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Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests 

-- This version of BCF should actually work properly for most files, assuming headers are properly defined.
-- Lots of bug fixes to BCF2 codec
-- Genotype getPhredScaledQual is now an int, returning -1 if there's no QUAL.  NOTE THIS SEMANTICS change
-- Equals() method for GenotypeLikelihoods, using PLs.
-- VCFCodec now longer adds empty bindings to missing input field values.  NOTE THIS CHANGE
-- VCs can be marked as fully decoded, so that when fullyDecode() is called it returns itself, instead of doing the decoding work.  The BCF2 codec now makes VCs marked as fully decoded
-- stringToBytes returns empty list for null or "" string in BCF2Encoder
-- Proper handling of genotype ordering in BCF2 reader / writer
-- Removed the crazy slow noDups and sameSamples tests that were slowing down unit and integration tests totally unnecessarily
-- Many failing MD5s now due to double -> int change in GQ, will update later
This commit is contained in:
Mark DePristo 2012-05-27 11:13:43 -04:00
parent 86e5a066fc
commit 5894d045cb
17 changed files with 303 additions and 1656 deletions
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25
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
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@ -84,7 +84,7 @@ public class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceDepende
decodeGenotypes(info, builder);
}
return builder.make();
return builder.fullyDecoded(true).make();
}
@Override
@ -321,34 +321,37 @@ public class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceDepende
for ( final Map.Entry<String, List<Object>> entry : fieldValues.entrySet() ) {
final String field = entry.getKey();
final List<Object> values = entry.getValue();
Object value = entry.getValue().get(i);
try {
if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
alleles = decodeGenotypeAlleles(siteInfo.alleles, (List<Integer>)values.get(i));
alleles = decodeGenotypeAlleles(siteInfo.alleles, (List<Integer>)value);
} else if ( field.equals(VCFConstants.GENOTYPE_QUALITY_KEY) ) {
final Integer value = (Integer)values.get(i);
if ( value != BCF2Type.INT8.getMissingJavaValue() )
log10PError = value / -10.0;
log10PError = ((Integer)value) / -10.0;
} else if ( field.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) ) {
final List<Integer> pls = (List<Integer>)values.get(i);
final List<Integer> pls = (List<Integer>)value;
if ( pls != null ) { // we have a PL field
log10Likelihoods = new double[pls.size()];
for ( int j = 0; j < log10Likelihoods.length; j++ )
log10Likelihoods[j] = pls.get(j) / -10.0;
for ( int j = 0; j < log10Likelihoods.length; j++ ) {
final double d = pls.get(j);
log10Likelihoods[j] = d == -0.0 ? 0.0 : d / -10.0;
}
}
} else if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
throw new ReviewedStingException("Genotype filters not implemented in GATK BCF2");
//filters = new HashSet<String>(values.get(i));
} else { // add to attributes
if ( values.get(i) != null ) { // don't add missing values
if ( value != null ) { // don't add missing values
if ( attributes == null ) attributes = new HashMap<String, Object>(nFields);
attributes.put(field, values.get(i));
if ( value instanceof List && ((List)value).size() == 1)
value = ((List)value).get(0);
attributes.put(field, value);
}
}
} catch ( ClassCastException e ) {
throw new UserException.MalformedBCF2("BUG: expected encoding of field " + field
+ " inconsistent with the value observed in the decoded value in the "
+ " BCF file. Value was " + Utils.join(",", values));
+ " BCF file. Value was " + value);
}
}

18
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Encoder.java
View File

@ -247,12 +247,14 @@ public class BCF2Encoder {
}
private final List<Byte> stringToBytes(final String v) throws IOException {
assert v != null && !v.equals("");
// TODO -- this needs to be optimized away for efficiency
final byte[] bytes = v.getBytes();
final List<Byte> l = new ArrayList<Byte>(bytes.length);
for ( int i = 0; i < bytes.length; i++) l.add(bytes[i]);
return l;
if ( v == null || v.equals("") )
return Collections.emptyList();
else {
// TODO -- this needs to be optimized away for efficiency
final byte[] bytes = v.getBytes();
final List<Byte> l = new ArrayList<Byte>(bytes.length);
for ( int i = 0; i < bytes.length; i++) l.add(bytes[i]);
return l;
}
}
}
}

4
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
View File

@ -217,9 +217,9 @@ public class VCFCodec extends AbstractVCFCodec {
} else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) {
genotypeFilters = missing ? parseFilters(VCFConstants.MISSING_VALUE_v4) : parseFilters(getCachedString(GTValueArray[i]));
} else if ( missing ) {
gtAttributes.put(gtKey, VCFConstants.MISSING_VALUE_v4);
// if its truly missing (there no provided value) skip adding it to the attributes
} else {
gtAttributes.put(gtKey, new String(GTValueArray[i]));
gtAttributes.put(gtKey, GTValueArray[i]);
}
}
}

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
View File

@ -111,7 +111,7 @@ public final class VCFConstants {
public static final String PER_GENOTYPE_COUNT = "G";
public static final String EMPTY_ALLELE = ".";
public static final String EMPTY_GENOTYPE = "./.";
public static final double MAX_GENOTYPE_QUAL = 99.0;
public static final int MAX_GENOTYPE_QUAL = 99;
public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
public static final String DOUBLE_PRECISION_INT_SUFFIX = ".00";

16
public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
View File

@ -268,13 +268,13 @@ public class Genotype implements Comparable<Genotype> {
}
public String toString() {
int Q = (int)Math.round(getPhredScaledQual());
int Q = getPhredScaledQual();
return String.format("[%s %s Q%s %s]", getSampleName(), getGenotypeString(false),
Q == -10 ? "." : String.format("%2d",Q), sortedString(getAttributes()));
Q == -1 ? "." : String.format("%2d",Q), sortedString(getAttributes()));
}
public String toBriefString() {
return String.format("%s:Q%.2f", getGenotypeString(false), getPhredScaledQual());
return String.format("%s:Q%d", getGenotypeString(false), getPhredScaledQual());
}
public boolean sameGenotype(Genotype other) {
@ -331,7 +331,15 @@ public class Genotype implements Comparable<Genotype> {
public boolean filtersWereApplied() { return commonInfo.filtersWereApplied(); }
public boolean hasLog10PError() { return commonInfo.hasLog10PError(); }
public double getLog10PError() { return commonInfo.getLog10PError(); }
public double getPhredScaledQual() { return commonInfo.getPhredScaledQual(); }
/**
* Returns a phred-scaled quality score, or -1 if none is available
* @return
*/
public int getPhredScaledQual() {
final int i = (int)Math.round(commonInfo.getPhredScaledQual());
return i < 0 ? -1 : i;
}
public Map<String, Object> getAttributes() { return commonInfo.getAttributes(); }
public boolean hasAttribute(String key) { return commonInfo.hasAttribute(key); }

85
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
View File

@ -30,6 +30,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.Arrays;
import java.util.EnumMap;
public class GenotypeLikelihoods {
@ -107,6 +108,18 @@ public class GenotypeLikelihoods {
return likelihoodsAsString_PLs;
}
@Override public boolean equals(Object aThat) {
//check for self-comparison
if ( this == aThat ) return true;
if ( !(aThat instanceof GenotypeLikelihoods) ) return false;
GenotypeLikelihoods that = (GenotypeLikelihoods)aThat;
// now a proper field-by-field evaluation can be made.
// GLs are considered equal if the corresponding PLs are equal
return Arrays.equals(getAsPLs(), that.getAsPLs());
}
//Return genotype likelihoods as an EnumMap with Genotypes as keys and likelihoods as values
//Returns null in case of missing likelihoods
public EnumMap<Genotype.Type,Double> getAsMap(boolean normalizeFromLog10){
@ -267,16 +280,16 @@ public class GenotypeLikelihoods {
// @Override public ListIterator<Double> listIterator(final int i) { notImplemented(); return null; }
// @Override public List<Double> subList(final int i, final int i1) { notImplemented(); return null; }
// -------------------------------------------------------------------------------------
//
// Static conversion utilities, going from GL/PL index to allele index and vice versa.
//
// -------------------------------------------------------------------------------------
// -------------------------------------------------------------------------------------
//
// Static conversion utilities, going from GL/PL index to allele index and vice versa.
//
// -------------------------------------------------------------------------------------
/*
* Class representing the 2 alleles (or rather their indexes into VariantContext.getAllele()) corresponding to a specific PL index.
* Note that the reference allele is always index=0.
*/
* Class representing the 2 alleles (or rather their indexes into VariantContext.getAllele()) corresponding to a specific PL index.
* Note that the reference allele is always index=0.
*/
public static class GenotypeLikelihoodsAllelePair {
public final int alleleIndex1, alleleIndex2;
@ -292,8 +305,8 @@ public class GenotypeLikelihoods {
public final static int MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED = 50;
/*
* a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles
*/
* a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles
*/
private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
private static GenotypeLikelihoodsAllelePair[] calculatePLcache(final int altAlleles) {
@ -312,35 +325,35 @@ public class GenotypeLikelihoods {
if ( cache[i] == null )
throw new ReviewedStingException("BUG: cache entry " + i + " is unexpected null");
}
return cache;
}
/**
* Compute how many likelihood elements are associated with the given number of alleles
* Equivalent to asking in how many ways N non-negative integers can add up to P is S(N,P)
* where P = ploidy (number of chromosomes) and N = total # of alleles.
* Each chromosome can be in one single state (0,...,N-1) and there are P of them.
* Naive solution would be to store N*P likelihoods, but this is not necessary because we can't distinguish chromosome states, but rather
* only total number of alt allele counts in all chromosomes.
*
* For example, S(3,2) = 6: For alleles A,B,C, on a diploid organism we have six possible genotypes:
* AA,AB,BB,AC,BC,CC.
* Another way of expressing is with vector (#of A alleles, # of B alleles, # of C alleles)
* which is then, for ordering above, (2,0,0), (1,1,0), (0,2,0), (1,1,0), (0,1,1), (0,0,2)
* In general, for P=2 (regular biallelic), then S(N,2) = N*(N+1)/2
*
* Recursive implementation:
* S(N,P) = sum_{k=0}^P S(N-1,P-k)
* because if we have N integers, we can condition 1 integer to be = k, and then N-1 integers have to sum to P-K
* With initial conditions
* S(N,1) = N (only way to have N integers add up to 1 is all-zeros except one element with a one. There are N of these vectors)
* S(1,P) = 1 (only way to have 1 integer add to P is with that integer P itself).
*
* @param numAlleles Number of alleles (including ref)
* @param ploidy Ploidy, or number of chromosomes in set
* @return Number of likelihood elements we need to hold.
*/
* Compute how many likelihood elements are associated with the given number of alleles
* Equivalent to asking in how many ways N non-negative integers can add up to P is S(N,P)
* where P = ploidy (number of chromosomes) and N = total # of alleles.
* Each chromosome can be in one single state (0,...,N-1) and there are P of them.
* Naive solution would be to store N*P likelihoods, but this is not necessary because we can't distinguish chromosome states, but rather
* only total number of alt allele counts in all chromosomes.
*
* For example, S(3,2) = 6: For alleles A,B,C, on a diploid organism we have six possible genotypes:
* AA,AB,BB,AC,BC,CC.
* Another way of expressing is with vector (#of A alleles, # of B alleles, # of C alleles)
* which is then, for ordering above, (2,0,0), (1,1,0), (0,2,0), (1,1,0), (0,1,1), (0,0,2)
* In general, for P=2 (regular biallelic), then S(N,2) = N*(N+1)/2
*
* Recursive implementation:
* S(N,P) = sum_{k=0}^P S(N-1,P-k)
* because if we have N integers, we can condition 1 integer to be = k, and then N-1 integers have to sum to P-K
* With initial conditions
* S(N,1) = N (only way to have N integers add up to 1 is all-zeros except one element with a one. There are N of these vectors)
* S(1,P) = 1 (only way to have 1 integer add to P is with that integer P itself).
*
* @param numAlleles Number of alleles (including ref)
* @param ploidy Ploidy, or number of chromosomes in set
* @return Number of likelihood elements we need to hold.
*/
public static int calculateNumLikelihoods(final int numAlleles, final int ploidy) {
// fast, closed form solution for diploid samples (most common use case)
@ -408,7 +421,7 @@ public class GenotypeLikelihoods {
* @return the PL indexes
*/
public static int[] getPLIndecesOfAlleles(final int allele1Index, final int allele2Index) {
final int[] indexes = new int[3];
indexes[0] = calculatePLindex(allele1Index, allele1Index);
indexes[1] = calculatePLindex(allele1Index, allele2Index);

49
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
View File

@ -88,7 +88,7 @@ public class GenotypesContext implements List<Genotype> {
/**
* Create an GenotypeContext containing genotypes
*/
@Requires({"genotypes != null", "noDups(genotypes)"})
@Requires("genotypes != null")
protected GenotypesContext(final ArrayList<Genotype> genotypes) {
this.notToBeDirectlyAccessedGenotypes = genotypes;
this.sampleNameToOffset = null;
@ -105,7 +105,7 @@ public class GenotypesContext implements List<Genotype> {
* @param sampleNamesInOrder a list of sample names, one for each genotype in genotypes, sorted in alphabetical
* order.
*/
@Requires({"genotypes != null", "noDups(genotypes)",
@Requires({"genotypes != null",
"sampleNameToOffset != null",
"sampleNamesInOrder != null",
"genotypes.size() == sampleNameToOffset.size()",
@ -157,9 +157,7 @@ public class GenotypesContext implements List<Genotype> {
*/
@Requires({"genotypes != null",
"sampleNameToOffset != null",
"sampleNamesInOrder != null",
"sameSamples(genotypes, sampleNamesInOrder)",
"sameSamples(genotypes, sampleNameToOffset.keySet())"})
"sampleNamesInOrder != null"})
@Ensures({"result != null"})
public static final GenotypesContext create(final ArrayList<Genotype> genotypes,
final Map<String, Integer> sampleNameToOffset,
@ -251,8 +249,7 @@ public class GenotypesContext implements List<Genotype> {
sampleNamesInOrder = null;
}
@Ensures({"sampleNamesInOrder != null",
"sameSamples(notToBeDirectlyAccessedGenotypes, sampleNamesInOrder)"})
@Ensures({"sampleNamesInOrder != null"})
protected void ensureSampleOrdering() {
if ( sampleNamesInOrder == null ) {
sampleNamesInOrder = new ArrayList<String>(size());
@ -264,8 +261,7 @@ public class GenotypesContext implements List<Genotype> {
}
}
@Ensures({"sampleNameToOffset != null",
"sameSamples(notToBeDirectlyAccessedGenotypes, sampleNameToOffset.keySet())"})
@Ensures({"sampleNameToOffset != null"})
protected void ensureSampleNameMap() {
if ( sampleNameToOffset == null ) {
sampleNameToOffset = new HashMap<String, Integer>(size());
@ -276,12 +272,6 @@ public class GenotypesContext implements List<Genotype> {
}
}
// for testing purposes
protected void ensureAll() {
ensureSampleNameMap();
ensureSampleOrdering();
}
// ---------------------------------------------------------------------------
//
// Map methods
@ -336,7 +326,6 @@ public class GenotypesContext implements List<Genotype> {
*/
@Override
@Requires({"genotype != null", "get(genotype.getSampleName()) == null"})
@Ensures("noDups(getGenotypes())")
public boolean add(final Genotype genotype) {
checkImmutability();
invalidateSampleOrdering();
@ -351,7 +340,6 @@ public class GenotypesContext implements List<Genotype> {
@Override
@Requires("! contains(genotype)")
@Ensures("noDups(getGenotypes())")
public void add(final int i, final Genotype genotype) {
throw new UnsupportedOperationException();
}
@ -367,7 +355,6 @@ public class GenotypesContext implements List<Genotype> {
*/
@Override
@Requires("! containsAny(genotypes)")
@Ensures("noDups(getGenotypes())")
public boolean addAll(final Collection<? extends Genotype> genotypes) {
checkImmutability();
invalidateSampleOrdering();
@ -511,7 +498,6 @@ public class GenotypesContext implements List<Genotype> {
}
@Override
@Ensures("noDups(getGenotypes())")
public Genotype set(final int i, final Genotype genotype) {
checkImmutability();
final Genotype prev = getGenotypes().set(i, genotype);
@ -696,29 +682,4 @@ public class GenotypesContext implements List<Genotype> {
}
}
}
protected final static boolean noDups(Collection<Genotype> genotypes) {
Set<String> names = new HashSet<String>(genotypes.size());
for ( final Genotype g : genotypes ) {
if ( names.contains(g.getSampleName()) )
return false;
names.add(g.getSampleName());
}
return true;
}
protected final static boolean sameSamples(List<Genotype> genotypes, Collection<String> sampleNamesInOrder) {
Set<String> names = new HashSet<String>(sampleNamesInOrder);
if ( names.size() != sampleNamesInOrder.size() )
return false;
if ( genotypes.size() != names.size() )
return false;
for ( final Genotype g : genotypes )
if ( ! names.contains(g.getSampleName()) )
return false;
return true;
}
}

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java
View File

@ -80,9 +80,7 @@ public class LazyGenotypesContext extends GenotypesContext {
final Map<String, Integer> sampleNameToOffset;
final List<String> sampleNamesInOrder;
@Requires({"genotypes != null", "sampleNamesInOrder != null", "sampleNameToOffset != null",
"sameSamples(genotypes, sampleNamesInOrder)",
"sameSamples(genotypes, sampleNameToOffset.keySet())"})
@Requires({"genotypes != null", "sampleNamesInOrder != null", "sampleNameToOffset != null"})
public LazyData(final ArrayList<Genotype> genotypes,
final List<String> sampleNamesInOrder,
final Map<String, Integer> sampleNameToOffset) {

70
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -159,9 +159,24 @@ import java.util.*;
* VariantContext vc1 = vc.subContextFromGenotypes(Arrays.asList(g1));
* </pre>
*
* <s3>
* Fully decoding. Currently VariantContexts support some fields, particularly those
* stored as generic attributes, to be of any type. For example, a field AB might
* be naturally a floating point number, 0.51, but when it's read into a VC its
* not decoded into the Java presentation but left as a string "0.51". A fully
* decoded VariantContext is one where all values have been converted to their
* corresponding Java object types, based on the types declared in a VCFHeader.
*
* The fullyDecode() takes a header object and creates a new fully decoded VariantContext
* where all fields are converted to their true java representation. The VCBuilder
* can be told that all fields are fully decoded, in which case no work is done when
* asking for a fully decoded version of the VC.
* </s3>
*
* @author depristo
*/
public class VariantContext implements Feature { // to enable tribble integration
private boolean fullyDecoded = false;
protected CommonInfo commonInfo = null;
public final static double NO_LOG10_PERROR = CommonInfo.NO_LOG10_PERROR;
@ -213,7 +228,6 @@ public class VariantContext implements Feature { // to enable tribble integratio
GENOTYPES
}
private final static EnumSet<Validation> ALL_VALIDATION = EnumSet.allOf(Validation.class);
private final static EnumSet<Validation> NO_VALIDATION = EnumSet.noneOf(Validation.class);
// ---------------------------------------------------------------------------------------------------------
@ -232,7 +246,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
other.getAlleles(), other.getGenotypes(), other.getLog10PError(),
other.getFiltersMaybeNull(),
other.getAttributes(), other.REFERENCE_BASE_FOR_INDEL,
NO_VALIDATION);
other.fullyDecoded, NO_VALIDATION);
}
/**
@ -250,12 +264,19 @@ public class VariantContext implements Feature { // to enable tribble integratio
* @param referenceBaseForIndel padded reference base
* @param validationToPerform set of validation steps to take
*/
protected VariantContext(String source, String ID,
String contig, long start, long stop,
Collection<Allele> alleles, GenotypesContext genotypes,
double log10PError, Set<String> filters, Map<String, Object> attributes,
Byte referenceBaseForIndel,
EnumSet<Validation> validationToPerform ) {
protected VariantContext(final String source,
final String ID,
final String contig,
final long start,
final long stop,
final Collection<Allele> alleles,
final GenotypesContext genotypes,
final double log10PError,
final Set<String> filters,
final Map<String, Object> attributes,
final Byte referenceBaseForIndel,
final boolean fullyDecoded,
final EnumSet<Validation> validationToPerform ) {
if ( contig == null ) { throw new IllegalArgumentException("Contig cannot be null"); }
this.contig = contig;
this.start = start;
@ -293,6 +314,8 @@ public class VariantContext implements Feature { // to enable tribble integratio
}
}
this.fullyDecoded = fullyDecoded;
if ( ! validationToPerform.isEmpty() ) {
validate(validationToPerform);
}
@ -1277,11 +1300,34 @@ public class VariantContext implements Feature { // to enable tribble integratio
// Fully decode
//
// ---------------------------------------------------------------------------------------------------------
/**
* Return a VC equivalent to this one but where all fields are fully decoded
*
* See VariantContext document about fully decoded
*
* @param header containing types about all fields in this VC
* @return a fully decoded version of this VC
*/
public VariantContext fullyDecode(final VCFHeader header) {
final VariantContextBuilder builder = new VariantContextBuilder(this);
fullyDecodeInfo(builder, header);
fullyDecodeGenotypes(builder, header);
return builder.make();
if ( isFullyDecoded() )
return this;
else {
// TODO -- warning this is potentially very expensive as it creates copies over and over
final VariantContextBuilder builder = new VariantContextBuilder(this);
fullyDecodeInfo(builder, header);
fullyDecodeGenotypes(builder, header);
builder.fullyDecoded(true);
return builder.make();
}
}
/**
* See VariantContext document about fully decoded
* @return true if this is a fully decoded VC
*/
public boolean isFullyDecoded() {
return fullyDecoded;
}
private final void fullyDecodeInfo(final VariantContextBuilder builder, final VCFHeader header) {

29
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
View File

@ -60,6 +60,7 @@ import java.util.*;
*/
public class VariantContextBuilder {
// required fields
private boolean fullyDecoded = false;
private String source = null;
private String contig = null;
private long start = -1;
@ -120,6 +121,7 @@ public class VariantContextBuilder {
this.source = parent.getSource();
this.start = parent.getStart();
this.stop = parent.getEnd();
this.fullyDecoded = parent.isFullyDecoded();
}
public VariantContextBuilder(VariantContextBuilder parent) {
@ -134,6 +136,7 @@ public class VariantContextBuilder {
this.source = parent.source;
this.start = parent.start;
this.stop = parent.stop;
this.fullyDecoded = parent.fullyDecoded;
this.attributes(parent.attributes);
this.filters(parent.filters);
@ -440,6 +443,30 @@ public class VariantContextBuilder {
return this;
}
/**
* @return true if this builder contains fully decoded data
*
* See VariantContext for more information
*/
public boolean isFullyDecoded() {
return fullyDecoded;
}
/**
* Sets this builder's fully decoded state to true.
*
* A fully decoded builder indicates that all fields are represented by their
* proper java objects (e.g., Integer(10) not "10").
*
* See VariantContext for more information
*
* @param isFullyDecoded
*/
public VariantContextBuilder fullyDecoded(boolean isFullyDecoded) {
this.fullyDecoded = isFullyDecoded;
return this;
}
/**
* Takes all of the builder data provided up to this point, and instantiates
* a freshly allocated VariantContext with all of the builder data. This
@ -452,6 +479,6 @@ public class VariantContextBuilder {
public VariantContext make() {
return new VariantContext(source, ID, contig, start, stop, alleles,
genotypes, log10PError, filters, attributes,
referenceBaseForIndel, toValidate);
referenceBaseForIndel, fullyDecoded, toValidate);
}
}

14
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
View File

@ -259,7 +259,8 @@ class BCF2Writer extends IndexingVariantContextWriter {
final VCFToBCFEncoding encoding = prepFieldValueForEncoding(field, null);
startGenotypeField(field, numInFormatField, encoding.BCF2Type);
for ( final Genotype g : vc.getGenotypes() ) {
for ( final String name : header.getGenotypeSamples() ) {
final Genotype g = vc.getGenotype(name); // todo -- can we optimize this?
try {
final Object fieldValue = g.getAttribute(field);
@ -357,9 +358,10 @@ class BCF2Writer extends IndexingVariantContextWriter {
private final void addGQ(final VariantContext vc) throws IOException {
startGenotypeField(VCFConstants.GENOTYPE_QUALITY_KEY, 1, BCF2Type.INT8);
for ( final Genotype g : vc.getGenotypes() ) {
for ( final String name : header.getGenotypeSamples() ) {
final Genotype g = vc.getGenotype(name); // todo -- can we optimize this?
if ( g.hasLog10PError() ) {
final int GQ = (int)Math.round(Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL));
final int GQ = Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL);
if ( GQ > VCFConstants.MAX_GENOTYPE_QUAL ) throw new ReviewedStingException("Unexpectedly large GQ " + GQ + " at " + vc);
encoder.encodeRawValue(GQ, BCF2Type.INT8);
} else {
@ -380,7 +382,8 @@ class BCF2Writer extends IndexingVariantContextWriter {
// collect all of the PLs into a single vector of values
int i = 0;
for ( final Genotype g : vc.getGenotypes() ) {
for ( final String name : header.getGenotypeSamples() ) {
final Genotype g = vc.getGenotype(name); // todo -- can we optimize this?
final GenotypeLikelihoods gls = g.getLikelihoods();
final int[] pls = gls != null ? g.getLikelihoods().getAsPLs() : null;
if ( pls == null )
@ -405,7 +408,8 @@ class BCF2Writer extends IndexingVariantContextWriter {
final Map<Allele, String> alleleMap = VCFWriter.buildAlleleMap(vc);
final int maxPloidy = vc.getMaxPloidy();
startGenotypeField(VCFConstants.GENOTYPE_KEY, maxPloidy, BCF2Type.INT8);
for ( final Genotype g : vc.getGenotypes() ) {
for ( final String name : header.getGenotypeSamples() ) {
final Genotype g = vc.getGenotype(name); // todo -- can we optimize this?
final List<Allele> alleles = g.getAlleles();
final int samplePloidy = alleles.size();
for ( int i = 0; i < maxPloidy; i++ ) {

24
public/java/test/org/broadinstitute/sting/BaseTest.java
View File

@ -9,6 +9,7 @@ import org.broadinstitute.sting.commandline.CommandLineUtils;
import org.broadinstitute.sting.utils.crypt.CryptUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.io.IOUtils;
import org.testng.Assert;
import org.testng.Reporter;
import java.io.File;
@ -264,4 +265,27 @@ public abstract class BaseTest {
public static void log(final String message) {
Reporter.log(message, true);
}
private static final double DEFAULT_FLOAT_TOLERANCE = 1e-4;
public static final void assertEqualsDoubleSmart(final Object actual, final Double expected) {
Assert.assertTrue(actual instanceof Double);
assertEqualsDoubleSmart((double)(Double)actual, (double)expected);
}
public static final void assertEqualsDoubleSmart(final double actual, final double expected) {
assertEqualsDoubleSmart(actual, expected, DEFAULT_FLOAT_TOLERANCE);
}
public static final void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance) {
if ( Double.isNaN(expected) ) // NaN == NaN => false unfortunately
Assert.assertTrue(Double.isNaN(actual));
else if ( Double.isInfinite(expected) ) // NaN == NaN => false unfortunately
Assert.assertTrue(Double.isInfinite(actual));
else {
final double delta = Math.abs(actual - expected);
final double ratio = Math.abs(actual / expected - 1.0);
Assert.assertTrue(delta < tolerance || ratio < tolerance);
}
}
}

4
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -335,7 +335,9 @@ public class WalkerTest extends BaseTest {
// run the executable
boolean gotAnException = false;
try {
System.out.println(String.format("Executing test %s with GATK arguments: %s", name, Utils.join(" ",command)));
final String now = new SimpleDateFormat("HH:mm:ss").format(new Date());
System.out.println(String.format("[%s] Executing test %s with GATK arguments: %s",
now, name, Utils.join(" ",command)));
CommandLineExecutable.start(instance, command);
} catch (Exception e) {
gotAnException = true;

10
public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java
View File

@ -388,15 +388,7 @@ public class BCF2EncoderDecoderUnitTest extends BaseTest {
final double valueFloat = (Double)tv.value;
final double decodedFloat = (Double)decoded;
if ( Double.isNaN(valueFloat) ) // NaN == NaN => false unfortunately
Assert.assertTrue(Double.isNaN(decodedFloat));
else if ( Double.isInfinite(valueFloat) ) // NaN == NaN => false unfortunately
Assert.assertTrue(Double.isInfinite(decodedFloat));
else {
final double delta = Math.abs(decodedFloat - valueFloat);
final double ratio = Math.abs(decodedFloat / valueFloat - 1.0);
Assert.assertTrue(delta < FLOAT_TOLERANCE || ratio < FLOAT_TOLERANCE);
}
BaseTest.assertEqualsDoubleSmart(decodedFloat, valueFloat, FLOAT_TOLERANCE);
} else
Assert.assertEquals(decoded, tv.value);
}

98
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
View File

@ -24,6 +24,7 @@
package org.broadinstitute.sting.utils.variantcontext;
import org.apache.log4j.Logger;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureCodecHeader;
import org.broad.tribble.readers.PositionalBufferedStream;
@ -47,9 +48,12 @@ import java.util.*;
* @since Date created
*/
public class VariantContextTestProvider {
final protected static Logger logger = Logger.getLogger(VariantContextTestProvider.class);
final private static boolean ENABLE_VARARRAY_TESTS = true;
final private static boolean ENABLE_PLOIDY_TESTS = true;
final private static boolean ENABLE_PL_TESTS = true;
final private static boolean ENABLE_SOURCE_VCF_TESTS = true;
private static VCFHeader syntheticHeader;
final static List<VariantContextTestData> TEST_DATAs = new ArrayList<VariantContextTestData>();
private static VariantContext ROOT;
@ -81,7 +85,7 @@ public class VariantContextTestProvider {
public List<VariantContext> vcs;
public VariantContextTestData(final VCFHeader header, final VariantContextBuilder builder) {
this(header, Collections.singletonList(builder.make()));
this(header, Collections.singletonList(builder.fullyDecoded(true).make()));
}
public VariantContextTestData(final VCFHeader header, final List<VariantContext> vcs) {
@ -125,13 +129,20 @@ public class VariantContextTestProvider {
}
private static void makeEmpiricalTests() throws IOException {
for ( final File file : testSourceVCFs ) {
VCFCodec codec = new VCFCodec();
Pair<VCFHeader, List<VariantContext>> x = readAllVCs( file, codec );
List<VariantContext> fullyDecoded = new ArrayList<VariantContext>(x.getSecond().size());
for ( final VariantContext raw : x.getSecond() )
fullyDecoded.add(raw.fullyDecode(x.getFirst()));
TEST_DATAs.add(new VariantContextTestData(x.getFirst(), x.getSecond()));
if ( ENABLE_SOURCE_VCF_TESTS ) {
for ( final File file : testSourceVCFs ) {
VCFCodec codec = new VCFCodec();
Pair<VCFHeader, List<VariantContext>> x = readAllVCs( file, codec );
List<VariantContext> fullyDecoded = new ArrayList<VariantContext>(x.getSecond().size());
int i = 0;
logger.warn("Reading records from " + file);
for ( final VariantContext raw : x.getSecond() ) {
fullyDecoded.add(raw.fullyDecode(x.getFirst()));
logger.warn("\t" + i++);
}
logger.warn("Done reading " + file);
TEST_DATAs.add(new VariantContextTestData(x.getFirst(), x.getSecond()));
}
}
}
@ -215,7 +226,7 @@ public class VariantContextTestProvider {
add(builder().attribute("FLOAT3", null));
add(builder().attribute("FLAG", true));
add(builder().attribute("FLAG", false));
//add(builder().attribute("FLAG", false)); // NOTE -- VCF doesn't allow false flags
add(builder().attribute("STRING1", "s1"));
add(builder().attribute("STRING1", null));
@ -255,7 +266,7 @@ public class VariantContextTestProvider {
// add all
add(builder.genotypes(Arrays.asList(genotypes)));
// add all with the last replicated 10x, 100x, 1000x times
// add all with the last replicated 10x and 100x times
for ( int nCopiesOfLast : Arrays.asList(10, 100, 1000) ) {
final GenotypesContext gc = new GenotypesContext();
final Genotype last = genotypes[genotypes.length-1];
@ -424,7 +435,7 @@ public class VariantContextTestProvider {
final List<VariantContext> read = new ArrayList<VariantContext>();
while ( ! pbs.isDone() ) {
final VariantContext vc = codec.decode(pbs);
if ( vc != null ) read.add(vc);
if ( vc != null ) read.add(vc.fullyDecode((VCFHeader)header.getHeaderValue()));
};
return new Pair<VCFHeader, List<VariantContext>>((VCFHeader)header.getHeaderValue(), read);
@ -454,7 +465,70 @@ public class VariantContextTestProvider {
Assert.assertEquals(actual.getChr(), expected.getChr());
Assert.assertEquals(actual.getStart(), expected.getStart());
Assert.assertEquals(actual.getEnd(), expected.getEnd());
// TODO -- expand me
Assert.assertEquals(actual.getID(), expected.getID());
Assert.assertEquals(actual.getAlleles(), expected.getAlleles());
assertAttributesEquals(actual.getAttributes(), expected.getAttributes());
Assert.assertEquals(actual.getFilters(), expected.getFilters());
BaseTest.assertEqualsDoubleSmart(actual.getPhredScaledQual(), expected.getPhredScaledQual());
Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes());
if ( expected.hasGenotypes() ) {
Assert.assertEquals(actual.getSampleNames(), expected.getSampleNames());
final Set<String> samples = expected.getSampleNames();
for ( final String sample : samples ) {
assertEquals(actual.getGenotype(sample), expected.getGenotype(sample));
}
}
}
public static void assertEquals(final Genotype actual, final Genotype expected) {
Assert.assertEquals(actual.getSampleName(), expected.getSampleName());
Assert.assertEquals(actual.getAlleles(), expected.getAlleles());
Assert.assertEquals(actual.getGenotypeString(), expected.getGenotypeString());
Assert.assertEquals(actual.getFilters(), expected.getFilters());
Assert.assertEquals(actual.getPhredScaledQual(), expected.getPhredScaledQual());
assertAttributesEquals(actual.getAttributes(), expected.getAttributes());
Assert.assertEquals(actual.isPhased(), expected.isPhased());
Assert.assertEquals(actual.getPloidy(), expected.getPloidy());
}
private static void assertAttributesEquals(final Map<String, Object> actual, Map<String, Object> expected) {
final Set<String> expectedKeys = new HashSet<String>(expected.keySet());
for ( final Map.Entry<String, Object> act : actual.entrySet() ) {
final Object actualValue = act.getValue();
if ( expected.containsKey(act.getKey()) && expected.get(act.getKey()) != null ) {
final Object expectedValue = expected.get(act.getKey());
if ( expectedValue instanceof List ) {
final List<Object> expectedList = (List<Object>)expectedValue;
Assert.assertTrue(actualValue instanceof List);
final List<Object> actualList = (List<Object>)actualValue;
Assert.assertEquals(actualList.size(), expectedList.size());
for ( int i = 0; i < expectedList.size(); i++ )
assertAttributesEquals(actualList.get(i), expectedList.get(i));
} else
assertAttributesEquals(actualValue, expectedValue);
} else {
// it's ok to have a binding in x -> null that's absent in y
Assert.assertNull(actualValue);
}
expectedKeys.remove(act.getKey());
}
// now expectedKeys contains only the keys found in expected but not in actual,
// and they must all be null
for ( final String missingExpected : expectedKeys ) {
final Object value = expected.get(missingExpected);
Assert.assertTrue(value == null || value.equals(VCFConstants.MISSING_VALUE_v4));
}
}
private static void assertAttributesEquals(final Object actual, final Object expected) {
if ( expected instanceof Double ) {
BaseTest.assertEqualsDoubleSmart(actual, (Double)expected);
} else
Assert.assertEquals(actual, expected);
}
public static void assertEquals(final VCFHeader actual, final VCFHeader expected) {

756
public/testdata/ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf vendored
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751
public/testdata/dbsnp_135.b37.1000.vcf vendored
View File

@ -247,754 +247,3 @@
1 58771 rs140128481 T C . PASS ASP;RSPOS=58771;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 58814 rs114420996 G A . PASS ASP;G5;GMAF=0.0982632541133455;KGPilot123;RSPOS=58814;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004050010000100;WGT=0;dbSNPBuildID=132
1 59040 rs149755937 T C . PASS ASP;KGPilot123;RSPOS=59040;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 60718 rs78395614 G A . PASS CFL;GNO;RSPOS=60718;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 60726 rs192328835 C A . PASS KGPilot123;RSPOS=60726;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 60791 rs76199781 A G . PASS CFL;GNO;RSPOS=60791;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 61442 rs74970982 A G . PASS CFL;GMAF=0.076782449725777;GNO;KGPilot123;RSPOS=61442;SAO=0;SSR=0;VC=SNV;VP=050000000008000110000100;WGT=0;dbSNPBuildID=131
1 61462 rs56992750 T A . PASS CFL;G5;G5A;GMAF=0.0383912248628885;GNO;KGPilot123;RSPOS=61462;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008030110000100;WGT=0;dbSNPBuildID=129
1 61480 rs75526266 G C . PASS CFL;GNO;RSPOS=61480;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 61499 rs75719746 G A . PASS CFL;GNO;RSPOS=61499;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 61743 rs184286948 G C . PASS KGPilot123;RSPOS=61743;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 61920 rs62637820 G A . PASS CFL;GMAF=0.0255941499085923;RSPOS=61920;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=129
1 61987 rs76735897 A G . PASS CFL;GMAF=0.292961608775137;GNO;KGPilot123;RSPOS=61987;SAO=0;SSR=0;VC=SNV;VP=050000000008000110000100;WGT=0;dbSNPBuildID=131
1 61989 rs77573425 G C . PASS CFL;GMAF=0.309414990859232;GNO;KGPilot123;RSPOS=61989;SAO=0;SSR=0;VC=SNV;VP=050000000008000110000100;WGT=0;dbSNPBuildID=131
1 61993 rs190553843 C T . PASS KGPilot123;RSPOS=61993;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 62156 rs181864839 C T . PASS KGPilot123;RSPOS=62156;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 62157 rs10399597 G A . PASS CFL;GMAF=0.00228519195612431;KGPilot123;RSPOS=62157;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040010000100;WGT=0;dbSNPBuildID=119
1 62162 rs140556834 G A . PASS ASP;KGPilot123;RSPOS=62162;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 62203 rs28402963 T C . PASS CFL;KGPilot123;RSPOS=62203;SAO=0;SSR=0;VC=SNV;VP=050000000008000010000100;WGT=0;dbSNPBuildID=125
1 62271 rs28599927 A G . PASS CFL;GMAF=0.138482632541133;RSPOS=62271;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=125
1 63268 rs75478250 T C . PASS CFL;GNO;RSPOS=63268;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 63276 rs185977555 G A . PASS KGPilot123;RSPOS=63276;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 63297 rs188886746 G A . PASS KGPilot123;RSPOS=63297;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 63671 rs116440577 G A . PASS ASP;G5;GMAF=0.170018281535649;KGPilot123;RSPOS=63671;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004050010000100;WGT=0;dbSNPBuildID=132
1 63737 rs77426996 TACT T,TCTA . PASS CFL;RSPOS=63738;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=131
1 64649 rs181431124 A C . PASS KGPilot123;RSPOS=64649;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 66008 rs2691286 C G . PASS CFL;GNO;RSPOS=66008;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=100
1 66162 rs62639105 A T . PASS CFL;GMAF=0.320383912248629;GNO;KGPilot123;RSPOS=66162;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000110000100;WGT=0;dbSNPBuildID=129
1 66176 rs28552463 T A . PASS CFL;GMAF=0.0484460694698355;KGPilot123;RSPOS=66176;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040010000100;WGT=0;dbSNPBuildID=125
1 66219 rs181028663 A T . PASS KGPilot123;RSPOS=66219;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 66238 rs113961546 T A . PASS CFL;GNO;RSPOS=66238;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=132
1 66314 rs28534012 T A . PASS CFL;RSPOS=66314;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=125
1 66331 rs186063952 A C . PASS KGPilot123;RSPOS=66331;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 66334 rs28464214 T A . PASS CFL;RSPOS=66334;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=125
1 66442 rs192044252 T A . PASS KGPilot123;RSPOS=66442;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 66457 rs13328655 T A . PASS CFL;GMAF=0.0795246800731261;KGPilot123;RSPOS=66457;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040010000100;WGT=0;dbSNPBuildID=121
1 66503 rs112350669 T A . PASS CFL;RSPOS=66503;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=132
1 66507 rs12401368 T A . PASS CFL;GMAF=0.479890310786106;KGPilot123;RSPOS=66507;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040010000100;WGT=0;dbSNPBuildID=120
1 66651 rs2257270 A T . PASS CFL;GNO;RSPOS=66651;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=100
1 67179 rs149952626 C G . PASS ASP;KGPilot123;RSPOS=67179;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 67181 rs77662731 A G . PASS ASP;G5;G5A;GENEINFO=OR4F5:79501;GMAF=0.0470749542961609;GNO;KGPilot123;RSPOS=67181;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070110000100;WGT=0;dbSNPBuildID=131
1 67223 rs78676975 C A . PASS ASP;GENEINFO=OR4F5:79501;GNO;RSPOS=67223;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 69428 rs140739101 T G . PASS ASP;RSPOS=69428;S3D;SAO=0;SSR=0;VC=SNV;VLD;VP=050200000004040000000100;WGT=0;dbSNPBuildID=134
1 69453 rs142004627 G A . PASS ASP;RSPOS=69453;S3D;SAO=0;SSR=0;VC=SNV;VP=050200000004000000000100;WGT=0;dbSNPBuildID=134
1 69476 rs148502021 T C . PASS ASP;RSPOS=69476;S3D;SAO=0;SSR=0;VC=SNV;VLD;VP=050200000004040000000100;WGT=0;dbSNPBuildID=134
1 69496 rs150690004 G A . PASS ASP;RSPOS=69496;S3D;SAO=0;SSR=0;VC=SNV;VLD;VP=050200000004040000000100;WGT=0;dbSNPBuildID=134
1 69511 rs75062661 A G . PASS GENEINFO=OR4F5:79501;GMAF=0.193784277879342;GNO;KGPilot123;RSPOS=69511;S3D;SAO=0;SSR=0;VC=SNV;VP=050200000000000110000100;WGT=0;dbSNPBuildID=131
1 69534 rs190717287 T C . PASS KGPilot123;RSPOS=69534;S3D;SAO=0;SSR=0;VC=SNV;VP=050200000000000010000100;WGT=0;dbSNPBuildID=135
1 69552 rs55874132 G C . PASS GENEINFO=OR4F5:79501;HD;RSPOS=69552;S3D;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050300000000040400000100;WGT=0;dbSNPBuildID=129
1 69590 rs141776804 T A . PASS ASP;RSPOS=69590;S3D;SAO=0;SSR=0;VC=SNV;VP=050200000004000000000100;WGT=0;dbSNPBuildID=134
1 69594 rs144967600 T C . PASS ASP;RSPOS=69594;S3D;SAO=0;SSR=0;VC=SNV;VP=050200000004000000000100;WGT=0;dbSNPBuildID=134
1 72148 rs182862337 C T . PASS KGPilot123;RSPOS=72148;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 73841 rs143773730 C T . PASS ASP;KGPilot123;RSPOS=73841;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 74651 rs62641291 G A . PASS RSPOS=74651;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=129
1 74681 rs13328683 G T . PASS CFL;GMAF=0.286106032906764;RSPOS=74681;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=121
1 74709 rs62641292 T A . PASS CFL;RSPOS=74709;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 74771 rs13328675 A G . PASS CFL;RSPOS=74771;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=121
1 74790 rs13328700 C G . PASS CFL;RSPOS=74790;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=121
1 74792 rs13328684 G A . PASS CFL;RSPOS=74792;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=121
1 77462 rs188023513 G A . PASS KGPilot123;RSPOS=77462;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 77470 rs192898053 T C . PASS KGPilot123;RSPOS=77470;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 77874 rs184538873 G A . PASS KGPilot123;RSPOS=77874;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 77961 rs78385339 G A . PASS GMAF=0.125685557586837;KGPilot123;RSPOS=77961;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040010000100;WGT=0;dbSNPBuildID=131
1 79033 rs62641298 A G . PASS GMAF=0.438299817184644;GNO;HD;KGPilot123;RSPOS=79033;SAO=0;SSR=0;VC=SNV;VP=050000000000000510000100;WGT=0;dbSNPBuildID=129
1 79050 rs62641299 G T . PASS GMAF=0.224405850091408;GNO;KGPilot123;RSPOS=79050;SAO=0;SSR=0;VC=SNV;VP=050000000000000110000100;WGT=0;dbSNPBuildID=129
1 79137 rs143777184 A T . PASS ASP;KGPilot123;RSPOS=79137;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 79417 rs184768190 C T . PASS KGPilot123;RSPOS=79417;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 79418 rs2691296 G C . PASS GMAF=0.0178244972577697;RSPOS=79418;RV;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000000040000000100;WGT=0;dbSNPBuildID=100
1 79538 rs2691295 C T . PASS RSPOS=79538;RV;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=100
1 79772 rs147215883 C G . PASS ASP;KGPilot123;RSPOS=79772;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 79872 rs189224661 T G . PASS KGPilot123;RSPOS=79872;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 80323 rs3942603 G C . PASS CFL;GNO;RSPOS=80323;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=108
1 80386 rs3878915 C A . PASS GMAF=0.0118829981718464;RSPOS=80386;RV;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000000040000000100;WGT=0;dbSNPBuildID=108
1 80454 rs144226842 G C . PASS ASP;KGPilot123;RSPOS=80454;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 81836 rs2259560 A T . PASS ASP;GNO;RSPOS=81836;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000100000100;WGT=0;dbSNPBuildID=100
1 81949 rs181567186 T C . PASS KGPilot123;RSPOS=81949;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 81962 rs4030308 T TAA . PASS ASP;RSPOS=81962;RV;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000004000000000200;WGT=0;dbSNPBuildID=108
1 82102 rs4030307 C T . PASS ASP;RSPOS=82102;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000000000100;WGT=0;dbSNPBuildID=108
1 82103 rs2020400 T C . PASS ASP;RSPOS=82103;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000000000100;WGT=0;dbSNPBuildID=92
1 82126 rs1815133 C T . PASS ASP;RSPOS=82126;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000000000100;WGT=0;dbSNPBuildID=92
1 82133 rs4030306 CA C,CAAAAAAAAAAAAAAA . PASS ASP;RSPOS=82136;RV;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000004000000000200;WGT=0;dbSNPBuildID=108
1 82154 rs4477212 A G . PASS ASP;HD;RSPOS=82154;SAO=0;SSR=0;VC=SNV;VP=050000000004000400000100;WGT=0;dbSNPBuildID=111
1 82162 rs1815132 C A . PASS ASP;GMAF=0.0351919561243144;GNO;RSPOS=82162;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000100000100;WGT=0;dbSNPBuildID=92
1 82163 rs139113303 G A . PASS ASP;KGPilot123;RSPOS=82163;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 82196 rs112844054 A T . PASS ASP;RSPOS=82196;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
1 82249 rs1851945 A G . PASS ASP;GMAF=0.0452468007312614;KGPilot123;RSPOS=82249;RV;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000004040010000100;WGT=0;dbSNPBuildID=92
1 82282 rs3871775 G A . PASS ASP;RSPOS=82282;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000000000100;WGT=0;dbSNPBuildID=108
1 82303 rs3871776 T C . PASS ASP;RSPOS=82303;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000000000100;WGT=0;dbSNPBuildID=108
1 82316 rs4030305 A C . PASS ASP;GNO;RSPOS=82316;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000100000100;WGT=0;dbSNPBuildID=108
1 82609 rs149189449 C G . PASS ASP;KGPilot123;RSPOS=82609;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 82676 rs185237834 T G . PASS KGPilot123;RSPOS=82676;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 82734 rs4030331 T C . PASS ASP;GMAF=0.261882998171846;KGPilot123;RSPOS=82734;RV;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000004040010000100;WGT=0;dbSNPBuildID=108
1 82957 rs189774606 C T . PASS KGPilot123;RSPOS=82957;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 83084 rs181193408 T A . PASS KGPilot123;RSPOS=83084;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 83088 rs186081601 G C . PASS KGPilot123;RSPOS=83088;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 83107 rs4405097 G C . PASS ASP;RSPOS=83107;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=111
1 83119 rs4030324 AA A,ATAAC . PASS ASP;RSPOS=83120;RV;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000004000000000200;WGT=0;dbSNPBuildID=108
1 83771 rs189906733 T G . PASS KGPilot123;RSPOS=83771;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 83786 rs58520670 T TA . PASS ASP;RSPOS=83794;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 83815 rs58857344 GAGAA G . PASS ASP;RSPOS=83827;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 83826 rs71281475 AAAGA A,AAA . PASS ASP;GNO;RSPOS=83827;RV;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000004000100000200;WGT=0;dbSNPBuildID=130
1 83855 rs59596480 GAA G . PASS ASP;RSPOS=83857;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 83872 rs59556914 AA A,AAGA . PASS ASP;RSPOS=83873;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 83884 rs59586754 GAAA G . PASS ASP;RSPOS=83885;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 83897 rs61330047 GAA G . PASS ASP;RSPOS=83899;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 83901 rs58254183 GAAAGAA G . PASS ASP;RSPOS=83903;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 83921 rs61338823 GAA G . PASS ASP;RSPOS=83923;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 83930 rs71281474 AG A,AGA . PASS ASP;GNO;RSPOS=83931;RV;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000004000100000200;WGT=0;dbSNPBuildID=130
1 83934 rs59235392 AG A,AGAAA . PASS ASP;RSPOS=83935;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 83977 rs180759811 A G . PASS KGPilot123;RSPOS=83977;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 84002 rs28850140 G A . PASS ASP;GMAF=0.138939670932358;KGPilot123;RSPOS=84002;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040010000100;WGT=0;dbSNPBuildID=125
1 84010 rs186443818 G A . PASS KGPilot123;RSPOS=84010;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 84018 rs61352176 GAA G . PASS ASP;RSPOS=84020;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
1 84079 rs190867312 T C . PASS KGPilot123;RSPOS=84079;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 84139 rs183605470 A T . PASS KGPilot123;RSPOS=84139;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 84156 rs188652299 A C . PASS KGPilot123;RSPOS=84156;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 84244 rs191297051 A C . PASS KGPilot123;RSPOS=84244;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 84295 rs183209871 G A . PASS KGPilot123;RSPOS=84295;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 84346 rs187855973 T C . PASS KGPilot123;RSPOS=84346;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 84453 rs191379015 C G . PASS KGPilot123;RSPOS=84453;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 84705 rs183470350 T G . PASS KGPilot123;RSPOS=84705;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 85063 rs187802690 T C . PASS KGPilot123;RSPOS=85063;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 85200 rs4030343 T C . PASS ASP;GMAF=0.0680987202925046;RSPOS=85200;RV;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000004040000000100;WGT=0;dbSNPBuildID=108
1 85302 rs4030342 A G . PASS ASP;RSPOS=85302;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000000000100;WGT=0;dbSNPBuildID=108
1 85420 rs4030341 T G . PASS ASP;GMAF=1;GNO;RSPOS=85420;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000100000100;WGT=0;dbSNPBuildID=108
1 85526 rs111645077 A C . PASS ASP;RSPOS=85526;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
1 85597 rs192472955 A C . PASS KGPilot123;RSPOS=85597;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 85622 rs185273034 A T . PASS KGPilot123;RSPOS=85622;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 85892 rs147185795 A G . PASS ASP;KGPilot123;RSPOS=85892;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 86000 rs140628094 A C . PASS ASP;KGPilot123;RSPOS=86000;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 86018 rs142878000 C G . PASS ASP;KGPilot123;RSPOS=86018;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 86028 rs114608975 T C . PASS ASP;G5;G5A;GMAF=0.0310786106032907;KGPilot123;RSPOS=86028;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070010000100;WGT=0;dbSNPBuildID=132
1 86064 rs190167736 G A . PASS KGPilot123;RSPOS=86064;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 86065 rs116504101 G C . PASS ASP;G5;G5A;GMAF=0.0315356489945155;KGPilot123;RSPOS=86065;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070010000100;WGT=0;dbSNPBuildID=132
1 86235 rs111577602 A C . PASS ASP;RSPOS=86235;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
1 86282 rs192830046 T G . PASS KGPilot123;RSPOS=86282;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 86303 rs2949417 G T . PASS ASP;GMAF=0.129798903107861;KGPilot123;RSPOS=86303;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040010000100;WGT=0;dbSNPBuildID=101
1 86331 rs115209712 A G . PASS ASP;G5;G5A;GMAF=0.126142595978062;KGPilot123;RSPOS=86331;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070010000100;WGT=0;dbSNPBuildID=132
1 86982 rs184970101 G A . PASS KGPilot123;RSPOS=86982;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 87021 rs188486692 T C . PASS KGPilot123;RSPOS=87021;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 87099 rs74807217 T A . PASS ASP;GNO;RSPOS=87099;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 87109 rs112601681 T C . PASS ASP;RSPOS=87109;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
1 87190 rs1524602 G A . PASS ASP;G5;G5A;GMAF=0.281078610603291;GNO;KGPilot123;RSPOS=87190;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004030110000100;WGT=0;dbSNPBuildID=88
1 87276 rs5772017 A AT . PASS CFL;PM;PMC;RSPOS=87285;SAO=0;SSR=0;VC=DIV;VP=050028000008000000000200;WGT=0;dbSNPBuildID=114
1 87303 rs113433457 G A . PASS CFL;GNO;RSPOS=87303;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=132
1 87360 rs180907504 C T . PASS KGPilot123;RSPOS=87360;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 87409 rs139490478 C T . PASS ASP;KGPilot123;RSPOS=87409;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 87590 rs185279164 G A . PASS KGPilot123;RSPOS=87590;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 87647 rs146836579 T C . PASS ASP;KGPilot123;RSPOS=87647;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 87683 rs113097605 T C . PASS CFL;GNO;RSPOS=87683;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=132
1 87702 rs111305205 G A . PASS CFL;GNO;RSPOS=87702;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=132
1 87755 rs140735660 G A . PASS ASP;KGPilot123;RSPOS=87755;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 87826 rs3855952 A G . PASS CFL;GNO;PH2;RSPOS=87826;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000102000100;WGT=0;dbSNPBuildID=108
1 87970 rs189643077 T C . PASS KGPilot123;RSPOS=87970;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 87978 rs182297743 G A . PASS KGPilot123;RSPOS=87978;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 88136 rs59529791 G A . PASS CFL;KGPilot123;RSPOS=88136;SAO=0;SSR=0;VC=SNV;VP=050000000008000010000100;WGT=0;dbSNPBuildID=129
1 88169 rs940550 C T . PASS CFL;G5;GMAF=0.25091407678245;GNO;KGPilot123;PH2;RSPOS=88169;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000008050112000100;WGT=0;dbSNPBuildID=86
1 88172 rs940551 G A . PASS CFL;G5;G5A;GMAF=0.030164533820841;KGPilot123;RSPOS=88172;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000008070010000100;WGT=0;dbSNPBuildID=86
1 88177 rs143215837 G C . PASS ASP;KGPilot123;RSPOS=88177;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 88188 rs148331237 C A . PASS ASP;KGPilot123;RSPOS=88188;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 88216 rs2103136 A G . PASS CFL;GNO;HD;RSPOS=88216;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000500000100;WGT=0;dbSNPBuildID=96
1 88236 rs186918018 C T . PASS KGPilot123;RSPOS=88236;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 88250 rs191950833 T A . PASS KGPilot123;RSPOS=88250;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 88265 rs940552 C T . PASS CFL;G5;GNO;RSPOS=88265;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008010100000100;WGT=0;dbSNPBuildID=86
1 88295 rs113378454 T A . PASS CFL;GNO;RSPOS=88295;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=132
1 88316 rs113759966 G A . PASS CFL;GMAF=0.033363802559415;GNO;KGPilot123;RSPOS=88316;SAO=0;SSR=0;VC=SNV;VP=050000000008000110000100;WGT=0;dbSNPBuildID=132
1 88324 rs183326616 A G . PASS KGPilot123;RSPOS=88324;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 88332 rs113199939 A C . PASS CFL;GNO;RSPOS=88332;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=132
1 88338 rs55700207 G A . PASS CFL;G5;GMAF=0.0836380255941499;GNO;KGPilot123;RSPOS=88338;SAO=0;SSR=0;VC=SNV;VP=050000000008010110000100;WGT=0;dbSNPBuildID=129
1 88370 rs185487977 G A . PASS KGPilot123;RSPOS=88370;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 88376 rs189954431 T G . PASS KGPilot123;RSPOS=88376;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 88388 rs182344336 C T . PASS KGPilot123;RSPOS=88388;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 88429 rs146027550 T C . PASS ASP;KGPilot123;RSPOS=88429;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 88710 rs186575039 C G . PASS KGPilot123;RSPOS=88710;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 89165 rs192631277 A C . PASS KGPilot123;RSPOS=89165;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 89744 rs184101761 A G . PASS KGPilot123;RSPOS=89744;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 89794 rs188661839 T C . PASS KGPilot123;RSPOS=89794;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 89946 rs138808727 A T . PASS ASP;KGPilot123;RSPOS=89946;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 90199 rs78751575 A T . PASS CFL;GMAF=0.0447897623400366;GNO;RSPOS=90199;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040100000100;WGT=0;dbSNPBuildID=131
1 90238 rs74728256 A C . PASS CFL;GNO;RSPOS=90238;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040100000100;WGT=0;dbSNPBuildID=131
1 90311 rs76894051 T C . PASS CFL;GNO;RSPOS=90311;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 91190 rs143856811 G A . PASS ASP;KGPilot123;RSPOS=91190;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 91228 rs139873689 A G . PASS ASP;KGPilot123;RSPOS=91228;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 91336 rs4245763 A T . PASS CFL;GNO;RSPOS=91336;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=111
1 91354 rs4245764 G A . PASS CFL;GMAF=0.00959780621572212;GNO;RSPOS=91354;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=111
1 91421 rs28619159 T C . PASS CFL;GMAF=0.0557586837294333;GNO;RSPOS=91421;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=125
1 91472 rs6680825 C T . PASS CFL;GMAF=0.00959780621572212;RSPOS=91472;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=116
1 91486 rs28555135 G C . PASS CFL;RSPOS=91486;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=125
1 91490 rs28662916 A G . PASS CFL;RSPOS=91490;SAO=0;SSR=1;VC=SNV;VP=050000000008000000000140;WGT=0;dbSNPBuildID=125
1 91536 rs77418980 G T . PASS CFL;G5;G5A;GMAF=0.338665447897623;HD;KGPilot123;RSPOS=91536;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008070410000100;WGT=0;dbSNPBuildID=131
1 91551 rs61483841 G GT . PASS CFL;RSPOS=91560;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 91581 rs151118460 G A . PASS ASP;KGPilot123;RSPOS=91581;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 91605 rs141083882 C T . PASS ASP;KGPilot123;RSPOS=91605;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 92593 rs75476593 C G . PASS CFL;GNO;RSPOS=92593;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 92633 rs149776517 C T . PASS ASP;KGPilot123;RSPOS=92633;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 92794 rs4628451 A G . PASS CFL;GMAF=0.0521023765996344;RSPOS=92794;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=111
1 92858 rs147061536 G T . PASS ASP;KGPilot123;RSPOS=92858;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 92875 rs193157612 T C . PASS KGPilot123;RSPOS=92875;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 94893 rs76199007 A G . PASS CFL;GNO;RSPOS=94893;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040100000100;WGT=0;dbSNPBuildID=131
1 94930 rs78828224 C T . PASS GNO;RSPOS=94930;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040100000100;WGT=0;dbSNPBuildID=131
1 94932 rs80302002 T C . PASS GNO;RSPOS=94932;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040100000100;WGT=0;dbSNPBuildID=131
1 94986 rs185004859 C T . PASS KGPilot123;RSPOS=94986;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 94990 rs76864342 T C . PASS GNO;RSPOS=94990;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040100000100;WGT=0;dbSNPBuildID=131
1 94991 rs188832636 G A . PASS KGPilot123;RSPOS=94991;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 95006 rs76774169 A T . PASS CFL;GNO;RSPOS=95006;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040100000100;WGT=0;dbSNPBuildID=131
1 95083 rs77653505 G A . PASS CFL;GMAF=0.00319926873857404;GNO;RSPOS=95083;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040100000100;WGT=0;dbSNPBuildID=131
1 98583 rs141344361 T A . PASS ASP;KGPilot123;RSPOS=98583;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 98919 rs1851938 T A . PASS CFL;RSPOS=98919;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000000000100;WGT=0;dbSNPBuildID=92
1 98926 rs79874388 G A . PASS GNO;RSPOS=98926;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040100000100;WGT=0;dbSNPBuildID=131
1 98929 rs12184306 A G . PASS CFL;GMAF=0.141224862888483;KGPilot123;RSPOS=98929;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040010000100;WGT=0;dbSNPBuildID=120
1 98945 rs75356303 C T . PASS CFL;GMAF=0.0521023765996344;GNO;RSPOS=98945;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 98946 rs191775802 C G . PASS KGPilot123;RSPOS=98946;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 98974 rs12184307 A G . PASS CFL;KGPilot123;RSPOS=98974;SAO=0;SSR=0;VC=SNV;VP=050000000008000010000100;WGT=0;dbSNPBuildID=120
1 98993 rs1851939 G A . PASS CFL;GMAF=0.0242230347349177;GNO;RSPOS=98993;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000008040100000100;WGT=0;dbSNPBuildID=92
1 99043 rs12184295 T A . PASS CFL;RSPOS=99043;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=120
1 99141 rs78611732 G C . PASS CFL;GNO;RSPOS=99141;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 99166 rs78627600 C T . PASS CFL;GNO;RSPOS=99166;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 99229 rs4109798 C A . PASS CFL;RSPOS=99229;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000000000100;WGT=0;dbSNPBuildID=108
1 99671 rs146209971 A T . PASS ASP;KGPilot123;RSPOS=99671;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 99687 rs139153227 C T . PASS ASP;KGPilot123;RSPOS=99687;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 99719 rs183898652 C T . PASS KGPilot123;RSPOS=99719;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 100676 rs188226172 A T . PASS KGPilot123;RSPOS=100676;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 101111 rs78180088 G T . PASS CFL;GMAF=0.0639853747714808;GNO;RSPOS=101111;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 101550 rs151255177 C T . PASS ASP;RSPOS=101550;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 103856 rs77787752 A C . PASS GMAF=0.000914076782449726;GNO;RSPOS=103856;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
1 103861 rs62642110 T C . PASS RSPOS=103861;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=129
1 103867 rs62642111 G A . PASS RSPOS=103867;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=129
1 103905 rs142403309 A G . PASS ASP;KGPilot123;RSPOS=103905;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 104033 rs4287120 T C . PASS GNO;RSPOS=104033;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=111
1 106544 rs180741296 C G . PASS KGPilot123;RSPOS=106544;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 107352 rs55952670 T C . PASS HD;RSPOS=107352;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000000400000100;WGT=0;dbSNPBuildID=129
1 108293 rs80353694 C T . PASS CFL;HD;RSPOS=108293;RV;SAO=0;SSR=0;VC=SNV;VP=050000000008000400000100;WGT=0;dbSNPBuildID=131
1 108310 rs74747225 T C . PASS CFL;GNO;RSPOS=108310;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 108365 rs79073610 A G . PASS CFL;GNO;RSPOS=108365;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 114699 rs187571096 A G . PASS KGPilot123;RSPOS=114699;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 115746 rs147538909 C T . PASS ASP;KGPilot123;RSPOS=115746;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 116549 rs190211768 C T . PASS KGPilot123;RSPOS=116549;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 120458 rs182017058 T C . PASS KGPilot123;RSPOS=120458;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 120705 rs4117992 T C . PASS CFL;GMAF=0.178244972577697;KGPilot123;RSPOS=120705;RV;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000008040010000100;WGT=0;dbSNPBuildID=108
1 120717 rs190208468 G A . PASS KGPilot123;RSPOS=120717;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 120833 rs57420544 C T . PASS CFL;RSPOS=120833;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 120983 rs182468771 C T . PASS KGPilot123;RSPOS=120983;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 120986 rs60176197 T TTA . PASS CFL;RSPOS=120994;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 120995 rs71218814 A ATAT . PASS CFL;GNO;RSPOS=120995;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000008000100000200;WGT=0;dbSNPBuildID=130
1 120995 rs60628823 A ATAT . PASS CFL;RSPOS=120998;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 121009 rs1851943 C T . PASS CFL;GMAF=0.475319926873857;KGPilot123;RSPOS=121009;RV;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000008040010000100;WGT=0;dbSNPBuildID=92
1 121017 rs61430945 A ATATC . PASS CFL;RSPOS=121020;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 121025 rs58419146 T C . PASS CFL;RSPOS=121025;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 121028 rs57409576 C A . PASS CFL;RSPOS=121028;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 121034 rs60444794 C T . PASS CFL;RSPOS=121034;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 121039 rs61570867 A C . PASS CFL;RSPOS=121039;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 121042 rs1856862 T A . PASS CFL;GNO;RSPOS=121042;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=92
1 121046 rs60712173 A ATAATAT . PASS CFL;RSPOS=121048;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 121050 rs57285429 G GATC . PASS CFL;RSPOS=121050;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 121062 rs59472517 T TAACA . PASS CFL;RSPOS=121062;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 121064 rs58377840 A ATTG . PASS CFL;RSPOS=121065;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 121069 rs60402600 T TC . PASS CFL;RSPOS=121069;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 121072 rs60992425 T TTAC . PASS CFL;RSPOS=121072;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 121077 rs58683621 G A . PASS CFL;RSPOS=121077;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 121082 rs61557411 A ATATCT . PASS CFL;RSPOS=121085;SAO=0;SSR=0;VC=DIV;VP=050000000008000000000200;WGT=0;dbSNPBuildID=129
1 121105 rs56889809 T C . PASS CFL;RSPOS=121105;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 121191 rs71220897 C A . PASS CFL;GMAF=0.0886654478976234;GNO;RSPOS=121191;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=130
1 121258 rs58797648 C T . PASS CFL;RSPOS=121258;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 121267 rs58782460 T C . PASS CFL;RSPOS=121267;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 126108 rs146756510 G A . PASS ASP;KGPilot123;RSPOS=126108;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 126113 rs79114531 C A . PASS CFL;GMAF=0.0603290676416819;GNO;KGPilot123;RSPOS=126113;SAO=0;SSR=0;VC=SNV;VP=050000000008000110000100;WGT=0;dbSNPBuildID=131
1 128658 rs185320873 G A . PASS KGPilot123;RSPOS=128658;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 133013 rs149496965 C T . PASS ASP;KGPilot123;RSPOS=133013;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 135032 rs148209574 G A . PASS ASP;KGPilot123;RSPOS=135032;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 135040 rs141523926 T C . PASS ASP;KGPilot123;RSPOS=135040;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 135203 rs147502335 G A . PASS ASP;KGPilot123;RSPOS=135203;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 136596 rs139210500 G C . PASS ASP;RSPOS=136596;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 137801 rs191107331 G A . PASS KGPilot123;RSPOS=137801;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 137825 rs147252685 G A . PASS ASP;KGPilot123;RSPOS=137825;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 139479 rs182357477 C T . PASS KGPilot123;RSPOS=139479;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 139841 rs62642133 T G . PASS CFL;GENEINFO=LOC729737:729737;GMAF=0.0319926873857404;RSPOS=139841;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=129
1 143736 rs72482377 C T . PASS ASP;RSPOS=143736;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=130
1 144044 rs141844601 G T . PASS ASP;RSPOS=144044;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 144827 rs75191913 C T . PASS CFL;GNO;RSPOS=144827;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 150056 rs4081358 G A . PASS CFL;GMAF=0.00228519195612431;RSPOS=150056;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000008040000000100;WGT=0;dbSNPBuildID=108
1 150059 rs4081359 G A . PASS CFL;GMAF=0.00411334552102377;RSPOS=150059;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000008040000000100;WGT=0;dbSNPBuildID=108
1 161483 rs189086610 C G . PASS KGPilot123;RSPOS=161483;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 161488 rs193081027 C T . PASS KGPilot123;RSPOS=161488;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 162463 rs143399298 T C . PASS ASP;KGPilot123;RSPOS=162463;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 168373 rs183198872 C T . PASS KGPilot123;RSPOS=168373;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 168964 rs187450123 A G . PASS KGPilot123;RSPOS=168964;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 171529 rs191891026 A G . PASS KGPilot123;RSPOS=171529;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 171841 rs184235219 A G . PASS KGPilot123;RSPOS=171841;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 172595 rs187071114 G A . PASS KGPilot123;RSPOS=172595;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 173103 rs77708150 C T . PASS CFL;HD;RSPOS=173103;RV;SAO=0;SSR=0;VC=SNV;VP=050000000008000400000100;WGT=0;dbSNPBuildID=131
1 173709 rs192722547 A C . PASS KGPilot123;RSPOS=173709;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 176230 rs72489570 A G . PASS CFL;GNO;RSPOS=176230;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=130
1 227622 rs184145725 C T . PASS KGPilot123;RSPOS=227622;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 227844 rs149969738 G A . PASS ASP;RSPOS=227844;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 227919 rs145680509 A T . PASS ASP;RSPOS=227919;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 229868 rs111293595 C T . PASS CFL;RSPOS=229868;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=132
1 229902 rs62642953 G T . PASS ASP;RSPOS=229902;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 230058 rs62635260 T G . PASS GNO;RSPOS=230058;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040100000100;WGT=0;dbSNPBuildID=129
1 230433 rs190807317 T C . PASS KGPilot123;RSPOS=230433;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 230804 rs111808888 C T . PASS GMAF=0.43418647166362;RSPOS=230804;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040000000100;WGT=0;dbSNPBuildID=132
1 231455 rs140386775 T A . PASS ASP;RSPOS=231455;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 232214 rs11490937 G A . PASS GNO;PH2;RSPOS=232214;SAO=0;SSR=0;VC=SNV;VP=050000000000000102000100;WGT=0;dbSNPBuildID=120
1 232449 rs144169752 G A . PASS ASP;RSPOS=232449;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 232930 rs146484642 C G . PASS ASP;RSPOS=232930;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 233473 rs115354837 C G . PASS ASP;G5;GMAF=0.176873857404022;KGPilot123;RSPOS=233473;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004050010000100;WGT=0;dbSNPBuildID=132
1 233476 rs141415251 G A . PASS ASP;KGPilot123;RSPOS=233476;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 234313 rs56055731 C T . PASS GMAF=0.151736745886654;HD;RSPOS=234313;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000000040400000100;WGT=0;dbSNPBuildID=129
1 234408 rs111659307 A G . PASS GMAF=0.0036563071297989;RSPOS=234408;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040000000100;WGT=0;dbSNPBuildID=132
1 234432 rs8179455 A G . PASS GNO;KGPilot123;RSPOS=234432;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000000110000100;WGT=0;dbSNPBuildID=117
1 234446 rs67749660 C T . PASS GNO;RSPOS=234446;RV;SAO=0;SLO;SSR=1;VC=SNV;VLD;VP=050100000000040100000140;WGT=0;dbSNPBuildID=130
1 234481 rs8179403 T A . PASS GMAF=0.491316270566728;GNO;RSPOS=234481;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000000040100000100;WGT=0;dbSNPBuildID=117
1 234534 rs111281142 A G . PASS GMAF=0.00457038391224863;RSPOS=234534;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040000000100;WGT=0;dbSNPBuildID=132
1 234556 rs113278145 C T . PASS GMAF=0.0653564899451554;RSPOS=234556;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040000000100;WGT=0;dbSNPBuildID=132
1 235844 rs138426292 C G . PASS ASP;RSPOS=235844;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 237490 rs184796003 C A . PASS RSPOS=237490;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 237684 rs113488767 G A . PASS CFL;RSPOS=237684;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=132
1 237763 rs112186068 G A . PASS CFL;GMAF=0.231718464351005;RSPOS=237763;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=132
1 237877 rs181999503 C T . PASS KGPilot123;RSPOS=237877;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 237881 rs114112614 G T . PASS ASP;GMAF=0.117915904936015;RSPOS=237881;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=134
1 239339 rs184451216 A G . PASS KGPilot123;RSPOS=239339;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 240435 rs143434963 C G . PASS ASP;RSPOS=240435;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 240789 rs147589465 T G . PASS ASP;KGPilot123;RSPOS=240789;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 240898 rs147990930 T G . PASS ASP;RSPOS=240898;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 241027 rs112327644 G A . PASS GMAF=0.163619744058501;RSPOS=241027;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040000000100;WGT=0;dbSNPBuildID=132
1 241159 rs71222010 T TTTC . PASS GNO;RSPOS=241159;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000000000100000200;WGT=0;dbSNPBuildID=130
1 241194 rs71222829 G T . PASS GMAF=0.00594149908592322;GNO;RSPOS=241194;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000000040100000100;WGT=0;dbSNPBuildID=130
1 241263 rs7415228 C T . PASS RSPOS=241263;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=116
1 241265 rs71222830 C T . PASS GNO;RSPOS=241265;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000000040100000100;WGT=0;dbSNPBuildID=130
1 241319 rs71222011 CACCCGGC CGCCCAGA . PASS GNO;RSPOS=241320;SAO=0;SLO;SSR=0;VC=MNV;VP=050100000000000100000800;WGT=0;dbSNPBuildID=130
1 241320 rs79974410 A G . PASS CFL;GNO;KGPilot123;RSPOS=241320;SAO=0;SSR=0;VC=SNV;VP=050000000008000110000100;WGT=0;dbSNPBuildID=131
1 241369 rs11490246 C T . PASS GMAF=0.0278793418647166;GNO;RSPOS=241369;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=120
1 243782 rs181434479 C A . PASS KGPilot123;RSPOS=243782;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 243850 rs140116466 CAAGT C . PASS ASP;KGPilot123;RSPOS=243851;SAO=0;SSR=0;VC=DIV;VP=050000000004000010000200;WGT=0;dbSNPBuildID=134
1 245024 rs192405071 C A . PASS RSPOS=245024;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 246060 rs185479292 G A . PASS KGPilot123;RSPOS=246060;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 249276 rs115018998 T C . PASS ASP;GMAF=0.00502742230347349;KGPilot123;RSPOS=249276;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040010000100;WGT=0;dbSNPBuildID=132
1 251627 rs72502741 AC A . PASS RSPOS=251628;SAO=0;SSR=0;VC=DIV;VP=050000000000000000000200;WGT=0;dbSNPBuildID=130
1 251627 rs149773139 AC A . PASS ASP;RSPOS=251628;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 252144 rs191013370 T C . PASS KGPilot123;RSPOS=252144;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 254186 rs148663102 T C . PASS ASP;KGPilot123;RSPOS=254186;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 254926 rs71236370 C T . PASS CFL;GNO;RSPOS=254926;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=130
1 255900 rs76982582 T C . PASS CFL;GNO;RSPOS=255900;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040100000100;WGT=0;dbSNPBuildID=131
1 255901 rs76003013 G A . PASS CFL;GNO;RSPOS=255901;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040100000100;WGT=0;dbSNPBuildID=131
1 256022 rs181053586 A G . PASS KGPilot123;RSPOS=256022;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 256586 rs140435168 T G . PASS ASP;KGPilot123;RSPOS=256586;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 258589 rs185940535 C A . PASS KGPilot123;RSPOS=258589;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 259207 rs143738566 A C . PASS ASP;KGPilot123;RSPOS=259207;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 261542 rs192416692 T C . PASS KGPilot123;RSPOS=261542;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 326957 rs138542627 C T . PASS ASP;RSPOS=326957;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 348458 rs80050187 T G . PASS CFL;GNO;RSPOS=348458;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 355280 rs2527589 G A . PASS CFL;GMAF=0.147623400365631;RSPOS=355280;RV;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=100
1 355528 rs77832493 T G . PASS CFL;GNO;RSPOS=355528;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 355531 rs78394685 C G . PASS CFL;GNO;RSPOS=355531;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 355532 rs75706905 C T . PASS CFL;GNO;RSPOS=355532;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 356537 rs183318141 G A . PASS KGPilot123;RSPOS=356537;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 358440 rs187762289 T A . PASS KGPilot123;RSPOS=358440;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 362895 rs190726048 A G . PASS KGPilot123;RSPOS=362895;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 362905 rs182870673 T G . PASS KGPilot123;RSPOS=362905;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 362907 rs138802168 G C . PASS ASP;KGPilot123;RSPOS=362907;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 383643 rs7418215 A C . PASS ASP;RSPOS=383643;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 384525 rs75295791 C T . PASS ASP;GNO;RSPOS=384525;RV;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 384597 rs4116902 T C . PASS ASP;RSPOS=384597;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000000000100;WGT=0;dbSNPBuildID=108
1 384621 rs1913420 T C . PASS ASP;RSPOS=384621;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000000000100;WGT=0;dbSNPBuildID=92
1 384627 rs62639158 C G . PASS ASP;RSPOS=384627;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 384655 rs62639153 C T . PASS ASP;RSPOS=384655;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 384665 rs62392173 T C . PASS ASP;RSPOS=384665;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 384686 rs62639154 T C . PASS ASP;RSPOS=384686;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 384713 rs62639157 C T . PASS ASP;RSPOS=384713;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 384819 rs62428671 T C . PASS ASP;RSPOS=384819;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 384833 rs62392174 C T . PASS ASP;RSPOS=384833;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 384896 rs62392175 T C . PASS ASP;RSPOS=384896;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 384951 rs62392176 G A . PASS ASP;RSPOS=384951;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 384973 rs62639155 T C . PASS ASP;RSPOS=384973;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 385051 rs62639156 G C . PASS ASP;RSPOS=385051;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 385053 rs113653250 A C . PASS ASP;GMAF=0.0671846435100548;RSPOS=385053;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=132
1 386315 rs138343296 T C . PASS ASP;RSPOS=386315;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 401320 rs75345457 C A . PASS ASP;GNO;RSPOS=401320;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 414172 rs143956329 A G . PASS ASP;RSPOS=414172;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 416202 rs150426163 G T . PASS ASP;KGPilot123;RSPOS=416202;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 437533 rs141313203 T C . PASS ASP;RSPOS=437533;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 437654 rs145099697 T C . PASS ASP;RSPOS=437654;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 437671 rs138983045 A G . PASS ASP;RSPOS=437671;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 437827 rs141572790 T A . PASS ASP;RSPOS=437827;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 437952 rs150904834 T C . PASS ASP;RSPOS=437952;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 449566 rs62639626 T C . PASS ASP;RSPOS=449566;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 450115 rs75542457 C T . PASS ASP;GNO;RSPOS=450115;RV;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040100000100;WGT=0;dbSNPBuildID=131
1 450209 rs79326384 T C . PASS ASP;GNO;RSPOS=450209;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 450425 rs78409573 G A . PASS ASP;GNO;RSPOS=450425;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 521973 rs3088262 A G . PASS CFL;GMAF=0.0146252285191956;RSPOS=521973;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000008040000000100;WGT=0;dbSNPBuildID=102
1 522476 rs188307237 A T . PASS KGPilot123;RSPOS=522476;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 523471 rs192687139 T C . PASS KGPilot123;RSPOS=523471;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 525698 rs2808353 A G . PASS GMAF=0.00137111517367459;GNO;KGPilot123;RSPOS=525698;RV;SAO=0;SSR=0;VC=SNV;VP=050000000000000110000100;WGT=0;dbSNPBuildID=100
1 526057 rs141459107 T C . PASS ASP;KGPilot123;RSPOS=526057;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 526692 rs143629215 C T . PASS ASP;KGPilot123;RSPOS=526692;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 526722 rs28782493 T C . PASS ASP;RSPOS=526722;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=125
1 526733 rs28760963 C T . PASS ASP;RSPOS=526733;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=125
1 526735 rs187540194 C T . PASS KGPilot123;RSPOS=526735;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 526736 rs28863004 C G . PASS ASP;GNO;HD;RSPOS=526736;SAO=0;SSR=0;VC=SNV;VP=050000000004000500000100;WGT=0;dbSNPBuildID=125
1 526771 rs140972083 G C . PASS ASP;KGPilot123;RSPOS=526771;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 526793 rs111822079 A G . PASS ASP;GMAF=0.0356489945155393;GNO;RSPOS=526793;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000100000100;WGT=0;dbSNPBuildID=132
1 526832 rs192574259 G C . PASS KGPilot123;RSPOS=526832;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 526840 rs60396226 T C . PASS ASP;GMAF=0.119744058500914;GNO;KGPilot123;RSPOS=526840;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000110000100;WGT=0;dbSNPBuildID=129
1 526843 rs12354290 G A . PASS ASP;GMAF=0.0173674588665448;RSPOS=526843;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=120
1 526970 rs60791385 T C . PASS ASP;GMAF=0.0813528336380256;KGPilot123;RSPOS=526970;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040010000100;WGT=0;dbSNPBuildID=129
1 527006 rs58575848 T C . PASS ASP;RSPOS=527006;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 527031 rs61539349 G A . PASS ASP;RSPOS=527031;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 527038 rs189135631 C T . PASS KGPilot123;RSPOS=527038;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 527069 rs55684445 C G . PASS ASP;RSPOS=527069;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 527090 rs60833825 A G . PASS ASP;RSPOS=527090;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 527108 rs61209377 T C . PASS ASP;GMAF=0.020109689213894;RSPOS=527108;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=129
1 527143 rs76728905 A C . PASS ASP;GNO;RSPOS=527143;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 527157 rs143773298 A G . PASS ASP;KGPilot123;RSPOS=527157;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 527186 rs111227194 A G . PASS ASP;GMAF=0.0356489945155393;GNO;KGPilot123;RSPOS=527186;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000110000100;WGT=0;dbSNPBuildID=132
1 527207 rs112901516 A G . PASS ASP;GMAF=0.0374771480804388;GNO;KGPilot123;RSPOS=527207;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000110000100;WGT=0;dbSNPBuildID=132
1 527219 rs181574093 G A . PASS KGPilot123;RSPOS=527219;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 529782 rs144425991 C T . PASS ASP;KGPilot123;RSPOS=529782;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 532051 rs184296032 A C . PASS KGPilot123;RSPOS=532051;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 532080 rs150672670 T C . PASS ASP;RSPOS=532080;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 532402 rs184573826 T C . PASS RSPOS=532402;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 532413 rs190029356 G A . PASS KGPilot123;RSPOS=532413;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 532447 rs181202492 A G . PASS KGPilot123;RSPOS=532447;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 533162 rs112369404 C T . PASS ASP;GMAF=0.0036563071297989;GNO;KGPilot123;RSPOS=533162;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000110000100;WGT=0;dbSNPBuildID=132
1 533163 rs186223690 G A . PASS KGPilot123;RSPOS=533163;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 533170 rs114617477 G T . PASS ASP;G5;G5A;GMAF=0.0758683729433272;KGPilot123;RSPOS=533170;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070010000100;WGT=0;dbSNPBuildID=132
1 533179 rs111501994 A G . PASS ASP;GMAF=0.0219378427787934;GNO;KGPilot123;RSPOS=533179;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000110000100;WGT=0;dbSNPBuildID=132
1 533187 rs190848289 C T . PASS KGPilot123;RSPOS=533187;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 533198 rs78497331 C T . PASS ASP;GMAF=0.112888482632541;KGPilot123;RSPOS=533198;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040010000100;WGT=0;dbSNPBuildID=131
1 533211 rs113525763 A G . PASS ASP;RSPOS=533211;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
1 533236 rs112576181 A G . PASS ASP;RSPOS=533236;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
1 533253 rs78702838 A G . PASS ASP;GNO;RSPOS=533253;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 533291 rs75693233 G A . PASS ASP;GNO;RSPOS=533291;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040100000100;WGT=0;dbSNPBuildID=131
1 533988 rs7367602 A G . PASS ASP;RSPOS=533988;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 533996 rs7367603 A G . PASS ASP;RSPOS=533996;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 534082 rs7367611 A G . PASS ASP;GNO;RSPOS=534082;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=116
1 534090 rs9438469 G A . PASS ASP;RSPOS=534090;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=119
1 534169 rs59089120 G A . PASS ASP;RSPOS=534169;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 534192 rs6680723 C T . PASS ASP;GMAF=0.236288848263254;GNO;HD;KGPilot123;RSPOS=534192;SAO=0;SSR=0;VC=SNV;VP=050000000004000510000100;WGT=0;dbSNPBuildID=116
1 534198 rs6680725 C T . PASS ASP;GMAF=0.11745886654479;KGPilot123;RSPOS=534198;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040010000100;WGT=0;dbSNPBuildID=116
1 534220 rs6702333 G A . PASS ASP;KGPilot123;RSPOS=534220;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=116
1 534234 rs6680731 C T . PASS ASP;RSPOS=534234;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 534259 rs6702342 G T . PASS ASP;GMAF=0.043418647166362;RSPOS=534259;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=116
1 534265 rs56781381 G C . PASS ASP;GMAF=0.0114259597806216;RSPOS=534265;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=129
1 534295 rs58567539 C T . PASS ASP;GMAF=0.00776965265082267;RSPOS=534295;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=129
1 534297 rs190879900 T C . PASS KGPilot123;RSPOS=534297;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 534315 rs74490954 G A . PASS ASP;RSPOS=534315;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=131
1 534317 rs3122004 G A . PASS ASP;RSPOS=534317;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=103
1 534323 rs61590446 G A . PASS ASP;RSPOS=534323;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 534447 rs111957886 CTGTT C . PASS ASP;GNO;RSPOS=534448;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000004000100000200;WGT=0;dbSNPBuildID=132
1 534540 rs183186584 G T . PASS KGPilot123;RSPOS=534540;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 534542 rs61767346 A G . PASS ASP;RSPOS=534542;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
1 534545 rs145971835 G A . PASS ASP;KGPilot123;RSPOS=534545;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 534546 rs6690870 T C . PASS ASP;RSPOS=534546;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 534547 rs188376087 G A . PASS KGPilot123;RSPOS=534547;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 534581 rs80197286 G C . PASS ASP;GNO;RSPOS=534581;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 534583 rs6683466 C G . PASS ASP;GNO;HD;PH2;RSPOS=534583;SAO=0;SSR=0;VC=SNV;VP=050000000004000502000100;WGT=0;dbSNPBuildID=116
1 534607 rs113273694 T A . PASS ASP;GNO;RSPOS=534607;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000100000100;WGT=0;dbSNPBuildID=132
1 534649 rs60383769 C T . PASS ASP;GMAF=0.0105118829981718;RSPOS=534649;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=129
1 535696 rs151048542 G A . PASS ASP;KGPilot123;RSPOS=535696;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 535879 rs6687203 C T . PASS ASP;RSPOS=535879;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 535916 rs139752812 A G . PASS ASP;RSPOS=535916;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 535932 rs6700508 A G . PASS ASP;RSPOS=535932;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 535937 rs6694734 T C . PASS ASP;RSPOS=535937;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 535952 rs6694742 T C . PASS ASP;GMAF=0.0415904936014625;RSPOS=535952;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=116
1 535958 rs6687227 C T . PASS ASP;GMAF=0.0114259597806216;RSPOS=535958;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=116
1 535986 rs6687297 C T . PASS ASP;GMAF=0.0118829981718464;RSPOS=535986;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=116
1 535989 rs6660439 G T . PASS ASP;RSPOS=535989;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 536021 rs6594020 T A . PASS ASP;RSPOS=536021;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 536095 rs189259765 C T . PASS RSPOS=536095;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 536134 rs2808303 C A,T . PASS ASP;RSPOS=536134;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=100
1 536153 rs6660590 G A . PASS ASP;RSPOS=536153;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 536170 rs113835516 T C . PASS ASP;RSPOS=536170;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
1 536202 rs149807327 T C . PASS ASP;RSPOS=536202;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 536205 rs6594021 A G . PASS ASP;RSPOS=536205;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=116
1 536210 rs111483111 T C . PASS ASP;RSPOS=536210;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
1 536213 rs2491326 A C . PASS ASP;GNO;RSPOS=536213;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=100
1 536480 rs79150575 T A . PASS ASP;RSPOS=536480;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=131
1 537487 rs144672821 C T . PASS ASP;RSPOS=537487;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 537630 rs192612652 C T . PASS RSPOS=537630;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 537646 rs113396932 C T . PASS ASP;RSPOS=537646;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
1 537658 rs12184344 T C . PASS ASP;RSPOS=537658;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=120
1 537680 rs12184252 G T . PASS ASP;GMAF=0.349177330895795;GNO;RSPOS=537680;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000100000100;WGT=0;dbSNPBuildID=120
1 537681 rs12184273 C T . PASS ASP;RSPOS=537681;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=120
1 537709 rs12184274 C G . PASS ASP;RSPOS=537709;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=120
1 539740 rs75816844 T C . PASS GNO;RSPOS=539740;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
1 540894 rs184327576 A G . PASS RSPOS=540894;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 540975 rs80246094 G A . PASS ASP;G5;G5A;GMAF=0.090036563071298;KGPilot123;RSPOS=540975;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070010000100;WGT=0;dbSNPBuildID=131
1 544778 rs2792865 G A . PASS CFL;GMAF=0.00137111517367459;RSPOS=544778;RV;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=100
1 544787 rs139562592 G C . PASS ASP;RSPOS=544787;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 544815 rs3121180 G A . PASS RSPOS=544815;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=103
1 544872 rs76880380 A T . PASS GNO;RSPOS=544872;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040100000100;WGT=0;dbSNPBuildID=131
1 544888 rs78306699 C T . PASS GNO;RSPOS=544888;RV;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
1 545088 rs61769280 C T . PASS CFL;RSPOS=545088;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 545249 rs80060025 C T . PASS CFL;GNO;RSPOS=545249;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 545412 rs79440074 T A . PASS CFL;GNO;RSPOS=545412;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 545816 rs75786306 T A . PASS CFL;GNO;RSPOS=545816;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 546088 rs2792863 T A . PASS CFL;RSPOS=546088;RV;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=100
1 546108 rs74566339 C T . PASS CFL;GNO;RSPOS=546108;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 546140 rs75192658 A C . PASS CFL;GNO;RSPOS=546140;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 546697 rs12025928 A G . PASS CFL;GMAF=0.059872029250457;GNO;PH2;RSPOS=546697;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000102000100;WGT=0;dbSNPBuildID=120
1 546709 rs111411573 G A . PASS CFL;GNO;RSPOS=546709;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=132
1 546732 rs77628483 C T . PASS CFL;RSPOS=546732;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=131
1 546739 rs112572037 T C . PASS CFL;GNO;RSPOS=546739;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=132
1 546758 rs181126194 T C . PASS RSPOS=546758;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 546778 rs61769281 C G . PASS CFL;RSPOS=546778;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 546800 rs61769282 T C . PASS CFL;RSPOS=546800;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 546802 rs113633859 G C . PASS CFL;GNO;RSPOS=546802;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000100000100;WGT=0;dbSNPBuildID=132
1 546803 rs111914532 GGT G . PASS CFL;GNO;RSPOS=546804;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000008000100000200;WGT=0;dbSNPBuildID=132
1 546805 rs61769283 T C . PASS CFL;RSPOS=546805;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 546823 rs61769284 G A . PASS CFL;RSPOS=546823;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=129
1 546882 rs9438485 T C . PASS CFL;RSPOS=546882;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=119
1 546897 rs142153100 G T . PASS ASP;RSPOS=546897;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 546925 rs9438486 G A . PASS CFL;GMAF=0.307129798903108;RSPOS=546925;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=119
1 546952 rs9438487 T C . PASS CFL;GMAF=0.361060329067642;RSPOS=546952;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040000000100;WGT=0;dbSNPBuildID=119
1 546964 rs137862440 C T . PASS ASP;RSPOS=546964;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 547029 rs9438488 G A . PASS CFL;GNO;RSPOS=547029;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000008040100000100;WGT=0;dbSNPBuildID=119
1 547042 rs9438489 C T . PASS CFL;RSPOS=547042;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=119
1 547068 rs2994589 C T . PASS ASP;RSPOS=547068;RV;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=101
1 547081 rs9438490 G T . PASS ASP;RSPOS=547081;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=119
1 547133 rs75048165 G A . PASS ASP;GNO;RSPOS=547133;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040100000100;WGT=0;dbSNPBuildID=131
1 547237 rs74914204 G A . PASS ASP;RSPOS=547237;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=131
1 547321 rs144203620 GGT G . PASS ASP;RSPOS=547327;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 547341 rs79201305 G A . PASS ASP;GNO;RSPOS=547341;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040100000100;WGT=0;dbSNPBuildID=131
1 547380 rs149461650 C T . PASS ASP;RSPOS=547380;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 547425 rs140188273 GGT G . PASS ASP;RSPOS=547431;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 547484 rs147158803 C T . PASS ASP;RSPOS=547484;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 547579 rs140376926 A G . PASS ASP;RSPOS=547579;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 547623 rs9728082 G A . PASS ASP;RSPOS=547623;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=119
1 547753 rs9326617 G A . PASS ASP;GMAF=0.264625228519196;RSPOS=547753;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=119
1 549548 rs191550559 T G . PASS KGPilot123;RSPOS=549548;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 553346 rs183055671 C G . PASS KGPilot123;RSPOS=553346;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 553742 rs140182652 G A . PASS ASP;RSPOS=553742;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 554807 rs78478702 C T . PASS GMAF=0.00228519195612431;GNO;RSPOS=554807;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
1 554808 rs78894760 G A . PASS GNO;RSPOS=554808;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
1 559081 rs188144421 G C . PASS KGPilot123;RSPOS=559081;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 559889 rs140313358 A G . PASS ASP;KGPilot123;RSPOS=559889;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 561156 rs150334593 T G . PASS ASP;RSPOS=561156;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 561200 rs141958416 C T . PASS ASP;KGPilot123;RSPOS=561200;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 563363 rs137905425 C T . PASS ASP;RSPOS=563363;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 563625 rs191286235 T C . PASS KGPilot123;RSPOS=563625;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 564340 rs2792857 G A . PASS CFL;RSPOS=564340;RV;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=100
1 564458 rs77440582 G C . PASS RSPOS=564458;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=131
1 564459 rs78251161 T C . PASS RSPOS=564459;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=131
1 564460 rs76160718 C G . PASS RSPOS=564460;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=131
1 564463 rs80141050 A G . PASS RSPOS=564463;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=131
1 564477 rs6650104 A G . PASS G5;GNO;HD;PH2;RSPOS=564477;SAO=0;SLO;SSR=1;VC=SNV;VLD;VP=050100000000050502000140;WGT=0;dbSNPBuildID=116
1 564505 rs11490923 G A . PASS RSPOS=564505;SAO=0;SSR=1;VC=SNV;VP=050000000000000000000140;WGT=0;dbSNPBuildID=120
1 564520 rs9629042 C G . PASS HD;RSPOS=564520;SAO=0;SSR=1;VC=SNV;VP=050000000000000400000140;WGT=0;dbSNPBuildID=119
1 564532 rs11240781 G A . PASS GNO;PH2;RSPOS=564532;SAO=0;SSR=1;VC=SNV;VP=050000000000000102000140;WGT=0;dbSNPBuildID=120
1 564591 rs9633435 A C . PASS GNO;HD;RSPOS=564591;SAO=0;SSR=1;VC=SNV;VP=050000000000000500000140;WGT=0;dbSNPBuildID=119
1 564598 rs144350286 A G . PASS ASP;RSPOS=564598;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 564618 rs10082168 C G . PASS RSPOS=564618;SAO=0;SSR=1;VC=SNV;VP=050000000000000000000140;WGT=0;dbSNPBuildID=119
1 564621 rs10458597 C T . PASS G5;GMAF=0.0173674588665448;GNO;HD;PH2;RSPOS=564621;SAO=0;SSR=1;VC=SNV;VLD;VP=050000000000050502000140;WGT=0;dbSNPBuildID=119
1 564654 rs147404388 G A . PASS ASP;RSPOS=564654;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 564886 rs148456289 T C . PASS ASP;RSPOS=564886;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565006 rs142650224 T C . PASS ASP;RSPOS=565006;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565097 rs143871052 ATT A,AT . PASS ASP;RSPOS=565098;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 565154 rs146386615 CA C . PASS ASP;RSPOS=565155;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 565164 rs151014821 A C . PASS ASP;RSPOS=565164;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565195 rs139723294 AT A . PASS ASP;RSPOS=565198;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 565286 rs140432825 C T . PASS ASP;RSPOS=565286;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565374 rs9701779 A G . PASS G5;GNO;HD;RSPOS=565374;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=050100000000050500000100;WGT=0;dbSNPBuildID=119
1 565400 rs8179414 C T . PASS HD;RSPOS=565400;SAO=0;SSR=1;VC=SNV;VP=050000000000000400000140;WGT=0;dbSNPBuildID=117
1 565406 rs144191907 C T . PASS ASP;RSPOS=565406;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565407 rs146557167 C T . PASS ASP;RSPOS=565407;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565419 rs55668158 C G . PASS RSPOS=565419;SAO=0;SSR=1;VC=SNV;VP=050000000000000000000140;WGT=0;dbSNPBuildID=129
1 565433 rs9701055 C T . PASS G5;G5A;GNO;HD;PH2;RSPOS=565433;SAO=0;SLO;SSR=1;VC=SNV;VLD;VP=050100000000070502000140;WGT=0;dbSNPBuildID=119
1 565490 rs141292355 T C . PASS ASP;RSPOS=565490;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565508 rs145079224 G A . PASS ASP;RSPOS=565508;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565541 rs145787647 A G . PASS ASP;RSPOS=565541;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565591 rs141914161 C T . PASS ASP;RSPOS=565591;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565596 rs9782892 G A . PASS HD;RSPOS=565596;SAO=0;SLO;SSR=1;VC=SNV;VP=050100000000000400000140;WGT=0;dbSNPBuildID=119
1 565697 rs143799743 A G . PASS ASP;RSPOS=565697;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565870 rs148172508 T C . PASS ASP;RSPOS=565870;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565901 rs142023194 G A . PASS ASP;RSPOS=565901;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565935 rs55973403 C T . PASS GMAF=0.0489031078610603;RSPOS=565935;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040000000100;WGT=0;dbSNPBuildID=129
1 565937 rs145759242 T C . PASS ASP;RSPOS=565937;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 565976 rs138694460 C T . PASS ASP;RSPOS=565976;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566041 rs7340021 C T . PASS RSPOS=566041;SAO=0;SSR=1;VC=SNV;VP=050000000000000000000140;WGT=0;dbSNPBuildID=116
1 566048 rs145777875 G A . PASS ASP;RSPOS=566048;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566130 rs147381188 C T . PASS ASP;RSPOS=566130;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566146 rs142917786 CA C . PASS ASP;RSPOS=566150;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 566205 rs139130884 T C . PASS ASP;RSPOS=566205;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566296 rs151181506 GA G . PASS ASP;RSPOS=566297;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 566371 rs149516726 A G . PASS ASP;RSPOS=566371;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566390 rs144069128 T C . PASS ASP;RSPOS=566390;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566541 rs148687159 G A . PASS ASP;RSPOS=566541;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566573 rs143522810 A G . PASS ASP;RSPOS=566573;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566771 rs146545403 C T . PASS ASP;RSPOS=566771;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566792 rs140024420 T C . PASS ASP;RSPOS=566792;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566805 rs143649721 G A . PASS ASP;RSPOS=566805;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566810 rs9645428 G A . PASS HD;RSPOS=566810;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000000400000100;WGT=0;dbSNPBuildID=119
1 566816 rs151278223 C A . PASS ASP;RSPOS=566816;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566843 rs182069836 T C . PASS KGPilot123;RSPOS=566843;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 566847 rs187911910 T C . PASS KGPilot123;RSPOS=566847;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 566849 rs140536240 G A . PASS ASP;RSPOS=566849;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566850 rs150449760 G A . PASS ASP;RSPOS=566850;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566916 rs145370722 A G . PASS ASP;RSPOS=566916;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566933 rs142636660 A G . PASS ASP;RSPOS=566933;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 566939 rs192480211 C T . PASS KGPilot123;RSPOS=566939;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 566960 rs146905624 T C . PASS ASP;RSPOS=566960;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567002 rs138612401 T C . PASS ASP;RSPOS=567002;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567033 rs142707378 T C . PASS ASP;RSPOS=567033;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567047 rs185393250 T C . PASS KGPilot123;RSPOS=567047;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 567062 rs143484473 C T . PASS ASP;RSPOS=567062;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567092 rs148002581 T C . PASS ASP;RSPOS=567092;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567098 rs189927567 C T . PASS KGPilot123;RSPOS=567098;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 567119 rs141701738 A C . PASS ASP;RSPOS=567119;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567133 rs139068045 ACC A,AC . PASS ASP;RSPOS=567134;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 567137 rs9326623 C T . PASS GMAF=0.00228519195612431;GNO;RSPOS=567137;SAO=0;SSR=1;VC=SNV;VLD;VP=050000000000040100000140;WGT=0;dbSNPBuildID=119
1 567191 rs139593516 C T . PASS ASP;RSPOS=567191;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567239 rs147555239 CG C . PASS ASP;RSPOS=567242;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 567239 rs149882676 CG C . PASS ASP;RSPOS=567240;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 567378 rs141798519 T C . PASS ASP;RSPOS=567378;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567540 rs146275198 A G . PASS ASP;RSPOS=567540;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567579 rs140006168 C T . PASS ASP;RSPOS=567579;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567604 rs143613086 G A . PASS ASP;RSPOS=567604;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567606 rs145723147 A G . PASS ASP;RSPOS=567606;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567697 rs148529803 G A . PASS ASP;RSPOS=567697;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567783 rs142895724 T C . PASS ASP;RSPOS=567783;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567807 rs151077676 T C . PASS ASP;RSPOS=567807;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567867 rs142547273 A G . PASS ASP;RSPOS=567867;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567940 rs144892194 T C . PASS ASP;RSPOS=567940;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 567986 rs141940943 TA T . PASS ASP;RSPOS=567990;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 567997 rs146234117 CA C . PASS ASP;RSPOS=568003;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 568072 rs147963388 A G . PASS ASP;RSPOS=568072;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568158 rs141891825 G A . PASS ASP;RSPOS=568158;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568169 rs138522592 C T . PASS ASP;RSPOS=568169;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568201 rs150293476 T C . PASS ASP;RSPOS=568201;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568256 rs137953150 C T . PASS ASP;RSPOS=568256;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568313 rs149057822 G A . PASS ASP;RSPOS=568313;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568361 rs143080150 T C . PASS ASP;RSPOS=568361;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568403 rs138635580 G A . PASS ASP;RSPOS=568403;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568419 rs141761147 T C . PASS ASP;RSPOS=568419;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568442 rs146264256 T C . PASS ASP;RSPOS=568442;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568451 rs78032279 C T . PASS GNO;RSPOS=568451;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
1 568463 rs138107770 A G . PASS ASP;RSPOS=568463;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568527 rs142696073 G A . PASS ASP;RSPOS=568527;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568562 rs150822004 A G . PASS ASP;RSPOS=568562;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568572 rs139256206 G A . PASS ASP;RSPOS=568572;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568589 rs149999337 T C . PASS ASP;RSPOS=568589;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568616 rs144294451 A G . PASS ASP;RSPOS=568616;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568631 rs76167418 C T . PASS CFL;GMAF=0.120201096892139;GNO;RSPOS=568631;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 568644 rs78639846 T C . PASS GNO;RSPOS=568644;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
1 568670 rs75654607 T C . PASS GNO;RSPOS=568670;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
1 568671 rs147940116 C T . PASS ASP;RSPOS=568671;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568673 rs78918217 A G . PASS GNO;RSPOS=568673;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
1 568691 rs141850957 T C . PASS ASP;RSPOS=568691;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568703 rs143001019 A G . PASS ASP;RSPOS=568703;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568709 rs148329687 A G . PASS ASP;KGPilot123;RSPOS=568709;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 568718 rs150918512 C T . PASS ASP;RSPOS=568718;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568797 rs140714337 A G . PASS ASP;RSPOS=568797;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 568941 rs150104574 A G . PASS ASP;RSPOS=568941;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569052 rs138605248 C T . PASS ASP;RSPOS=569052;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569094 rs140303844 A G . PASS ASP;RSPOS=569094;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569204 rs145433303 T C . PASS ASP;RSPOS=569204;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569226 rs138069586 C A . PASS ASP;RSPOS=569226;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569250 rs149524355 G A . PASS ASP;RSPOS=569250;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569267 rs144154237 G A . PASS ASP;RSPOS=569267;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569268 rs148077852 G A . PASS ASP;RSPOS=569268;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569304 rs147848402 AT A . PASS ASP;RSPOS=569309;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 569396 rs141851735 C T . PASS ASP;RSPOS=569396;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569492 rs147253560 T C . PASS ASP;RSPOS=569492;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569609 rs140803461 A C . PASS ASP;RSPOS=569609;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569624 rs144764545 T C . PASS ASP;RSPOS=569624;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569717 rs147510063 T C . PASS ASP;RSPOS=569717;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569763 rs140083384 A G . PASS ASP;RSPOS=569763;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569803 rs150050719 G A . PASS ASP;RSPOS=569803;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 569983 rs145414098 G A . PASS ASP;RSPOS=569983;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 570026 rs148603765 G A . PASS ASP;RSPOS=570026;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 570027 rs142049128 T G . PASS ASP;RSPOS=570027;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 570060 rs148889850 AC A . PASS ASP;RSPOS=570061;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 570076 rs144125246 T C . PASS ASP;RSPOS=570076;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 570108 rs143527354 CA C . PASS ASP;RSPOS=570109;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 570178 rs146675873 G A . PASS ASP;RSPOS=570178;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 570196 rs10449773 T C . PASS ASP;GNO;PH2;RSPOS=570196;SAO=0;SSR=1;VC=SNV;VP=050000000004000102000140;WGT=0;dbSNPBuildID=119
1 570305 rs74903230 G T . PASS ASP;RSPOS=570305;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=131
1 570306 rs75635644 T C . PASS ASP;RSPOS=570306;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=131
1 570308 rs77524690 A C . PASS ASP;RSPOS=570308;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=131
1 570309 rs78888785 A C . PASS ASP;RSPOS=570309;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=131
1 570337 rs193042102 G T . PASS KGPilot123;RSPOS=570337;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 570573 rs184868172 T G . PASS KGPilot123;RSPOS=570573;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 570663 rs189669695 C T . PASS KGPilot123;RSPOS=570663;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 571923 rs186361076 G T . PASS RSPOS=571923;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 574151 rs74047006 A T . PASS CFL;GNO;KGPilot123;RSPOS=574151;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000008000110000100;WGT=0;dbSNPBuildID=130
1 574329 rs185282956 A G . PASS KGPilot123;RSPOS=574329;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 585859 rs189649164 G A . PASS KGPilot123;RSPOS=585859;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 585863 rs181868443 C T . PASS KGPilot123;RSPOS=585863;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 586195 rs55870831 G T . PASS HD;RSPOS=586195;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000000400000100;WGT=0;dbSNPBuildID=129
1 589082 rs187234864 G A . PASS KGPilot123;RSPOS=589082;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 592051 rs79746121 C T . PASS ASP;GMAF=0.0105118829981718;GNO;RSPOS=592051;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 592051 rs10218594 C T . PASS ASP;RSPOS=592051;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=119
1 592058 rs11589730 G A . PASS ASP;RSPOS=592058;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=120
1 592060 rs28730494 T C . PASS ASP;RSPOS=592060;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=125
1 592075 rs6681105 T C . PASS ASP;G5;GMAF=0.00137111517367459;GNO;HD;PH2;RSPOS=592075;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004050502000100;WGT=0;dbSNPBuildID=116
1 592101 rs11588491 A T . PASS ASP;RSPOS=592101;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=120
1 592117 rs11578815 C T . PASS ASP;RSPOS=592117;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=120
1 592136 rs2487374 A C . PASS ASP;RSPOS=592136;RV;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=100
1 592146 rs12064670 C A . PASS ASP;GMAF=0.00457038391224863;RSPOS=592146;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=120
1 592183 rs4113310 A T . PASS ASP;RSPOS=592183;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000000000100;WGT=0;dbSNPBuildID=108
1 592185 rs11578827 C G . PASS ASP;RSPOS=592185;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=120
1 592190 rs11240784 T C . PASS ASP;RSPOS=592190;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=120
1 592305 rs11578847 C T . PASS ASP;GMAF=0.00228519195612431;RSPOS=592305;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=120
1 597681 rs191662915 T C . PASS KGPilot123;RSPOS=597681;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 600478 rs114979547 G A . PASS ASP;G5;G5A;GMAF=0.0973491773308958;KGPilot123;RSPOS=600478;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070010000100;WGT=0;dbSNPBuildID=132
1 600495 rs147241137 G C . PASS ASP;KGPilot123;RSPOS=600495;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 601055 rs183469249 T C . PASS KGPilot123;RSPOS=601055;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 601141 rs140845213 C T . PASS ASP;KGPilot123;RSPOS=601141;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 601142 rs78960661 G A . PASS RSPOS=601142;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=131
1 601408 rs143332664 G A . PASS ASP;RSPOS=601408;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 601550 rs78266750 G A . PASS HD;RSPOS=601550;SAO=0;SSR=0;VC=SNV;VP=050000000000000400000100;WGT=0;dbSNPBuildID=131
1 601583 rs79221329 G A . PASS GMAF=0.0164533820840951;HD;KGPilot123;RSPOS=601583;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040410000100;WGT=0;dbSNPBuildID=131
1 601841 rs148361140 G C . PASS ASP;RSPOS=601841;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 602101 rs141465832 G A . PASS ASP;RSPOS=602101;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 603331 rs186375515 T C . PASS KGPilot123;RSPOS=603331;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 603354 rs111125843 G T . PASS GNO;RSPOS=603354;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=132
1 603505 rs140832136 A C . PASS ASP;KGPilot123;RSPOS=603505;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 603515 rs190065153 C A . PASS KGPilot123;RSPOS=603515;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 603516 rs182349900 C A . PASS KGPilot123;RSPOS=603516;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 603589 rs149712121 A C . PASS ASP;KGPilot123;RSPOS=603589;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 603710 rs186580270 G C . PASS KGPilot123;RSPOS=603710;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 603938 rs61769313 C G . PASS ASP;GMAF=0.00137111517367459;RSPOS=603938;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=129
1 603971 rs189352986 A C . PASS RSPOS=603971;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 604172 rs413981 G T . PASS ASP;RSPOS=604172;RV;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=80
1 604877 rs79439412 G A . PASS ASP;GNO;RSPOS=604877;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 604921 rs76965970 G A . PASS ASP;GNO;RSPOS=604921;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
1 608913 rs2998413 G A . PASS CFL;RSPOS=608913;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=101
1 609603 rs76650282 A T . PASS ASP;GNO;RSPOS=609603;RV;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040100000100;WGT=0;dbSNPBuildID=131
1 618463 rs114496243 G A . PASS ASP;G5;G5A;GMAF=0.189213893967093;KGPilot123;RSPOS=618463;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070010000100;WGT=0;dbSNPBuildID=132
1 622507 rs111891105 G A . PASS GENEINFO=OR4F16:81399;HD;RSPOS=622507;RV;SAO=0;SSR=0;VC=SNV;VP=050000000000000400000100;WGT=0;dbSNPBuildID=132
1 626321 rs77242874 A G . PASS CFL;GNO;RSPOS=626321;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 633582 rs192643069 C T . PASS KGPilot123;RSPOS=633582;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 636021 rs75919195 G A . PASS CFL;GMAF=0.313985374771481;GNO;RSPOS=636021;RV;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=131
1 636044 rs150838338 G A . PASS ASP;RSPOS=636044;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 636116 rs139627507 G C . PASS ASP;RSPOS=636116;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 636673 rs140723072 C T . PASS ASP;KGPilot123;RSPOS=636673;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 636710 rs183948244 C T . PASS KGPilot123;RSPOS=636710;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 636975 rs144572927 G A . PASS ASP;KGPilot123;RSPOS=636975;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 637753 rs188948234 C A . PASS KGPilot123;RSPOS=637753;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 644420 rs144745434 T C . PASS ASP;KGPilot123;RSPOS=644420;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 645399 rs192911354 T C . PASS KGPilot123;RSPOS=645399;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 645605 rs185127847 T A . PASS KGPilot123;RSPOS=645605;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 653518 rs148115286 AAG A . PASS ASP;RSPOS=653519;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
1 657635 rs111878790 T A . PASS CFL;GENEINFO=LOC100287654:100287654;RSPOS=657635;SAO=0;SSR=0;VC=SNV;VP=050000000008000000000100;WGT=0;dbSNPBuildID=132
1 658404 rs112428783 A G . PASS GENEINFO=LOC100287654:100287654;HD;RSPOS=658404;RV;SAO=0;SSR=0;VC=SNV;VP=050000000000000400000100;WGT=0;dbSNPBuildID=132
1 658426 rs188842781 G T . PASS KGPilot123;RSPOS=658426;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 662571 rs191780594 C T . PASS KGPilot123;RSPOS=662571;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 662613 rs151190501 G A . PASS ASP;KGPilot123;RSPOS=662613;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
1 662622 rs61769339 G A . PASS CFL;GMAF=0.11563071297989;GNO;KGPilot123;RSPOS=662622;SAO=0;SSR=0;VC=SNV;VP=050000000008000110000100;WGT=0;dbSNPBuildID=129
1 663097 rs142727405 G C . PASS ASP;RSPOS=663097;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
1 664010 rs183901648 A C . PASS KGPilot123;RSPOS=664010;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 668329 rs180933589 G A . PASS RSPOS=668329;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
1 668340 rs188337135 G C . PASS KGPilot123;RSPOS=668340;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
1 668346 rs115048193 G A . PASS ASP;G5;G5A;GMAF=0.00228519195612431;KGPilot123;RSPOS=668346;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070010000100;WGT=0;dbSNPBuildID=132
1 668374 rs138476838 G A . PASS ASP;KGPilot123;RSPOS=668374;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134