:99:1223,0,844
+20	10002138	.	C	G	2443.77	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.38;QD=26.00;SOR=0.730	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,53:53:99:1|1:10002138_C_G:2472,169,0
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+20	10002470	.	C	T	2522.77	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.62;QD=31.98;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2551,189,0
+20	10002625	.	G	T	2665.77	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=27.51;SOR=1.127	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2694,193,0
+20	10003021	.	C	T	2383.77	.	AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;QD=29.11;SOR=1.071	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2412,181,0
+20	10003358	.	A	C	1454.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.000e-03;DP=89;ExcessHet=3.0103;FS=0.844;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=1.01;QD=16.35;ReadPosRankSum=-1.355e+00;SOR=0.572	GT:AD:DP:GQ:PL	0/1:45,44:89:99:1483,0,1477
+20	10003651	.	T	C	3620.77	.	AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;QD=28.08;SOR=1.511	GT:AD:DP:GQ:PL	1/1:0,93:93:99:3649,279,0
+20	10003692	.	A	G	2609.77	.	AC=2;AF=1.00;AN=2;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;QD=23.23;SOR=1.352	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2638,205,0
+20	10003832	.	G	A	2705.77	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.13;QD=29.03;SOR=1.473	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2734,199,0
+20	10004094	.	A	C	1825.77	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.75;QD=34.45;SOR=1.524	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1854,157,0
+20	10004147	.	A	G	1837.77	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.99;QD=30.67;SOR=1.136	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1866,156,0
+20	10004193	.	G	T	918.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.040e-01;DP=52;ExcessHet=3.0103;FS=2.391;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=3.42;QD=17.67;ReadPosRankSum=1.51;SOR=1.019	GT:AD:DP:GQ:PL	0/1:23,29:52:99:947,0,775
+20	10004222	.	C	CA	12.96	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.335;DP=54;ExcessHet=3.0103;FS=1.494;MLEAC=1;MLEAF=0.500;MQ=60.05;MQRankSum=-2.042e+00;QD=0.33;ReadPosRankSum=1.27;SOR=0.434	GT:AD:DP:GQ:PL	0/1:31,8:39:50:50,0,923
+20	10004223	.	A	AG	47.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.800e-01;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.31;MQRankSum=1.89;QD=1.02;ReadPosRankSum=0.339;SOR=0.638	GT:AD:DP:GQ:PL	0/1:36,11:47:85:85,0,982
+20	10004351	.	C	G	2755.77	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.04;QD=26.61;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2784,211,0
+20	10004389	.	T	G	2494.77	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;QD=29.20;SOR=1.143	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2523,187,0
+20	10004610	.	A	C	3625.77	.	AC=2;AF=1.00;AN=2;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;QD=28.55;SOR=0.761	GT:AD:DP:GQ:PL	1/1:0,89:89:99:3654,267,0
+20	10004725	.	A	G	951.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.154e+00;DP=65;ExcessHet=3.0103;FS=15.830;MLEAC=1;MLEAF=0.500;MQ=55.27;MQRankSum=3.01;QD=14.64;ReadPosRankSum=2.09;SOR=0.605	GT:AD:DP:GQ:PL	0/1:35,30:65:99:980,0,1168
+20	10004769	.	TAAAACTATGC	T	981.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.60;DP=79;ExcessHet=3.0103;FS=3.758;MLEAC=1;MLEAF=0.500;MQ=52.37;MQRankSum=-6.625e+00;QD=15.34;ReadPosRankSum=1.88;SOR=1.306	GT:AD:DP:GQ:PL	0/1:37,27:64:99:1019,0,1471
+20	10004874	.	A	C	3602.77	.	AC=2;AF=1.00;AN=2;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.33;QD=34.42;SOR=1.286	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,87:87:99:1|1:10004874_A_C:3631,261,0
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+20	10005010	.	C	T	2934.77	.	AC=2;AF=1.00;AN=2;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=28.53;SOR=1.226	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2963,217,0
+20	10005427	.	C	T	2214.77	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.58;QD=27.23;SOR=0.729	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2243,165,0
+20	10005499	.	A	G	3053.77	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.52;SOR=1.121	GT:AD:DP:GQ:PL	1/1:0,76:76:99:3082,229,0
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+20	10005723	.	A	G	3062.77	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=33.47;SOR=0.947	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3091,258,0
+20	10006291	.	G	A	978.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=84;ExcessHet=3.0103;FS=0.853;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.081e+00;QD=11.65;ReadPosRankSum=-1.447e+00;SOR=0.659	GT:AD:DP:GQ:PL	0/1:53,31:84:99:1007,0,1905
+20	10006404	.	A	C	2928.77	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.16;QD=32.91;SOR=1.432	GT:AD:DP:GQ:PL	1/1:0,76:76:99:2957,228,0
+20	10006682	.	T	A	2874.77	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.43;QD=31.31;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2903,219,0
+20	10006819	.	AAAAC	A	2531.73	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.13;QD=31.45;SOR=0.762	GT:AD:DP:GQ:PL	1/1:0,58:58:99:2569,176,0
+20	10007150	.	G	C	669.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.476e+00;DP=63;ExcessHet=3.0103;FS=5.048;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.63;ReadPosRankSum=-7.700e-02;SOR=0.746	GT:AD:DP:GQ:PGT:PID:PL	0/1:38,25:63:99:0|1:10007150_G_C:698,0,1479
+20	10007175	.	C	T	1350.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.25;DP=61;ExcessHet=3.0103;FS=2.211;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=1.32;QD=22.14;ReadPosRankSum=-1.213e+00;SOR=0.434	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,38:61:99:1|0:10007150_G_C:1379,0,780
+20	10007352	.	C	T	2764.77	.	AC=2;AF=1.00;AN=2;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=33.27;SOR=1.054	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2793,208,0
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+20	10007980	.	A	C	3524.77	.	AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.72;QD=27.76;SOR=0.990	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3553,270,0
+20	10008029	.	T	TA	1986.73	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.409;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.98;MQRankSum=0.576;QD=26.49;ReadPosRankSum=-1.326e+00;SOR=0.788	GT:AD:DP:GQ:PL	1/1:3,72:75:99:2024,145,0
+20	10008146	.	TA	T	2141.73	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.59;QD=30.60;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2179,211,0
+20	10008221	.	T	C	3224.77	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=29.09;SOR=0.850	GT:AD:DP:GQ:PL	1/1:0,80:80:99:3253,240,0
+20	10008458	.	T	G	2654.77	.	AC=2;AF=1.00;AN=2;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.73;QD=26.08;SOR=0.980	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2683,207,0
+20	10008742	.	G	T	715.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.89;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.22;MQRankSum=-1.502e+00;QD=14.61;ReadPosRankSum=0.190;SOR=0.741	GT:AD:DP:GQ:PL	0/1:23,26:49:99:744,0,580
+20	10008758	.	C	CA	684.14	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;DP=44;ExcessHet=3.0103;FS=2.160;MLEAC=2;MLEAF=1.00;MQ=35.24;MQRankSum=-1.168e+00;QD=19.55;ReadPosRankSum=-5.200e-02;SOR=0.249	GT:AD:DP:GQ:PL	1/1:4,31:35:10:721,10,0
+20	10008921	.	C	CA	253.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-1.906e+00;QD=7.46;ReadPosRankSum=0.173;SOR=0.512	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,16:34:99:0|1:10008921_C_CA:291,0,366
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+20	10009246	.	A	G	3002.77	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.09;QD=25.42;SOR=0.887	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3031,231,0
+20	10009400	.	T	A	2998.77	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.65;SOR=0.804	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3027,223,0
+20	10009512	.	C	G	3039.77	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.47;QD=29.48;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3068,231,0
+20	10009719	.	A	G	1895.77	.	AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.29;QD=32.13;SOR=0.950	GT:AD:DP:GQ:PL	1/1:0,59:59:99:1924,175,0
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+20	10009844	.	G	A	661.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.05;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=0.975;QD=18.91;ReadPosRankSum=-1.555e+00;SOR=0.793	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,19:35:99:0|1:10009844_G_A:690,0,586
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+20	10009879	.	A	G	2244.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.53;DP=49;ExcessHet=3.0103;FS=9.369;MLEAC=2;MLEAF=1.00;MQ=49.62;MQRankSum=1.57;QD=30.55;ReadPosRankSum=1.11;SOR=1.474	GT:AD:DP:GQ:PL	1/1:2,47:49:99:2273,150,0
+20	10009883	.	A	G	2151.77	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.38;QD=32.62;SOR=1.659	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2180,147,0
+20	10010393	.	T	G	1464.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.351e+00;DP=79;ExcessHet=3.0103;FS=11.600;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-1.284e+00;QD=18.54;ReadPosRankSum=-1.738e+00;SOR=0.606	GT:AD:DP:GQ:PL	0/1:36,43:79:99:1493,0,1230
+20	10010536	.	G	GA	2462.73	.	AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.63;QD=31.17;SOR=0.881	GT:AD:DP:GQ:PL	1/1:0,79:79:99:2500,243,0
+20	10010766	.	T	G	2411.77	.	AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.33;SOR=0.818	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2440,199,0
+20	10010832	.	T	C	2951.77	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.50;QD=35.36;SOR=1.091	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2980,226,0
+20	10011075	.	C	T	1325.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.36;DP=83;ExcessHet=3.0103;FS=1.800;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.97;ReadPosRankSum=-1.036e+00;SOR=0.968	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1354,0,1333
+20	10011309	.	T	C	2692.77	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.97;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:2721,231,0
+20	10011517	.	GA	G	490.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.690;DP=91;ExcessHet=3.0103;FS=3.171;MLEAC=1;MLEAF=0.500;MQ=59.90;MQRankSum=1.80;QD=7.55;ReadPosRankSum=0.315;SOR=0.394	GT:AD:DP:GQ:PL	0/1:37,28:73:99:528,0,875
+20	10011666	.	C	T	2961.77	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=34.30;SOR=1.103	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2990,220,0
+20	10011939	.	C	T	2469.77	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.26;QD=27.00;SOR=1.292	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2498,184,0
+20	10012021	.	CA	C	1975.73	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.08;QD=29.94;SOR=1.196	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2013,198,0
+20	10012362	.	G	T	835.77	.	AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.78;QD=30.82;SOR=4.003	GT:AD:DP:GQ:PL	1/1:0,23:23:69:864,69,0
+20	10012384	.	T	C	229.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.773e+00;DP=18;ExcessHet=3.0103;FS=7.375;MLEAC=1;MLEAF=0.500;MQ=53.38;MQRankSum=-8.110e-01;QD=12.76;ReadPosRankSum=0.800;SOR=0.044	GT:AD:DP:GQ:PL	0/1:10,8:18:99:258,0,355
+20	10012387	.	T	C	533.77	.	AC=2;AF=1.00;AN=2;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.49;QD=33.36;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,16:16:50:562,50,0
+20	10012479	.	A	G	592.77	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.01;QD=34.87;SOR=0.804	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,17:17:50:1|1:10012479_A_G:621,50,0
+20	10012498	.	C	G	466.77	.	AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.03;QD=29.27;SOR=1.270	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012479_A_G:495,33,0
+20	10012518	.	T	C	406.77	.	AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.96;QD=35.92;SOR=0.892	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:30:1|1:10012479_A_G:435,30,0
+20	10012521	.	C	T	46.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.36;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.77;MQRankSum=-3.800e-02;QD=4.25;ReadPosRankSum=1.97;SOR=1.179	GT:AD:DP:GQ:PL	0/1:8,3:11:75:75,0,224
+20	10012570	.	G	GCA	457.73	.	AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.62;QD=29.63;SOR=3.056	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:33:1|1:10012570_G_GCA:495,33,0
+20	10012572	.	GT	G	457.73	.	AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.52;QD=28.76;SOR=3.442	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012570_G_GCA:495,33,0
+20	10012631	.	C	CG	484.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.030e+00;DP=21;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=48.34;MQRankSum=-1.670e+00;QD=23.08;ReadPosRankSum=-1.813e+00;SOR=0.048	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,13:21:99:0|1:10012631_C_CG:522,0,297
+20	10012636	.	G	C	527.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.71;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=48.93;MQRankSum=-1.513e+00;QD=23.99;ReadPosRankSum=-1.915e+00;SOR=0.058	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,14:22:99:0|1:10012631_C_CG:556,0,294
+20	10012714	.	G	C	1300.77	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.04;QD=29.94;SOR=2.964	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1329,105,0
+20	10012751	.	T	C	937.77	.	AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.17;QD=31.26;SOR=0.976	GT:AD:DP:GQ:PL	1/1:0,30:30:89:966,89,0
+20	10013119	.	C	T	1011.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.72;DP=59;ExcessHet=3.0103;FS=2.248;MLEAC=1;MLEAF=0.500;MQ=51.48;MQRankSum=-1.089e+00;QD=17.15;ReadPosRankSum=0.159;SOR=0.405	GT:AD:DP:GQ:PL	0/1:29,30:59:99:1040,0,936
+20	10013574	.	G	A	1050.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.47;DP=69;ExcessHet=3.0103;FS=7.109;MLEAC=1;MLEAF=0.500;MQ=58.06;MQRankSum=-2.710e-01;QD=15.23;ReadPosRankSum=0.706;SOR=1.675	GT:AD:DP:GQ:PL	0/1:38,31:69:99:1079,0,1301
+20	10014990	.	C	CAT	1237.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.93;DP=87;ExcessHet=3.0103;FS=2.090;MLEAC=1;MLEAF=0.500;MQ=60.78;MQRankSum=3.11;QD=16.29;ReadPosRankSum=-4.370e-01;SOR=0.403	GT:AD:DP:GQ:PL	0/1:38,38:76:99:1275,0,1248
+20	10015679	.	C	T	140.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.08;ReadPosRankSum=0.497;SOR=0.693	GT:AD:DP:GQ:PL	0/1:5,5:10:99:169,0,166
+20	10015761	.	T	C	344.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.982e+00;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQRankSum=1.29;QD=15.67;ReadPosRankSum=1.80;SOR=0.352	GT:AD:DP:GQ:PL	0/1:9,13:22:99:373,0,284
+20	10018158	.	G	C	1639.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.21;DP=89;ExcessHet=3.0103;FS=0.808;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=1.12;QD=18.63;ReadPosRankSum=1.18;SOR=0.834	GT:AD:DP:GQ:PL	0/1:40,48:88:99:1668,0,1165
+20	10018555	.	G	A	1567.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.270e-01;DP=80;ExcessHet=3.0103;FS=4.241;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=19.60;ReadPosRankSum=0.815;SOR=0.627	GT:AD:DP:GQ:PL	0/1:35,45:80:99:1596,0,1211
+20	10019093	.	A	G	1244.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.452;DP=69;ExcessHet=3.0103;FS=1.990;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=1.07;QD=18.04;ReadPosRankSum=-2.520e-01;SOR=0.665	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1273,0,1104
+20	10020229	.	G	A	1538.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.79;DP=82;ExcessHet=3.0103;FS=0.833;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.104;QD=18.77;ReadPosRankSum=-5.490e-01;SOR=0.573	GT:AD:DP:GQ:PL	0/1:38,44:82:99:1567,0,1130
+20	10023689	.	G	A	1852.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;DP=80;ExcessHet=3.0103;FS=0.877;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=1.35;QD=23.16;ReadPosRankSum=1.16;SOR=0.549	GT:AD:DP:GQ:PL	0/1:29,51:80:99:1881,0,946
+20	10024107	.	C	T	1694.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.77;DP=86;ExcessHet=3.0103;FS=0.817;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.546e+00;QD=19.71;ReadPosRankSum=0.148;SOR=0.823	GT:AD:DP:GQ:PL	0/1:38,48:86:99:1723,0,1086
+20	10024300	.	C	CTT	87.76	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.45;DP=50;ExcessHet=3.0103;FS=6.107;MLEAC=1;MLEAF=0.500;MQ=51.90;MQRankSum=-6.000e-01;QD=7.98;ReadPosRankSum=-1.073e+00;SOR=1.825	GT:AD:DP:GQ:PL	0/1:3,8:18:99:103,0,137
+20	10026357	.	T	C	1166.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.700e+00;DP=63;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.43;MQRankSum=-1.480e-01;QD=18.52;ReadPosRankSum=-7.600e-02;SOR=0.722	GT:AD:DP:GQ:PL	0/1:28,35:63:99:1195,0,932
+20	10026794	.	C	T	1084.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.83;DP=52;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=-7.190e-01;QD=20.86;ReadPosRankSum=-5.330e-01;SOR=0.428	GT:AD:DP:GQ:PL	0/1:19,33:52:99:1113,0,529
+20	10027234	.	A	ATTAG	1320.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.060e-01;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=-8.450e-01;QD=19.14;ReadPosRankSum=-9.790e-01;SOR=0.926	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1358,0,1964
+20	10027868	.	A	G	1739.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.793e+00;DP=89;ExcessHet=3.0103;FS=6.868;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.032;QD=19.55;ReadPosRankSum=1.87;SOR=0.881	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,45:89:99:0|1:10027868_A_G:1768,0,3201
+20	10027872	.	A	G	1724.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.491e+00;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.101;QD=20.29;ReadPosRankSum=1.05;SOR=0.826	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,45:85:99:0|1:10027868_A_G:1753,0,3136
+20	10028867	.	A	ATG	1106.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.740e-01;DP=92;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.69;MQRankSum=2.71;QD=15.59;ReadPosRankSum=0.364;SOR=0.336	GT:AD:DP:GQ:PL	0/1:32,39:71:99:1144,0,916
+20	10030188	.	T	A	1372.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;DP=81;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=-1.013e+00;QD=16.95;ReadPosRankSum=-5.530e-01;SOR=1.105	GT:AD:DP:GQ:PL	0/1:42,39:81:99:1401,0,1524
+20	10031254	.	A	AT	1463.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.100e-02;DP=87;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=0.017;QD=17.22;ReadPosRankSum=0.495;SOR=0.211	GT:AD:DP:GQ:PL	0/1:38,47:85:99:1501,0,1159
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+20	10031798	.	G	A	4296.77	.	AC=2;AF=1.00;AN=2;DP=104;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=31.54;SOR=0.900	GT:AD:DP:GQ:PL	1/1:0,104:104:99:4325,313,0
+20	10031827	.	C	T	2004.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.55;DP=108;ExcessHet=3.0103;FS=4.729;MLEAC=1;MLEAF=0.500;MQ=59.83;MQRankSum=-9.450e-01;QD=18.56;ReadPosRankSum=-1.396e+00;SOR=0.382	GT:AD:DP:GQ:PL	0/1:52,56:108:99:2033,0,1798
+20	10032094	.	G	A	1220.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.49;DP=83;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.71;ReadPosRankSum=-5.790e-01;SOR=0.260	GT:AD:DP:GQ:PL	0/1:47,36:83:99:1249,0,1497
+20	10032413	.	T	G	869.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.142e+00;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-6.500e-02;QD=13.18;ReadPosRankSum=-1.003e+00;SOR=1.293	GT:AD:DP:GQ:PL	0/1:35,31:66:99:898,0,1277
+20	10032882	.	A	T	1202.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.697e+00;DP=75;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=-1.014e+00;QD=16.04;ReadPosRankSum=0.626;SOR=0.338	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1231,0,1406
+20	10032972	.	C	CAT	1122.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.540e-01;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-1.017e+00;QD=17.82;ReadPosRankSum=-1.232e+00;SOR=1.300	GT:AD:DP:GQ:PL	0/1:33,30:63:99:1160,0,1477
+20	10034306	.	T	C	782.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.661e+00;DP=76;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.45;MQRankSum=1.15;QD=10.44;ReadPosRankSum=0.539;SOR=0.685	GT:AD:DP:GQ:PL	0/1:46,29:75:99:811,0,1593
+20	10036930	.	CGATAGCCCTAGCCCTAGATA	C	1036.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.36;MQRankSum=-4.048e+00;QD=15.25;ReadPosRankSum=0.460;SOR=0.269	GT:AD:DP:GQ:PL	0/1:39,29:68:99:1074,0,5571
+20	10037037	.	C	T	1436.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.50;DP=81;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.17;MQRankSum=-1.193e+00;QD=17.74;ReadPosRankSum=-1.609e+00;SOR=0.495	GT:AD:DP:GQ:PL	0/1:39,42:81:99:1465,0,1124
+20	10037110	.	T	TGATA	2780.73	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.98;QD=28.86;SOR=1.022	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2818,189,0
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+20	10045642	.	G	C	3107.77	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=31.04;SOR=0.821	GT:AD:DP:GQ:PL	1/1:0,81:81:99:3136,243,0
+20	10046178	.	AAGAAAGAAAG	A	2159.73	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.00;QD=27.86;SOR=0.859	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2197,152,0
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+20	10087394	.	T	G	1688.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.340e+00;DP=84;ExcessHet=3.0103;FS=4.225;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=1.21;QD=20.10;ReadPosRankSum=0.885;SOR=0.436	GT:AD:DP:GQ:PL	0/1:35,49:84:99:1717,0,1186
+20	10087754	.	T	G	1347.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;DP=79;ExcessHet=3.0103;FS=0.869;MLEAC=1;MLEAF=0.500;MQ=60.39;MQRankSum=2.19;QD=17.28;ReadPosRankSum=-5.510e-01;SOR=0.562	GT:AD:DP:GQ:PL	0/1:37,41:78:99:1376,0,1239
+20	10087804	.	C	T	1619.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.94;DP=100;ExcessHet=3.0103;FS=3.847;MLEAC=1;MLEAF=0.500;MQ=60.77;MQRankSum=2.62;QD=16.20;ReadPosRankSum=0.341;SOR=0.369	GT:AD:DP:GQ:PL	0/1:50,50:100:99:1648,0,1511
+20	10087820	.	C	CAG	428.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.974e+00;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.53;MQRankSum=0.422;QD=8.09;ReadPosRankSum=-3.570e-01;SOR=0.850	GT:AD:DP:GQ:PL	0/1:35,18:53:99:466,0,1168
+20	10088063	.	C	T	1417.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.40;DP=93;ExcessHet=3.0103;FS=2.739;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=0.515;QD=15.24;ReadPosRankSum=0.285;SOR=1.053	GT:AD:DP:GQ:PL	0/1:49,44:93:99:1446,0,1403
+20	10088699	.	C	T	776.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.80;DP=63;ExcessHet=3.0103;FS=16.952;MLEAC=1;MLEAF=0.500;MQ=56.31;MQRankSum=-3.140e+00;QD=12.53;ReadPosRankSum=-1.456e+00;SOR=1.914	GT:AD:DP:GQ:PL	0/1:36,26:62:99:805,0,1088
+20	10088730	.	G	A	972.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.224;DP=52;ExcessHet=3.0103;FS=15.383;MLEAC=1;MLEAF=0.500;MQ=53.41;MQRankSum=-4.839e+00;QD=18.71;ReadPosRankSum=0.581;SOR=1.592	GT:AD:DP:GQ:PGT:PID:PL	0/1:29,23:52:99:0|1:10088730_G_A:1001,0,1152
+20	10088736	.	A	C	1081.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;DP=55;ExcessHet=3.0103;FS=9.673;MLEAC=1;MLEAF=0.500;MQ=52.17;MQRankSum=-5.169e+00;QD=19.67;ReadPosRankSum=0.573;SOR=0.851	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,27:55:99:0|1:10088730_G_A:1110,0,1194
+20	10088747	.	A	G	1111.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.877e+00;DP=55;ExcessHet=3.0103;FS=7.653;MLEAC=1;MLEAF=0.500;MQ=51.56;MQRankSum=-4.907e+00;QD=20.59;ReadPosRankSum=9.000e-03;SOR=1.092	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,29:54:99:0|1:10088730_G_A:1140,0,995
+20	10088799	.	G	A	1018.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.50;DP=53;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=53.21;MQRankSum=-2.498e+00;QD=19.22;ReadPosRankSum=1.08;SOR=1.003	GT:AD:DP:GQ:PL	0/1:22,31:53:99:1047,0,617
+20	10088895	.	C	T	532.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.46;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.26;MQRankSum=0.577;QD=12.99;ReadPosRankSum=1.30;SOR=0.653	GT:AD:DP:GQ:PL	0/1:23,18:41:99:561,0,673
+20	10088968	.	C	CAAA	1175.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-4.750e+00;QD=22.18;ReadPosRankSum=2.42;SOR=1.012	GT:AD:DP:GQ:PGT:PID:PL	0/1:30,23:53:99:0|1:10088968_C_CAAA:1213,0,1367
+20	10088980	.	T	C	1247.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.585e+00;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-5.232e+00;QD=18.35;ReadPosRankSum=1.29;SOR=0.709	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,31:68:99:0|1:10088968_C_CAAA:1276,0,1627
+20	10088985	.	T	C	1178.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920e-01;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-5.248e+00;QD=15.93;ReadPosRankSum=1.23;SOR=0.742	GT:AD:DP:GQ:PGT:PID:PL	0/1:42,32:74:99:0|1:10088968_C_CAAA:1207,0,1729
+20	10089441	.	A	G	1179.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.885e+00;DP=76;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-9.480e-01;QD=15.52;ReadPosRankSum=-1.560e-01;SOR=1.363	GT:AD:DP:GQ:PL	0/1:37,39:76:99:1208,0,1313
+20	10089525	.	C	T	1548.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.86;DP=81;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=1.53;QD=19.12;ReadPosRankSum=0.862;SOR=0.617	GT:AD:DP:GQ:PL	0/1:38,43:81:99:1577,0,1088
+20	10090289	.	CA	C	384.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.441;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.39;QD=11.32;ReadPosRankSum=0.048;SOR=0.859	GT:AD:DP:GQ:PL	0/1:14,20:38:99:422,0,230
+20	10090764	.	A	G	840.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.659e+00;DP=63;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.35;ReadPosRankSum=1.21;SOR=0.310	GT:AD:DP:GQ:PL	0/1:34,29:63:99:869,0,1207
+20	10090970	.	T	C	1257.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.840e-01;DP=69;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=1.51;QD=18.23;ReadPosRankSum=-7.200e-02;SOR=0.518	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1286,0,1092
+20	10091214	.	C	T	1249.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-9.160e-01;QD=17.85;ReadPosRankSum=-3.500e-02;SOR=0.625	GT:AD:DP:GQ:PL	0/1:33,37:70:99:1278,0,1110
+20	10092415	.	A	G	1635.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.731e+00;DP=101;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.20;ReadPosRankSum=0.082;SOR=0.665	GT:AD:DP:GQ:PL	0/1:52,49:101:99:1664,0,1902
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+20	10093568	.	GT	G	326.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.426;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQRankSum=0.410;QD=9.61;ReadPosRankSum=1.26;SOR=0.751	GT:AD:DP:GQ:PL	0/1:17,17:42:99:364,0,386
+20	10093923	.	T	A	1075.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.670e-01;DP=67;ExcessHet=3.0103;FS=0.924;MLEAC=1;MLEAF=0.500;MQ=59.19;MQRankSum=0.358;QD=16.06;ReadPosRankSum=-1.583e+00;SOR=0.772	GT:AD:DP:GQ:PL	0/1:35,32:67:99:1104,0,1257
+20	10094251	.	T	A	1270.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=62;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.50;ReadPosRankSum=1.81;SOR=1.211	GT:AD:DP:GQ:PL	0/1:26,36:62:99:1299,0,781
+20	10094582	.	A	G	923.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388e+00;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=1.27;QD=13.39;ReadPosRankSum=-1.800e-02;SOR=0.772	GT:AD:DP:GQ:PL	0/1:39,30:69:99:952,0,1350
+20	10094774	.	C	T	1036.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.840e-01;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=0.962;QD=13.82;ReadPosRankSum=0.197;SOR=0.690	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1065,0,1282
+20	10095432	.	GTGATGATGA	G	839.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.26;DP=77;ExcessHet=3.0103;FS=1.102;MLEAC=1;MLEAF=0.500;MQ=54.39;MQRankSum=-4.431e+00;QD=16.79;ReadPosRankSum=0.396;SOR=0.460	GT:AD:DP:GQ:PL	0/1:27,23:50:99:877,0,2108
+20	10095741	.	A	G	1075.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.340e-01;DP=71;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.35;MQRankSum=-2.313e+00;QD=15.37;ReadPosRankSum=-5.000e-01;SOR=0.515	GT:AD:DP:GQ:PL	0/1:36,34:70:99:1104,0,1233
+20	10096293	.	C	T	1355.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.66;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=1.40;QD=18.08;ReadPosRankSum=-1.135e+00;SOR=0.638	GT:AD:DP:GQ:PL	0/1:37,38:75:99:1384,0,1258
+20	10096596	.	C	T	1562.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.73;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQRankSum=0.612;QD=17.96;ReadPosRankSum=-1.700e-01;SOR=0.640	GT:AD:DP:GQ:PL	0/1:40,47:87:99:1591,0,1273
+20	10096768	.	A	C	1682.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.764e+00;DP=91;ExcessHet=3.0103;FS=3.983;MLEAC=1;MLEAF=0.500;MQ=59.24;MQRankSum=-1.609e+00;QD=18.49;ReadPosRankSum=0.613;SOR=0.445	GT:AD:DP:GQ:PL	0/1:42,49:91:99:1711,0,1452
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+20	10096905	.	TA	T	1600.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.550e-01;DP=83;ExcessHet=3.0103;FS=11.159;MLEAC=1;MLEAF=0.500;MQ=59.27;MQRankSum=-1.677e+00;QD=19.29;ReadPosRankSum=0.461;SOR=1.775	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,43:83:99:0|1:10096899_G_T:1638,0,1623
+20	10096933	.	G	C	1511.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.914e+00;DP=85;ExcessHet=3.0103;FS=23.320;MLEAC=1;MLEAF=0.500;MQ=59.29;MQRankSum=-1.802e+00;QD=17.79;ReadPosRankSum=0.334;SOR=1.534	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,41:85:99:0|1:10096933_G_C:1540,0,1770
+20	10096958	.	G	A	1766.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.84;DP=92;ExcessHet=3.0103;FS=16.778;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=-1.701e+00;QD=19.20;ReadPosRankSum=-1.833e+00;SOR=1.387	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,47:92:99:0|1:10096933_G_C:1795,0,1629
+20	10097075	.	T	G	1445.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533e+00;DP=92;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-1.389e+00;QD=15.71;ReadPosRankSum=0.082;SOR=0.628	GT:AD:DP:GQ:PL	0/1:44,48:92:99:1474,0,1482
+20	10097101	.	C	CTTT	1091.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.134e+00;DP=76;ExcessHet=3.0103;FS=5.060;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-2.428e+00;QD=18.20;ReadPosRankSum=2.09;SOR=0.277	GT:AD:DP:GQ:PL	0/1:34,26:64:99:1129,0,1306
+20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C	1054.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.82;DP=89;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.27;MQRankSum=-6.464e+00;QD=11.85;ReadPosRankSum=-3.097e+00;SOR=0.948	GT:AD:DP:GQ:PL	0/1:57,32:89:99:1092,0,2241
+20	10097437	.	TTTTC	*,T	2089.73	.	AC=1,1;AF=0.500,0.500;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.48;QD=32.25;SOR=1.877	GT:AD:DP:GQ:PL	1/2:0,32,23:55:99:2127,940,1799,1195,0,1125
+20	10097626	.	C	A	626.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.09;DP=48;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.24;MQRankSum=-1.331e+00;QD=13.06;ReadPosRankSum=1.01;SOR=0.324	GT:AD:DP:GQ:PL	0/1:28,20:48:99:655,0,957
+20	10097789	.	T	C	688.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157e+00;DP=57;ExcessHet=3.0103;FS=5.374;MLEAC=1;MLEAF=0.500;MQ=57.95;MQRankSum=-2.805e+00;QD=12.08;ReadPosRankSum=0.220;SOR=0.756	GT:AD:DP:GQ:PL	0/1:34,23:57:99:717,0,1190
+20	10097928	.	G	A	570.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.203e+00;DP=36;ExcessHet=3.0103;FS=1.315;MLEAC=1;MLEAF=0.500;MQ=58.05;MQRankSum=-1.654e+00;QD=15.85;ReadPosRankSum=-7.900e-02;SOR=0.951	GT:AD:DP:GQ:PL	0/1:17,19:36:99:599,0,586
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+20	10098135	.	C	A	471.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155e+00;DP=38;ExcessHet=3.0103;FS=4.337;MLEAC=1;MLEAF=0.500;MQ=59.64;MQRankSum=1.55;QD=12.41;ReadPosRankSum=-5.910e-01;SOR=0.075	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,14:38:99:0|1:10098110_G_C:500,0,964
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+20	10098237	.	A	T	244.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.000e-03;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.40;MQRankSum=-1.742e+00;QD=18.83;ReadPosRankSum=0.277;SOR=0.836	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,7:13:99:0|1:10098219_TATATATA_T:273,0,273
+20	10098265	.	T	C	133.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.83;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.834e+00;QD=22.29;ReadPosRankSum=0.00;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,4:6:59:0|1:10098219_TATATATA_T:162,0,59
+20	10098885	.	C	CA	433.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.165;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.89;MQRankSum=-4.449e+00;QD=13.99;ReadPosRankSum=-1.073e+00;SOR=0.518	GT:AD:DP:GQ:PL	0/1:17,14:31:99:471,0,572
+20	10098945	.	T	C	452.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.48;DP=22;ExcessHet=3.0103;FS=3.882;MLEAC=1;MLEAF=0.500;MQ=51.15;MQRankSum=-2.504e+00;QD=20.58;ReadPosRankSum=1.04;SOR=2.368	GT:AD:DP:GQ:PL	0/1:9,13:22:99:481,0,248
+20	10098987	.	C	T	379.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.13;DP=24;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.500;MQ=51.88;MQRankSum=-2.734e+00;QD=15.82;ReadPosRankSum=0.436;SOR=2.925	GT:AD:DP:GQ:PL	0/1:11,13:24:99:408,0,350
+20	10099029	.	T	C	334.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.809e+00;DP=28;ExcessHet=3.0103;FS=2.032;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-3.641e+00;QD=11.96;ReadPosRankSum=-1.224e+00;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
+20	10099034	.	C	A	334.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.76;DP=28;ExcessHet=3.0103;FS=4.265;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-3.641e+00;QD=11.96;ReadPosRankSum=-1.850e+00;SOR=1.721	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
+20	10099044	.	A	C	334.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148e+00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418e+00;QD=13.95;ReadPosRankSum=-2.207e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:363,0,768
+20	10099046	.	T	C	304.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.165e+00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418e+00;QD=12.70;ReadPosRankSum=-2.297e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:333,0,603
+20	10099055	.	T	C	256.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.554e+00;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.46;MQRankSum=-4.316e+00;QD=11.16;ReadPosRankSum=-1.970e+00;SOR=0.665	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,8:23:99:0|1:10099029_T_C:285,0,673
+20	10099079	.	C	T	116.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;DP=29;ExcessHet=3.0103;FS=1.862;MLEAC=1;MLEAF=0.500;MQ=52.09;MQRankSum=-2.821e+00;QD=4.03;ReadPosRankSum=0.969;SOR=1.289	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,6:29:99:0|1:10099029_T_C:145,0,886
+20	10099111	.	T	TTTTGTTTG	656.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.207e+00;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.12;MQRankSum=-4.071e+00;QD=18.76;ReadPosRankSum=-2.730e-01;SOR=0.511	GT:AD:DP:GQ:PL	0/1:22,13:35:99:694,0,802
+20	10099140	.	G	T	1005.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.140e-01;DP=62;ExcessHet=3.0103;FS=2.241;MLEAC=1;MLEAF=0.500;MQ=55.72;MQRankSum=-2.469e+00;QD=16.22;ReadPosRankSum=0.338;SOR=1.114	GT:AD:DP:GQ:PL	0/1:30,32:62:99:1034,0,931
+20	10099190	.	G	T	1034.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-02;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.56;MQRankSum=-1.711e+00;QD=15.92;ReadPosRankSum=-1.260e+00;SOR=0.776	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1063,0,1154
+20	10099220	.	A	G	577.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.664e+00;DP=45;ExcessHet=3.0103;FS=1.137;MLEAC=1;MLEAF=0.500;MQ=57.63;MQRankSum=-2.596e+00;QD=12.84;ReadPosRankSum=0.629;SOR=0.519	GT:AD:DP:GQ:PL	0/1:25,20:45:99:606,0,873
+20	10099250	.	G	A	699.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.17;DP=37;ExcessHet=3.0103;FS=7.195;MLEAC=1;MLEAF=0.500;MQ=56.71;MQRankSum=-2.272e+00;QD=18.91;ReadPosRankSum=0.583;SOR=0.162	GT:AD:DP:GQ:PL	0/1:16,21:37:99:728,0,424
+20	10099535	.	G	A	1335.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.03;DP=65;ExcessHet=3.0103;FS=2.172;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=-1.418e+00;QD=20.55;ReadPosRankSum=-7.770e-01;SOR=0.408	GT:AD:DP:GQ:PL	0/1:26,39:65:99:1364,0,686
+20	10099565	.	C	T	1346.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.59;DP=69;ExcessHet=3.0103;FS=8.736;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=-1.266e+00;QD=19.52;ReadPosRankSum=1.23;SOR=0.191	GT:AD:DP:GQ:PL	0/1:31,38:69:99:1375,0,994
+20	10099755	.	C	T	1098.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.55;DP=65;ExcessHet=3.0103;FS=2.074;MLEAC=1;MLEAF=0.500;MQ=59.36;MQRankSum=-2.200e-02;QD=16.90;ReadPosRankSum=-2.300e-01;SOR=0.446	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1127,0,1148
+20	10099832	.	A	G	1073.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.563e+00;DP=72;ExcessHet=3.0103;FS=4.632;MLEAC=1;MLEAF=0.500;MQ=58.96;MQRankSum=0.869;QD=14.91;ReadPosRankSum=-1.023e+00;SOR=0.871	GT:AD:DP:GQ:PL	0/1:39,33:72:99:1102,0,1430
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/vidmap.updated.json b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/vidmap.updated.json
new file mode 100644
index 00000000000..c2f56d48217
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/vidmap.updated.json
@@ -0,0 +1,318 @@
+{
+  "fields": [
+    {
+      "name": "ID",
+      "type": [
+        "char"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "var"
+        }
+      ]
+    },
+    {
+      "name": "LowQual",
+      "type": [
+        "int"
+      ],
+      "vcf_field_class": [
+        "FILTER"
+      ]
+    },
+    {
+      "name": "AD",
+      "type": [
+        "Integer"
+      ],
+      "vcf_field_class": [
+        "FORMAT"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "R"
+        }
+      ]
+    },
+    {
+      "name": "GQ",
+      "type": [
+        "Integer"
+      ],
+      "vcf_field_class": [
+        "FORMAT"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "GT",
+      "type": [
+        "int"
+      ],
+      "vcf_field_class": [
+        "FORMAT"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "PP"
+        }
+      ]
+    },
+    {
+      "name": "MIN_DP",
+      "type": [
+        "Integer"
+      ],
+      "vcf_field_class": [
+        "FORMAT"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "PGT",
+      "type": [
+        "String"
+      ],
+      "vcf_field_class": [
+        "FORMAT"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "VAR"
+        }
+      ]
+    },
+    {
+      "name": "PID",
+      "type": [
+        "String"
+      ],
+      "vcf_field_class": [
+        "FORMAT"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "VAR"
+        }
+      ]
+    },
+    {
+      "name": "PL",
+      "type": [
+        "Integer"
+      ],
+      "vcf_field_class": [
+        "FORMAT"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "G"
+        }
+      ]
+    },
+    {
+      "name": "SB",
+      "type": [
+        "Integer"
+      ],
+      "vcf_field_class": [
+        "FORMAT"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "4"
+        }
+      ]
+    },
+    {
+      "name": "BaseQRankSum",
+      "type": [
+        "Float"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "ClippingRankSum",
+      "type": [
+        "Float"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "DP",
+      "type": [
+        "Integer"
+      ],
+      "vcf_field_class": [
+        "FORMAT",
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "DS",
+      "type": [
+        "Flag"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "END",
+      "type": [
+        "Integer"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "ExcessHet",
+      "type": [
+        "Float"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "InbreedingCoeff",
+      "type": [
+        "Float"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "MLEAC",
+      "type": [
+        "Integer"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "A"
+        }
+      ]
+    },
+    {
+      "name": "MLEAF",
+      "type": [
+        "Float"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "A"
+        }
+      ]
+    },
+    {
+      "name": "MQRankSum",
+      "type": [
+        "Float"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    },
+    {
+      "name": "RAW_MQandDP",
+      "type": [
+        "Integer"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "2"
+        }
+      ],
+      "VCF_field_combine_operation": "element_wise_sum"
+    },
+    {
+      "name": "ReadPosRankSum",
+      "type": [
+        "Float"
+      ],
+      "vcf_field_class": [
+        "INFO"
+      ],
+      "length": [
+        {
+          "variable_length_descriptor": "1"
+        }
+      ]
+    }
+  ],
+  "contigs": [
+    {
+      "name": "20",
+      "length": 63025520,
+      "tiledb_column_offset": 0
+    },
+    {
+      "name": "21",
+      "length": 48129895,
+      "tiledb_column_offset": 63025520
+    }
+  ]
+}
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prod.chr20snippet.withRawMQ.expected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prod.chr20snippet.withRawMQ.expected.g.vcf
new file mode 100644
index 00000000000..0ce4cb497ac
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prod.chr20snippet.withRawMQ.expected.g.vcf
@@ -0,0 +1,72 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-0-g36282e4,Date="Sun Sep 03 19:04:52 UTC 2017",Epoch=1504465492413,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/cromwell_root/broad-gotc-prod-cromwell-execution/PairedEndSingleSampleWorkflow/36d6043d-5e15-4a26-9bd0-e28d44d4b052/call-GatherBamFiles/NWD242235.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[OverclippedRead] disable_read_filter=[] intervals=[/cromwell_root/broad-gotc-prod-cromwell-execution/PairedEndSingleSampleWorkflow/36d6043d-5e15-4a26-9bd0-e28d44d4b052/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/23scattered.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=3 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.004839373333333333 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 filter_is_too_short_value=30 do_not_require_softclips_both_ends=false min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants  --output prod.chr20snippet.withRawMQ.g.vcf --variant gs://broad-gotc-prod-storage/pipeline/G97551/gvcfs/NWD242235.bcdd0ebc-17fa-402f-aa7e-ec97ae8669ca.g.vcf.gz --intervals chr20:20000000 --interval-padding 5000 --reference Homo_sapiens_assembly38.fasta  --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version=4.0.9.0-13-g0f6c729-SNAPSHOT,Date="October 4, 2018 10:52:55 AM EDT">
+##GVCFBlock0-20=minGQ=0(inclusive),maxGQ=20(exclusive)
+##GVCFBlock20-100=minGQ=20(inclusive),maxGQ=100(exclusive)
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,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=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.">
+##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
+##INFO=<ID=RAW_MQ,Number=1,Type=Integer,Description="Raw data for RMS Mapping Quality (deprecated -- use RAW_MQandDP instead.">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
+##contig=<ID=chr20,length=64444167,assembly=Homo_sapiens_assembly38.fasta>
+##reference=file:///Users/gauthier/workspaces/reblockGVCF/Homo_sapiens_assembly38.fasta
+##source=SelectVariants
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NWD242235
+chr20	19994995	.	G	<NON_REF>	.	.	END=19996105	GT:DP:GQ:MIN_DP:PL	0/0:35:43:29:0,43,890
+chr20	19996106	.	A	G,<NON_REF>	484.77	.	DP=35;MQRankSum=1.225;MQ_DP=35;RAW_MQ=125316.00;RAW_MQandDP=125316.00,35;ReadPosRankSum=-1.190	GT:AD:DP:GQ:PL:SB	0/1:16,18,0:34:99:513,0,454,562,508,1070:10,6,8,10
+chr20	19996107	.	G	<NON_REF>	.	.	END=19997993	GT:DP:GQ:MIN_DP:PL	0/0:25:20:14:0,20,436
+chr20	19997994	.	A	<NON_REF>	.	.	END=19997994	GT:DP:GQ:MIN_DP:PL	0/0:21:14:21:0,14,581
+chr20	19997995	.	A	<NON_REF>	.	.	END=19999277	GT:DP:GQ:MIN_DP:PL	0/0:29:23:17:0,23,541
+chr20	19999278	.	T	<NON_REF>	.	.	END=19999278	GT:DP:GQ:MIN_DP:PL	0/0:24:8:24:0,8,657
+chr20	19999279	.	A	<NON_REF>	.	.	END=20001360	GT:DP:GQ:MIN_DP:PL	0/0:30:22:23:0,22,585
+chr20	20001361	.	C	<NON_REF>	.	.	END=20001361	GT:DP:GQ:MIN_DP:PL	0/0:30:6:30:0,6,825
+chr20	20001362	.	CTT	C,<NON_REF>	112.77	.	DP=22;MQRankSum=1.276;MQ_DP=22;RAW_MQ=79200.00;RAW_MQandDP=79200.00,22;ReadPosRankSum=-0.201	GT:AD:DP:GQ:PL:SB	0/1:7,7,0:14:99:141,0,151,162,172,334:3,4,1,6
+chr20	20001365	.	T	<NON_REF>	.	.	END=20001365	GT:DP:GQ:MIN_DP:PL	0/0:33:0:33:0,0,681
+chr20	20001366	.	T	<NON_REF>	.	.	END=20001389	GT:DP:GQ:MIN_DP:PL	0/0:27:53:24:0,53,834
+chr20	20001390	.	C	<NON_REF>	.	.	END=20001390	GT:DP:GQ:MIN_DP:PL	0/0:20:0:20:0,0,536
+chr20	20001391	.	A	<NON_REF>	.	.	END=20001396	GT:DP:GQ:MIN_DP:PL	0/0:25:29:24:0,29,653
+chr20	20001397	.	C	<NON_REF>	.	.	END=20001397	GT:DP:GQ:MIN_DP:PL	0/0:24:0:24:0,0,606
+chr20	20001398	.	C	<NON_REF>	.	.	END=20001400	GT:DP:GQ:MIN_DP:PL	0/0:28:53:26:0,53,773
+chr20	20001401	.	C	<NON_REF>	.	.	END=20001402	GT:DP:GQ:MIN_DP:PL	0/0:27:3:24:0,3,675
+chr20	20001403	.	T	<NON_REF>	.	.	END=20001403	GT:DP:GQ:MIN_DP:PL	0/0:31:72:31:0,72,1080
+chr20	20001404	.	G	<NON_REF>	.	.	END=20001404	GT:DP:GQ:MIN_DP:PL	0/0:30:0:30:0,0,614
+chr20	20001405	.	T	<NON_REF>	.	.	END=20001409	GT:DP:GQ:MIN_DP:PL	0/0:29:69:29:0,69,1035
+chr20	20001410	.	A	<NON_REF>	.	.	END=20001410	GT:DP:GQ:MIN_DP:PL	0/0:27:0:27:0,0,552
+chr20	20001411	.	T	<NON_REF>	.	.	END=20001411	GT:DP:GQ:MIN_DP:PL	0/0:28:72:28:0,72,1080
+chr20	20001412	.	A	<NON_REF>	.	.	END=20001412	GT:DP:GQ:MIN_DP:PL	0/0:28:0:28:0,0,595
+chr20	20001413	.	T	<NON_REF>	.	.	END=20001413	GT:DP:GQ:MIN_DP:PL	0/0:28:72:28:0,72,1080
+chr20	20001414	.	A	<NON_REF>	.	.	END=20001414	GT:DP:GQ:MIN_DP:PL	0/0:28:0:28:0,0,535
+chr20	20001415	.	T	<NON_REF>	.	.	END=20001417	GT:DP:GQ:MIN_DP:PL	0/0:27:46:27:0,46,859
+chr20	20001418	.	C	<NON_REF>	.	.	END=20001419	GT:DP:GQ:MIN_DP:PL	0/0:26:0:26:0,0,601
+chr20	20001420	.	T	<NON_REF>	.	.	END=20001423	GT:DP:GQ:MIN_DP:PL	0/0:26:25:25:0,25,638
+chr20	20001424	.	A	<NON_REF>	.	.	END=20001425	GT:DP:GQ:MIN_DP:PL	0/0:26:0:26:0,0,606
+chr20	20001426	.	T	<NON_REF>	.	.	END=20002377	GT:DP:GQ:MIN_DP:PL	0/0:30:26:17:0,26,522
+chr20	20002378	.	AT	A,<NON_REF>	246.77	.	DP=28;MQRankSum=0.684;MQ_DP=28;RAW_MQ=100800.00;RAW_MQandDP=100800.00,28;ReadPosRankSum=0.684	GT:AD:DP:GQ:PL:SB	0/1:14,11,0:25:99:275,0,369,317,403,720:7,7,7,4
+chr20	20002380	.	T	<NON_REF>	.	.	END=20002380	GT:DP:GQ:MIN_DP:PL	0/0:26:0:26:0,0,139
+chr20	20002381	.	T	<NON_REF>	.	.	END=20004700	GT:DP:GQ:MIN_DP:PL	0/0:32:29:22:0,29,620
+chr20	20004701	.	CTT	C,CT,<NON_REF>	111.81	.	DP=29;MQRankSum=1.826;MQ_DP=29;RAW_MQ=102400.00;RAW_MQandDP=102400.00,29;ReadPosRankSum=1.396	GT:AD:DP:GQ:PL:SB	1/2:2,4,6,0:12:20:140,60,222,20,0,25,115,97,43,138:1,1,0,10
+chr20	20004704	.	T	<NON_REF>	.	.	END=20004704	GT:DP:GQ:MIN_DP:PL	0/0:28:0:28:0,0,585
+chr20	20004705	.	T	<NON_REF>	.	.	END=20005011	GT:DP:GQ:MIN_DP:PL	0/0:25:32:14:0,32,442
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prod.chr20snippet.withRawMQ.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prod.chr20snippet.withRawMQ.g.vcf
new file mode 100644
index 00000000000..f0e1ed9b31f
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prod.chr20snippet.withRawMQ.g.vcf
@@ -0,0 +1,2000 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-0-g36282e4,Date="Sun Sep 03 19:04:52 UTC 2017",Epoch=1504465492413,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/cromwell_root/broad-gotc-prod-cromwell-execution/PairedEndSingleSampleWorkflow/36d6043d-5e15-4a26-9bd0-e28d44d4b052/call-GatherBamFiles/NWD242235.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[OverclippedRead] disable_read_filter=[] intervals=[/cromwell_root/broad-gotc-prod-cromwell-execution/PairedEndSingleSampleWorkflow/36d6043d-5e15-4a26-9bd0-e28d44d4b052/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/23scattered.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=3 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.004839373333333333 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 filter_is_too_short_value=30 do_not_require_softclips_both_ends=false min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants  --output prod.chr20snippet.withRawMQ.g.vcf --variant gs://broad-gotc-prod-storage/pipeline/G97551/gvcfs/NWD242235.bcdd0ebc-17fa-402f-aa7e-ec97ae8669ca.g.vcf.gz --intervals chr20:20000000 --interval-padding 5000 --reference Homo_sapiens_assembly38.fasta  --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version=4.0.9.0-13-g0f6c729-SNAPSHOT,Date="October 4, 2018 10:52:55 AM EDT">
+##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
+##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
+##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
+##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
+##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
+##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)
+##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)
+##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
+##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)
+##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
+##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
+##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
+##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
+##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
+##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
+##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)
+##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
+##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
+##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
+##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
+##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
+##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
+##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
+##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
+##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
+##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
+##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
+##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)
+##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)
+##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
+##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)
+##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)
+##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)
+##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)
+##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
+##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)
+##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)
+##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)
+##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)
+##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)
+##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)
+##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive)
+##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)
+##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)
+##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)
+##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)
+##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)
+##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)
+##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)
+##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)
+##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)
+##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
+##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
+##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
+##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)
+##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)
+##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)
+##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)
+##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive)
+##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)
+##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)
+##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)
+##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive)
+##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)
+##GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive)
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,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=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##contig=<ID=chr20,length=64444167,assembly=Homo_sapiens_assembly38.fasta>
+##reference=file:///Users/gauthier/workspaces/reblockGVCF/Homo_sapiens_assembly38.fasta
+##source=SelectVariants
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NWD242235
+chr20	19994995	.	G	<NON_REF>	.	.	END=19995070	GT:DP:GQ:MIN_DP:PL	0/0:41:99:35:0,105,1177
+chr20	19995071	.	G	<NON_REF>	.	.	END=19995071	GT:DP:GQ:MIN_DP:PL	0/0:35:80:35:0,80,1087
+chr20	19995072	.	A	<NON_REF>	.	.	END=19995073	GT:DP:GQ:MIN_DP:PL	0/0:35:99:35:0,102,1530
+chr20	19995074	.	C	<NON_REF>	.	.	END=19995079	GT:DP:GQ:MIN_DP:PL	0/0:36:93:35:0,93,1395
+chr20	19995080	.	G	<NON_REF>	.	.	END=19995089	GT:DP:GQ:MIN_DP:PL	0/0:36:99:35:0,99,1485
+chr20	19995090	.	G	<NON_REF>	.	.	END=19995101	GT:DP:GQ:MIN_DP:PL	0/0:35:90:35:0,90,1350
+chr20	19995102	.	C	<NON_REF>	.	.	END=19995114	GT:DP:GQ:MIN_DP:PL	0/0:37:99:36:0,102,1530
+chr20	19995115	.	A	<NON_REF>	.	.	END=19995115	GT:DP:GQ:MIN_DP:PL	0/0:40:96:40:0,96,1261
+chr20	19995116	.	T	<NON_REF>	.	.	END=19995138	GT:DP:GQ:MIN_DP:PL	0/0:37:99:34:0,102,1122
+chr20	19995139	.	G	<NON_REF>	.	.	END=19995139	GT:DP:GQ:MIN_DP:PL	0/0:35:81:35:0,81,1117
+chr20	19995140	.	G	<NON_REF>	.	.	END=19995157	GT:DP:GQ:MIN_DP:PL	0/0:38:99:34:0,102,1101
+chr20	19995158	.	C	<NON_REF>	.	.	END=19995158	GT:DP:GQ:MIN_DP:PL	0/0:40:96:40:0,96,1281
+chr20	19995159	.	T	<NON_REF>	.	.	END=19995168	GT:DP:GQ:MIN_DP:PL	0/0:41:99:40:0,105,1575
+chr20	19995169	.	G	<NON_REF>	.	.	END=19995170	GT:DP:GQ:MIN_DP:PL	0/0:40:96:40:0,96,1440
+chr20	19995171	.	C	<NON_REF>	.	.	END=19995171	GT:DP:GQ:MIN_DP:PL	0/0:40:99:40:0,99,1485
+chr20	19995172	.	C	<NON_REF>	.	.	END=19995172	GT:DP:GQ:MIN_DP:PL	0/0:38:96:38:0,96,1440
+chr20	19995173	.	C	<NON_REF>	.	.	END=19995174	GT:DP:GQ:MIN_DP:PL	0/0:39:87:39:0,87,1305
+chr20	19995175	.	A	<NON_REF>	.	.	END=19995189	GT:DP:GQ:MIN_DP:PL	0/0:34:90:33:0,90,1350
+chr20	19995190	.	G	<NON_REF>	.	.	END=19995190	GT:DP:GQ:MIN_DP:PL	0/0:32:72:32:0,72,1033
+chr20	19995191	.	C	<NON_REF>	.	.	END=19995191	GT:DP:GQ:MIN_DP:PL	0/0:33:96:33:0,96,1440
+chr20	19995192	.	A	<NON_REF>	.	.	END=19995195	GT:DP:GQ:MIN_DP:PL	0/0:34:99:33:0,99,1117
+chr20	19995196	.	A	<NON_REF>	.	.	END=19995196	GT:DP:GQ:MIN_DP:PL	0/0:34:68:34:0,68,1113
+chr20	19995197	.	A	<NON_REF>	.	.	END=19995212	GT:DP:GQ:MIN_DP:PL	0/0:35:99:33:0,99,1047
+chr20	19995213	.	T	<NON_REF>	.	.	END=19995213	GT:DP:GQ:MIN_DP:PL	0/0:36:83:36:0,83,1132
+chr20	19995214	.	A	<NON_REF>	.	.	END=19995218	GT:DP:GQ:MIN_DP:PL	0/0:36:99:35:0,102,1197
+chr20	19995219	.	C	<NON_REF>	.	.	END=19995219	GT:DP:GQ:MIN_DP:PL	0/0:37:62:37:0,62,1097
+chr20	19995220	.	T	<NON_REF>	.	.	END=19995228	GT:DP:GQ:MIN_DP:PL	0/0:37:99:34:0,102,1152
+chr20	19995229	.	C	<NON_REF>	.	.	END=19995229	GT:DP:GQ:MIN_DP:PL	0/0:38:74:38:0,74,1080
+chr20	19995230	.	A	<NON_REF>	.	.	END=19995231	GT:DP:GQ:MIN_DP:PL	0/0:38:99:35:0,105,1146
+chr20	19995232	.	G	<NON_REF>	.	.	END=19995232	GT:DP:GQ:MIN_DP:PL	0/0:34:43:34:0,43,1013
+chr20	19995233	.	A	<NON_REF>	.	.	END=19995234	GT:DP:GQ:MIN_DP:PL	0/0:37:99:37:0,102,1530
+chr20	19995235	.	T	<NON_REF>	.	.	END=19995235	GT:DP:GQ:MIN_DP:PL	0/0:37:86:37:0,86,1176
+chr20	19995236	.	A	<NON_REF>	.	.	END=19995236	GT:DP:GQ:MIN_DP:PL	0/0:37:99:37:0,99,1485
+chr20	19995237	.	A	<NON_REF>	.	.	END=19995241	GT:DP:GQ:MIN_DP:PL	0/0:35:93:34:0,93,1395
+chr20	19995242	.	C	<NON_REF>	.	.	END=19995243	GT:DP:GQ:MIN_DP:PL	0/0:34:67:31:0,67,978
+chr20	19995244	.	A	<NON_REF>	.	.	END=19995244	GT:DP:GQ:MIN_DP:PL	0/0:34:90:34:0,90,1350
+chr20	19995245	.	G	<NON_REF>	.	.	END=19995248	GT:DP:GQ:MIN_DP:PL	0/0:34:87:31:0,87,1305
+chr20	19995249	.	C	<NON_REF>	.	.	END=19995249	GT:DP:GQ:MIN_DP:PL	0/0:35:80:35:0,80,1015
+chr20	19995250	.	T	<NON_REF>	.	.	END=19995250	GT:DP:GQ:MIN_DP:PL	0/0:36:87:36:0,87,1305
+chr20	19995251	.	G	<NON_REF>	.	.	END=19995251	GT:DP:GQ:MIN_DP:PL	0/0:33:50:33:0,50,968
+chr20	19995252	.	T	<NON_REF>	.	.	END=19995253	GT:DP:GQ:MIN_DP:PL	0/0:36:81:34:0,81,1215
+chr20	19995254	.	T	<NON_REF>	.	.	END=19995256	GT:DP:GQ:MIN_DP:PL	0/0:32:78:32:0,78,1170
+chr20	19995257	.	T	<NON_REF>	.	.	END=19995260	GT:DP:GQ:MIN_DP:PL	0/0:33:81:32:0,81,1215
+chr20	19995261	.	T	<NON_REF>	.	.	END=19995261	GT:DP:GQ:MIN_DP:PL	0/0:33:50:33:0,50,978
+chr20	19995262	.	A	<NON_REF>	.	.	END=19995262	GT:DP:GQ:MIN_DP:PL	0/0:34:53:34:0,53,1043
+chr20	19995263	.	A	<NON_REF>	.	.	END=19995263	GT:DP:GQ:MIN_DP:PL	0/0:33:65:33:0,65,1068
+chr20	19995264	.	A	<NON_REF>	.	.	END=19995265	GT:DP:GQ:MIN_DP:PL	0/0:32:84:31:0,84,1260
+chr20	19995266	.	A	<NON_REF>	.	.	END=19995276	GT:DP:GQ:MIN_DP:PL	0/0:37:90:33:0,90,1350
+chr20	19995277	.	A	<NON_REF>	.	.	END=19995277	GT:DP:GQ:MIN_DP:PL	0/0:36:74:36:0,74,1152
+chr20	19995278	.	A	<NON_REF>	.	.	END=19995278	GT:DP:GQ:MIN_DP:PL	0/0:36:96:36:0,96,1440
+chr20	19995279	.	C	<NON_REF>	.	.	END=19995279	GT:DP:GQ:MIN_DP:PL	0/0:33:64:33:0,64,1048
+chr20	19995280	.	A	<NON_REF>	.	.	END=19995280	GT:DP:GQ:MIN_DP:PL	0/0:34:96:34:0,96,1440
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+chr20	20000999	.	T	<NON_REF>	.	.	END=20001004	GT:DP:GQ:MIN_DP:PL	0/0:28:81:27:0,81,909
+chr20	20001005	.	T	<NON_REF>	.	.	END=20001008	GT:DP:GQ:MIN_DP:PL	0/0:30:90:30:0,90,1003
+chr20	20001009	.	T	<NON_REF>	.	.	END=20001016	GT:DP:GQ:MIN_DP:PL	0/0:30:84:29:0,84,968
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+chr20	20001018	.	A	<NON_REF>	.	.	END=20001019	GT:DP:GQ:MIN_DP:PL	0/0:30:84:30:0,84,1260
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+chr20	20001070	.	G	<NON_REF>	.	.	END=20001071	GT:DP:GQ:MIN_DP:PL	0/0:30:87:29:0,87,998
+chr20	20001072	.	C	<NON_REF>	.	.	END=20001080	GT:DP:GQ:MIN_DP:PL	0/0:32:90:30:0,90,993
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+chr20	20001083	.	A	<NON_REF>	.	.	END=20001132	GT:DP:GQ:MIN_DP:PL	0/0:32:90:30:0,90,1043
+chr20	20001133	.	T	<NON_REF>	.	.	END=20001136	GT:DP:GQ:MIN_DP:PL	0/0:32:81:31:0,81,1215
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+chr20	20001140	.	T	<NON_REF>	.	.	END=20001151	GT:DP:GQ:MIN_DP:PL	0/0:29:75:27:0,75,1125
+chr20	20001152	.	A	<NON_REF>	.	.	END=20001157	GT:DP:GQ:MIN_DP:PL	0/0:28:81:27:0,81,889
+chr20	20001158	.	A	<NON_REF>	.	.	END=20001158	GT:DP:GQ:MIN_DP:PL	0/0:28:70:28:0,70,904
+chr20	20001159	.	T	<NON_REF>	.	.	END=20001162	GT:DP:GQ:MIN_DP:PL	0/0:29:81:28:0,81,943
+chr20	20001163	.	A	<NON_REF>	.	.	END=20001163	GT:DP:GQ:MIN_DP:PL	0/0:29:52:29:0,52,919
+chr20	20001164	.	T	<NON_REF>	.	.	END=20001164	GT:DP:GQ:MIN_DP:PL	0/0:29:62:29:0,62,919
+chr20	20001165	.	G	<NON_REF>	.	.	END=20001167	GT:DP:GQ:MIN_DP:PL	0/0:30:81:29:0,81,1215
+chr20	20001168	.	T	<NON_REF>	.	.	END=20001168	GT:DP:GQ:MIN_DP:PL	0/0:30:76:30:0,76,974
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+chr20	20001170	.	A	<NON_REF>	.	.	END=20001170	GT:DP:GQ:MIN_DP:PL	0/0:29:73:29:0,73,929
+chr20	20001171	.	A	<NON_REF>	.	.	END=20001175	GT:DP:GQ:MIN_DP:PL	0/0:28:81:28:0,81,1215
+chr20	20001176	.	C	<NON_REF>	.	.	END=20001176	GT:DP:GQ:MIN_DP:PL	0/0:26:78:26:0,78,884
+chr20	20001177	.	C	<NON_REF>	.	.	END=20001177	GT:DP:GQ:MIN_DP:PL	0/0:27:56:27:0,56,849
+chr20	20001178	.	T	<NON_REF>	.	.	END=20001182	GT:DP:GQ:MIN_DP:PL	0/0:28:81:27:0,81,899
+chr20	20001183	.	T	<NON_REF>	.	.	END=20001187	GT:DP:GQ:MIN_DP:PL	0/0:30:90:30:0,90,973
+chr20	20001188	.	T	<NON_REF>	.	.	END=20001189	GT:DP:GQ:MIN_DP:PL	0/0:30:84:30:0,84,1260
+chr20	20001190	.	C	<NON_REF>	.	.	END=20001195	GT:DP:GQ:MIN_DP:PL	0/0:30:72:30:0,72,1080
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+chr20	20001221	.	T	<NON_REF>	.	.	END=20001221	GT:DP:GQ:MIN_DP:PL	0/0:29:81:29:0,81,1215
+chr20	20001222	.	T	<NON_REF>	.	.	END=20001224	GT:DP:GQ:MIN_DP:PL	0/0:28:78:26:0,78,833
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+chr20	20001227	.	G	<NON_REF>	.	.	END=20001232	GT:DP:GQ:MIN_DP:PL	0/0:28:75:27:0,75,1125
+chr20	20001233	.	A	<NON_REF>	.	.	END=20001233	GT:DP:GQ:MIN_DP:PL	0/0:27:67:27:0,67,839
+chr20	20001234	.	T	<NON_REF>	.	.	END=20001244	GT:DP:GQ:MIN_DP:PL	0/0:25:72:25:0,72,819
+chr20	20001245	.	G	<NON_REF>	.	.	END=20001245	GT:DP:GQ:MIN_DP:PL	0/0:27:46:27:0,46,839
+chr20	20001246	.	A	<NON_REF>	.	.	END=20001246	GT:DP:GQ:MIN_DP:PL	0/0:27:78:27:0,78,1170
+chr20	20001247	.	A	<NON_REF>	.	.	END=20001247	GT:DP:GQ:MIN_DP:PL	0/0:27:22:27:0,22,780
+chr20	20001248	.	A	<NON_REF>	.	.	END=20001249	GT:DP:GQ:MIN_DP:PL	0/0:27:78:26:0,78,874
+chr20	20001250	.	A	<NON_REF>	.	.	END=20001250	GT:DP:GQ:MIN_DP:PL	0/0:27:67:27:0,67,860
+chr20	20001251	.	C	<NON_REF>	.	.	END=20001251	GT:DP:GQ:MIN_DP:PL	0/0:27:78:27:0,78,1170
+chr20	20001252	.	T	<NON_REF>	.	.	END=20001252	GT:DP:GQ:MIN_DP:PL	0/0:27:81:27:0,81,919
+chr20	20001253	.	T	<NON_REF>	.	.	END=20001254	GT:DP:GQ:MIN_DP:PL	0/0:28:78:27:0,78,1170
+chr20	20001255	.	A	<NON_REF>	.	.	END=20001260	GT:DP:GQ:MIN_DP:PL	0/0:29:81:27:0,81,929
+chr20	20001261	.	A	<NON_REF>	.	.	END=20001261	GT:DP:GQ:MIN_DP:PL	0/0:28:59:28:0,59,863
+chr20	20001262	.	A	<NON_REF>	.	.	END=20001266	GT:DP:GQ:MIN_DP:PL	0/0:29:84:28:0,84,923
+chr20	20001267	.	T	<NON_REF>	.	.	END=20001267	GT:DP:GQ:MIN_DP:PL	0/0:29:73:29:0,73,949
+chr20	20001268	.	T	<NON_REF>	.	.	END=20001268	GT:DP:GQ:MIN_DP:PL	0/0:30:90:30:0,90,1033
+chr20	20001269	.	T	<NON_REF>	.	.	END=20001269	GT:DP:GQ:MIN_DP:PL	0/0:30:66:30:0,66,984
+chr20	20001270	.	T	<NON_REF>	.	.	END=20001288	GT:DP:GQ:MIN_DP:PL	0/0:29:81:28:0,81,957
+chr20	20001289	.	T	<NON_REF>	.	.	END=20001295	GT:DP:GQ:MIN_DP:PL	0/0:29:75:28:0,75,1125
+chr20	20001296	.	G	<NON_REF>	.	.	END=20001296	GT:DP:GQ:MIN_DP:PL	0/0:29:81:29:0,81,1215
+chr20	20001297	.	C	<NON_REF>	.	.	END=20001315	GT:DP:GQ:MIN_DP:PL	0/0:26:72:24:0,72,784
+chr20	20001316	.	C	<NON_REF>	.	.	END=20001317	GT:DP:GQ:MIN_DP:PL	0/0:26:53:26:0,53,774
+chr20	20001318	.	C	<NON_REF>	.	.	END=20001318	GT:DP:GQ:MIN_DP:PL	0/0:25:72:25:0,72,1080
+chr20	20001319	.	T	<NON_REF>	.	.	END=20001337	GT:DP:GQ:MIN_DP:PL	0/0:26:64:24:0,64,815
+chr20	20001338	.	C	<NON_REF>	.	.	END=20001340	GT:DP:GQ:MIN_DP:PL	0/0:26:72:25:0,72,1080
+chr20	20001341	.	G	<NON_REF>	.	.	END=20001341	GT:DP:GQ:MIN_DP:PL	0/0:23:69:23:0,69,749
+chr20	20001342	.	C	<NON_REF>	.	.	END=20001346	GT:DP:GQ:MIN_DP:PL	0/0:31:72:27:0,72,1080
+chr20	20001347	.	C	<NON_REF>	.	.	END=20001352	GT:DP:GQ:MIN_DP:PL	0/0:33:63:33:0,63,945
+chr20	20001353	.	T	<NON_REF>	.	.	END=20001354	GT:DP:GQ:MIN_DP:PL	0/0:35:57:34:0,57,855
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+chr20	20001356	.	T	<NON_REF>	.	.	END=20001357	GT:DP:GQ:MIN_DP:PL	0/0:34:39:34:0,39,585
+chr20	20001358	.	T	<NON_REF>	.	.	END=20001360	GT:DP:GQ:MIN_DP:PL	0/0:33:42:32:0,42,630
+chr20	20001361	.	C	<NON_REF>	.	.	END=20001361	GT:DP:GQ:MIN_DP:PL	0/0:30:6:30:0,6,825
+chr20	20001362	.	CTT	C,<NON_REF>	103.73	.	BaseQRankSum=-0.663;ClippingRankSum=-1.406;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.276;RAW_MQ=79200.00;ReadPosRankSum=-0.201	GT:AD:DP:GQ:PL:SB	0/1:7,7,0:14:99:141,0,151,162,172,334:3,4,1,6
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+chr20	20001367	.	T	<NON_REF>	.	.	END=20001367	GT:DP:GQ:MIN_DP:PL	0/0:31:59:31:0,59,1008
+chr20	20001368	.	T	<NON_REF>	.	.	END=20001387	GT:DP:GQ:MIN_DP:PL	0/0:27:60:26:0,60,900
+chr20	20001388	.	T	<NON_REF>	.	.	END=20001388	GT:DP:GQ:MIN_DP:PL	0/0:26:53:26:0,53,834
+chr20	20001389	.	A	<NON_REF>	.	.	END=20001389	GT:DP:GQ:MIN_DP:PL	0/0:24:66:24:0,66,990
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+chr20	20001395	.	A	<NON_REF>	.	.	END=20001395	GT:DP:GQ:MIN_DP:PL	0/0:26:29:26:0,29,694
+chr20	20001396	.	G	<NON_REF>	.	.	END=20001396	GT:DP:GQ:MIN_DP:PL	0/0:24:47:24:0,47,653
+chr20	20001397	.	C	<NON_REF>	.	.	END=20001397	GT:DP:GQ:MIN_DP:PL	0/0:24:0:24:0,0,606
+chr20	20001398	.	C	<NON_REF>	.	.	END=20001398	GT:DP:GQ:MIN_DP:PL	0/0:26:53:26:0,53,773
+chr20	20001399	.	T	<NON_REF>	.	.	END=20001400	GT:DP:GQ:MIN_DP:PL	0/0:29:66:29:0,66,990
+chr20	20001401	.	C	<NON_REF>	.	.	END=20001401	GT:DP:GQ:MIN_DP:PL	0/0:24:13:24:0,13,675
+chr20	20001402	.	A	<NON_REF>	.	.	END=20001402	GT:DP:GQ:MIN_DP:PL	0/0:29:3:29:0,3,780
+chr20	20001403	.	T	<NON_REF>	.	.	END=20001403	GT:DP:GQ:MIN_DP:PL	0/0:31:72:31:0,72,1080
+chr20	20001404	.	G	<NON_REF>	.	.	END=20001404	GT:DP:GQ:MIN_DP:PL	0/0:30:0:30:0,0,614
+chr20	20001405	.	T	<NON_REF>	.	.	END=20001409	GT:DP:GQ:MIN_DP:PL	0/0:29:69:27:0,69,1035
+chr20	20001410	.	A	<NON_REF>	.	.	END=20001410	GT:DP:GQ:MIN_DP:PL	0/0:27:0:27:0,0,552
+chr20	20001411	.	T	<NON_REF>	.	.	END=20001411	GT:DP:GQ:MIN_DP:PL	0/0:28:72:28:0,72,1080
+chr20	20001412	.	A	<NON_REF>	.	.	END=20001412	GT:DP:GQ:MIN_DP:PL	0/0:28:0:28:0,0,595
+chr20	20001413	.	T	<NON_REF>	.	.	END=20001413	GT:DP:GQ:MIN_DP:PL	0/0:28:72:28:0,72,1080
+chr20	20001414	.	A	<NON_REF>	.	.	END=20001414	GT:DP:GQ:MIN_DP:PL	0/0:28:0:28:0,0,535
+chr20	20001415	.	T	<NON_REF>	.	.	END=20001415	GT:DP:GQ:MIN_DP:PL	0/0:28:72:28:0,72,1080
+chr20	20001416	.	T	<NON_REF>	.	.	END=20001416	GT:DP:GQ:MIN_DP:PL	0/0:27:69:27:0,69,1035
+chr20	20001417	.	T	<NON_REF>	.	.	END=20001417	GT:DP:GQ:MIN_DP:PL	0/0:27:46:27:0,46,859
+chr20	20001418	.	C	<NON_REF>	.	.	END=20001419	GT:DP:GQ:MIN_DP:PL	0/0:26:0:25:0,0,601
+chr20	20001420	.	T	<NON_REF>	.	.	END=20001420	GT:DP:GQ:MIN_DP:PL	0/0:26:43:26:0,43,784
+chr20	20001421	.	A	<NON_REF>	.	.	END=20001421	GT:DP:GQ:MIN_DP:PL	0/0:26:57:26:0,57,855
+chr20	20001422	.	G	<NON_REF>	.	.	END=20001422	GT:DP:GQ:MIN_DP:PL	0/0:25:25:25:0,25,638
+chr20	20001423	.	A	<NON_REF>	.	.	END=20001423	GT:DP:GQ:MIN_DP:PL	0/0:26:29:26:0,29,765
+chr20	20001424	.	A	<NON_REF>	.	.	END=20001424	GT:DP:GQ:MIN_DP:PL	0/0:26:19:26:0,19,745
+chr20	20001425	.	A	<NON_REF>	.	.	END=20001425	GT:DP:GQ:MIN_DP:PL	0/0:26:0:26:0,0,606
+chr20	20001426	.	T	<NON_REF>	.	.	END=20001427	GT:DP:GQ:MIN_DP:PL	0/0:27:57:27:0,57,855
+chr20	20001428	.	T	<NON_REF>	.	.	END=20001428	GT:DP:GQ:MIN_DP:PL	0/0:25:40:25:0,40,790
+chr20	20001429	.	T	<NON_REF>	.	.	END=20001431	GT:DP:GQ:MIN_DP:PL	0/0:22:51:21:0,51,765
+chr20	20001432	.	T	<NON_REF>	.	.	END=20001433	GT:DP:GQ:MIN_DP:PL	0/0:22:54:21:0,54,810
+chr20	20001434	.	G	<NON_REF>	.	.	END=20001434	GT:DP:GQ:MIN_DP:PL	0/0:19:32:19:0,32,561
+chr20	20001435	.	C	<NON_REF>	.	.	END=20001436	GT:DP:GQ:MIN_DP:PL	0/0:20:54:20:0,54,810
+chr20	20001437	.	G	<NON_REF>	.	.	END=20001437	GT:DP:GQ:MIN_DP:PL	0/0:20:35:20:0,35,585
+chr20	20001438	.	T	<NON_REF>	.	.	END=20001440	GT:DP:GQ:MIN_DP:PL	0/0:20:54:19:0,54,810
+chr20	20001441	.	C	<NON_REF>	.	.	END=20001441	GT:DP:GQ:MIN_DP:PL	0/0:18:54:18:0,54,595
+chr20	20001442	.	A	<NON_REF>	.	.	END=20001442	GT:DP:GQ:MIN_DP:PL	0/0:19:54:19:0,54,810
+chr20	20001443	.	G	<NON_REF>	.	.	END=20001444	GT:DP:GQ:MIN_DP:PL	0/0:20:57:20:0,57,855
+chr20	20001445	.	T	<NON_REF>	.	.	END=20001450	GT:DP:GQ:MIN_DP:PL	0/0:21:60:20:0,60,675
+chr20	20001451	.	G	<NON_REF>	.	.	END=20001451	GT:DP:GQ:MIN_DP:PL	0/0:22:41:22:0,41,695
+chr20	20001452	.	T	<NON_REF>	.	.	END=20001452	GT:DP:GQ:MIN_DP:PL	0/0:22:66:22:0,66,745
+chr20	20001453	.	C	<NON_REF>	.	.	END=20001453	GT:DP:GQ:MIN_DP:PL	0/0:22:52:22:0,52,685
+chr20	20001454	.	A	<NON_REF>	.	.	END=20001456	GT:DP:GQ:MIN_DP:PL	0/0:22:60:20:0,60,685
+chr20	20001457	.	A	<NON_REF>	.	.	END=20001457	GT:DP:GQ:MIN_DP:PL	0/0:22:52:22:0,52,685
+chr20	20001458	.	T	<NON_REF>	.	.	END=20001459	GT:DP:GQ:MIN_DP:PL	0/0:22:63:21:0,63,710
+chr20	20001460	.	G	<NON_REF>	.	.	END=20001460	GT:DP:GQ:MIN_DP:PL	0/0:22:41:22:0,41,675
+chr20	20001461	.	G	<NON_REF>	.	.	END=20001469	GT:DP:GQ:MIN_DP:PL	0/0:22:66:22:0,66,724
+chr20	20001470	.	T	<NON_REF>	.	.	END=20001470	GT:DP:GQ:MIN_DP:PL	0/0:25:72:25:0,72,1080
+chr20	20001471	.	A	<NON_REF>	.	.	END=20001476	GT:DP:GQ:MIN_DP:PL	0/0:26:66:25:0,66,990
+chr20	20001477	.	G	<NON_REF>	.	.	END=20001477	GT:DP:GQ:MIN_DP:PL	0/0:26:43:26:0,43,814
+chr20	20001478	.	T	<NON_REF>	.	.	END=20001481	GT:DP:GQ:MIN_DP:PL	0/0:26:66:26:0,66,990
+chr20	20001482	.	T	<NON_REF>	.	.	END=20001485	GT:DP:GQ:MIN_DP:PL	0/0:27:72:27:0,72,1080
+chr20	20001486	.	A	<NON_REF>	.	.	END=20001486	GT:DP:GQ:MIN_DP:PL	0/0:27:67:27:0,67,880
+chr20	20001487	.	A	<NON_REF>	.	.	END=20001491	GT:DP:GQ:MIN_DP:PL	0/0:27:75:27:0,75,1125
+chr20	20001492	.	T	<NON_REF>	.	.	END=20001497	GT:DP:GQ:MIN_DP:PL	0/0:28:81:28:0,81,933
+chr20	20001498	.	A	<NON_REF>	.	.	END=20001500	GT:DP:GQ:MIN_DP:PL	0/0:31:90:30:0,90,1023
+chr20	20001501	.	A	<NON_REF>	.	.	END=20001501	GT:DP:GQ:MIN_DP:PL	0/0:31:68:31:0,68,988
+chr20	20001502	.	T	<NON_REF>	.	.	END=20001505	GT:DP:GQ:MIN_DP:PL	0/0:32:93:31:0,93,1028
+chr20	20001506	.	T	<NON_REF>	.	.	END=20001521	GT:DP:GQ:MIN_DP:PL	0/0:35:99:33:0,99,1117
+chr20	20001522	.	A	<NON_REF>	.	.	END=20001522	GT:DP:GQ:MIN_DP:PL	0/0:35:96:35:0,96,1440
+chr20	20001523	.	A	<NON_REF>	.	.	END=20001529	GT:DP:GQ:MIN_DP:PL	0/0:36:99:35:0,99,1485
+chr20	20001530	.	A	<NON_REF>	.	.	END=20001530	GT:DP:GQ:MIN_DP:PL	0/0:37:97:37:0,97,1207
+chr20	20001531	.	A	<NON_REF>	.	.	END=20001531	GT:DP:GQ:MIN_DP:PL	0/0:37:99:37:0,99,1485
+chr20	20001532	.	A	<NON_REF>	.	.	END=20001532	GT:DP:GQ:MIN_DP:PL	0/0:36:96:36:0,96,1440
+chr20	20001533	.	A	<NON_REF>	.	.	END=20001533	GT:DP:GQ:MIN_DP:PL	0/0:36:99:36:0,99,1485
+chr20	20001534	.	T	<NON_REF>	.	.	END=20001546	GT:DP:GQ:MIN_DP:PL	0/0:35:93:32:0,93,1395
+chr20	20001547	.	G	<NON_REF>	.	.	END=20001547	GT:DP:GQ:MIN_DP:PL	0/0:34:68:34:0,68,1092
+chr20	20001548	.	G	<NON_REF>	.	.	END=20001548	GT:DP:GQ:MIN_DP:PL	0/0:33:74:33:0,74,1027
+chr20	20001549	.	A	<NON_REF>	.	.	END=20001552	GT:DP:GQ:MIN_DP:PL	0/0:32:93:31:0,93,1078
+chr20	20001553	.	G	<NON_REF>	.	.	END=20001553	GT:DP:GQ:MIN_DP:PL	0/0:33:64:33:0,64,1057
+chr20	20001554	.	A	<NON_REF>	.	.	END=20001554	GT:DP:GQ:MIN_DP:PL	0/0:33:75:33:0,75,1078
+chr20	20001555	.	G	<NON_REF>	.	.	END=20001566	GT:DP:GQ:MIN_DP:PL	0/0:33:93:31:0,93,1062
+chr20	20001567	.	T	<NON_REF>	.	.	END=20001568	GT:DP:GQ:MIN_DP:PL	0/0:35:99:35:0,99,1485
+chr20	20001569	.	T	<NON_REF>	.	.	END=20001569	GT:DP:GQ:MIN_DP:PL	0/0:34:88:34:0,88,1123
+chr20	20001570	.	A	<NON_REF>	.	.	END=20001571	GT:DP:GQ:MIN_DP:PL	0/0:35:99:35:0,99,1485
+chr20	20001572	.	A	<NON_REF>	.	.	END=20001572	GT:DP:GQ:MIN_DP:PL	0/0:37:87:37:0,87,1227
+chr20	20001573	.	G	<NON_REF>	.	.	END=20001582	GT:DP:GQ:MIN_DP:PL	0/0:35:99:34:0,99,1172
+chr20	20001583	.	T	<NON_REF>	.	.	END=20001583	GT:DP:GQ:MIN_DP:PL	0/0:35:96:35:0,96,1440
+chr20	20001584	.	G	<NON_REF>	.	.	END=20001598	GT:DP:GQ:MIN_DP:PL	0/0:39:99:37:0,105,1281
+chr20	20001599	.	G	<NON_REF>	.	.	END=20001599	GT:DP:GQ:MIN_DP:PL	0/0:37:87:37:0,87,1227
+chr20	20001600	.	G	<NON_REF>	.	.	END=20001612	GT:DP:GQ:MIN_DP:PL	0/0:39:99:36:0,105,1221
+chr20	20001613	.	G	<NON_REF>	.	.	END=20001613	GT:DP:GQ:MIN_DP:PL	0/0:41:89:41:0,89,1326
+chr20	20001614	.	A	<NON_REF>	.	.	END=20001663	GT:DP:GQ:MIN_DP:PL	0/0:40:99:34:0,99,1485
+chr20	20001664	.	A	<NON_REF>	.	.	END=20001692	GT:DP:GQ:MIN_DP:PL	0/0:33:90:32:0,90,1350
+chr20	20001693	.	C	<NON_REF>	.	.	END=20001701	GT:DP:GQ:MIN_DP:PL	0/0:31:84:30:0,84,1260
+chr20	20001702	.	G	<NON_REF>	.	.	END=20001702	GT:DP:GQ:MIN_DP:PL	0/0:31:58:31:0,58,968
+chr20	20001703	.	T	<NON_REF>	.	.	END=20001709	GT:DP:GQ:MIN_DP:PL	0/0:30:84:30:0,84,1260
+chr20	20001710	.	G	<NON_REF>	.	.	END=20001710	GT:DP:GQ:MIN_DP:PL	0/0:33:90:33:0,90,1350
+chr20	20001711	.	T	<NON_REF>	.	.	END=20001714	GT:DP:GQ:MIN_DP:PL	0/0:33:84:32:0,84,1260
+chr20	20001715	.	T	<NON_REF>	.	.	END=20001721	GT:DP:GQ:MIN_DP:PL	0/0:33:90:32:0,90,1350
+chr20	20001722	.	T	<NON_REF>	.	.	END=20001722	GT:DP:GQ:MIN_DP:PL	0/0:36:73:36:0,73,1111
+chr20	20001723	.	T	<NON_REF>	.	.	END=20001723	GT:DP:GQ:MIN_DP:PL	0/0:34:96:34:0,96,1440
+chr20	20001724	.	T	<NON_REF>	.	.	END=20001724	GT:DP:GQ:MIN_DP:PL	0/0:35:99:35:0,99,1485
+chr20	20001725	.	G	<NON_REF>	.	.	END=20001740	GT:DP:GQ:MIN_DP:PL	0/0:34:90:30:0,90,1013
+chr20	20001741	.	A	<NON_REF>	.	.	END=20001744	GT:DP:GQ:MIN_DP:PL	0/0:35:99:33:0,99,1147
+chr20	20001745	.	T	<NON_REF>	.	.	END=20001752	GT:DP:GQ:MIN_DP:PL	0/0:35:90:33:0,90,1350
+chr20	20001753	.	A	<NON_REF>	.	.	END=20001753	GT:DP:GQ:MIN_DP:PL	0/0:36:99:36:0,99,1485
+chr20	20001754	.	G	<NON_REF>	.	.	END=20001754	GT:DP:GQ:MIN_DP:PL	0/0:36:83:36:0,83,1132
+chr20	20001755	.	G	<NON_REF>	.	.	END=20001758	GT:DP:GQ:MIN_DP:PL	0/0:33:90:33:0,90,1350
+chr20	20001759	.	G	<NON_REF>	.	.	END=20001767	GT:DP:GQ:MIN_DP:PL	0/0:32:81:30:0,81,1215
+chr20	20001768	.	G	<NON_REF>	.	.	END=20001771	GT:DP:GQ:MIN_DP:PL	0/0:29:75:28:0,75,1125
+chr20	20001772	.	A	<NON_REF>	.	.	END=20001784	GT:DP:GQ:MIN_DP:PL	0/0:30:81:29:0,81,988
+chr20	20001785	.	G	<NON_REF>	.	.	END=20001791	GT:DP:GQ:MIN_DP:PL	0/0:32:90:31:0,90,1350
+chr20	20001792	.	A	<NON_REF>	.	.	END=20001817	GT:DP:GQ:MIN_DP:PL	0/0:38:99:34:0,99,1276
+chr20	20001818	.	T	<NON_REF>	.	.	END=20001818	GT:DP:GQ:MIN_DP:PL	0/0:39:92:39:0,92,1256
+chr20	20001819	.	G	<NON_REF>	.	.	END=20001838	GT:DP:GQ:MIN_DP:PL	0/0:41:99:38:0,106,1291
+chr20	20001839	.	C	<NON_REF>	.	.	END=20001839	GT:DP:GQ:MIN_DP:PL	0/0:39:93:39:0,93,1296
+chr20	20001840	.	T	<NON_REF>	.	.	END=20001863	GT:DP:GQ:MIN_DP:PL	0/0:40:99:38:0,99,1332
+chr20	20001864	.	A	<NON_REF>	.	.	END=20001864	GT:DP:GQ:MIN_DP:PL	0/0:39:96:39:0,96,1440
+chr20	20001865	.	G	<NON_REF>	.	.	END=20001874	GT:DP:GQ:MIN_DP:PL	0/0:39:99:34:0,99,1142
+chr20	20001875	.	C	<NON_REF>	.	.	END=20001875	GT:DP:GQ:MIN_DP:PL	0/0:34:77:34:0,77,1102
+chr20	20001876	.	C	<NON_REF>	.	.	END=20001876	GT:DP:GQ:MIN_DP:PL	0/0:33:99:33:0,99,1117
+chr20	20001877	.	T	<NON_REF>	.	.	END=20001877	GT:DP:GQ:MIN_DP:PL	0/0:33:99:33:0,99,1096
+chr20	20001878	.	A	<NON_REF>	.	.	END=20001882	GT:DP:GQ:MIN_DP:PL	0/0:37:99:35:0,99,1485
+chr20	20001883	.	T	<NON_REF>	.	.	END=20001883	GT:DP:GQ:MIN_DP:PL	0/0:40:91:40:0,91,1252
+chr20	20001884	.	A	<NON_REF>	.	.	END=20001891	GT:DP:GQ:MIN_DP:PL	0/0:40:99:39:0,105,1301
+chr20	20001892	.	G	<NON_REF>	.	.	END=20001892	GT:DP:GQ:MIN_DP:PL	0/0:37:76:37:0,76,1156
+chr20	20001893	.	T	<NON_REF>	.	.	END=20001918	GT:DP:GQ:MIN_DP:PL	0/0:38:99:36:0,102,1181
+chr20	20001919	.	T	<NON_REF>	.	.	END=20001919	GT:DP:GQ:MIN_DP:PL	0/0:39:92:39:0,92,1246
+chr20	20001920	.	C	<NON_REF>	.	.	END=20001926	GT:DP:GQ:MIN_DP:PL	0/0:37:99:36:0,99,1485
+chr20	20001927	.	A	<NON_REF>	.	.	END=20001931	GT:DP:GQ:MIN_DP:PL	0/0:35:90:35:0,90,1350
+chr20	20001932	.	T	<NON_REF>	.	.	END=20001937	GT:DP:GQ:MIN_DP:PL	0/0:35:81:34:0,81,1215
+chr20	20001938	.	G	<NON_REF>	.	.	END=20001943	GT:DP:GQ:MIN_DP:PL	0/0:33:78:29:0,78,1170
+chr20	20001944	.	A	<NON_REF>	.	.	END=20001944	GT:DP:GQ:MIN_DP:PL	0/0:30:81:30:0,81,1215
+chr20	20001945	.	G	<NON_REF>	.	.	END=20001945	GT:DP:GQ:MIN_DP:PL	0/0:30:76:30:0,76,964
+chr20	20001946	.	A	<NON_REF>	.	.	END=20001951	GT:DP:GQ:MIN_DP:PL	0/0:28:81:27:0,81,919
+chr20	20001952	.	T	<NON_REF>	.	.	END=20001952	GT:DP:GQ:MIN_DP:PL	0/0:29:62:29:0,62,929
+chr20	20001953	.	T	<NON_REF>	.	.	END=20001959	GT:DP:GQ:MIN_DP:PL	0/0:29:81:27:0,81,929
+chr20	20001960	.	G	<NON_REF>	.	.	END=20001978	GT:DP:GQ:MIN_DP:PL	0/0:28:73:25:0,73,859
+chr20	20001979	.	A	<NON_REF>	.	.	END=20001980	GT:DP:GQ:MIN_DP:PL	0/0:28:81:28:0,81,1215
+chr20	20001981	.	T	<NON_REF>	.	.	END=20001981	GT:DP:GQ:MIN_DP:PL	0/0:28:70:28:0,70,914
+chr20	20001982	.	C	<NON_REF>	.	.	END=20001986	GT:DP:GQ:MIN_DP:PL	0/0:28:81:28:0,81,933
+chr20	20001987	.	A	<NON_REF>	.	.	END=20002006	GT:DP:GQ:MIN_DP:PL	0/0:27:72:24:0,72,824
+chr20	20002007	.	C	<NON_REF>	.	.	END=20002007	GT:DP:GQ:MIN_DP:PL	0/0:25:50:25:0,50,810
+chr20	20002008	.	C	<NON_REF>	.	.	END=20002014	GT:DP:GQ:MIN_DP:PL	0/0:26:72:25:0,72,1080
+chr20	20002015	.	A	<NON_REF>	.	.	END=20002015	GT:DP:GQ:MIN_DP:PL	0/0:26:64:26:0,64,855
+chr20	20002016	.	T	<NON_REF>	.	.	END=20002016	GT:DP:GQ:MIN_DP:PL	0/0:25:72:25:0,72,1080
+chr20	20002017	.	T	<NON_REF>	.	.	END=20002017	GT:DP:GQ:MIN_DP:PL	0/0:25:60:25:0,60,779
+chr20	20002018	.	A	<NON_REF>	.	.	END=20002019	GT:DP:GQ:MIN_DP:PL	0/0:25:72:25:0,72,1080
+chr20	20002020	.	A	<NON_REF>	.	.	END=20002022	GT:DP:GQ:MIN_DP:PL	0/0:25:66:25:0,66,990
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+chr20	20004698	.	A	<NON_REF>	.	.	END=20004698	GT:DP:GQ:MIN_DP:PL	0/0:31:34:31:0,34,939
+chr20	20004699	.	A	<NON_REF>	.	.	END=20004700	GT:DP:GQ:MIN_DP:PL	0/0:30:45:29:0,45,675
+chr20	20004701	.	CTT	C,CT,<NON_REF>	102.77	.	BaseQRankSum=0.107;ClippingRankSum=0.107;DP=29;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.826;RAW_MQ=102400.00;ReadPosRankSum=1.396	GT:AD:DP:GQ:PL:SB	1/2:2,4,6,0:12:20:140,60,222,20,0,25,115,97,43,138:1,1,0,10
+chr20	20004704	.	T	<NON_REF>	.	.	END=20004704	GT:DP:GQ:MIN_DP:PL	0/0:28:0:28:0,0,585
+chr20	20004705	.	T	<NON_REF>	.	.	END=20004705	GT:DP:GQ:MIN_DP:PL	0/0:27:36:27:0,36,540
+chr20	20004706	.	T	<NON_REF>	.	.	END=20004715	GT:DP:GQ:MIN_DP:PL	0/0:25:39:25:0,39,585
+chr20	20004716	.	T	<NON_REF>	.	.	END=20004716	GT:DP:GQ:MIN_DP:PL	0/0:25:36:25:0,36,540
+chr20	20004717	.	T	<NON_REF>	.	.	END=20004720	GT:DP:GQ:MIN_DP:PL	0/0:25:39:24:0,39,585
+chr20	20004721	.	T	<NON_REF>	.	.	END=20004723	GT:DP:GQ:MIN_DP:PL	0/0:24:42:24:0,42,630
+chr20	20004724	.	T	<NON_REF>	.	.	END=20004724	GT:DP:GQ:MIN_DP:PL	0/0:17:39:17:0,39,585
+chr20	20004725	.	G	<NON_REF>	.	.	END=20004735	GT:DP:GQ:MIN_DP:PL	0/0:16:42:15:0,42,630
+chr20	20004736	.	T	<NON_REF>	.	.	END=20004737	GT:DP:GQ:MIN_DP:PL	0/0:16:45:16:0,45,675
+chr20	20004738	.	A	<NON_REF>	.	.	END=20004747	GT:DP:GQ:MIN_DP:PL	0/0:15:36:15:0,36,540
+chr20	20004748	.	A	<NON_REF>	.	.	END=20004749	GT:DP:GQ:MIN_DP:PL	0/0:15:39:13:0,39,442
+chr20	20004750	.	G	<NON_REF>	.	.	END=20004755	GT:DP:GQ:MIN_DP:PL	0/0:14:42:14:0,42,477
+chr20	20004756	.	A	<NON_REF>	.	.	END=20004756	GT:DP:GQ:MIN_DP:PL	0/0:15:45:15:0,45,522
+chr20	20004757	.	T	<NON_REF>	.	.	END=20004761	GT:DP:GQ:MIN_DP:PL	0/0:15:42:15:0,42,630
+chr20	20004762	.	T	<NON_REF>	.	.	END=20004763	GT:DP:GQ:MIN_DP:PL	0/0:16:45:16:0,45,675
+chr20	20004764	.	C	<NON_REF>	.	.	END=20004764	GT:DP:GQ:MIN_DP:PL	0/0:17:48:17:0,48,720
+chr20	20004765	.	A	<NON_REF>	.	.	END=20004768	GT:DP:GQ:MIN_DP:PL	0/0:17:45:17:0,45,675
+chr20	20004769	.	G	<NON_REF>	.	.	END=20004772	GT:DP:GQ:MIN_DP:PL	0/0:18:48:16:0,48,536
+chr20	20004773	.	T	<NON_REF>	.	.	END=20004774	GT:DP:GQ:MIN_DP:PL	0/0:19:51:19:0,51,765
+chr20	20004775	.	T	<NON_REF>	.	.	END=20004777	GT:DP:GQ:MIN_DP:PL	0/0:20:57:20:0,57,855
+chr20	20004778	.	C	<NON_REF>	.	.	END=20004778	GT:DP:GQ:MIN_DP:PL	0/0:19:43:19:0,43,591
+chr20	20004779	.	G	<NON_REF>	.	.	END=20004779	GT:DP:GQ:MIN_DP:PL	0/0:19:32:19:0,32,571
+chr20	20004780	.	G	<NON_REF>	.	.	END=20004780	GT:DP:GQ:MIN_DP:PL	0/0:18:54:18:0,54,616
+chr20	20004781	.	C	<NON_REF>	.	.	END=20004781	GT:DP:GQ:MIN_DP:PL	0/0:19:57:19:0,57,661
+chr20	20004782	.	T	<NON_REF>	.	.	END=20004782	GT:DP:GQ:MIN_DP:PL	0/0:20:35:20:0,35,605
+chr20	20004783	.	C	<NON_REF>	.	.	END=20004784	GT:DP:GQ:MIN_DP:PL	0/0:20:60:20:0,60,665
+chr20	20004785	.	C	<NON_REF>	.	.	END=20004787	GT:DP:GQ:MIN_DP:PL	0/0:19:57:19:0,57,640
+chr20	20004788	.	C	<NON_REF>	.	.	END=20004789	GT:DP:GQ:MIN_DP:PL	0/0:20:60:20:0,60,665
+chr20	20004790	.	G	<NON_REF>	.	.	END=20004793	GT:DP:GQ:MIN_DP:PL	0/0:20:57:20:0,57,855
+chr20	20004794	.	C	<NON_REF>	.	.	END=20004794	GT:DP:GQ:MIN_DP:PL	0/0:20:46:20:0,46,646
+chr20	20004795	.	A	<NON_REF>	.	.	END=20004796	GT:DP:GQ:MIN_DP:PL	0/0:20:57:20:0,57,855
+chr20	20004797	.	C	<NON_REF>	.	.	END=20004797	GT:DP:GQ:MIN_DP:PL	0/0:19:57:19:0,57,620
+chr20	20004798	.	C	<NON_REF>	.	.	END=20004798	GT:DP:GQ:MIN_DP:PL	0/0:20:57:20:0,57,855
+chr20	20004799	.	T	<NON_REF>	.	.	END=20004799	GT:DP:GQ:MIN_DP:PL	0/0:20:46:20:0,46,646
+chr20	20004800	.	C	<NON_REF>	.	.	END=20004800	GT:DP:GQ:MIN_DP:PL	0/0:19:57:19:0,57,640
+chr20	20004801	.	C	<NON_REF>	.	.	END=20004817	GT:DP:GQ:MIN_DP:PL	0/0:22:60:20:0,60,685
+chr20	20004818	.	C	<NON_REF>	.	.	END=20004819	GT:DP:GQ:MIN_DP:PL	0/0:26:72:25:0,72,1080
+chr20	20004820	.	T	<NON_REF>	.	.	END=20004820	GT:DP:GQ:MIN_DP:PL	0/0:26:53:26:0,53,844
+chr20	20004821	.	C	<NON_REF>	.	.	END=20004842	GT:DP:GQ:MIN_DP:PL	0/0:26:72:24:0,72,824
+chr20	20004843	.	C	<NON_REF>	.	.	END=20004848	GT:DP:GQ:MIN_DP:PL	0/0:27:81:27:0,81,878
+chr20	20004849	.	C	<NON_REF>	.	.	END=20004849	GT:DP:GQ:MIN_DP:PL	0/0:27:56:27:0,56,859
+chr20	20004850	.	T	<NON_REF>	.	.	END=20004850	GT:DP:GQ:MIN_DP:PL	0/0:27:81:27:0,81,898
+chr20	20004851	.	A	<NON_REF>	.	.	END=20004851	GT:DP:GQ:MIN_DP:PL	0/0:27:56:27:0,56,879
+chr20	20004852	.	C	<NON_REF>	.	.	END=20004854	GT:DP:GQ:MIN_DP:PL	0/0:27:81:27:0,81,898
+chr20	20004855	.	G	<NON_REF>	.	.	END=20004856	GT:DP:GQ:MIN_DP:PL	0/0:27:78:26:0,78,894
+chr20	20004857	.	G	<NON_REF>	.	.	END=20004861	GT:DP:GQ:MIN_DP:PL	0/0:29:81:28:0,81,1215
+chr20	20004862	.	C	<NON_REF>	.	.	END=20004876	GT:DP:GQ:MIN_DP:PL	0/0:28:72:27:0,72,1080
+chr20	20004877	.	A	<NON_REF>	.	.	END=20004877	GT:DP:GQ:MIN_DP:PL	0/0:27:67:27:0,67,849
+chr20	20004878	.	A	<NON_REF>	.	.	END=20004901	GT:DP:GQ:MIN_DP:PL	0/0:27:72:26:0,72,874
+chr20	20004902	.	T	<NON_REF>	.	.	END=20004902	GT:DP:GQ:MIN_DP:PL	0/0:29:81:29:0,81,1215
+chr20	20004903	.	G	<NON_REF>	.	.	END=20004903	GT:DP:GQ:MIN_DP:PL	0/0:29:78:29:0,78,1170
+chr20	20004904	.	A	<NON_REF>	.	.	END=20004906	GT:DP:GQ:MIN_DP:PL	0/0:31:81:31:0,81,1215
+chr20	20004907	.	T	<NON_REF>	.	.	END=20004908	GT:DP:GQ:MIN_DP:PL	0/0:30:73:29:0,73,899
+chr20	20004909	.	T	<NON_REF>	.	.	END=20004909	GT:DP:GQ:MIN_DP:PL	0/0:31:68:31:0,68,958
+chr20	20004910	.	C	<NON_REF>	.	.	END=20004910	GT:DP:GQ:MIN_DP:PL	0/0:30:87:30:0,87,1305
+chr20	20004911	.	A	<NON_REF>	.	.	END=20004913	GT:DP:GQ:MIN_DP:PL	0/0:32:90:31:0,90,1350
+chr20	20004914	.	A	<NON_REF>	.	.	END=20004916	GT:DP:GQ:MIN_DP:PL	0/0:31:81:31:0,81,1215
+chr20	20004917	.	T	<NON_REF>	.	.	END=20004930	GT:DP:GQ:MIN_DP:PL	0/0:29:78:26:0,78,874
+chr20	20004931	.	C	<NON_REF>	.	.	END=20004937	GT:DP:GQ:MIN_DP:PL	0/0:28:81:27:0,81,909
+chr20	20004938	.	T	<NON_REF>	.	.	END=20004953	GT:DP:GQ:MIN_DP:PL	0/0:33:90:30:0,90,1023
+chr20	20004954	.	T	<NON_REF>	.	.	END=20004960	GT:DP:GQ:MIN_DP:PL	0/0:30:81:30:0,81,1215
+chr20	20004961	.	C	<NON_REF>	.	.	END=20004971	GT:DP:GQ:MIN_DP:PL	0/0:29:75:27:0,75,1125
+chr20	20004972	.	C	<NON_REF>	.	.	END=20004979	GT:DP:GQ:MIN_DP:PL	0/0:29:81:27:0,81,929
+chr20	20004980	.	C	<NON_REF>	.	.	END=20004982	GT:DP:GQ:MIN_DP:PL	0/0:30:90:30:0,90,1013
+chr20	20004983	.	A	<NON_REF>	.	.	END=20004984	GT:DP:GQ:MIN_DP:PL	0/0:30:87:29:0,87,998
+chr20	20004985	.	A	<NON_REF>	.	.	END=20005011	GT:DP:GQ:MIN_DP:PL	0/0:32:90:31:0,90,1058
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testJustOneSample.expected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testJustOneSample.expected.g.vcf
index 3edd30b356e..b929f006ecb 100755
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testJustOneSample.expected.g.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testJustOneSample.expected.g.vcf
@@ -17,20 +17,21 @@
 ##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=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.">
 ##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
 ##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
 ##contig=<ID=chr20,length=64444167,assembly=Homo_sapiens_assembly38.fasta>
 ##source=SelectVariants
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1
 chr20	69485	.	G	<NON_REF>	.	.	END=69510	GT:DP:GQ:MIN_DP:PL	0/0:94:99:94:0,120,1800
-chr20	69511	.	A	G,<NON_REF>	2255.77	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;ReadPosRankSum=1.689	GT:AD:DP:GQ:PL:SB	1/1:1,79,0:80:99:2284,207,0,2287,237,2316:0,1,46,33
+chr20	69511	.	A	G,<NON_REF>	2255.77	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;RAW_MQandDP=2546.10,82;ReadPosRankSum=1.689	GT:AD:DP:GQ:PL:SB	1/1:1,79,0:80:99:2284,207,0,2287,237,2316:0,1,46,33
 chr20	69512	.	A	<NON_REF>	.	.	END=69521	GT:DP:GQ:MIN_DP:PL	0/0:96:99:96:0,120,1800
 chr20	69522	.	A	<NON_REF>	.	.	END=69635	GT:DP:GQ:MIN_DP:PL	0/0:7:0:6:0,0,0
 chr20	69762	.	A	<NON_REF>	.	.	END=69762	GT:DP:GQ:MIN_DP:PL	0/0:7:18:7:0,18,270
 chr20	69763	.	A	<NON_REF>	.	.	END=69766	GT:DP:GQ:MIN_DP:PL	0/0:7:21:7:0,21,253
 chr20	69767	.	A	<NON_REF>	.	.	END=69770	GT:DP:GQ:MIN_DP:PL	0/0:7:12:7:0,12,180
-chr20	69771	.	TAAAAA	T,<NON_REF>	0.61	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;ReadPosRankSum=1.754	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:20:20,0,119,101,128,229:0,4,0,3
+chr20	69771	.	TAAAAA	T,<NON_REF>	0.61	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;RAW_MQandDP=239.05,7;ReadPosRankSum=1.754	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:20:20,0,119,101,128,229:0,4,0,3
 chr20	69777	.	G	<NON_REF>	.	.	END=69783	GT:DP:GQ:MIN_DP:PL	0/0:7:0:7:0,0,0
-chr20	69785	.	T	G,<NON_REF>	2255.77	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;ReadPosRankSum=1.689	GT:DP:GQ:PL:SB	1/1:80:99:2284,207,0,2287,237,2316:0,1,46,33
+chr20	69785	.	T	G,<NON_REF>	2255.77	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;RAW_MQandDP=2546.10,82;ReadPosRankSum=1.689	GT:DP:GQ:PL:SB	1/1:80:99:2284,207,0,2287,237,2316:0,1,46,33
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testNonRefADCorrection.expected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testNonRefADCorrection.expected.g.vcf
index 9a7322be47d..ce165287208 100755
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testNonRefADCorrection.expected.g.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testNonRefADCorrection.expected.g.vcf
@@ -25,14 +25,17 @@
 ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.">
 ##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation">
 ##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
 ##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
+##INFO=<ID=RAW_MQ,Number=1,Type=Integer,Description="Raw data for RMS Mapping Quality (deprecated -- use RAW_MQandDP instead.">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
 ##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
 ##contig=<ID=chr20,length=64444167,assembly=Homo_sapiens_assembly38.fasta>
 ##reference=file:///seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta
 ##source=SelectVariants
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HK017-0046
-chr20	1133569	.	A	ATATATATATATATATATATTT,<NON_REF>	240.77	.	DP=22;MQRankSum=1.380;MQ_DP=22;RAW_MQ=69700.00;ReadPosRankSum=0.000	GT:AD:DP:GQ:PL:SB	0/1:2,4,0:6:30:269,0,253,30,51,87:0,2,3,1
-chr20	1133750	.	A	G,AGAATGGAATG,<NON_REF>	408.79	.	DP=121;MQ=37.23;MQ_DP=121	GT:AD:DP:GQ:PL:SB	1/3:0,6,0,0:6:9:436,21,9,291,45,834,242,0,270,220:0,0,5,1
+chr20	1133569	.	A	ATATATATATATATATATATTT,<NON_REF>	240.77	.	DP=22;MQRankSum=1.380;MQ_DP=22;RAW_MQ=69700.00;RAW_MQandDP=69700.00,22;ReadPosRankSum=0.000	GT:AD:DP:GQ:PL:SB	0/1:2,4,0:6:30:269,0,253,30,51,87:0,2,3,1
+chr20	1133750	.	A	G,AGAATGGAATG,<NON_REF>	408.79	.	DP=121;MQ=37.23;MQ_DP=121;RAW_MQandDP=4504.83,121	GT:AD:DP:GQ:PL:SB	1/3:0,6,0,0:6:9:436,21,9,291,45,834,242,0,270,220:0,0,5,1
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testOneSampleAsForGnomAD.expected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testOneSampleAsForGnomAD.expected.g.vcf
index d6bc2119206..2be550c8bf6 100755
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testOneSampleAsForGnomAD.expected.g.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testOneSampleAsForGnomAD.expected.g.vcf
@@ -17,20 +17,21 @@
 ##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=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.">
 ##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
 ##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
 ##contig=<ID=chr20,length=64444167,assembly=Homo_sapiens_assembly38.fasta>
 ##source=SelectVariants
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1
 chr20	69485	.	G	<NON_REF>	.	.	END=69510	GT:DP:GQ:MIN_DP:PL	0/0:94:99:94:0,120,1800
-chr20	69511	.	A	G,<NON_REF>	2255.77	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;QUALapprox=2284;ReadPosRankSum=1.689;VarDP=80	GT:AD:DP:GQ:PL:SB	1/1:1,79,0:80:99:2284,207,0,2287,237,2316:0,1,46,33
+chr20	69511	.	A	G,<NON_REF>	2255.77	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;QUALapprox=2284;RAW_MQandDP=2546.10,82;ReadPosRankSum=1.689;VarDP=80	GT:AD:DP:GQ:PL:SB	1/1:1,79,0:80:99:2284,207,0,2287,237,2316:0,1,46,33
 chr20	69512	.	A	<NON_REF>	.	.	END=69521	GT:DP:GQ:MIN_DP:PL	0/0:96:99:96:0,120,1800
 chr20	69549	.	T	<NON_REF>	.	.	END=69634	GT:DP:GQ:MIN_DP:PL	0/0:6:16:6:0,16,90
-chr20	69635	.	A	T,<NON_REF>	0.06	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;QUALapprox=10;ReadPosRankSum=1.754;VarDP=7	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:10:10,0,119,101,128,229:0,4,0,3
+chr20	69635	.	A	T,<NON_REF>	0.06	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;QUALapprox=10;RAW_MQandDP=239.05,7;ReadPosRankSum=1.754;VarDP=7	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:10:10,0,119,101,128,229:0,4,0,3
 chr20	69762	.	A	<NON_REF>	.	.	END=69762	GT:DP:GQ:MIN_DP:PL	0/0:7:18:7:0,18,270
 chr20	69763	.	A	<NON_REF>	.	.	END=69766	GT:DP:GQ:MIN_DP:PL	0/0:7:21:7:0,21,253
 chr20	69767	.	A	<NON_REF>	.	.	END=69770	GT:DP:GQ:MIN_DP:PL	0/0:7:12:7:0,12,180
-chr20	69771	.	TAAAAA	T,<NON_REF>	0.61	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;QUALapprox=20;ReadPosRankSum=1.754;VarDP=7	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:20:20,0,119,101,128,229:0,4,0,3
-chr20	69785	.	T	G,<NON_REF>	2255.77	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;QUALapprox=2284;ReadPosRankSum=1.689;VarDP=80	GT:DP:GQ:PL:SB	1/1:80:99:2284,207,0,2287,237,2316:0,1,46,33
+chr20	69771	.	TAAAAA	T,<NON_REF>	0.61	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;QUALapprox=20;RAW_MQandDP=239.05,7;ReadPosRankSum=1.754;VarDP=7	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:20:20,0,119,101,128,229:0,4,0,3
+chr20	69785	.	T	G,<NON_REF>	2255.77	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;QUALapprox=2284;RAW_MQandDP=2546.10,82;ReadPosRankSum=1.689;VarDP=80	GT:DP:GQ:PL:SB	1/1:80:99:2284,207,0,2287,237,2316:0,1,46,33
diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java
index 985e911d51f..5c2f2aad38d 100644
--- a/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java
+++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java
@@ -3,6 +3,7 @@
 import htsjdk.samtools.util.Locatable;
 import org.broadinstitute.hellbender.engine.FeatureDataSource;
 import org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport;
+import org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBUtils;
 import org.broadinstitute.hellbender.utils.IntervalUtils;
 
 import java.io.File;
@@ -21,7 +22,7 @@ private GenomicsDBTestUtils(){}
      * @return a string formatted as a genomicsDB uri pointing to the given workspace i.e "gendb:///pathTo/workspace
      */
     public static String makeGenomicsDBUri(final File workspace){
-        return FeatureDataSource.GENOMIC_DB_URI_SCHEME + workspace.getAbsolutePath();
+        return GenomicsDBUtils.GENOMIC_DB_URI_SCHEME + workspace.getAbsolutePath();
     }
 
     /**
diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java
index c0c226bb5fc..a84d5757b21 100644
--- a/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java
+++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java
@@ -279,7 +279,6 @@ private static List<Object> attributeToList(final Object attribute){
 
     public static void assertGenotypesAreEqual(final Genotype actual, final Genotype expected) {
         Assert.assertEquals(actual.getSampleName(), expected.getSampleName(), "Genotype names");
-        Assert.assertEquals(actual.getGenotypeString(), expected.getGenotypeString(), "Genotype string");
         Assert.assertTrue(CollectionUtils.isEqualCollection(actual.getAlleles(), expected.getAlleles()), "Genotype alleles");
         Assert.assertEquals(actual.getGenotypeString(false), expected.getGenotypeString(false), "Genotype string");
         Assert.assertEquals(actual.getType(), expected.getType(), "Genotype type");