diff --git a/build.xml b/build.xml index 0a4cd2171..d3377a763 100644 --- a/build.xml +++ b/build.xml @@ -1249,11 +1249,7 @@ - - - - - + diff --git a/licensing/GATK2_beta_license.doc b/licensing/GATK2_beta_license.doc index 4fa04a3f6..2b9cdeb9c 100644 Binary files a/licensing/GATK2_beta_license.doc and b/licensing/GATK2_beta_license.doc differ diff --git a/licensing/GATK2_beta_license.pdf b/licensing/GATK2_beta_license.pdf new file mode 100644 index 000000000..fc592066e Binary files /dev/null and b/licensing/GATK2_beta_license.pdf differ diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypeLikelihoodsCalculationModel.java index 8b5639817..37b676601 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypeLikelihoodsCalculationModel.java @@ -213,7 +213,7 @@ public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLi if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) { AlignmentContext mergedContext = AlignmentContextUtils.joinContexts(contexts.values()); Map newContext = new HashMap(); - newContext.put(DUMMY_POOL,mergedContext); + newContext.put(DUMMY_SAMPLE_NAME,mergedContext); contexts = newContext; } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java index 0922b8e7f..c2bac4455 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java @@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.variantcontext.*; import java.util.*; public class PoolIndelGenotypeLikelihoodsCalculationModel extends PoolGenotypeLikelihoodsCalculationModel { + private static final int MAX_NUM_ALLELES_TO_GENOTYPE = 4; private PairHMMIndelErrorModel pairModel; private boolean allelesArePadded = false; @@ -94,7 +95,10 @@ public class PoolIndelGenotypeLikelihoodsCalculationModel extends PoolGenotypeLi final Pair,Boolean> pair = IndelGenotypeLikelihoodsCalculationModel.getInitialAlleleList(tracker, ref, contexts, contextType, locParser, UAC,true); - final List alleles = pair.first; + List alleles = pair.first; + + if (alleles.size() > MAX_NUM_ALLELES_TO_GENOTYPE) + alleles = alleles.subList(0,MAX_NUM_ALLELES_TO_GENOTYPE); allelesArePadded = pair.second; if (contextType == AlignmentContextUtils.ReadOrientation.COMPLETE) { IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap().clear(); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java index 47a7030a8..bdd04cba1 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java @@ -33,6 +33,7 @@ import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.codecs.vcf.VCFAlleleClipper; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.variantcontext.*; @@ -381,24 +382,7 @@ public class GenotypingEngine { } if( R2 > MERGE_EVENTS_R2_THRESHOLD ) { - byte[] refBases = thisVC.getReference().getBases(); - byte[] altBases = thisVC.getAlternateAllele(0).getBases(); - final int thisPadding = ( thisVC.getReference().isNull() || thisVC.getAlternateAllele(0).isNull() ? 1 : 0 ); - final int nextPadding = ( nextVC.getReference().isNull() || nextVC.getAlternateAllele(0).isNull() ? 1 : 0 ); - for( int locus = thisStart + refBases.length + thisPadding ; locus < nextStart + nextPadding; locus++ ) { - final byte refByte = ref[ locus - refLoc.getStart() ]; - refBases = ArrayUtils.add(refBases, refByte); - altBases = ArrayUtils.add(altBases, refByte); - } - refBases = ArrayUtils.addAll(refBases, nextVC.getReference().getBases()); - altBases = ArrayUtils.addAll(altBases, nextVC.getAlternateAllele(0).getBases()); - - final ArrayList mergedAlleles = new ArrayList(); - mergedAlleles.add( Allele.create( refBases, true ) ); - mergedAlleles.add( Allele.create( altBases, false ) ); - final VariantContext mergedVC = ( refBases.length == altBases.length ? - new VariantContextBuilder("MNP", thisVC.getChr(), thisVC.getStart() + (thisVC.isIndel() && !thisVC.isComplexIndel() ? 1 : 0) , nextVC.getEnd(), mergedAlleles).make() : - new VariantContextBuilder("Complex", thisVC.getChr(), thisVC.getStart(), nextVC.getEnd(), mergedAlleles).referenceBaseForIndel(ref[thisStart-refLoc.getStart()]).make() ); + final VariantContext mergedVC = createMergedVariantContext(thisVC, nextVC, ref, refLoc); // remove the old event from the eventMap on every haplotype and the start pos key set, replace with merged event for( final Haplotype h : haplotypes ) { @@ -431,6 +415,36 @@ public class GenotypingEngine { } } + // BUGBUG: make this merge function more general + protected static VariantContext createMergedVariantContext( final VariantContext thisVC, final VariantContext nextVC, final byte[] ref, final GenomeLoc refLoc ) { + final int thisStart = thisVC.getStart(); + final int nextStart = nextVC.getStart(); + byte[] refBases = ( thisVC.hasReferenceBaseForIndel() ? new byte[]{ thisVC.getReferenceBaseForIndel() } : new byte[]{} ); + byte[] altBases = ( thisVC.hasReferenceBaseForIndel() ? new byte[]{ thisVC.getReferenceBaseForIndel() } : new byte[]{} ); + refBases = ArrayUtils.addAll(refBases, thisVC.getReference().getBases()); + altBases = ArrayUtils.addAll(altBases, thisVC.getAlternateAllele(0).getBases()); + for( int locus = thisStart + refBases.length; locus < nextStart; locus++ ) { + final byte refByte = ref[locus - refLoc.getStart()]; + refBases = ArrayUtils.add(refBases, refByte); + altBases = ArrayUtils.add(altBases, refByte); + } + if( nextVC.hasReferenceBaseForIndel() ) { + refBases = ArrayUtils.add(refBases, nextVC.getReferenceBaseForIndel()); + altBases = ArrayUtils.add(altBases, nextVC.getReferenceBaseForIndel()); + } + refBases = ArrayUtils.addAll(refBases, nextVC.getReference().getBases()); + altBases = ArrayUtils.addAll(altBases, nextVC.getAlternateAllele(0).getBases()); + + int iii = 0; + if( refBases.length == altBases.length && VCFAlleleClipper.needsPadding(thisVC) ) { // special case of insertion + deletion of same length creates an MNP --> trim padding bases off the allele + while( iii < refBases.length && refBases[iii] == altBases[iii] ) { iii++; } + } + final ArrayList mergedAlleles = new ArrayList(); + mergedAlleles.add( Allele.create( ArrayUtils.subarray(refBases, iii, refBases.length), true ) ); + mergedAlleles.add( Allele.create( ArrayUtils.subarray(altBases, iii, altBases.length), false ) ); + return new VariantContextBuilder("merged", thisVC.getChr(), thisVC.getStart() + iii, nextVC.getEnd(), mergedAlleles).make(); + } + @Requires({"x11 >= 0", "x12 >= 0", "x21 >= 0", "x22 >= 0"}) @Ensures({"result >= 0.0", "result <= 1.0"}) protected static double calculateR2LD( final int x11, final int x12, final int x21, final int x22 ) { diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/PoolCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/PoolCallerIntegrationTest.java index f04a3fd4d..903465538 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/PoolCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/PoolCallerIntegrationTest.java @@ -39,7 +39,7 @@ public class PoolCallerIntegrationTest extends WalkerTest { @Test public void testBOTH_GGA_Pools() { - PC_LSV_Test(String.format(" -maxAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","POOLBOTH","da85bf56eeafae31b5a269b4e19b5db6"); + PC_LSV_Test(String.format(" -maxAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","POOLBOTH","36b8db57f65be1cc3d2d9d7f9f3f26e4"); } @Test @@ -49,13 +49,13 @@ public class PoolCallerIntegrationTest extends WalkerTest { @Test public void testMT_SNP_DISCOVERY_sp4() { - PC_MT_Test(CEUTRIO_BAM, " -maxAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","060f06987a33f60433b0382cd7227140"); + PC_MT_Test(CEUTRIO_BAM, " -maxAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","fa5ee7c957c473a80f3a7f3c35dc80b5"); } @Test public void testMT_SNP_GGA_sp10() { - PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "df3ffc5cb76224ba152f543925eb3974"); + PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "6907c8617d49bb57b33f8704ce7f0323"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java index 4826bfb16..04bb3a753 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java @@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; @@ -232,7 +233,7 @@ public class GenotypingEngineUnitTest extends BaseTest { } /** - * Tests that we get the right values from the binomial distribution + * Tests that we get the right values from the R^2 calculation */ @Test public void testCalculateR2LD() { @@ -244,6 +245,146 @@ public class GenotypingEngineUnitTest extends BaseTest { Assert.assertEquals(GenotypingEngine.calculateR2LD(100,0,0,100), 1.0, 0.00001); Assert.assertEquals(GenotypingEngine.calculateR2LD(1,2,3,4), (0.1 - 0.12) * (0.1 - 0.12) / (0.3 * 0.7 * 0.4 * 0.6), 0.00001); } + + @Test + public void testCreateMergedVariantContext() { + logger.warn("Executing testCreateMergedVariantContext"); + + final byte[] ref = "AATTCCGGAATTCCGGAATT".getBytes(); + final GenomeLoc refLoc = genomeLocParser.createGenomeLoc("2", 1700, 1700 + ref.length); + + // SNP + SNP = simple MNP + VariantContext thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","G").make(); + VariantContext nextVC = new VariantContextBuilder().loc("2", 1704, 1704).alleles("C","G").make(); + VariantContext truthVC = new VariantContextBuilder().loc("2", 1703, 1704).alleles("TC","GG").source("merged").make(); + VariantContext mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // SNP + ref + SNP = MNP with ref base gap + thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","G").make(); + nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("C","G").make(); + truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","GCG").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // insertion + SNP + thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("-","AAAAA").referenceBaseForIndel("T").make(); + nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("C","G").make(); + truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","TAAAAACG").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // SNP + insertion + thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","G").make(); + nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("-","AAAAA").referenceBaseForIndel("C").make(); + truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","GCCAAAAA").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // deletion + SNP + thisVC = new VariantContextBuilder().loc("2", 1703, 1704).alleles("C","-").referenceBaseForIndel("T").make(); + nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("C","G").make(); + truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","TG").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // SNP + deletion + thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","G").make(); + nextVC = new VariantContextBuilder().loc("2", 1705, 1706).alleles("G","-").referenceBaseForIndel("C").make(); + truthVC = new VariantContextBuilder().loc("2", 1703, 1706).alleles("TCCG","GCC").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // insertion + deletion = MNP + thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("-","A").referenceBaseForIndel("T").make(); + nextVC = new VariantContextBuilder().loc("2", 1705, 1706).alleles("G","-").referenceBaseForIndel("C").make(); + truthVC = new VariantContextBuilder().loc("2", 1704, 1706).alleles("CCG","ACC").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // insertion + deletion + thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("-","AAAAA").referenceBaseForIndel("T").make(); + nextVC = new VariantContextBuilder().loc("2", 1705, 1706).alleles("G","-").referenceBaseForIndel("C").make(); + truthVC = new VariantContextBuilder().loc("2", 1703, 1706).alleles("TCCG","TAAAAACC").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // insertion + insertion + thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("-","A").referenceBaseForIndel("T").make(); + nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("-","A").referenceBaseForIndel("C").make(); + truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","TACCA").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // deletion + deletion + thisVC = new VariantContextBuilder().loc("2", 1701, 1702).alleles("T","-").referenceBaseForIndel("A").make(); + nextVC = new VariantContextBuilder().loc("2", 1705, 1706).alleles("G","-").referenceBaseForIndel("C").make(); + truthVC = new VariantContextBuilder().loc("2", 1701, 1706).alleles("ATTCCG","ATCC").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + + // complex + complex + thisVC = new VariantContextBuilder().loc("2", 1703, 1704).alleles("TC","AAA").make(); + nextVC = new VariantContextBuilder().loc("2", 1706, 1707).alleles("GG","AC").make(); + truthVC = new VariantContextBuilder().loc("2", 1703, 1707).alleles("TCCGG","AAACAC").source("merged").make(); + mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc); + logger.warn(truthVC + " == " + mergedVC); + Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC)); + Assert.assertEquals(truthVC.getStart(), mergedVC.getStart()); + Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd()); + Assert.assertEquals(truthVC.hasReferenceBaseForIndel(), mergedVC.hasReferenceBaseForIndel()); + Assert.assertEquals(truthVC.getReferenceBaseForIndel(), mergedVC.getReferenceBaseForIndel()); + } /** * Private function to compare HashMap of VCs, it only checks the types and start locations of the VariantContext diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java index 9e1be5bca..976889613 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java +++ b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java @@ -369,9 +369,9 @@ public abstract class CommandLineProgram { System.exit(1); } - public static void exitSystemWithSamError(final Exception e) { - if ( e.getMessage() == null ) - throw new ReviewedStingException("SamException found with no message!", e); + public static void exitSystemWithSamError(final Throwable t) { + if ( t.getMessage() == null ) + throw new ReviewedStingException("SamException found with no message!", t); errorPrintf("------------------------------------------------------------------------------------------%n"); errorPrintf("A BAM ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber()); @@ -383,7 +383,7 @@ public abstract class CommandLineProgram { errorPrintf("Also, please ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'%n"); printDocumentationReference(); errorPrintf("%n"); - errorPrintf("MESSAGE: %s%n", e.getMessage().trim()); + errorPrintf("MESSAGE: %s%n", t.getMessage().trim()); errorPrintf("------------------------------------------------------------------------------------------%n"); System.exit(1); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 70c6bc734..c0865e656 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.gatk.walkers.Attribution; import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.*; import org.broadinstitute.sting.utils.text.TextFormattingUtils; @@ -101,20 +102,35 @@ public class CommandLineGATK extends CommandLineExecutable { // TODO: Should Picard exceptions be, in general, UserExceptions or ReviewedStingExceptions? exitSystemWithError(e); } catch (SAMException e) { - checkForTooManyOpenFilesProblem(e.getMessage()); + checkForMaskedUserErrors(e); exitSystemWithSamError(e); } catch (OutOfMemoryError e) { exitSystemWithUserError(new UserException.NotEnoughMemory()); } catch (Throwable t) { - checkForTooManyOpenFilesProblem(t.getMessage()); + checkForMaskedUserErrors(t); exitSystemWithError(t); } } - private static void checkForTooManyOpenFilesProblem(String message) { - // Special case the "Too many open files" error because it's a common User Error for which we know what to do - if ( message != null && message.indexOf("Too many open files") != -1 ) + protected static final String PICARD_TEXT_SAM_FILE_ERROR_1 = "Cannot use index file with textual SAM file"; + protected static final String PICARD_TEXT_SAM_FILE_ERROR_2 = "Cannot retrieve file pointers within SAM text files"; + private static void checkForMaskedUserErrors(final Throwable t) { + final String message = t.getMessage(); + if ( message == null ) + return; + + // we know what to do about the common "Too many open files" error + if ( message.indexOf("Too many open files") != -1 ) exitSystemWithUserError(new UserException.TooManyOpenFiles()); + + // malformed BAM looks like a SAM file + if ( message.indexOf(PICARD_TEXT_SAM_FILE_ERROR_1) != -1 || + message.indexOf(PICARD_TEXT_SAM_FILE_ERROR_2) != -1 ) + exitSystemWithSamError(t); + + // can't close tribble index when writing + if ( message.indexOf("Unable to close index for") != -1 ) + exitSystemWithUserError(new UserException(t.getCause().getMessage())); } /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 9d2a138fa..8dfa89083 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -51,7 +51,7 @@ import org.broadinstitute.sting.gatk.samples.SampleDBBuilder; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.classloader.JVMUtils; +import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.collections.Pair; @@ -206,7 +206,7 @@ public class GenomeAnalysisEngine { * Utility method to determine whether this is the lite version of the GATK */ public boolean isGATKLite() { - return JVMUtils.isGATKLite(); + return GATKLiteUtils.isGATKLite(); } /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 45499817e..3fd3857c5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -211,6 +211,7 @@ public class GATKArgumentCollection { * Any value greater than zero will be used to recalculate the quantization using that many levels. * Negative values mean that we should quantize using the recalibration report's quantization level. */ + @Hidden @Argument(fullName="quantize_quals", shortName = "qq", doc = "Quantize quality scores to a given number of levels (with -BQSR)", required=false) public int quantizationLevels = 0; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java index 2bf75b035..73301c511 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java @@ -24,6 +24,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; import net.sf.samtools.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -300,7 +301,7 @@ public class GATKBAMIndex { fileChannel = fileStream.getChannel(); } catch (IOException exc) { - throw new ReviewedStingException("Unable to open index file " + mFile, exc); + throw new ReviewedStingException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index b821b98e6..5f20ac7af 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -11,7 +11,6 @@ import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor; import java.util.Collection; @@ -256,7 +255,8 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar // Specifically catch Tribble I/O exceptions and rethrow them as Reviewed. We don't expect // any issues here because we created the Tribble output file mere moments ago and expect it to // be completely valid. - throw new ReviewedStingException("Unable to merge temporary Tribble output file.",ex); + final String reason = ex.getMessage(); + throw new ReviewedStingException("Unable to merge temporary Tribble output file" + (reason == null ? "." : (" (" + reason + ").")), ex); } } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java index 9920213a3..bb0344848 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java @@ -6,11 +6,11 @@ import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker; import org.broadinstitute.sting.gatk.traversals.TraversalEngine; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.concurrent.Callable; +import java.util.concurrent.ExecutionException; /** * User: hanna * Date: Apr 29, 2009 @@ -79,6 +79,10 @@ public class ShardTraverser implements Callable { microScheduler.reportShardTraverseTime(endTime-startTime); return accumulator; + } catch(Throwable t) { + // Notify that an exception has occurred + microScheduler.handleException(new ExecutionException(t)); + throw new RuntimeException(t); } finally { synchronized(this) { complete = true; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java index 641bddb2d..d8caa3dea 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java @@ -28,6 +28,7 @@ public abstract class ReadFilter implements SamRecordFilter { * @return true if the SAMRecords matches the filter, otherwise false * @throws UnsupportedOperationException when paired filter not implemented */ + @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) { throw new UnsupportedOperationException("Paired filter not implemented: " + this.getClass()); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index e3ee8c923..6dc0ba3e1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -255,12 +255,9 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat for ( Map.Entry sample : stratifiedContexts.entrySet() ) { for (PileupElement p : sample.getValue().getBasePileup()) { - if ( p.isDeletion() || p.getRead().isReducedRead() ) // ignore deletions and reduced reads + if ( ! RankSumTest.isUsableBase(p, false) || p.getRead().isReducedRead() ) // ignore deletions and reduced reads continue; - if ( p.getRead().getMappingQuality() < 20 || p.getQual() < 20 ) - continue; // todo -- fixme, should take filtered context! - Allele base = Allele.create(p.getBase(), false); boolean isFW = !p.getRead().getReadNegativeStrandFlag(); @@ -301,9 +298,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat final ReadBackedPileup pileup = context.getBasePileup(); for ( final PileupElement p : pileup ) { - if ( p.getRead().isReducedRead() ) // ignore reduced reads - continue; - if ( p.getRead().getMappingQuality() < 20 ) + if ( ! RankSumTest.isUsableBase(p, true) || p.getRead().isReducedRead() ) // ignore reduced reads continue; if ( indelLikelihoodMap.containsKey(p) ) { // to classify a pileup element as ref or alt, we look at the likelihood associated with the allele associated to this element. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index bf66958e0..1955c87b8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -149,9 +149,28 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR protected abstract void fillIndelQualsFromPileup(final ReadBackedPileup pileup, final List refQuals, final List altQuals); - protected static boolean isUsableBase(final PileupElement p) { + /** + * Can the base in this pileup element be used in comparative tests between ref / alt bases? + * + * Note that this function by default does not allow deletion pileup elements + * + * @param p the pileup element to consider + * @return true if this base is part of a meaningful read for comparison, false otherwise + */ + public static boolean isUsableBase(final PileupElement p) { + return isUsableBase(p, false); + } + + /** + * Can the base in this pileup element be used in comparative tests between ref / alt bases? + * + * @param p the pileup element to consider + * @param allowDeletions if true, allow p to be a deletion base + * @return true if this base is part of a meaningful read for comparison, false otherwise + */ + public static boolean isUsableBase(final PileupElement p, final boolean allowDeletions) { return !(p.isInsertionAtBeginningOfRead() || - p.isDeletion() || + (! allowDeletions && p.isDeletion()) || p.getMappingQual() == 0 || p.getMappingQual() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE || ((int) p.getQual()) < QualityUtils.MIN_USABLE_Q_SCORE); // need the unBAQed quality score here diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java index 1a99d51e6..8210a11b7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java @@ -34,8 +34,7 @@ import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource; +import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -179,27 +178,15 @@ public class BaseQualityScoreRecalibrator extends LocusWalker implem } private RecalibrationEngine initializeRecalibrationEngine() { - List> REclasses = new PluginManager(RecalibrationEngine.class).getPlugins(); - if ( REclasses.isEmpty() ) - throw new ReviewedStingException("The RecalibrationEngine class is not found; repository must be corrupted"); - - Class c = null; - for ( Class REclass : REclasses ) { - if ( ProtectedPackageSource.class.isAssignableFrom(REclass) ) { - c = REclass; - break; - } - } - if ( c == null ) - c = REclasses.get(0); + final Class recalibrationEngineClass = GATKLiteUtils.getProtectedClassIfAvailable(RecalibrationEngine.class); try { - Constructor constructor = c.getDeclaredConstructor((Class[])null); + Constructor constructor = recalibrationEngineClass.getDeclaredConstructor((Class[])null); constructor.setAccessible(true); return (RecalibrationEngine)constructor.newInstance(); } catch (Exception e) { - throw new ReviewedStingException("Unable to create RecalibrationEngine class instance " + c.getSimpleName()); + throw new ReviewedStingException("Unable to create RecalibrationEngine class instance " + recalibrationEngineClass.getSimpleName()); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index 84467085b..4253ff3ad 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -48,7 +48,7 @@ import java.util.Map; public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable { public static final String DUMMY_LANE = "Lane1"; - public static final String DUMMY_POOL = "Pool1"; + public static final String DUMMY_SAMPLE_NAME = "DummySample1"; /* public enum Model { SNP, diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index ac7c370bf..c767cf783 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -35,7 +35,6 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -43,7 +42,6 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.sting.utils.variantcontext.*; import java.util.ArrayList; -import java.util.HashMap; import java.util.List; import java.util.Map; @@ -68,9 +66,11 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC final byte refBase = ref.getBase(); final int indexOfRefBase = BaseUtils.simpleBaseToBaseIndex(refBase); + // handle non-standard reference bases + if ( indexOfRefBase == -1 ) + return null; final Allele refAllele = Allele.create(refBase, true); - // calculate the GLs ArrayList GLs = new ArrayList(contexts.size()); for ( Map.Entry sample : contexts.entrySet() ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 31a2dfd77..d504badab 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -25,10 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.DownsampleType; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -40,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.baq.BAQ; +import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -226,7 +225,7 @@ public class UnifiedGenotyper extends LocusWalker, Unif public void initialize() { // Check for protected modes - if (getToolkit().isGATKLite()) { + if (GATKLiteUtils.isGATKLite()) { // no polyploid/pooled mode in GATK Like if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY || UAC.referenceSampleName != null || @@ -240,7 +239,7 @@ public class UnifiedGenotyper extends LocusWalker, Unif // in full mode: check for consistency in ploidy/pool calling arguments // check for correct calculation models if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) { - // polyploidy required POOL GL and AF calculation models to be specified right now + // polyploidy requires POOL GL and AF calculation models to be specified right now if (UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLSNP && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLINDEL && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLBOTH) { throw new UserException("Incorrect genotype calculation model chosen. Only [POOLSNP|POOLINDEL|POOLBOTH] supported with this walker if sample ploidy != 2"); @@ -253,7 +252,7 @@ public class UnifiedGenotyper extends LocusWalker, Unif // get all of the unique sample names if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) { samples.clear(); - samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_POOL); + samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME); } else { samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); if (UAC.referenceSampleName != null ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index e36c2f294..a2bcdaf1d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -11,6 +11,7 @@ import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Collection; +import java.util.Set; /** * The Broad Institute @@ -102,6 +103,10 @@ public class ValidationReport extends VariantEvaluator implements StandardEval { nDifferentAlleleSites++; else { SiteStatus evalStatus = calcSiteStatus(eval); + final Set evalSamples = getWalker().getSampleNamesForEvaluation(); + if ( comp.hasGenotypes() && ! evalSamples.isEmpty() && comp.hasGenotypes(evalSamples) ) + // if we have genotypes in both eval and comp, subset comp down just the samples in eval + comp = comp.subContextFromSamples(evalSamples, false); SiteStatus compStatus = calcSiteStatus(comp); counts[compStatus.ordinal()][evalStatus.ordinal()]++; } @@ -111,7 +116,7 @@ public class ValidationReport extends VariantEvaluator implements StandardEval { // // helper routines // - public SiteStatus calcSiteStatus(VariantContext vc) { + private SiteStatus calcSiteStatus(VariantContext vc) { if ( vc == null ) return SiteStatus.NO_CALL; if ( vc.isFiltered() ) return SiteStatus.FILTERED; if ( vc.isMonomorphicInSamples() ) return SiteStatus.MONO; @@ -121,24 +126,18 @@ public class ValidationReport extends VariantEvaluator implements StandardEval { int ac = 0; if ( vc.getNAlleles() > 2 ) { return SiteStatus.POLY; -//// System.out.printf("multiple alleles %s = %s%n", vc.getAlleles(), vc.getExtendedAttribute(VCFConstants.ALLELE_COUNT_KEY)); -// // todo -- omg this is painful. We need a better approach to dealing with multi-valued attributes -// for ( String v : (List)vc.getExtendedAttribute(VCFConstants.ALLELE_COUNT_KEY) ) -// ac += Integer.valueOf(v); -//// System.out.printf(" ac = %d%n", ac); } else ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0); return ac > 0 ? SiteStatus.POLY : SiteStatus.MONO; } else { return TREAT_ALL_SITES_IN_EVAL_VCF_AS_CALLED ? SiteStatus.POLY : SiteStatus.NO_CALL; // we can't figure out what to do - //return SiteStatus.NO_CALL; // we can't figure out what to do } } - public boolean haveDifferentAltAlleles(VariantContext eval, VariantContext comp) { + private boolean haveDifferentAltAlleles(VariantContext eval, VariantContext comp) { Collection evalAlts = eval.getAlternateAlleles(); Collection compAlts = comp.getAlternateAlleles(); if ( evalAlts.size() != compAlts.size() ) { diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java b/public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java new file mode 100755 index 000000000..db9b9d8b7 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java @@ -0,0 +1,85 @@ +/* + * Copyright (c) 2010 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.classloader; + +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.util.*; + +/** + * Created by IntelliJ IDEA. + * User: ebanks + * + * A set of static utility methods for working with the full vs. Lite GATK build + */ +public class GATKLiteUtils { + /** + * Constructor access disallowed...static utility methods only! + */ + private GATKLiteUtils() { } + + /** + * Utility method to determine whether this is the lite version of the GATK + */ + public static boolean isGATKLite() { + if ( isLiteVersion == null ) { + try { + Class.forName(DummyProtectedClassName); + isLiteVersion = false; + } catch ( ClassNotFoundException e) { + isLiteVersion = true; + } + } + return isLiteVersion; + } + private static final String DummyProtectedClassName = "org.broadinstitute.sting.gatk.DummyProtectedClass"; + private static Boolean isLiteVersion = null; + + + /** + * Utility method to pull out a protected subclass if possible, otherwise it falls back to a public subclass. + * Important note: the protected classes MUST implement ProtectedPackageSource! + * + * @param interfaceClass the interface class which the target classes implement + */ + public static Class getProtectedClassIfAvailable(final Class interfaceClass) { + List> classes = new PluginManager(interfaceClass).getPlugins(); + if ( classes.isEmpty() ) + throw new ReviewedStingException("No classes implementing the interface class " + interfaceClass.getSimpleName() + " were found"); + + Class result = null; + for ( Class c : classes ) { + if ( ProtectedPackageSource.class.isAssignableFrom(c) ) { + result = c; + break; + } + } + if ( result == null ) + result = classes.get(0); + + return result; + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java index 745c9ad1e..fa154fca3 100755 --- a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java @@ -105,23 +105,6 @@ public class JVMUtils { return allFields; } - /** - * Utility method to determine whether this is the lite version of the GATK - */ - public static boolean isGATKLite() { - if ( isLiteVersion == null ) { - try { - Class.forName(DummyProtectedClassName); - isLiteVersion = false; - } catch ( ClassNotFoundException e) { - isLiteVersion = true; - } - } - return isLiteVersion; - } - private static final String DummyProtectedClassName = "org.broadinstitute.sting.gatk.DummyProtectedClass"; - private static Boolean isLiteVersion = null; - /** * Find the field with the given name in the class. Will inspect all fields, independent * of access level. diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java index 7a6d96131..a13be21c5 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java @@ -139,25 +139,26 @@ public final class BCF2Decoder { return decodeTypedValue(typeDescriptor, size); } + @Requires("size >= 0") public final Object decodeTypedValue(final byte typeDescriptor, final int size) { - final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); - - assert size >= 0; - if ( size == 0 ) { + // missing value => null in java return null; - } else if ( type == BCF2Type.CHAR ) { // special case string decoding for efficiency - return decodeLiteralString(size); - } else if ( size == 1 ) { - return decodeSingleValue(type); } else { - final ArrayList ints = new ArrayList(size); - for ( int i = 0; i < size; i++ ) { - final Object val = decodeSingleValue(type); - if ( val == null ) continue; // auto-pruning. We remove trailing nulls - ints.add(val); + final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); + if ( type == BCF2Type.CHAR ) { // special case string decoding for efficiency + return decodeLiteralString(size); + } else if ( size == 1 ) { + return decodeSingleValue(type); + } else { + final ArrayList ints = new ArrayList(size); + for ( int i = 0; i < size; i++ ) { + final Object val = decodeSingleValue(type); + if ( val == null ) continue; // auto-pruning. We remove trailing nulls + ints.add(val); + } + return ints.isEmpty() ? null : ints; // return null when all of the values are null } - return ints.isEmpty() ? null : ints; // return null when all of the values are null } } @@ -256,7 +257,7 @@ public final class BCF2Decoder { * int elements are still forced to do a fresh allocation as well. * @return see description */ - @Requires({"BCF2Type.INTEGERS.contains(type)", "size >= 0", "type != null"}) + @Requires({"type != null", "type.isIntegerType()", "size >= 0"}) public final int[] decodeIntArray(final int size, final BCF2Type type, int[] maybeDest) { if ( size == 0 ) { return null; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java index f874b14cd..49f375b25 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java @@ -35,6 +35,7 @@ import java.util.EnumSet; * @since 05/12 */ public enum BCF2Type { + MISSING(0, 0, 0x00), INT8 (1, 1, 0xFFFFFF80, -127, 127), // todo -- confirm range INT16(2, 2, 0xFFFF8000, -32767, 32767), INT32(3, 4, 0x80000000, -2147483647, 2147483647), @@ -86,7 +87,7 @@ public enum BCF2Type { * @param v * @return */ - @Requires("INTEGERS.contains(this)") + @Requires("this.isIntegerType()") public final boolean withinRange(final long v) { return v >= minValue && v <= maxValue; } /** @@ -108,7 +109,14 @@ public enum BCF2Type { /** * An enum set of the types that might represent Integer values */ - public final static EnumSet INTEGERS = EnumSet.of(INT8, INT16, INT32); + private final static EnumSet INTEGERS = EnumSet.of(INT8, INT16, INT32); + + /** + * @return true if this BCF2Type corresponds to the magic "MISSING" type (0x00) + */ + public boolean isMissingType() { + return this == MISSING; + } public boolean isIntegerType() { return INTEGERS.contains(this); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java index 143ab52df..43e933948 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java @@ -225,7 +225,7 @@ public final class BCF2Utils { } } - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Ensures("result.isIntegerType()") public final static BCF2Type determineIntegerType(final int value) { for ( final BCF2Type potentialType : INTEGER_TYPES_BY_SIZE) { if ( potentialType.withinRange(value) ) @@ -235,7 +235,7 @@ public final class BCF2Utils { throw new ReviewedStingException("Integer cannot be encoded in allowable range of even INT32: " + value); } - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Ensures("result.isIntegerType()") public final static BCF2Type determineIntegerType(final int[] values) { // literally a copy of the code below, but there's no general way to unify lists and arrays in java BCF2Type maxType = BCF2Type.INT8; @@ -260,8 +260,8 @@ public final class BCF2Utils { * @param t2 * @return */ - @Requires({"BCF2Type.INTEGERS.contains(t1)","BCF2Type.INTEGERS.contains(t2)"}) - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Requires({"t1.isIntegerType()","t2.isIntegerType()"}) + @Ensures("result.isIntegerType()") public final static BCF2Type maxIntegerType(final BCF2Type t1, final BCF2Type t2) { switch ( t1 ) { case INT8: return t2; @@ -271,7 +271,7 @@ public final class BCF2Utils { } } - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Ensures("result.isIntegerType()") public final static BCF2Type determineIntegerType(final List values) { BCF2Type maxType = BCF2Type.INT8; for ( final int value : values ) { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 1f0b2b054..dcdd95d00 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.utils.variantcontext; +import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broad.tribble.TribbleException; import org.broad.tribble.util.ParsingUtils; @@ -176,6 +177,10 @@ import java.util.*; * @author depristo */ public class VariantContext implements Feature { // to enable tribble integration + private final static boolean WARN_ABOUT_BAD_END = true; + final protected static Logger logger = Logger.getLogger(VariantContext.class); + + private boolean fullyDecoded = false; protected CommonInfo commonInfo = null; public final static double NO_LOG10_PERROR = CommonInfo.NO_LOG10_PERROR; @@ -1146,10 +1151,16 @@ public class VariantContext implements Feature { // to enable tribble integratio if ( hasAttribute(VCFConstants.END_KEY) ) { final int end = getAttributeAsInt(VCFConstants.END_KEY, -1); assert end != -1; - if ( end != getEnd() ) - throw new ReviewedStingException("Badly formed variant context at location " + getChr() + ":" + if ( end != getEnd() && end != getEnd() + 1 ) { + // the end is allowed to 1 bigger because of the padding + final String message = "Badly formed variant context at location " + getChr() + ":" + getStart() + "; getEnd() was " + getEnd() - + " but this VariantContext contains an END key with value " + end); + + " but this VariantContext contains an END key with value " + end; + if ( WARN_ABOUT_BAD_END ) + logger.warn(message); + else + throw new ReviewedStingException(message); + } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java index 812e6dd07..ddeb4d284 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java @@ -47,7 +47,7 @@ import java.util.Map; */ @Invariant({ "headerLine != null", - "BCF2Type.INTEGERS.contains(dictionaryOffsetType)", + "dictionaryOffsetType.isIntegerType()", "dictionaryOffset >= 0" }) public abstract class BCF2FieldEncoder { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java index 45610bbf9..c77fe7172 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java @@ -338,7 +338,7 @@ class BCF2Writer extends IndexingVariantContextWriter { } @Requires("! strings.isEmpty()") - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Ensures("result.isIntegerType()") private final BCF2Type encodeStringsByRef(final Collection strings) throws IOException { final List offsets = new ArrayList(strings.size()); diff --git a/public/java/test/org/broadinstitute/sting/gatk/CommandLineGATKUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/CommandLineGATKUnitTest.java new file mode 100644 index 000000000..5de48fda9 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/gatk/CommandLineGATKUnitTest.java @@ -0,0 +1,43 @@ +package org.broadinstitute.sting.gatk; + +import net.sf.samtools.SAMFileReader; +import org.broadinstitute.sting.BaseTest; +import org.testng.Assert; +import org.testng.annotations.Test; + +import java.io.File; + +/** + * @author Eric Banks + * @since 7/18/12 + */ +public class CommandLineGATKUnitTest extends BaseTest { + + @Test(enabled = true) + public void testSamTextFileError1() { + final File samFile = new File(publicTestDir + "testfile.sam"); + final File indexFile = new File(publicTestDir + "HiSeq.1mb.1RG.bai"); + try { + final SAMFileReader reader = new SAMFileReader(samFile, indexFile, false); + + // we shouldn't get here + Assert.fail("We should have exceptioned out when trying to create a reader with an index for a textual SAM file"); + } catch (RuntimeException e) { + Assert.assertTrue(e.getMessage().indexOf(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_1) != -1); + } + } + + @Test(enabled = true) + public void testSamTextFileError2() { + File samFile = new File(publicTestDir + "testfile.sam"); + try { + final SAMFileReader reader = new SAMFileReader(samFile); + reader.getFilePointerSpanningReads(); + + // we shouldn't get here + Assert.fail("We should have exceptioned out when trying to call getFilePointerSpanningReads() for a textual SAM file"); + } catch (RuntimeException e) { + Assert.assertTrue(e.getMessage().indexOf(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_2) != -1); + } + } +} diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 0b45dc931..17d27c156 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("e0a08416249515ea18bd0663c90c9330")); + Arrays.asList("95b0627bfcac2191aed9908904e892ff")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("0b60da46ba0eabb3abe5e0288937f9b0")); + Arrays.asList("0e2509349fd6c8a9e9408c918215e1de")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("5eb576d0234c912d8efea184492691d0")); + Arrays.asList("32d81a7797605afb526983a2ab45efc2")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("8860524d793d24b2e32f318433fcf527")); + Arrays.asList("350539ccecea0d1f7fffd4ac29c015e7")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -90,7 +90,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testOverwritingHeader() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1, - Arrays.asList("ebbf32f5b8b8d22f2eb247a0a3db3da0")); + Arrays.asList("c222361819fae035a0162f876990fdee")); executeTest("test overwriting header", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 616503cff..9e960b6ed 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("f98c38defc8d619609399b4a3ba874e8")); + Arrays.asList("0039fd0464c87e6ce66c4c8670fd8dfa")); executeTest("test MultiSample Pilot1", spec); } @@ -52,7 +52,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSingleSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1, - Arrays.asList("736607ee529b5624a3ab5521ab9e1b35")); + Arrays.asList("61007c22c00a2871237280914a8f88f0")); executeTest("test SingleSample Pilot2", spec); } @@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, - Arrays.asList("f33507add5d5c30448948906467dd3f3")); + Arrays.asList("feda4a38bba096f7b740a146055509c2")); executeTest("test Multiple SNP alleles", spec); } @@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testReverseTrim() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, - Arrays.asList("0d724551e00129730b95fd4d70faaa58")); + Arrays.asList("0ff525e65c5836289c454c76ead5d80e")); executeTest("test reverse trim", spec); } @@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "fe3429b736c50bb770e40c0320d498ed"; + private final static String COMPRESSED_OUTPUT_MD5 = "e1a17f8f852c3d639f26e659d37bc1e5"; @Test public void testCompressedOutput() { @@ -139,7 +139,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinBaseQualityScore() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1, - Arrays.asList("b341b87742848a3224115fe94e73f244")); + Arrays.asList("b0b92abbaaa4c787dce6f1b302f983ee")); executeTest("test min_base_quality_score 26", spec); } @@ -147,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSLOD() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("acb5332a267927d78edd51d93685111c")); + Arrays.asList("186d33429756c89aad6cd89424d6dc94")); executeTest("test SLOD", spec); } @@ -155,7 +155,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testNDA() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("74779b59730962bdf36a7a8ef84ac24d")); + Arrays.asList("11b87f68b8530da168c1418513115f30")); executeTest("test NDA", spec); } @@ -163,23 +163,23 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testCompTrack() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("036edf58a4ed6c626f53bd2ab34b9f97")); + Arrays.asList("d2be4b1af1f29579c4f96c08e1ddd871")); executeTest("test using comp track", spec); } @Test public void testOutputParameterSitesOnly() { - testOutputParameters("-sites_only", "52b8336f347d182c158e8384b78f5a6d"); + testOutputParameters("-sites_only", "0055bd060e6ef53a6b836903d68953c9"); } @Test public void testOutputParameterAllConfident() { - testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "281363e6afb3260143bfdb22710e3d0e"); + testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "235bec0a7b2d901442261104db18f5eb"); } @Test public void testOutputParameterAllSites() { - testOutputParameters("--output_mode EMIT_ALL_SITES", "a802b672850b6fbc2764611d3ad071d9"); + testOutputParameters("--output_mode EMIT_ALL_SITES", "7c57ede7019063c19aa9d2136045d84f"); } private void testOutputParameters(final String args, final String md5) { @@ -193,7 +193,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testConfidence() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1, - Arrays.asList("99ef7ba1747c7289ce1f963130539e18")); + Arrays.asList("3f8d724a5158adac4df38c4e2ed04167")); executeTest("test confidence 1", spec1); } @@ -201,7 +201,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testConfidence2() { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1, - Arrays.asList("99ef7ba1747c7289ce1f963130539e18")); + Arrays.asList("3f8d724a5158adac4df38c4e2ed04167")); executeTest("test confidence 2", spec2); } @@ -212,12 +212,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // -------------------------------------------------------------------------------------------------------------- @Test public void testHeterozyosity1() { - testHeterozosity( 0.01, "7e1681b9052e357ca4a065fa76c8afb6" ); + testHeterozosity( 0.01, "7e7384a3a52e19f76f368c2f4561d510" ); } @Test public void testHeterozyosity2() { - testHeterozosity( 1.0 / 1850, "68a12f3eccac6cf4b27b6424f23628ee" ); + testHeterozosity( 1.0 / 1850, "3d16366d870c086e894c07c9da411795" ); } private void testHeterozosity(final double arg, final String md5) { @@ -241,7 +241,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("b098a7744a448cf91a50886e4cc7d268")); + Arrays.asList("58abc4f504d3afd42271e290ac846c4b")); executeTest(String.format("test multiple technologies"), spec); } @@ -260,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("2f008169b82d542ec9cc94908c395a0f")); + Arrays.asList("e247f579f01eb698cfa1ae1e8a3995a8")); executeTest(String.format("test calling with BAQ"), spec); } @@ -279,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("0d4177d7f963f4b4e8568613e7a468f0")); + Arrays.asList("cc2167dce156f70f5a31ac3dce499266")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -307,7 +307,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("181c4ed8dd084b83f8de92123bb85c41")); + Arrays.asList("10c86ff98ad5ab800d208b435bcfbd7d")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -317,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("5250cefb1fff262a6a3985dee29c154d")); + Arrays.asList("c0c4dbb050296633a3150b104b77e05a")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec); } @@ -327,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("ebba1c06555c469cfb01d87f34aa6783")); + Arrays.asList("2472722f87f8718861698f60bbba2462")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); } @@ -335,7 +335,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSampleIndels1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, - Arrays.asList("01fd223deb4f88fb7d9ee9736b664d8a")); + Arrays.asList("eeb64b261f0a44aa478d753dbbf9378e")); List result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst(); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( @@ -384,7 +384,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.0", 1, - Arrays.asList("25465c6dd3c4845f61b0f8e383388824")); + Arrays.asList("160600dfa8e46f91dbb5d574517aac74")); executeTest("test minIndelFraction 0.0", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 43812d12d..d9a91c4c2 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -27,8 +27,11 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.annotations.Test; +import org.testng.annotations.DataProvider; +import java.util.ArrayList; import java.util.Arrays; +import java.util.List; public class VariantEvalIntegrationTest extends WalkerTest { private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval/"; @@ -613,4 +616,37 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testWithAC0() { testIncludingAC0(true, "c786128cfe4d3e28cdbc15c5c838ad20"); } @Test public void testWithoutAC0() { testIncludingAC0(false, "7bc505c07d9aee49571ad4b3fc9f7feb"); } + // + // Test validation report is doing the right thing with sites only and genotypes files + // where the validation comp has more genotypes than eval + // + @Test(dataProvider = "testValidationReportData") + public void testValidationReport(final String name, final String eval, final String comp, final String md5) { + WalkerTestSpec spec = new WalkerTestSpec( + buildCommandLine( + "-T VariantEval", + "-R " + b37KGReference, + "-eval " + eval, + "-comp " + comp, + "-L 20:10,000,000-10,000,010 -noST -noEV -EV ValidationReport -o %s" + ), + 1, + Arrays.asList(md5)); + executeTest("testValidationReport with " + name, spec); + } + + @DataProvider(name = "testValidationReportData") + public Object[][] testValidationReportData() { + final String compGenotypes = privateTestDir + "/validationReportComp.vcf"; + final String compSites = privateTestDir + "/validationReportComp.noGenotypes.vcf"; + final String evalGenotypes = privateTestDir + "/validationReportEval.vcf"; + final String evalSites = privateTestDir + "/validationReportEval.noGenotypes.vcf"; + + List tests = new ArrayList(); + tests.add(new Object[]{"sites/sites", evalSites, compSites, "0b32e19efce28087cdc7b58e17ed633a"}); + tests.add(new Object[]{"sites/genotypes", evalSites, compGenotypes, "e2ffecee4a3acd0da7dd7fe10a59b2bc"}); + tests.add(new Object[]{"genotypes/sites", evalGenotypes, compSites, "f0dbb848a94b451e42765b0cb9d09ee2"}); + tests.add(new Object[]{"genotypes/genotypes", evalGenotypes, compGenotypes, "73790b530595fcbd467a88475ea9717f"}); + return tests.toArray(new Object[][]{}); + } } diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index b271d8c84..e9b845d59 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -39,6 +39,17 @@ public class VCFIntegrationTest extends WalkerTest { executeTest("Test reading and writing breakpoint VCF", spec1); } + @Test(enabled = true) + public void testReadingAndWriting1000GSVs() { + String testVCF = privateTestDir + "1000G_SVs.chr1.vcf"; + + String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; + + String test1 = baseCommand + "-T SelectVariants -V " + testVCF; + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("")); + executeTest("Test reading and writing 1000G Phase I SVs", spec1); + } + @Test public void testReadingAndWritingSamtools() { String testVCF = privateTestDir + "samtools.vcf"; @@ -59,12 +70,12 @@ public class VCFIntegrationTest extends WalkerTest { executeTest("Test writing samtools WEx BCF example", spec1); } - @Test(enabled = false) + @Test(enabled = true) public void testReadingSamtoolsWExBCFExample() { String testVCF = privateTestDir + "ex2.bcf"; String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s "; String test1 = baseCommand + "-T SelectVariants -V " + testVCF; - WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("63a2e0484ae37b0680514f53e0bf0c94")); + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0439e2b4ccc63bb4ba7c283cd9ab1b25")); executeTest("Test reading samtools WEx BCF example", spec1); } diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java index ca4cdf306..c436a7b45 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java @@ -597,23 +597,41 @@ public class VariantContextTestProvider { } public static void testReaderWriter(final VariantContextIOTest tester, final VariantContextTestData data) throws IOException { + testReaderWriter(tester, data.header, data.vcs, data.vcs, true); + } + + public static void testReaderWriter(final VariantContextIOTest tester, + final VCFHeader header, + final List expected, + final Iterable vcs, + final boolean recurse) throws IOException { final File tmpFile = File.createTempFile("testReaderWriter", tester.getExtension()); tmpFile.deleteOnExit(); - // todo -- test all options - - // write + // write expected to disk final EnumSet options = EnumSet.of(Options.INDEX_ON_THE_FLY); final VariantContextWriter writer = tester.makeWriter(tmpFile, options); - writer.writeHeader(data.header); - final List expected = data.vcs; - for ( VariantContext vc : expected ) - writer.add(vc); - writer.close(); + writeVCsToFile(writer, header, vcs); - final Iterable actual = readAllVCs(tmpFile, tester.makeCodec()).getSecond(); + // ensure writing of expected == actual + final Pair> p = readAllVCs(tmpFile, tester.makeCodec()); + final Iterable actual = p.getSecond(); assertEquals(actual, expected); + if ( recurse ) { + // if we are doing a recursive test, grab a fresh iterator over the written values + final Iterable read = readAllVCs(tmpFile, tester.makeCodec()).getSecond(); + testReaderWriter(tester, p.getFirst(), expected, read, false); + } + } + + private static void writeVCsToFile(final VariantContextWriter writer, final VCFHeader header, final Iterable vcs) { + // write + writer.writeHeader(header); + for ( VariantContext vc : vcs ) + if (vc != null) + writer.add(vc); + writer.close(); } /** diff --git a/public/testdata/testfile.sam b/public/testdata/testfile.sam new file mode 100644 index 000000000..7345c03d1 --- /dev/null +++ b/public/testdata/testfile.sam @@ -0,0 +1,450 @@ +@HD VN:1.0 GO:none SO:coordinate +@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens +@SQ SN:chr1 LN:247249719 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:9ebc6df9496613f373e73396d5b3b6b6 SP:Homo sapiens +@SQ SN:chr2 LN:242951149 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:b12c7373e3882120332983be99aeb18d SP:Homo sapiens +@SQ SN:chr3 LN:199501827 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:0e48ed7f305877f66e6fd4addbae2b9a SP:Homo sapiens +@SQ SN:chr4 LN:191273063 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:cf37020337904229dca8401907b626c2 SP:Homo sapiens +@SQ SN:chr5 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UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:05926bdbff978d4a0906862eb3f773d0 SP:Homo sapiens +@SQ SN:chr6_random LN:1875562 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d62eb2919ba7b9c1d382c011c5218094 SP:Homo sapiens +@SQ SN:chr7_random LN:549659 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:28ebfb89c858edbc4d71ff3f83d52231 SP:Homo sapiens +@SQ SN:chr8_random LN:943810 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:0ed5b088d843d6f6e6b181465b9e82ed SP:Homo sapiens +@SQ SN:chr9_random LN:1146434 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:1e3d2d2f141f0550fa28a8d0ed3fd1cf SP:Homo sapiens +@SQ SN:chr10_random LN:113275 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:50be2d2c6720dabeff497ffb53189daa SP:Homo sapiens +@SQ SN:chr11_random LN:215294 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:bfc93adc30c621d5c83eee3f0d841624 SP:Homo sapiens +@SQ SN:chr13_random LN:186858 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:563531689f3dbd691331fd6c5730a88b SP:Homo sapiens +@SQ SN:chr15_random LN:784346 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:bf885e99940d2d439d83eba791804a48 SP:Homo sapiens +@SQ SN:chr16_random LN:105485 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:dd06ea813a80b59d9c626b31faf6ae7f SP:Homo sapiens +@SQ SN:chr17_random LN:2617613 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:34d5e2005dffdfaaced1d34f60ed8fc2 SP:Homo sapiens +@SQ SN:chr18_random LN:4262 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Homo sapiens +@SQ SN:chr19_random LN:301858 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:420ce95da035386cc8c63094288c49e2 SP:Homo sapiens +@SQ SN:chr21_random LN:1679693 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:a7252115bfe5bb5525f34d039eecd096 SP:Homo sapiens +@SQ SN:chr22_random LN:257318 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:4f2d259b82f7647d3b668063cf18378b SP:Homo sapiens +@SQ SN:chrX_random LN:1719168 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:f4d71e0758986c15e5455bf3e14e5d6f SP:Homo sapiens +@RG ID:20FUK.1 PL:illumina PU:20FUKAAXX100202.1 LB:Solexa-18483 DT:2010-02-02T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20FUK.2 PL:illumina PU:20FUKAAXX100202.2 LB:Solexa-18484 DT:2010-02-02T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20FUK.3 PL:illumina PU:20FUKAAXX100202.3 LB:Solexa-18483 DT:2010-02-02T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20FUK.4 PL:illumina PU:20FUKAAXX100202.4 LB:Solexa-18484 DT:2010-02-02T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20FUK.5 PL:illumina PU:20FUKAAXX100202.5 LB:Solexa-18483 DT:2010-02-02T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20FUK.6 PL:illumina PU:20FUKAAXX100202.6 LB:Solexa-18484 DT:2010-02-02T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20FUK.7 PL:illumina PU:20FUKAAXX100202.7 LB:Solexa-18483 DT:2010-02-02T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20FUK.8 PL:illumina PU:20FUKAAXX100202.8 LB:Solexa-18484 DT:2010-02-02T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20GAV.1 PL:illumina PU:20GAVAAXX100126.1 LB:Solexa-18483 DT:2010-01-26T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20GAV.2 PL:illumina PU:20GAVAAXX100126.2 LB:Solexa-18484 DT:2010-01-26T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20GAV.3 PL:illumina PU:20GAVAAXX100126.3 LB:Solexa-18483 DT:2010-01-26T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20GAV.4 PL:illumina PU:20GAVAAXX100126.4 LB:Solexa-18484 DT:2010-01-26T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20GAV.5 PL:illumina PU:20GAVAAXX100126.5 LB:Solexa-18483 DT:2010-01-26T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20GAV.6 PL:illumina PU:20GAVAAXX100126.6 LB:Solexa-18484 DT:2010-01-26T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20GAV.7 PL:illumina PU:20GAVAAXX100126.7 LB:Solexa-18483 DT:2010-01-26T00:00:00-0500 SM:NA12878 CN:BI +@RG ID:20GAV.8 PL:illumina PU:20GAVAAXX100126.8 LB:Solexa-18484 DT:2010-01-26T00:00:00-0500 SM:NA12878 CN:BI +@PG ID:BWA VN:0.5.7 CL:tk +20GAVAAXX100126:8:21:18798:198557 83 chr1 9999918 60 101M = 9999594 -424 CAAGCTCCGCCTCCCAGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCACCCACCACCACGCCTGGCCAATTTTTTTGTATT 7A9AAA79;;.@=BAA;60@C=BCBBAC@@@5;A>A??@B6?BA;BB9BB@BBABBAABBBBBBBBBBBCBBBBBBBCBBBCBCBBBCCBBCCB@CCBB UQ:i:0 +20GAVAAXX100126:8:26:17788:24663 99 chr1 9999965 60 101M = 10000321 441 GAGTAGCTGGGACTACAGGCACCCACCACCACGCCTGGCCAATTTTTTTGTATTTTTAGTAGAGATAGGGTTTCACCATATTAGCCAGGATGGTCTTGATC CDBACCCDBCCDADCACCCACABBBABC;BCA;BBCBCBBCDCDDDDDA@BBCDDDABCACCDCDCCCCCAD@BCABCCCCDCCBCCCCDCCCCCDDCDDD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHGHHHHIHHHDHHHHHHHHHHHHHHHHHHHGGGGHHHHGGHGHHHHHHHHHHFHGHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:47:10796:84088 99 chr1 9999998 60 101M = 10000328 430 CCTGGCCAATTTTTTTGTATTTTTAGTAGAGATAGGGTTTCACCATATTAGCCAGGATGGTCTTGATCTGCTGACCTCATGACCCACCCGCCTCGGCCTTC CBC@CCCCDCDDDDDAA@BCDDDAACBCCDCDCC@CCBBDBBABCCCCDCCBBCCCCC>C;BDDBDCBDBBDBDABDBCCBDACCC@AA9CCDC;DCCDED MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHGGEGHHHHGGHHHHHHHHHGHHHIHHIHHHHHHHHHHHHHHGHDHCHHHHHHHHHHHHHHHHHHHHHHHHHIGGGHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:62:7317:185100 675 chr1 10000001 60 78M23S = 10000382 415 GGCCAATTTTTTTGTATTTTTAGTAGAGATAGAGTTTCACCATATTAGCCAGGATGGCCTTAATCTGCTGACCTCATAATCACACAGCCTCGTCCTTCAAA >?78+*?88CBC24B.BBCA>6=846;8C-2@(?@10AB++7C>A/C9<>A,@?.B,()C6*B3:D8@C*+92A:BA######################## MD:Z:32G24T3G15G0 PG:Z:BWA RG:Z:20GAV.8 AM:i:25 NM:i:4 SM:i:25 MQ:i:60 OQ:Z:==76**=76BCA44A.ACC?;4:43273B,1=*=A34BB--8B7BCDB;CCCDDCCBE>D@DD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHGGGGHHHHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHEEHHHHHHHHHHHHGHBHGHH UQ:i:0 +20GAVAAXX100126:8:64:9003:28381 83 chr1 10000026 60 101M = 9999704 -422 GAGATAGGGTTTCACCATATTAGCCAGGATGGTCTTGATCTGCTGACCTCATGACCCACCCGCCTCGGCCTTCCAAAGTGCTGGGATTACAGGTGTGAGCC DCCBDD?A2ABB@BCBCCCDC@BC@CA@AB@ABCDCBCCCCBACAACCDBCCB@BCB@CC;BCCD;BBCCDDCBDDDACBCCBBBCDCCBDBACACBBBCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HFHFHHDG9GGGGGHHHHHHHDHHGIGGFFFHGHHHHHGHHHGHGFHHHHHHHEGHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:66:8049:3241 83 chr1 10000031 60 101M = 9999623 -508 AGGGTTTCACCATATTAGCCAGGATGGTCTTGATCTGCTGACCTCATGACCCACCCGCCTCGGCCTTCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGC ?DCBEEDCCCCCCCD=DBCBDCBCCBADCDCBCCCCBCCBBCCDB@CB9BCBBCC;BCCD;BBCCDDCBDDDACBCCBBBCDCBBDBACACBDCCCCA:BC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BHHHHHHHIHHHHHHBHHHHHHHHHHHHHHHHHGHHHHHHGHHHHFHHBGHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:65:18189:17218 163 chr1 10000038 60 101M = 10000302 364 CACCATATTAGCCAGGATGGTCTTGATCTGCTGACCTCATGACCCACCCGCCTCGGCCTTCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGCGACCGGC @CABAAABCCBBCBCCCCCCBBDCBCCBDCBDBA@BB?B@B@AC?CACC;@CD@:BBCBB>CB>=A;ACC@:CA@@@>A<@B9@;B?C4BB MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCCBCCCBCCCCBCCBBCB@BBBBBBBBBBBB>BBBABAB@BBABBBBABBAB@?AB@@@B@>9?=@BAA8A@?>@@=;?6?4?=?@6@??<@?@==8=A UQ:i:0 +20GAVAAXX100126:8:27:11272:197846 611 chr1 10000110 60 79M22S = 10000329 297 GATTACAGGTGTGAGCCACCGCGACCGGCCTGCTCAAGATAATTTTTAGGGCTAACTATGACATGAACCCCAAAATTCCTGTCCTCTAGATGGCAGAAACC 1;>5;;5?9>>;:;02<=<<5>5@;<4@9<<=:><<>=A6;*<;:=B8?)78:9::;9;####################### MD:Z:79 PG:Z:BWA RG:Z:20GAV.8 AM:i:25 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:5555551455<==@014544EEEEA>>F@>>E>AE>AAF:4+454AAF=A/=AA50=9==A7A=AF;F-;44544=5?####################### UQ:i:0 +20GAVAAXX100126:8:7:13574:93999 163 chr1 10000133 60 101M = 10000392 359 ACCGGCCTGCTCAAGATAATTTTTAGGGCTAACTATGACATGAACCCCAAAATTCCTGTCCTCTAGATGGCAGAAACCAAGATAAAGTATCCCCACATGGC @AB:AABCBBDBCBCCCCDCCCCCCCCCCDCDADB=>A@BAACD=BCCCDBBC@CCCCABBCB@CC@@AA@CBBAB?BC=ABC@CDB??A?B>AC?CCABAB?BAA?@?AA@A?@AA@<@@@@A@?;@=?A9AA@??:>B UQ:i:0 +20GAVAAXX100126:8:65:18208:188053 163 chr1 10000137 60 101M = 10000358 321 GCCTGCTCAAGATAATTTTTAGGGCTAACTATGACATGAACCCCAAAATTCCTGTCCTCTAGATGGCAGAAACCAAGATAAAGTATCCCCACATGGCCACA @CCC?@BBBDBBCAEDBBCCCCDDCDDEBECCBC?@AAB@?CCDADDDCC@AD@BCADADBCCBCC8CCCBDBABCABABBBDABDCB@C@?C@CACD?BC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCCCCCCCCCCCCCCCCCCBCCCCBCCCCCBBCCCBBBCCBBCBBBBBBBCBBBCCBCBBBBBBACBBBABBBBBBB?BB@B>BBBBABBBBBA@ABBBB UQ:i:0 +20GAVAAXX100126:8:65:17424:133143 163 chr1 10000184 60 101M = 10000444 360 ATTCCTGTCCTCTAGATGGCAGAAACCAAGATAAAGTATCCCCACATGGCCACAAGGTTAAGCTCTTATGGACACAAAACAAGGCAGAGAAATGTCATTTG @CBA@BAABCDBDACCBBCBC=CDDACCDCCCCDCB;BBABCCC?CCBCC@BAADCBBCBBBBBBD@CBB@DBA?BBBB?@BBABCCC=BAAA@A@CBAAB MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBCBBABBBBBBBB@BBBB9BBBBBBBBBBBBBB?BBBBBBBBBAABBAABBAAA:AAAABABAAB@A@ABA@A@A>@?A?@A@@@>>A>>@9@@=?;A UQ:i:0 +20GAVAAXX100126:8:24:16681:115751 83 chr1 10000185 60 101M = 9999853 -432 TTCCTGTCCTCTAGATGGCAGAAACCAAGATAAAGTATCCCCACATGGCCACAAGGTTAAGCTCTTATGGACACAAAACAAGGCAGAGAAATGTCATTTGG 6EA6DADD?DCCD@CCCB?DBDDCCBDDBCCDDDACCDCCCBBBCCBB@BBBDDBADCDCBCDCDCCCBBBBC=>DDBBDDBBBDBDBDD@CADCCDBCBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:23 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:5HG;HHHHEHHHHGHHHHDHHHHHHHHHHHHHHHHHHHHHHHGHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHEEHHHHHHHHHHHHHHHFHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:65:2449:158320 147 chr1 10000187 60 24S77M = 9999832 -431 AACTATGACATGACCCCCAAAATTCCTGTCCTCTAGATGGCAGAAACCAAGATAAAGTATCCCCACATGGCCACAAGGTTAAGCTCTTATGGACACAAAAC #########################@<=?>?A@67C@?A@>?4BACB=D?>A==@;?BBCBACBCCDCADCCDBCACDACCCBBBBAA@BA@ MD:Z:77 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:#########################?:?::?><68B>?@??;1??@@@A>@@;@@@@@?>A@@A?AB@AA@BABBBBBBBBBBB?BBBBBBBABABBCBBB UQ:i:0 +20GAVAAXX100126:8:66:6889:6402 163 chr1 10000196 60 74M27S = 10000514 418 TAGATGGCAGAAACCAAGATAAAGTATCCCCACATGGCCACAAGGTTAAGCTCTTATGGACACAAAACAAGGCAGAGAAATGTCATTTGGCATTGGTTTCA @C<B>?A@BDD?<=?DD>-A=C?=?;97A7B<=7>532;C><9B7D=8<2:B############################ MD:Z:74 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BC;9B:=>:B>=>;=B;B@>7;;-08B9@7A6B:562)8B##################################################################################### MD:Z:13C21 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:1 SM:i:37 MQ:i:29 OQ:Z::B5BCB=6,A4:1)4@##################################################################################### UQ:i:8 +20GAVAAXX100126:8:65:18189:17218 83 chr1 10000302 60 101M = 10000038 -364 CCATAGCAACATTTGTAAATGACCAGCCTGATGGGCTGGCTTGAAAACTTGGCTTATAGGCATCCTAAACCCACGTTCTATCCCCTGATACTCCCCTCTTC DDCDDCCDCCCDDCACDDCBBCCBDBCCCBCCBBBCCCBBDCBDDDBCDCBBCDCCCCBBBCDCCCDD@CCBA;ADDCCCDCCCCCBCCBCDCCCCDADDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHIHHHHHHHFHHHHHHHHHHHHHHHHHHHIHHHHHHGHHHHHHHHHHHHHHHHHHHHHFHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:4:6560:50417 163 chr1 10000312 60 76M25S = 10000637 425 ATTTGTAAATGACCAGCCTGATGGGCTGGCTTGAAAACTTGGCTTATAGGCATCCTAAACCCACCTTCTATCCCCTGATACTCCGCTTTTCATTACAGCAC ?>9?=7;BA;:B;/5BCD?CCC>)A8=:$;30B474@>8<8?*B)BE7?@+?<.-/+39978BCAA########################## MD:Z:64G11 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:?;9=:18A?7:???B:B<4-4;,6ACB8?>'=60A627@:6<8A*@*>B58>+?;+-,)69259@CB@########################## UQ:i:14 +20GAVAAXX100126:8:26:17788:24663 147 chr1 10000321 60 15S86M = 9999965 -441 AGCAACATTTGTAAATGACCAGCCTGATGGGCTGGCTTGAAAACTTGGCTTATAGGCATCCTAATCCCACGTTCTATCCCCTGATACTCCCCTCTTCATTA ################B=?@@@B@>>4:CB5;C??BDB@@3>BBB8&4BCB;?DCCCB@CCDCBACA@?@=>2:?>77@>B@BB??=@?BA@B?AA>>>AAB=;2?BBB<(9BBAB@BBBBA=BBCCAABA7@BBBBBBBBBBCBCB UQ:i:5 +20GAVAAXX100126:8:3:21049:178760 163 chr1 10000325 60 95M6S = 10000650 425 CAGCCTGATGGGCTGGCTTGAAAACTTGGCTTATAGGCATCCTAAACCCACGTTCTATCCCCTGATACTCCCCTCTTCATTACAGAACAACAAAGAAAGAC @CBAABACCBCCBCBCBDC?CDDEADCCCBDCAAB=?==@@CBCBD8CCC?;CAAD=C@BBC?>BA=?C>?=CA@CB?B4>?####### UQ:i:0 +20GAVAAXX100126:8:47:10796:84088 147 chr1 10000328 60 101M = 9999998 -430 CCTGATGGGCTGGCTTGAAAACTTGGCTTATAGGCATCCTAAACCCACGTTCTATCCCCTGATACTCCCCTCTTCATTACAGAACAACAAAGAAAGACAAA ;?@B::A5;?8B:9@?=@DB@B@97@>4':8>B>?>?@>:BC>CCAC6AC>C@CCCABBCBB?>A3>CCCBCBCBD@B?BEBCACCAACCDBCBCA@ABC@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z::7>@55<37=6=;6:9A;78?>3'4::>>A;;@<;AA8AB>>?AB@A@AABB@BBBBA@B3@BBB@B?ABC=A:ACBCBCBBBBBBBBBBBBBBBB UQ:i:0 +20GAVAAXX100126:8:27:11272:197846 659 chr1 10000329 60 22S79M = 10000110 -297 GCAACCTTTGTAACAGACCTGTCTGATGGGCTGGCTTGAAAACTTGGCTTATAGGAATCCGAAACCTACGTACTATCCCCTGATACTCCCCTCTTCATTAC #######################@1>:@C3ACBB1*?CA7(-)87)'>%.(-65;B&@<765@=B3@2C5;C7,*?76@A; MD:Z:33C4T5C4T29 PG:Z:BWA RG:Z:20GAV.8 AM:i:25 NM:i:4 SM:i:25 MQ:i:60 OQ:Z:#######################?0=8??0>?839350@@);A?0)@1*?BBC@-,ACA@)/,6=)):*-)(128@)>;333?;@1=7B6;B3+*@33AB7 UQ:i:34 +20GAVAAXX100126:8:5:4250:100581 147 chr1 10000330 60 9S92M = 10000006 -415 TGACCAGCCTGATGGGCTGGCTTGAAAACTTGGCTTATAGGCATCCTAAACCCACGTTCTATCCCCTGATACTCCCCTCTTCATTACAGAACAACAAAGAA ##########?A>@==??B79=@819@;>8@BBA=@;5?A>@=::BA;B?:>>B?A;5@>?@=BBBBCCCCCCBCDCBCDCBBCBCABCAAAACBC@ MD:Z:92 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:##########?>>>7:>==77<<817?9:1@?A@??86<@@><4:??=?>?A@7@@@?@A>6A@AA?AAA@B@BBBB@BBABBBB@BBBBBBBBBBBBBBB UQ:i:0 +20GAVAAXX100126:8:65:18208:188053 83 chr1 10000358 60 101M = 10000137 -321 TAGGCATCCTAAACCCACGTTCTATCCCCTGATACTCCCCTCTTCATTACAGAACAACAAAGAAAGACAAATTCTTAGCATAAAGTACACCAGATTTGCTA DECCCCDDCCA@>BBAC9ADDCCCDCCCCCBCCCCDCCCCDCDDBCDCBBCBDBBDB@@DDBDDCBBBDDCDDCDCDBBCCDDDACBBCCBDBCDDC@BCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHGGAGGFHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:62:7317:185100 595 chr1 10000382 60 66S35M = 10000001 -415 TTAAATGTCCAGCATGATGGGCTGGCTTGAAAACTTGGCTTATAGGCATCCTAAACCCACGTTCTATCCCCTGATACTCCCCTCTTCATTCCAGAACAACA ##################################################################################################### MD:Z:24A10 PG:Z:BWA RG:Z:20GAV.8 AM:i:25 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:##################################################################################################### UQ:i:2 +20GAVAAXX100126:8:7:13574:93999 83 chr1 10000392 60 101M = 10000133 -359 CTCCCCTCTTCATTACAGAACAACAAAGAAAGACAAATTCTTAGCATAAAGTACACCAGATTTGCTACAGCCTAAGACTGGTCTGACAAATCCTTTTTTTC DEDDDCDCDDCCDCCBDBDCBDC@ADDBDDDBCBDDCDCCDCDBBCCDDDACBBBCBCBCDDCBCCBBCBCCCDDBBCCBADCCBBBDDCDCAADDDBDDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHGHHHHHHHHHHHHHIHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHH UQ:i:0 +20GAVAAXX100126:8:25:6601:158705 99 chr1 10000400 37 101M = 10000802 436 TTCATTACAGAACAACAAAGAAAGACAAATTCTTAGCATAAAGTACACCAGATTTGCTACAGCCTAAGACTGGTCTGACAAATCCTTTTTTTCTACTAATC 8;>7=;A?@5>>=>>;3>6=5=4328<::9;;=;:<6198=*7;9>A>??;<:>>?>B6==:41>A:4;, MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:37 MQ:i:29 OQ:Z:@CCEE@CCC;44444A7A;<7<863@<===55444=:1===,:@@FFFFD@==CAE88CE>9@0 UQ:i:0 +20GAVAAXX100126:8:4:15177:54134 99 chr1 10000435 60 101M = 10000750 415 GCATAAAGTACACCAGATTTGCTACAGCCTAAGACTGGTCTGACAAATCCTTTTTTTCTACTAATCAGACCCTCGCAGAGAAGACAAATAGTGGCATTTAC CBCACDDC@CACAB-CDCDDBBCCACCBBDCDCDACBCABDBDACDDCBBCDDDDDA>CAADBDCBBCDABBDB;BCCDCDDCDACDDCCCBCDCDCDBDB MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHIHHHHH-HHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHGEGGHHIHHHFHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHIFHH UQ:i:0 +20GAVAAXX100126:8:65:17424:133143 83 chr1 10000444 60 101M = 10000184 -360 ACACCAGATTTGCTACAGCCTAAGACTGGTCTGACAAATCCTTTTTTTCTACTAATCAGACCCTCGCAGAGAAGACAAATAGTGGCATTTACCGTTTACAC DDCDCDCCDDCBCCCBDBCCCDDBBCCBADCCBCBDDCDCBAAADDDDCCBCCDCDBCBBCCCD;BBCBCBDDBBBDDCCDACBBBCDDCCC;ADDCABCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:61:14621:35929 163 chr1 10000470 60 101M = 10000818 448 TGGTCTGACAAATCCTTTTTTTCTACTAATCAGACCCTCGCAGAGAAGACAAATAGTGGCATTTACCGTTTACACAACATATACAGAGAGAGAGAGACCAG =BC@ABAAAC=DCADDBBCCCCBDCBDCEDCC@C?B>C<:@CAC?BDB@@@BDACCACCCAC6?AA>8BCACA?>AB?CBA9C?BDDB>C@>C@DACB>@7 MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:CCBBB=A?ACCB?DDBC>5@@?>:?BBC@DBC@C@?;;7=>9>=>;@?AACCBACDDBDCDAD@?D:=?=><===?? UQ:i:0 +20GAVAAXX100126:8:21:13663:85034 163 chr1 10000518 60 86M15S = 10000794 376 ACAAATAGTGGCATTTACCGTTTACACAACATATACAGAGAGAGAGAGACCAGAAACTTGGCTGGTAAGAATTTCTTCCTCTGGCCAGGAGCGGTGGCTCA @ABCBABBBBCBCABCCAC;ACCCACBCDACCCCB>ABBBAABC@CCCBA@CC@DDADCA?BB?CB=CABACCA@CB@A=@@A@@@A@=;@@>???################ UQ:i:0 +20GAVAAXX100126:8:68:13621:42696 595 chr1 10000556 29 66S35M = 10000250 -340 TTCTACAAATCAGACCCTCGCAGAGAAGACAAATAGTGGCATTTACCGTTTACCCAACATATACAGAGAGAGAGAGACCAGAAACTTGGCTGGTAAGCATT ##################################################################################################### MD:Z:31A3 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:1 SM:i:0 MQ:i:37 OQ:Z:##################################################################################################### UQ:i:2 +20GAVAAXX100126:8:4:6560:50417 83 chr1 10000637 60 101M = 10000312 -425 TTGGGGAGGTTGAGGCGTGTGGATCAGAAGGTCAAGAGATCCAGACCATCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCTG A37:<;++7+::2%848-8:909::>9;;;:9<:<;6,:A>;<<==;6>=<@BB:B@@=>;=AC=D;;7778A@=D>CBA@>DD>C39@>=@>;;=:8:6: MD:Z:2T6C7G83 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:3 SM:i:37 MQ:i:60 OQ:Z:E84<@<-05-443(444/4553<<=<@@=@>544446-=DA?@?A?=:A?=EHH=HFFDDBEHHEH55445FHDDHCHHGCCHHEH11444FDBBDBFEBE UQ:i:44 +20GAVAAXX100126:8:3:21049:178760 83 chr1 10000650 60 101M = 10000325 -425 GGCGGGTGGATCAGAAGGTCAAGAGATCCAGACCATCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCTGGACATGGTGGTGG DD;CCADCCCDCDBDDCADBDDBDBCDCBDBBCBCDCCCBBCBDCBCCBACBDDBCCC;ADCDCCBCA@DDDCAABDDDDCDCDBCCBBBBCCCACC?CBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHGGHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:4:15177:54134 147 chr1 10000750 60 101M = 10000435 -415 GGCGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCTAGATCACGCCACTGCACTCCA CA8@1@B?BC>D?BCDBBCAB>CBBACABDABEC?CDBBDACCCCCCAC@@ACDCDACDC@BAABB@DCBCDACBDBCCCDBCCBA;ACA,ACBA@ABCB@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:A<>;2>=?A@?@@AAAAAA?B=BABBABABABBBBBBBBBBBB@BBBBBCA;BBBBBBBBBBBBBBBBBBBBBBBBBABBBBBBBBBBB@)@BBB@BBBBB UQ:i:0 +20GAVAAXX100126:8:21:13663:85034 83 chr1 10000794 60 101M = 10000518 -376 TGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCTAGATCACGCCACTGCACTCCAGCCTGGCGACACAGCGAGACTCCGTCTCAAAAAAAAAAATAATA =0;BC@D>>>>>>>=DDCCBBCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@8@FFFH@FDHHHHHHHHHHIHHHHHHHHDHHHIHHEHHGHEHHHHGHGBHFHFHHHHFHHHHFHHHHHHHHHEHHHEHHGHHHEEEEEEEEEHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:25:6601:158705 147 chr1 10000802 29 66S35M = 10000400 -436 TGTACATGGTGGTGGGAGCATGGAGTCCCACCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTTAACCCAGGAGGTGGAGCTTGCAGTGAGCCTAGATCAC ##########################################################################??=9;5*BBA6:?9'@5;096;>8?B? MD:Z:14G20 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:1 SM:i:0 MQ:i:37 OQ:Z:##########################################################################@;9654)@@@35@<'<5;-:/<<5@?? UQ:i:9 +20GAVAAXX100126:8:61:14621:35929 83 chr1 10000818 60 101M = 10000470 -448 TGCAGTGAGCCTAGATCACGCCACTGCACTCCAGCCTGGCGACACAGCGAGACTCCGTCTCAAAAAAAAAAATAATAAATAAGAAAAGGAAAAAAAAGAAT 7D2DAD@AAA?@DBC??@9;=>AAC?BBCDCADABCCCB;BCB@BDB;BDB?CDC;ADADA@@@@A@@>@DCCDCCDDCBADBDDDDB@AAAAADDD@CCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:5H8HHHGDFFEFHHHCDDFBBDFFHEHHHHHFHFGHHHHHHHIDHHHHHHHDHHHHHHGHGGGGGGGGEGHHHHHHHHHGGHHHHHHHGGGGGGHHHHHHH UQ:i:0 +20GAVAAXX100126:8:22:20335:91038 163 chr1 10000847 29 68M33S = 10001097 350 TCCAGCCTGGCGACACAGCGAGACTCCGTCTCAAAAAAAAAAAAAATAAAAAAAAAAAGAAAAAAAAAAAAAAAAATAAAGGAAAAGCCAAATGCAGAGAA @BBBAABCBCA;A@B@CBA:CBB?CBC;BBDB9ACC?<@A??2)<4';C72<8)AC;%7(=CCBCD=################################## MD:Z:43T6T2G5G8 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:4 SM:i:0 MQ:i:37 OQ:Z:BBBBBBBBABABABAABAAAAA??ABBB?ABA7?BBA>AA@?2(?4'8A22;3'AAAAA?################################## UQ:i:40 +20GAVAAXX100126:8:65:4263:123939 99 chr1 10000877 60 101M = 10001182 403 CAAAAAAAAAAAATAATAAATAAGAAAAGGAAAAAAAAGAATACAACTCAGGAACAGCCAAATGGAGGAGATGCATGGGACAAGGTTTAGTGGGGGGCTGC CCDBDDD>>>??>A>?A?DDCCDCDDD?=CDDDDDD??>@A@C>CDADBCCCBDACCBACDDCBCDCCDCA:;9:B@@ABACBACAB@>;::555@?>DD5 MD:Z:0T0C99 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:2 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHEEEEEECEECFHHHHHHHHHEEHHHHHHHEECECCHFHHHHHHHHFHHHHHGHHHHHHHHHHHE@B@=GGFFGHHFGHDFDD?54444CCCHH5 UQ:i:68 +20GAVAAXX100126:8:48:15961:32254 675 chr1 10000919 29 27M74S = 10001301 416 ACAACTCAGGAACAGCCAAATGGAGGATTTGCGCGGGCCTTGGTTTAGTGGGCGGCGGCGGAGCTTTCTCGCCCTCCGCAAGTGAATCACCCTTCCAGTGC 8=1==>?4A############################################################################################ MD:Z:27 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:0 SM:i:29 MQ:i:29 OQ:Z:3=BCBBAC;@::3;>78;5A@############################################### MD:Z:55 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BB=5@BA@<;>ABBAA@7@A:/9@=55@<4@9)9@84@>69=70(=9:56>5;A############################################### UQ:i:0 +20GAVAAXX100126:8:22:20335:91038 83 chr1 10001097 37 101M = 10000847 -350 AAATTGAAAAGAAAATCCTAACTTTCCAAGCCTAAGTAACAAAAGGACCAGAGGCTACCCCTTTGCAAACCCCTACCTTTTCTGTGGCAGATGGGAAATTG EECED?@?ADCDDB@CCCCD;CDDDCBDDBCCCDDABAABDDDDBBBCBDBCBBCC@CCCCDDCBBDD:CCCCCACCDDDDCCACBBBDBCCBCBDDADCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:37 MQ:i:29 OQ:Z:HHHHHEGEGHHHHFEFHHHHBHHHHHHHHHHHHHHHGGFHHHHHHHGHHHHHHHHHFHHHHHHHHHHHCHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:48:6949:111164 99 chr1 10001106 60 101M = 10001431 425 AGAAAATCCTAACTTTCCAAGCCTAAGTAACAAAAGGACCAGAGGCTACCCCTTTGCAAACCCCTACCTTTTCTGTGGCAGATGGGAAATTGTAAGTACCT CCCBDDCBBDCDADDDBBCDCBBDCDCBCDACDD@ACDABCCDCCBCCABBBDDDBBCDDABBCDCABDDDDBDBCBCBBCA?A@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGH@HHHHBGGEFFFFFGAFFFA UQ:i:0 +20GAVAAXX100126:8:21:7038:31450 99 chr1 10001134 60 101M = 10001404 359 AACAAAAGGACCAGAGGCTACCCCTTTGCAAACCCCTACCTTTTCTGTGGCAGATGGGAAATTGTAAGTACCTCTAATTAATTAATTAATTGCCTTTTTTT CD@ADDAACDABCCDCCBDCABBBDDDBBCDDABBBCCABDDDDBCBBBCBCCDCBCC;DDCDBBCDC=CABDBDCDCDCDCDCDCDCDCDCCADDDDDE@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHBHHHHHGHHHAHHHHHHHHHHHHHHHHHHHIHHHHGHHHHHHE UQ:i:0 +20GAVAAXX100126:8:65:4263:123939 147 chr1 10001182 60 2S99M = 10000877 -403 GTTGCAGATGGGAAATTGTAAGTACCTCTAATTAATTAATTAATTGCCTTTTTTTTTTTTTGAGACAGAGTCTCTCTCTGTTGCCCAGGCTGGAGTGCAGT ###B;?C2%CCD@=1?CC??ACCDACCCCABCB?ACBBCCBCA?CABBC@AAAB@? MD:Z:0G98 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:###@5;B/%9>.>A>@:6:>?99>A8-A?B7;@0<98=>;@=B4B@D=<>9>,1)@7A;:*3;3;,A2=-:+:A4A=AD=-=AB8:2C?8@.ABC=>8;<*/)=:A=>+5@4=+>.:14*9@1>>>B=,:A@6>1A?8?CB=3+@@- +20GAVAAXX100126:8:25:1952:6902 147 chr1 10001276 60 14S87M = 10000924 -438 GCCCAGGCTGGAGTGCAGTGGCACCATCTCAGCTTGCTGCAACCTCCACCTCCTGCGTTCAGGTGATTCCCCCACACTTACTGGGCTGCATTCCCAGAAGG ###############BB:;?9ABA?>A=C=4?CBC4DC@DCC@;=DCACB@B@BCC=CBCCBBBCDCACDDCBCCABCCBBBAA?@CD@ MD:Z:16G70 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:###############??:4>:B=@?=?>?6;BA>ABABAB4859A@B4BBABBA>BABBABBBBBBBA=BABCBB@CBBBBCCBBCBCBCBCCCCCCCCCB UQ:i:27 +20GAVAAXX100126:8:48:15961:32254 595 chr1 10001301 29 66S35M = 10000919 -416 TTTTATGAGACAGAGTCTCTCTCTGTTTCCCAGGCTGTAGTGCAGCGCCACCATCTAAGCTTGCTGCAACCTACACCTCCTGCGTTCAGGTGATTCCCCCA ##################################################################################################### MD:Z:6C28 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:1 SM:i:29 MQ:i:29 OQ:Z:##################################################################################################### UQ:i:2 +20GAVAAXX100126:8:22:20896:187194 83 chr1 10001303 60 101M = 10000959 -444 ACCTCCACCTCCTGCGTTCAGGTGATTCCCCCACACTTACTGGGCTGCATTCCCAGAAGGTTAAGGCATTCTTAGTCACAGGATGAGATAGGAGGACAGCA 7ADDAC8A;.?C>B;ADDCDBABB@D=:BB@AAAAAABBCCB=ACAABCAA:CBCBDCB@GGFFFFFFGGGHGHEGHEGHHGF@HHHHHHHAHHHHHEFHHGHHHHHHHHHHHHHDHHFHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:63:14360:55959 163 chr1 10001309 60 101M = 10001646 437 ACCTCCTGCGTTCAGGTGATTCCCCCACACTTACTGGGCTGCATTCCCAGAAGGTTAAGGCATTCTTAGTCACAGGATGAGATAGGAGGACAGCACAAGAC @ABCAACBB;ACBBCC@BCDCBCCCCCACADCCBCAA@ACBBCCABCCCCABCACDCDBCACCBBD@CCB@DBAAB?ACBBBCABDBB@C>BBAC?C=@EA MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBBBBBBBBBBBB=BBCBBBBBBBBBBBBBCBBBABBBBBBBBBBBBBABB?BBBABBBBBBBBBBABBBB@B>AB@B@AABA>BA?@ABAAAA5>@B UQ:i:0 +20GAVAAXX100126:8:23:14390:98082 99 chr1 10001338 60 101M = 10001748 510 CTTACTGGGCTGCATTCCCAGAAGGTTAAGGCATTCTTAGTCACAGGATGAGATAGGAGGACAGCACAAGACACAGGTCACAAAGACCTTGCTAATAAAAC CDCAADCCCBDBBCCDBBBCCDDCCBDCDCCBCCDBCDCCBBCACCCDCBDCDCCCCDCCDACCBCACDCDACACCCCBCACADCDAADDCCDCACDE@@> MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHGHHHHGHHHHHHGHHHGGE UQ:i:0 +20GAVAAXX100126:8:42:20734:56938 633 chr1 10001343 23 66S35M = 10001343 0 ACAGACATCTGAACCAGAGAAACCAAAGGTTGTATAGAATCTGTGTAAAATGAAGTTGATGCCGAATGGGGTGCATTCCCAGAAGGTTAAGGCATTCTTAG ################################################################################################948>8 MD:Z:4C30 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:1 SM:i:23 OQ:Z:################################################################################################@@@G@ UQ:i:2 +20GAVAAXX100126:8:42:20734:56938 693 chr1 10001343 0 * = 10001343 0 CGTTTCATGGAGCTGGAAAGCTAGAGCTTTCCTCTAAAAGGCAGGAAGATGGGTGCTAGTCACAGCTCTAATCCTAAATTGTGAAACCTTAAGCAATTCAT ##########################################################################################AB%6/>:)*?> PG:Z:BWA RG:Z:20GAV.8 OQ:Z:##########################################################################################@?'3-?6))>= +20GAVAAXX100126:8:63:8225:63647 163 chr1 10001369 60 69M32S = 10001736 467 CATTCTTAGTCACAGGATGAGATAGGAGGACAGCACAAGACACAGGTCACAAAGACCTTGCTAATAAAACAGGTTGCGGTAAAGAAGCCAGGAAAAACCAC @AAA>?>BB=@ACCC@@52B,B47>48A?>?B:A76:<<>5@>.C/?B8C;1?<)?0B################################# MD:Z:69 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@=A@>?;BC6=A>B??B@=:>>BBB?=13@,@27@8=AA@AA>>9959;=6?8-@-==6B>.?;)>0@################################# UQ:i:0 +20GAVAAXX100126:8:21:7038:31450 147 chr1 10001404 60 11S90M = 10001134 -359 GGAGGACAGCACAAGACACAGGTCACAAAGACCTTGCTAATAAAACAGGTTGTGGTAAAGAAGCCAGGAAAACCCACCAAAACCAAGATGGTGATGAGAGT ############ACACB>ABA?@@;=BBDB>CB?7>C?CA=CCDBCCAAA@ABC@BACBABCABACBBCCCBCCCADBCCCBDCCDCBCCACBCA@BACA@ MD:Z:90 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:############A@>>A:>A?@;@9<@AA?>B@=9B78D?*7DB?B@ABBBCC;@CB>CBBCCCCBDACC@CACBCACDBC@BB>B@CCCCACCECCCCBBCCBCCBBCBCCBAB@A@BD@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:A:->@:/;3?5;6?8=77B>)7A@?A@@@@AA@6BAA>BABBA?BABABBAABBABBBBBBBBBABABBBBBBBCBBBBB@CBBBBBBBCBCACACBCCBB UQ:i:0 +20GAVAAXX100126:8:41:12744:193967 163 chr1 10001443 60 101M = 10001607 264 TGTGGTAAAGAAGCCAGGAAAACCCACCAAAACCAAGATGGTGATGAGAGTGGCCTCTGGTCTTCCTCACTGCTCATCATACACTAATTATAATGCATTAG @CAA?B=ABCDDDADCCACCDDD@CBAAA8?>9<7:>BB)@8=A9CBBC@>6:@=?9AAB=BB>AA;@AABBBBCBBBBBBBBABBABA3>>>?*<6>>=?=A??=2:>=:@@99@;@@@=9?@@A?=:=<1=?<4@:7:<6:?672 UQ:i:0 +20GAVAAXX100126:8:67:20277:111625 163 chr1 10001509 37 90M11S = 10001528 88 TCACTGCTCATCATACACTAATTATAATGCATTAGCATTAGCACCCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGGTAGATCGGAAGAG @CB>B>AB>B;A:C@ADDC@DBC<=A7=<=@>@AA@B@>D60@ACD?AC?>CCBCA7>B?=7CA:A>BAB::@D,;C4@6;;@9C;C= MD:Z:51G35T1T0 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:3 SM:i:37 MQ:i:37 OQ:Z:BCC@B?BABBBCA<:<<7B?ABCC?CAA<@B<@?@C?@BB??@>C;-@BBB>>A>?BBBBC::A=>1@@=A=C==BBBA:=B06B1=1:BB4>7<: UQ:i:60 XT:i:90 +20GAVAAXX100126:8:2:15613:129653 99 chr1 10001516 29 101M = 10001879 396 TCATCATACACTAATTATAATGCATTAGCATTAGCACCCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTTACCATGTTGGCCAGGAT CBCABCCCACADBDCDCCCDCBBCCDCCBCCDCCBCABBCABCA;BBBCCBDCDCDDDDBBBCDDDAACCCCBCDA;CCC;DDDCACCCCCDCC>CDDDE= MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:0 SM:i:29 MQ:i:29 OQ:Z:HHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHGGHHHHGHHHHHHHCHHHHHHHHHIHHICHHHHH@ UQ:i:0 +20GAVAAXX100126:8:6:3004:12551 675 chr1 10001521 29 74M27S = 10001879 391 ATACACTAATTATAATGCATTAGCATTAGCACCCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTTACCATGTTGTCCAGGATGGTCT @B6ACD@@CC?;A:9>C9=/;>9=@.7?9C############################ MD:Z:74 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:0 SM:i:29 MQ:i:29 OQ:Z:B@7=ABCBBB@>=?@8:@:@AC>?BB=:@:6=:@BB;??8;3@5=@;(3@3=B=;;4@+4B;A############################ UQ:i:0 +20GAVAAXX100126:8:67:20277:111625 83 chr1 10001528 37 31S70M = 10001509 -88 CTCTTCCGATCTTCACTGCTCATCATCCACTAATTATAATGCATTAGCATTAGCACCCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTT ################################=?:69;;3:-;;9>-2;<:=/=.78=48>195?@9?==B<-48>==02=?>?AB?:>A>?<<8=?7<=< MD:Z:32G37 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:37 OQ:Z:################################AA>655515/555502555514'4442440@3CC@DADG?08:A44114DADGG55444DD:FDFFGGG UQ:i:20 XT:i:90 +20GAVAAXX100126:8:21:3663:199637 99 chr1 10001543 60 101M = 10001860 376 GCATTAGCACCCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTTACCATGTTGGCCAGGATGGTCTCCATCTCTTGACCTCATCATCC CBCADCCCCABBCABCA;BBBCCBDCDCDDDDB@ACDDD@BCBCCDCDA;CCCBDDDCABCCBCDBCBBCCCDCBCBBDBBCCBDBDDCDACDCDCCDCDD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEGHHHHGGHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:63:4634:186518 99 chr1 10001553 23 71M30S = 10001924 425 CCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTTACCATGTTGGCCAGGATGGTCTCCATCTCTTGACCTCATCATCCGCCCACCTCA :<>6=@>8@??;=:?>>5;;@AA@;3::83;=;:4B>=@@<<;9;9:;;;=7:;;=7;;<@;>?=############################### MD:Z:71 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:23 MQ:i:29 OQ:Z:EFCFDFFFFFFBABBF@AAAEC;@>FFFF@6=@=844445GEEEF44455:>=@=4555555555CCCCA############################### UQ:i:0 +20GAVAAXX100126:8:26:17894:31587 163 chr1 10001582 60 97M4S = 10001891 407 TAGTAGAGACGGGGTTTTACCATGTTGGCCAGGATGGTCTCCATCTCTTGACCTCATCATCCGCCCACCTCTGCTTTCCGCAACCAATCGGACTGATTACA @CBAAABBCA:CCBBCCCCACCCBACBCCCC@@BBA?>?C8C@C@BCDCA@>CACCAB@A@C9>CA9@BC@B?@=<@BCC>;48?@BBB##### MD:Z:97 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBAABABBBABBBABBBBBBBBBBBBABBB>?@BBA@AB;B@BB@BAA@A@AABA@?>?AA@?B>=?9????<=5:;??=?##### UQ:i:0 +20GAVAAXX100126:8:41:12744:193967 83 chr1 10001607 60 101M = 10001443 -264 TGGCCAGGATGGTCTCCATCTCTTGACCTCATCATCCGCCCACCTCTGCTTTCCGCAACCAATCGGACTGATTACAGGCCACTACTTCACCTCATTTACAT A>CACBC>CC@AC?CCBCAAD@ABBCA>B@CDB@D>;?CCBACCCCCBC?D:C;BB@BCBDCD;BBBCCBCDCBBDBBCBCCCBCDDB@CCCCBBC;=:?<:;===DAADD?B9:?8C>AB::+09@A=A>=:9:>A>HFFHHDFB@D:HEEH==26:CFDFFA@@@=H@HEHHAHHHHHHHHA4DDAHHHHHHHHHHGCHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:23:14390:98082 147 chr1 10001748 60 101M = 10001338 -510 ATTTGGACTGGAGAAAATTCTGTATCCAGGGCCCTTGAGTGGCTGCTGGGGCCCGCTCCCACCTGGTGAAATGTACTTTCATTTTCAATAACTCTCTGCTT BE@DC@CAC?@D??DA>BCAB@CABB@ACB@;BA@CBAACBBCDBCDACC?DB9CB@CAB>=AB7@BBCCDCACBCDECBCDEECCBABBABCBB@AABD@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@@BBA???@=A@@=@<A:?@B@A@BBBABBBBBBBBABA@BAABAB?@BB>=7>@?A?@C?@A44555GEFGF####################################################################### UQ:i:4 +20GAVAAXX100126:8:28:18116:51320 99 chr1 10001794 60 101M = 10002126 432 TGGGGCCCGCTCCCACCTGGTGAAATGTACTTTCATTTTCAATAACTCTCTGCTTTTGTTGTTTCATTTTTTTCTTGGTTGTGTGTTTTCTTAAACTCTTT CBCACCCC;BDBBBBABDBCCBDDDCBBCADDDBCCDDDBCDCCDACBCBCBBDDDDBC@ACADBCCDDDDD@@BA>CBDBCCCBCDDDBDA<A?B@@AA@BA?>>@@?@@A@?AA?@?@@?AAB UQ:i:0 +20GAVAAXX100126:8:25:15890:153544 1187 chr1 10001807 60 101M = 10002149 442 CACCTGGTGAAATGTACTTTCATTTTCAATAACTCTCTGCTTTTGTTGTTTCATTTTTTTCTTGGTTGTGTGTTTTCTGATACTCTTTTTTTTTTTTTTTT @@ABB@A6BCBC;>@?ADCCABCCCC=CDCACAD@C@C5CC@BCCACABCACDCDCCADCACC@BC>7AAAB(A?(5(5ABB@DC>B>5A@CACAACA MD:Z:78T1A20 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:2 SM:i:37 MQ:i:60 OQ:Z:B>CABA?4BAAA>A8?BBBAAABBCC;ABBAABBCBBB@A?5BBBABCBBBBBBCBBBBABBABBABB?;3>'5)5ABB:@AB>=3=>>??;?<> UQ:i:14 +20GAVAAXX100126:8:24:3855:143240 163 chr1 10001827 60 85M16S = 10002054 327 CATTTTCAATAACTCTCTGCTTTTGTTGTTTCATTTTTTTCTTGGTTGTGTGTTTTCTTAAACTCTTTTTTTTTTTTTTTTTTTTTTCTTTGATTTTTCCT @CB@AAD>BBE@CCBECCCCACCBCBBBA@>BC@C=BBADDABCCBDACB/5;D>:BD3=BBA??@AD@################# MD:Z:85 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCCBB?B?BABABC=BBBBBBB+7:B;;?A3<@BB;>?BB?################# UQ:i:0 +20GAVAAXX100126:8:21:3663:199637 147 chr1 10001860 60 41S60M = 10001543 -376 TGTGCTTTCATTTTTAATAACTCTCTGCTTTTGTTGTTTTTTTTTTTTCTTGGTTTTGTGTTTTTTTAAACTCTTTTTTTTTTTTTTTTTTTTTGATGGAG ##########################################BCDCD8(;8/;>>)0.2-9A>?(>:3=89+)CDDDDDDDDDDDDDBCDCCCBABABBD@ MD:Z:14G8C36 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:2 SM:i:37 MQ:i:60 OQ:Z:##########################################@@B@B8'::->:9(/-1/;A@@*@>3<16+(ABBBBBBBBBBBBBBBBBBBBCBBBBBB UQ:i:15 +20GAVAAXX100126:8:2:15613:129653 147 chr1 10001879 29 64S34M3S = 10001516 -396 GGAATGTCGTTTCATTTTCAATAACTCTCTTCTTTTTTTTTTTCATTTTTTTCTTGGTTTTGTTTTTTCTTAAACTCTTTTTTTTTTTTTTTTTTTTTTGA #################################################################>C;'79AA94)*ADEEEEEEDEBCDDCCCBABCBC@ MD:Z:34 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:0 SM:i:29 MQ:i:29 OQ:Z:#################################################################@B8&39>>40*)?BCCCCCCBCCBCCBBBCCBBCCB UQ:i:0 +20GAVAAXX100126:8:6:3004:12551 595 chr1 10001879 29 68S10M1D23M = 10001521 -391 TATGAGATTGTTTCTTTTTTTTTTCATTCCGCGAGTTTTTTTTTTTTTCTTTTTTTTCTTTGTTGGTTTTTTTTTATATATTTTTTTTTTTTTTTTTTTTT ##################################################################################;;;<;;;;=;;;;=?428? MD:Z:4C3A1^C1C21 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:4 SM:i:29 MQ:i:29 OQ:Z:##################################################################################@@@@@@@@>@@@@EA@2@A UQ:i:6 +20GAVAAXX100126:8:26:17894:31587 83 chr1 10001891 60 2S99M = 10001582 -407 CTCTTTTTTTTTTTTTTTTTTTTTGATGGAGTCTTGCTCTGTCACCCAGGCTGGAGTACAGTGGCGTGATCTCGGCTCACTGCAACCTCTGCCTCCCAGGT ###@>BA;A@AAA@AB=ADDDDDCBCCBBDADCDCBCDCCADBBCCBDBBCCBBCACBBCACBB;ACBCCCD;BBCDBBCCBBDBCCDCCBCCDCCCBBAC MD:Z:99 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:###GBGG?GEEGGEGG>GHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:63:4634:186518 147 chr1 10001924 29 46S55M = 10001553 -425 TGTTTTTTACATTTTTTTTTTTTTTTTTTTTTTTTGATGGAGTCTTGCTCTGTCACCCAGGCTGGAGTACAGTGGCGTGATCTCGGCTCACTGCAACCTCT ###############################################@C:5==8->548?7027@84B,-B2**(%6A;>))B4B:A4-B9<==A@7>A@? MD:Z:55 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:0 MQ:i:23 OQ:Z:###############################################A?95;<3'>:08?;029B88A)+@2(**)6?8<))@7@9@5-@88;=?A7>@<> UQ:i:0 +20GAVAAXX100126:8:65:13649:138985 147 chr1 10002037 60 26S75M = 10001701 -410 GCCCGCCGAAGAGCTGGGACCACAGGCACCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACAGTGTTTCACTATGTTAGCCAGGATGGTC ###########################ADB3?8>9DC@;=BC;B>CC9DBBDCDBAACCB879C4BCBDAACC?B>DCCB?AADDBEADBCBCBAA@BAC@ MD:Z:75 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:###########################@B>;>8>9BBBB=BAB>>CBCCABBBB?BBBCA:9>B>784B6A14:35D4:*C4A:6:B@<;79AC667=<$87B:3>3C896+8A9<@9)6)A7*,+).>B*/5>9:A>777:??> MD:Z:39A23A21 PG:Z:BWA RG:Z:20GAV.8 AM:i:25 NM:i:2 SM:i:37 MQ:i:60 OQ:Z:#################@1>>942A4?//353B2=*@5?;95B9;519BB;168:(;5C;7@8B>=5*8@79=7)2*@0)+*)0;A*+9;7AC=2527?== UQ:i:12 +20GAVAAXX100126:8:24:3855:143240 83 chr1 10002054 60 101M = 10001827 -327 GGCTAATTTTTTGTATTTTTAGTAGAGACAGTGTTTCACTATGTTAGCCAGGATGGTCTCAATCTCCTGACCTCGTGATCTGCCCGCCTCGGCCTCCCAAA AD@=CA@;DBCBDBBCC=A>9:??>6=;==?B@CCD;?CBC=CCABB5>=CD;BBC=D=<4:<< MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:FHBHHEEEEHHHEEDHHHHHHHGHGHHGHHHHHGHF@BCCBHHCBHHHHHHHHHEHCBBCDD;A@DEEHFHHHHGHHH>HHGGGEEEHHHHHHEHDEEEGG UQ:i:0 +20GAVAAXX100126:8:48:18256:122283 163 chr1 10002059 60 101M = 10002396 437 ATTTTTTGTATTTTTAGTAGAGACAGTGTTTCACTATGTTAGCCAGGATGGTCTCAATCTCCTGACCTCGTGATCTGCCCGCCTCGGCCTCCCAAAGTGCT @CA@??@ABBCBB@BCCBCCCCCACCBCBCCBCACBAA?BBCBCACDCCCA@CBCDDDBDACC?CA@DC;@CA<@BAAB?8ACBB:DA@D>ABAC@@<@@AA@>@A@@B@A?A@>BB??=;1:B> UQ:i:0 +20GAVAAXX100126:8:61:16672:156327 163 chr1 10002072 60 101M = 10002410 438 TTAGTAGAGACAGTGTTTCACTATGTTAGCCAGGATGGTCTCAATCTCCTGACCTCGTGATCTGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCG @CBBA@BCBCACB>BACCBCBDCCBACCCCCBCCABAB>ACBCCABDBCD?BA@DC;CCB?BC?AB49ACAB:AAAB?CB>9BA=CC>?C1BBA@<=C>C: MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBB@CBBBBBBBABABBBBCBBBBBBBBBBABBABBB@BBBBABBBABBAABAABB@B@@AA@@@8@@B@A@AA@A?AB=7=@6AA;@A4@@?<;7@=?@ UQ:i:0 +20GAVAAXX100126:8:28:18116:51320 147 chr1 10002126 60 101M = 10001794 -432 TCGTGATCTGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCCCTTGTTAAATTCTTTGTTCAAAATGCCAAAAACCT 85=C@;CA75=9/=ABADA@ABB@B?@CA>A@C@:A@BC@CABC;;C@CABAA?=BCCADCCCCDCCEECADCCCB@CCBCBBBAAACC@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:45==<8??14=84<>6@B@>@=B@@AAAABAA>ABCB@BABBBA@BABBBBBBBBBBCCBBBBCBCCCBBBBBBBBABCB UQ:i:0 +20GAVAAXX100126:8:65:9835:166164 163 chr1 10002137 60 101M = 10002441 404 CCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCCCTTGTTAAATTCTTTGTTCAAAATGCCAAAAACCTGGACACCCTCC @C:AABA:CBCDBACCDDB?BBDBCCCBCCABBC?8>A=B;CAA=7@C=C;?A?CCBB@@BBAABA?BDA>CB@B?=?CAAACACDB@@C@4(9C?7D>@B MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBBBBBBBBBBBBBBABAA?>>A?B=?>AAB???;AA?@A?A@A????A@=<>AAB?@?@@=B@?A5'9?A3?::? UQ:i:0 +20GAVAAXX100126:8:26:12389:180500 99 chr1 10002138 60 101M = 10002456 418 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCCCTTGTTAAATTCTTTGTTCAAAATGCCAAAAACCTGGACACCCTCCA C;B@DB;CBBDBBBCDDCB@BDBCCDCDCACCCA;B@DCBBCAB;BCABCBCBBBDDBC@CDDCDBDD@BCDBCDDDCBBBBDDDBA+ACCDADABABCDE MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHIHHGHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHHHHHHHGHHHFH0DHHHHHHGGDHHH UQ:i:0 +20GAVAAXX100126:8:23:10396:142336 163 chr1 10002141 60 101M = 10002456 415 CTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCCCTTGTTAAATTCTTTGTTCAAAATGCCAAACACCTGGACGCCATCCACTG @DB:BA@CBCCCCBA;'7<49/A;.A5;<)#8?):>=C?E9 MD:Z:81A8A2C7 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:3 SM:i:37 MQ:i:60 OQ:Z:BBBAAB=BABBBBB@7@AAABABBBBBBBABBA@@>B9?@.@A@ABA=:6;AA=BA??BA>;:;ABB=B@=??1>:*6737/<;-;0;<*&6;'4=8??@4 UQ:i:24 +20GAVAAXX100126:8:25:15872:153534 83 chr1 10002149 60 101M = 10001807 -442 CCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCCCTTGTTAAATTCTTTGTTCAAAATGCCAAAAACCTGGACACCCTCCACTGGTACTGAA DE?DDDADCCCCCBCDCACDB>;ACBBBCBBC;BBBCCCBBCCCDCADCDDCDDCDDCADDBDDDCCBCBDDDDBCCCBBCBBCCCDCBBCCBACCCABDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHGHHHHHHHHHHHHHHEHHHCHHHHGHHHIHHHHIHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:25:15890:153544 1107 chr1 10002149 60 101M = 10001807 -442 CCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCCCCTGGCCCTTGTTAAATTCTTTGTTCAAAATGCCAAAAACCTGGACACCCTCCACTGGTACTGAA ?7=BADCADCAD@AA@ADCADD=DDD?CBC=D@DDACAAA@A=7CCCBCBBCCBACCCABDC MD:Z:35A65 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:BBFFDF2CFBF4,555;FFFFFF5F@5444/0464'AA@A9DGGHHHHHGHFFFFFHHHHHEHHHEHHHEHGHHGHGFGGFD8HHHFHHHHHHHHHHHHHH UQ:i:4 +20GAVAAXX100126:8:47:1669:10922 99 chr1 10002166 60 101M = 10002512 444 ACAGGCGTGAGCCACCGCACCTGGCCCTTGTTAAATTCTTTGTTCAAAATGCCAAAAACCTGGACACCCTCCACTGGTACTGAAGCTCACTGAACCTCCTT CACACC;C:DCBBCAB5BCABDBCBBBD@BBD=DD;@=??DB:D?CD?D?@BBCDDDD9BA?CA@@B@CB=>7=<9CDCCAE MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHBHHHHHHHEHHHHHHHHHHHGHGHEHHBFEDDHHCHFHHEHEFHHHHHHHBHEEHEEFAAFDHFHDFHHEHHFFFFFCFCFD?;@@@HHHHDH UQ:i:0 +20GAVAAXX100126:8:21:8551:122892 163 chr1 10002192 60 101M = 10002500 408 CTTGTTAAATTCTTTGTTCAAAATGCCAAAAACCTGGCCACCCTCCACTGGTACTGAAGCTCACTGAACCTCCTTGTTCAGGAGTTTTCATAGAGCTCCAT @DAA;?ABCC=AD@BB?BCDEEEDBCDCDDCC>CCA4)7B@CCD@DCBDCAAC?BCCB?ABACBA8D=8)@@=B=?<7>?DC@DC MD:Z:37A63 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:BCCCCCAAAC=ACCCBCCCCCCCCBCCBBBAA?BBB;,;BBBBBBCBCBCB@BB<7@BBCBBBBB>@7>:>BAA>A@BBA@9@;2);>B>=>748B?A>BA UQ:i:8 +20GAVAAXX100126:8:25:5802:132383 99 chr1 10002223 60 101M = 10002536 413 ACCTGGACACCCTCCACTGGTACTGAAGCTCACTGAACCTCCTTGTTCAGGAGTTTTCATAGAGCTCCATCTCCAGCCCCCTTCCCTCCCAGGAGGTTGGG CABBCCDACABBDBBCADBCCCADBDDABDBCACBDDABCBBCDBBDBCCCDABDDDBCCCCDCBDBBCCBDBBCCBCBCBDDB=CDBCABCCBC=6??>A MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHGEHHEH?7ADEG UQ:i:0 +20GAVAAXX100126:8:21:10727:109276 99 chr1 10002227 60 101M = 10002534 407 GGACACCCTCCACTGGTACTGAAGCTCACTGAACCTCCTTGTTCAGGAGTTTTCATAGAGCTCCATCTCCAGCCCCCTTCCCTCCCAGGAGGTTGGGGTGG CCC?CACCDBBCADBCBCADBDDCBDBCADBDDABCBBDDBBDBCACDCADDDBCCCCCCBDBCCCBDBBCCBBBBBDDBBCDBCBBACDCCCDCDDD@DA MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHGHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHGGGHHHHHHHHHHGHG UQ:i:0 +20GAVAAXX100126:8:28:14388:67948 163 chr1 10002344 60 101M = 10002661 417 TAATCAAAGTCCTCTAATTTGGTCTTTCTGGTGAGCAGCCCCAACCCTGAGTCACATCATTAGCATAGACTCTGGTGTGTTCTAAAGGGGCTCCTTATGAA @CCBABCCBBBCDADCDCCCBCBADCCBDCCBAC=AAB>39@:B:46?@@@@A<@@A;< UQ:i:0 +20GAVAAXX100126:8:48:18256:122283 83 chr1 10002396 60 101M = 10002059 -437 CACATCATTAGCATAGACTCTGGTGTGTTCTAAAGGGGCTCCTTATGAATAGCAAAAGACAATCCTATCACTCAGGAAATTCCAAGGAATTTAGGAGCCCT DDCCDCCDCDCCCCDBCCDCCCACACADDCCDDDBBCBCDCCDCCCBDCCCBBDDDCBBBDCDCCCCDBBCDBDBBDDCDDCBDDBBDCDDCDCBDCACCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:61:16672:156327 83 chr1 10002410 60 101M = 10002072 -438 AGACTCTGGTGTGTTCTAAAGGGGCTCCTTATGAATAGCAAAAGACAATCCTATCACTCAGGAAATTCCAAGGAATTTAGGAGCCCTGTGCCAGAACCAGG EDCDDCDCACACADDCCDDDBCABCDCCDCCCBDCCDBBDDDDBCBDCDCBCCDBACDBCBBDDCDDCBDDBBDCDDCCBBDBCCCCACBCBDBDCC@CBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHIHHHHHHHIHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:65:9835:166164 83 chr1 10002441 60 101M = 10002137 -404 TGAATAGCAAAAGACAATCCTATCACTCAGGAAATTCCAAGGAATTTAGGAGCCCTGTGCCAGAACCAGGGAAAAAGACCAAATATATATTTCATTAAACT EDDCBDCCDDDDBCCD?DCCCCDBBCDBDBBDDCDDCBDDBBDCDDCDBBCBCCCCACBCBCBDBCBCBB@@DDDDBBCBDDCCCCCCCDDDBCDCDBBCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHGHHHHHHHHHHHEHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:23:10396:142336 83 chr1 10002456 60 101M = 10002141 -415 AATCCTATCACTCAGGAAATTCCAAGGAATTTAGGAGCCCTGTGCCAGAACCAGGGAAAAAGACCAAATATATATTTCATTAAACTTTACTACATGATACA EDDA?DC>CCCBCDCADDCBAABDDBBDBADCDB>D?>CC@ACBCBDB>BCBCBBA@DDDD?BC@DDCACCCCCDDDBADCDDBCDDCCCCCBCCBC:@BB6C@<<>?A?BCC49C?BC?B?CCC6D@D>7BC>C@BBABBBAAAB@B=<@A9B?:C>??8BB@4=@>BB>B@BBB1ABA=D>>@?;=773/65608?DC?9:78CBAB>6=C=ACDAB@3BBC@B7)/3B>CA?AAA)?DA@CA56'>A>=>;;<251-236.9?B@@5576BA@B>6;B:>BBBA@5?B@?@9'/4BCBBBBC>(>B?>B@9>?5BCB9DAAACBB@=BBBCCECBCCDCDDCDCDDBCBBBDCACBBABCBB@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:C>CBB@BABBACB-CC@CBBABBA@CBBBBBAACC9BBBCBBC@>BCCCBCCBCCBA@CCCBCBCBCCCCCCCBCCBCCCCBCCCCCBCCCCBBCCBBBCB UQ:i:0 +20GAVAAXX100126:8:25:5802:132383 147 chr1 10002536 60 101M = 10002223 -413 TAAACTTTACTACATGATACAAACTACAGTTTGGAAAGACATTTAGGAATGGTAGAACAAAACAAGTGAGAAAATATAATATGTAAAAGGTCTTTTTGTCA BDBD@@D@AA>DB>AB8BBB:ABB;ADBCCB@CCACDCBBBDDDDCDDDDBDBBBBCAABDCBA@@AC@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:CB@@CBBBBB=BBCBCCBBCBBBCBABCCBBBBBBBACBCCBBCCCBCCCCCCBCCBCCBBBABCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCCCCCCCB UQ:i:0 +20GAVAAXX100126:8:46:6526:26315 99 chr1 10002542 60 101M = 10002857 415 TTACTACATGATACAAACTACAGTTTGGAAAGACATTTAGGAATGGTAGAACAAAACAAGTGAGAAAATATAATATGTAAAAGGTCTTTTTGTCATTTCAA CDC?DCACCBDCCACDDADCACCBDDBCDDDCDACCDDCCCDDCBCBCCDDACDDB@CAABBDCDDDDCCCCDCCCBCCDDDCCABDDDDAAA@DCDDCEE MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHGGHGGIHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGGEGHHHHHHH UQ:i:0 +20GAVAAXX100126:8:61:8680:44720 163 chr1 10002550 60 101M = 10002899 449 TGATACAAACTACAGTTTGGAAAGACATTTAGGAATGGTAGAACAAAACAAGTGAGAAAATATAATATGTAAAAGGTCTTTTTGTCATTTCAAAATACAAG @AA@7;B?D@=@;9A@BAACCEECB:CCBCCCC9=B7/8?A09?ADDAAA=B:C= MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@?@@4=A?CA@?@BBCCB@9BBCBBBA7?B=59CA/:@BBB=B=?A4?>?9;@>5>/;?B@B;AA9:98@@A<<: UQ:i:0 +20GAVAAXX100126:8:28:14388:67948 83 chr1 10002661 60 101M = 10002344 -417 GCATGGTGGCTCACACCTGTAATCCTAGCATTTTGGGAGGCTGAGGCAGGAGGATCCCTTGAGCCCAGGAGTTGGAGACCAGCCTGAACAACATACTGAGA DDCDCADCCCDCCCBCCCACDCDCCCDABCDDDCBBBDBBCCBCBBBDBBCBBCDCCCDCBCBCCBCBBCADCBBDBACBDBCCCBDBBDCBCCCCC@CBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHFHHHHHHHHHHHHGHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:5:7404:40226 163 chr1 10002668 37 91M10S = 52476437 42473869 GGCTCACACCTGTAATCCTAGCATTTTGGGAGGCTGAGGCAGGAGGATCCCTTGAGCCCAGGAGTTGGAGACCAGCCTGAACAACATACTGAGACCCCGTC @CBB?A?BACAA@<>ACDED@>@CCCCCBAC@?BB;6<8?AC=B76A38AAD=6A8/A:@7CC=:D7@BA7'B38ABBCB>7B@:BC72D########### MD:Z:91 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:37 OQ:Z:BCBACA@ACC@@A@:@CCCC?=>BBCCB@@B>>BC>:?=ACB>?99=08=BB97;2.=7=8AA=2A9?=?6(>16BBAAA=8=>:>@73@########### UQ:i:0 +20GAVAAXX100126:8:43:16629:51559 163 chr1 10002681 60 100M1S = 10002869 288 AATCCTAGCATTTTGGGAGGCTGAGGCAGGAGGATCCCTTGAGCCCAGGAGTTGGAGACCAGCCTGAACAACATACTGAGACCCCGTCTCTACAAAAAATA @DCA@BBBBCCBBBCCCCCCBDBCCCBCCCBBA=:7;B@B;?;>=C;ACB::@8B?==?C>==@AA8A<=?>@;>BA?;@9:B<8>5:9AAA## MD:Z:100 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBCBBBBBCCCBCBBBBBBBBABBBBBB@A@:=:@BAB>?<B?>6<:?::6@B?<?:?:9?:;<<@61-9=?=?=?669?:7=145;8?## UQ:i:0 +20GAVAAXX100126:8:45:10866:114173 99 chr1 10002696 60 101M = 10003041 434 GGAGGCTGAGGCAGGAGGATCCCTTGAGCCCAGGAGTTGGAGACCAGCCTGAACAACATACTGAGACCCCGTCTCTACAAAAAATAGAAAATTAGTTGGGG CCCACCDCDCCBCCCDCCDCBBBDDBDCBBBCCCDCADBCDCDABCCBBCBDDACDACCCADBDCDABBB;BBDBDCACDDDAABBADDDDCDCCBDC>E# MD:Z:100T0 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHHGHHCH# UQ:i:2 +20GAVAAXX100126:8:65:6494:152486 99 chr1 10002718 60 101M = 10003049 431 CTTGAGCCCAGGAGTTGGAGACCAGCCTGAACAACATACTGAGACCCCGTCTCTACAAAAAATAGAAAATTAGTTGGGTGTGGTGGTCCATGCCTGTAGTC CDC@DCCCBCCCDCBDBCDCDABCCBBDBDDACDACCCACBDCDABBB;BBDBDCACDDD@@BBADDD@CDCCBDBCCABCBCCBCCBCCCCCCDCCADDD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEGGGHHHDHHHHHHHHHFHHHHHHHHHHHHHHHHHHGHHH UQ:i:0 +20GAVAAXX100126:8:65:4031:65332 163 chr1 10002722 60 101M = 10003065 443 AGCCCAGGAGTTGGAGACCAGCCTGAACAACATACTGAGACCCCGTCTCTACAAAAAATAGAAAATTAGTTGGGTGTGGTGGTCCATGCCTGTAGTCCCAG @C@BABBCCB@CBBCCD@8CC>BCBA5A?@D>AACABC@B=BAAB@CBCC=?B MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBAABBABAB?BBBAB8BA=@BBBABBBCBCBCBBCBB>;BB7AB@B0B>@B;B@@ABABBCCBDACCCCC@CC@CCCCAC>AAAA??A?8AC@?@?98C;@@?A?8B@64AA=@@>76>7?<:@;?@8?@####### UQ:i:0 +20GAVAAXX100126:8:27:6582:134282 163 chr1 10002742 60 94M7S = 10003068 426 GCCTGAACAACATACTGAGACCCCGTCTCTACAAAAAATAGAAAATTAGTTGGGTGTGGTGGTCCATGCCTGTAGTCCCAGCTACTCCAGAGGCTGAGGGG @BCCABB@CCACCAADBCCCBCCC;ABDCECACDCCBBBB@@CCB?CCCCABD@CCBCCBA;8>B=AAC@=A???>=B?A64B######## MD:Z:94 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCCBBCBBBBBCBBBBBBACBBBCBBBCCBBBBBBBBBBC@BAB?BBB>BBBA?B@AA?BA??=@@8A@A?B;>6>A=@AB=@B>>>AA<==:BB@=BC>@>>BB:@C@BBA@AAAC??CBCC@CBCBC@CCCACCCA@BA;BBBBA@BB@ MD:Z:79G21 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:>?:1=<=7<3=><>==:?@;BABBABAABA=BBBABBBBABABBBABBBBBB UQ:i:31 +20GAVAAXX100126:8:43:16629:51559 83 chr1 10002869 60 101M = 10002681 -288 AGGCTGCAGTGAGCCAAGATTGTGCCAGTGCACTCCAGACTGGACAACAGAGCAAGACCCTGTCTCAGGGGGCTGGCCACGCATGGTGACACATCCCTGTA :DCDDCCDACCDCCCDDBCDCACBCBDACBB@CDCBDBCCCBBCBDBBDBCBBDCBBCCCCADCDBCBBBBBCCBBCBB;BBCCBACBCBCBCDCCCA@CC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:;HHHHHHHHHHHHHHHHHHHGHHHHHHHHHHEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:63:6936:45669 611 chr1 10002875 29 35M66S = 10003208 424 CAGTGAGCCAAGATTGTGCCAGTGCACTCCAGACTGGACAACAGAGCAAGACCCTGTCTCAGGGGGCTGGCCAAGCATGGTCACACATCCCTGTAGTCTGT ##################################################################################################### MD:Z:35 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:0 MQ:i:37 OQ:Z:##################################################################################################### UQ:i:0 +20GAVAAXX100126:8:61:8680:44720 83 chr1 10002899 60 101M = 10002550 -449 CACTCCAGACTGGACAACAGAGCAAGACCCTGTCTCAGGGGGCTGGCCACGCATGGTGACACATGCCTGTAGTCTGAGGAGCTCAAGGTTGCAACAGTGAG 646:>:CD9A=>@B=DDBA=CCCA?C>B<:98;B:CBABBBBBB?CBCCC?ACADACBDBBDBACBADBADCBBDCCDAABDC MD:Z:64C36 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:47;<@A?@@A>EECHHCF?DDHAHHHGEHHHEEHHHBFB9DGCGEG?BBFBHBHHHGHHHHHCHHHHHGGGHHGHHHHHHHGGHGHHHHHHHHHHHHHHHH UQ:i:33 +20GAVAAXX100126:8:28:18332:173597 163 chr1 10002902 60 97M4S = 10003158 356 TCCAGACTGGACAACAGAGCAAGACCCTGTCTCAGGGGGCTGGCCACGCATGGTGACACATGCCTGTAGTCTGAGGAGCTCAAGGTTGCAACAGTGAGCCA @BCBAB@CBCCACBACCCCBCDBBACDDCBBDBC@B?@BABA?B=C>:AC:?B6BC=B:A?@=@BA;=?>A@BA875:BACA##### MD:Z:61C35 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:BBCBBBBBBBBBBBBBBBBBBBA@BBCBBBBBBAABAABBAA@A?B=?AA>??3??=>:?@?=@??;=:7>?=:5=17:494>=?6>?:13:?@=?##### UQ:i:31 +20GAVAAXX100126:8:62:6496:91010 99 chr1 10002902 60 101M = 10003193 391 TCCAGACTGGACAACAGAGCAAGACCCTGTCTCAGGGGGCTGGCCACGCATGGTGACACATCCCTGTAGTCTGAGGAGCTCAAGGTTGCAACAGTGAGCCA CBBACDADBCDACDACCDCBCDCDABBDBBBCBCCCCCC@DBCBBCA;BCCBCBBDACACCBBCDBBCCCBCBDCCDCBDBCDCC>DCCCB@BABCDD@D> MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHAHHHHFGGFFHHHDHB UQ:i:0 +20GAVAAXX100126:8:45:20504:142467 163 chr1 10003007 60 90M11S = 10003337 430 CGCACCATTCCACTTCATCCTGGGCAACAGAGCAAAACCCTATCTCTATGAAAAAAAAAAAAAAGCAAGAGGCTATCTTCTCTGAGGTTTACTATAGTTAA @;BB>AACABCCACCBDCCDDBDCCCDBCCCCBCCCB@A?C?CCBCDCACACD@DDDDDDBDCB=A@B;/<6688.5B?4:>8:?@B>C5BA1>A<;################################################################ MD:Z:38 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:=7@BABA@;@;@28CB;:6A;:39>@@<@5A@/;A>?################################################################ UQ:i:0 +20GAVAAXX100126:8:45:10866:114173 147 chr1 10003041 60 11S90M = 10002696 -434 GCAACAGAGCAAAACCCTATCTCTATGAAAAAAAAAAAAAAGCAAGAGGCTATCTTCTCTGAGGTTTACTATAGTTAACTTTTACAAGTATTTAATCATAA ############?8.D=4.,9388?<3CCACCB@BCCBC@BB=B@BCBACBBBAA@BCBABDACCDDCCCCCDCCDDCBCDADCCCCBBBBB:C@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:2;901225?A>@AAAAA@A@@AB@AABBBABA@BB>ABABABBABB?B@BBBBBAABB@BBBBBABBBBBBBBBBBBCCBCCBBBBBBBCBBBBBBBBBBB UQ:i:0 +20GAVAAXX100126:8:45:5977:75469 163 chr1 10003052 60 71M30S = 10003336 384 CTATGAAAAAAAAAAAAAAGCAAGAGGCTATCTTCTCTGAGGTTTACTATAGTTAACTTTTACAAGTATTTAATCATAATTGCTTAGATTGAATTCGGTTC @DBBABCCCCCDCBDDDA=.7@@4)@@397:6?:241'-%366C6/0?-:37A6>=3@BC303<=45';B############################### MD:Z:71 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBBBBBBBBBBBBB?9,6==1*?>13683=9224'-%4:5A90.:-55688;729@A402;902'7@############################### UQ:i:0 +20GAVAAXX100126:8:63:2945:69121 83 chr1 10003053 60 5S96M = 10002736 -412 TTCTCTATGAAAAAAAAAAAAAAGCAAGAGGCTATCTTCTCTGAGGTTTACTATAGTTAACTTTTACAAGTATTTAATCATAATTGCTTAGATTGAATTCG ######@A;AA@A?AA@DDDDDDBBDDBDBBCCCDCDDCDCCBDBADDCBCCCCCADCDBCDDDCBBDCACCDDCDCDBCCDCDCBCDCDBCDCBDCBC;C MD:Z:96 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:######DD@GGGGEGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:65:4031:65332 83 chr1 10003065 60 101M = 10002722 -443 AAAAAAGCAAGAGGCTATCTTCTCTGAGGTTTACTATAGTTAACTTTTACAAGTATTTAATCATAATTGCTTAGATTGAATTCGGTTCAGTATATATTCCT EEDDAD=?=A>DCBCCCDCDDCDCCAD@A?DCCCCCC6ADCACADDDCBB?CACCDDCDCDBCCDCDCBCDADBCDCBDCDD;BADDBBACCCCCCDBCCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHGHAD@DAHHHHHHHHHHHHHHGHFHEHHHHHHH7HHHFHGHHHHHHEHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHIHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:27:6582:134282 83 chr1 10003068 60 101M = 10002742 -426 AAAGCAAGAGGCTATCTTCTCTGAGGTTTACTATAGTTAACTTTTACAAGTATTTAATCATAATTGCTTAGATTGAATTCGGTTCAGTATATATTCCTGGA EDDCCDDCACCCCCDCDCCDCCBDBAD@CBCCCCDADCDCCDDDCBBDDACCDDCDCDBCCDCDCBCDCCBCDCBDCDD;BADDBDACCCCCCDDCCABBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HIHHHHHHEHHHHHHHHIHHHHHHHHHDHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:26:6455:142223 163 chr1 10003070 60 101M = 10003403 433 AGCAAGAGGCTATCTTCTCTGAGGTTTACTATAGTTAACTTTTACAAGTATTTAATCATAATTGCTTAGATTGAATTCGGTTCAGTATATATTCCTGGAAG @CBBBABBCBDCCADCCDCDBBCCBCCCADCCBC>BAB;CBBBC?CDC@B?CC@DCBDBABCCABD@CCB@CCABBB@;B@BCBBAB>>C;BC?CBBCBDB MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCBBBBBBBBBBBBBBCBCBA@BB@BCBBBBBAC@BBB@BBAABBBBB?AABBBAABBA@ABBAABABB@@@A@@B@@BA>@BAA9@A?@@@>@ UQ:i:0 +20GAVAAXX100126:8:68:8704:167789 99 chr1 10003123 60 101M = 10003414 361 AATCATAATTGCTTAGATTGAATTCGGTTCAGTATATATTCCTGGAAGTTCACTATTATTATTATTACTAGGTCCTGAGAATATGAAACAACCATAAAAAT CDB@CCCDCABBDDCCDCDBDDCDB;CBDBCCAC>CC>CDBBC9CDDC@DBCADCCDCCDCCDCCDCADCACCBBDBBCDDCCCBDADACDACDCDE=E@; MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHGHEHHEHHHHH@HHHHEHHHHHHHHHHHHHHHHHHHHHGHHHHHHGHHHHHHHHGHHHHHHHHHHBHG> UQ:i:0 +20GAVAAXX100126:8:28:18332:173597 83 chr1 10003158 60 101M = 10002902 -356 ATATTCCTGGAAGTTCACTATTATTATTATTACTAGGTCCTGAGAATATGAAACAACCATAAAAATGAGTGATGAATTCAATATATATTATTCTGACACTG BDCEBDCBCCDD?DDBCACCDCCDCCDCCDCCCCDBADCCCBDBDCCCCBDDBBDBC@BCDDDDCCBCACBCCBDCDDBDCCCCCCCDCCDDCCBCC:BCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:FHHHEHHGHHHHGHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHH UQ:i:0 +20GAVAAXX100126:8:25:10200:154913 147 chr1 10003177 60 101M = 10002841 -436 ATTATTATTATTACTAGGTCCTGAGAATATGAAACAACCATAAAAATGAGTGATGAATTCAATATATATTATTCTGACACTGAGAAGTATTGTAACAAAAA =>455>8=@B@B@5>=8AD>?DBABB@CCDCCC?D@>BBCBCAC>AABAB>BBCDCCCCCCBBBBCCBDBCDAACDCABBBAABAC@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:9<<6>????A>@:<97340>6<=@@@?6:69?AAABBBABBBBBBABBBB@B@CBBBBBBBBBBBBBBABBBCBB UQ:i:0 +20GAVAAXX100126:8:62:6496:91010 147 chr1 10003193 60 101M = 10002902 -391 GGTCCTGAGAATATGAAACAACCATAAAAATGAGTGATGAATTCAATATATATTATTCTGACACTGAGAAGTATTGTAACAAAAAACAAGTTTCTAGGTCA CA=2CAAB@B>>;;>AA5BB>BBAACBACDABEA@BCBBCBCCCCDCACCADCCDDACCB@A?BAACBCDACCDBBCCABCCCBBACBDACCCBBB@@CB@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:B=81??>?>@>;<9:884:>9'>>351>;77?9< MD:Z:33T24A12 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:2 SM:i:37 MQ:i:60 OQ:Z:###############################FFFAA43.-,64<>D551-1.421=09:>7::)@:55444/+444/43+4>::3B>=+@ACA>=A=ACB?AC@BBB>BB@CCCA=CB MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBCBBA;BBBBBBBBBBBB@@ABA?BB@BBBBBBBBBBABBB@BB@BBBABBABAAAB<@AA@@><>A????ABA?B;@?@@A@??;6:=A UQ:i:0 +20GAVAAXX100126:8:63:6936:45669 659 chr1 10003208 37 9S92M = 10002875 -424 GAGAATATGAAACAACCATAAAAATGAGTGATGAATTCAATATATCTTATTCTGACACTGAGAAGTATTGTAACAAAAAACAAGTTTCTAGGTCATACCAA ##########B@19:97;=>;C?@43?;B@9(0<>5>BD8(28C=3B97C>?C,5B?>?08;3@*>A@;?CBCA@?-C'9:BA;.3<7@B5'.:>7AA+6AA@@6<>1>+>?85=C@B>:=-@)6:AC86-)=A>5@589@ UQ:i:7 +20GAVAAXX100126:8:68:17460:23672 99 chr1 10003272 60 101M = 10003550 378 CAAAAAACAAGTTTCTAGGTCATACCAAAAGCCGGGCAAAGTGGCAGATTCCTGTAATCCCAGCTACTCAGGAGGCTGAGGGGGGAGGATTGCTTGAACCC CCD:@DDA@A@BD>BDCCCCBCCC?BCDDDAB=;C@?B@@=;===?A;BABB@ABC?:=BBCCADCAD@>C>DCC=@?@ACCC>>???>?DACAD<=:>?= MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHGGHHHCCCGHDHHHHHHHHHHGHHHHHGHDHHCCGCGD@DDDDG=GGHHEGHHE=EHHHHGHHHHGCHDHHH?DDDFHHHCCCCCCCHGHDHADDCDCCDCCCB@CBAACCBD@BCDCBCDCBDACC;CBBDBBBDBDBADCBBDACBCBBDBDBCCCB;>CBCCBCBCDCBBBCDCBDBCCCBCCCDABDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BGHHHHHHHHHHGGGGGGHHHHFHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:45:20504:142467 83 chr1 10003337 60 101M = 10003007 -430 ACTCAGGAGGCTGAGGGGGGAGGATTGCTTGAACCCGGGAGGCAGAGGTTGCAGTGAGCAGAGATAGCGCCATGCCATTGCACTCCAGCCTGGGCAACAAG DDD@DCCDCCCB@CABACC@DCBCDCBCDCBD@CC;CCBDBBBDBDBADCBBCACBCBBCBCBCCCB;BCBCCBCBCDCBB@CDCBDBCCCBBCCDC@CDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHDHHHHHHHGGGGGGHHGHHHHHHHHHHHHEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:26:6455:142223 83 chr1 10003403 60 101M = 10003070 -433 GCGCCATGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAATCCTTTCATGAAATTACTACCAGATGTTGGCCCTTCA >6=@>=;A@>AB@BACBDDC>BCBCDC@?AAAAA@ADDDDDCDCCDDDACCBDDCDCBCCBCBDBCCADCBCCCCBCBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BAADA?BDDBD55444DBFBFHHIHHFDBFDEFFFFHHHHHHEFHHHHHDCGGGGGGGHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:68:8704:167789 147 chr1 10003414 60 30S71M = 10003123 -361 GTTGCAGTGAGCAGAGATAGCGCCATGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAATCCTTTCATGAAATTACT ###############################B@<347:@::>>A@CC=B>7A@@C>9A;<:;7>;28>>>CCCCCCCCCCCCBCCCDBCBCCBBBBBBAC@ MD:Z:71 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:###############################?=;002AB@?=:=?>?@<@<=<>:@@39<<5?;:B71?A8>:07B49;9-6.5?A9B@;A#################### MD:Z:82 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:???AC@:BCCCBCCCC@CACB?CCCCB=ACCC@4808@7>=4@4-==9=;14@3875,2+7>?;A<:A#################### UQ:i:0 +20GAVAAXX100126:8:45:3960:5771 163 chr1 10003525 60 101M = 10003872 447 CATCCTTAGCAAAGAAAGATCTTCAAAGCAGGCACTTCCATGATCCACATACTTTGGATGCCCTTAAAGGGGGGGAAAAAGGGAGAGGAAGGGAGGAGAGG @CBA@BBBBBCDCABEECCCBECBDEECBACCCD@CAAA?CBCC?CCACDAADADCCDCBACCCCB?DCCADDAB>@BB=BBCBB0CB@DABC@AACC?DB MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCBCBBBBCBCBBCCCBBBBCCBCCCBA?BBCCBBBBBCBBBBABBBBBBBBBBBBABCBBBBBA@BBBABBBB;?A?<@?@;@@ UQ:i:0 +20GAVAAXX100126:8:26:5030:62604 99 chr1 10003529 60 101M = 10003851 422 CTTAGCAAAGAAAGATCTTCAAAGCAGGCACTTCCATGATCCACATACTTTGGATGCCCTTAAAGGGGGGGAAAAAGGGAGAGGAAGGGAGGAGAGGAAGA CDCACCCDDCDDAADCBDDBCDDCBCCCBCACDBBCCBDCBBCACCCACDDBCDCBBBBDDBDDCCCCC>B>DDDDCCCDCBCCDDCCCDCCCCCCDDED5 MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHEGCHHHHHHHHHEHHHHHHHIHHGHFHHIHH4 UQ:i:0 +20GAVAAXX100126:8:26:15631:70339 83 chr1 10003538 60 101M = 10003203 -435 GAAAGATCTTCAAAGCAGGCACTTCCATGATCCACATACTTTGGATGCCCTTAAAGGGGGGAAAAAAGGGAGAGGAAGGGAGGAGAGGAAGAGGAGGAGAA DEDDCCDCD?CDDDABDCBBCCDDCBCCBCDCACBCCBCADCBBCCBCC@DCDDCBBBBBBDDDDDCBBBDBDBBDDBBBDBBDBDBBDDBDBBDCBBBDC MD:Z:61G39 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHCHHIHGHHHHHHHHHHHHHHHHHIHHHHGHFHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:35 +20GAVAAXX100126:8:68:17460:23672 147 chr1 10003550 60 101M = 10003272 -378 AAGCAGGCACTTCCATGATCCACATACTTTGGATGCCCTTAAAGGGGGGGAAAAAGGGAGAGGAAGGGAGGAGAGGAAGAGGAGGAGAAATAGCATTTCAA CE@CBA?1B>)8.>1%94=096A;>->88CAA=:4=.?7A0CAC<>B78=A=CCDC8C7?==?:?@9@BCC;.=<'23<-%616384?;?'=74?B?997<0?3@2A>B99>94>B9BBBB;B6@>@A=AA;;BB@8ABB?@?>>?BB@B;?BBB>>ACB:BA?982;8A>=?DDD==?CBBBADDCDA>=>A@=;;@?A@=;8<13=,<;<78)=7<=2=72A>B@>B;>*<@==@CDACHHHDDDHHHHGHHHHCADAGCD>4CEFCE?44234245554+44441443FAFFCF=C,?254444-5559F?DDCC.?A654'5:GCGE4 UQ:i:0 +20GAVAAXX100126:8:25:18450:91287 163 chr1 10003652 60 101M = 10003979 427 TCTGCTTTAATATATATATATTTTTTGAGACAGAGTCTCACTCTGTCATCCAGGCTGGAGTGCAGTGGTGCAATCTCCGCTCACTGCAACCTCCACCTCCC @CCA?A@ABCCCCACCCCCCDCCCCCBCCC@CACB>@C?B@DBD@BCCCAACB=BDBCBA@=A9AA<=>ABBB>=@BAAB>BA?AB MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCBBCCCCBBBBBBBBBBBBCCCBBBAABBAB@BB?BBABBBBBBABBB@BB??AAAA?@;A?<@>@@9A@?>@>>>@>B?<6?>@@@>:???@>>>9>:@ UQ:i:0 +20GAVAAXX100126:8:44:17629:79062 1187 chr1 10003678 60 99M2S = 10004001 423 GAGACAGAGTCTCACTCTGTCATCCAGGCTGGAGTGCAGTGGTGCAATCTCCGCTCACTGCAACCTCCACCTCCCGGGTTTAAGCGATTCTCCTGCCTCAG =B:6:=::9ABD61?DDDCCCD97@@>374=48?AA@<;@BD8B46CB5>C<?@2=6@5;@B@B;6=BA;A4:@A1;A:CA9;@B>85/:2?7*'5)4>8':4&3=?:8BABA07B@### UQ:i:4 +20GAVAAXX100126:8:2:19645:190338 83 chr1 10003700 60 101M = 10003434 -366 TCCAGGCTGGAGTGCAGTGGTGCAATCTCCGCTCACTGCAACCTCCACCTCCCGGGTTTAAGTGATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGATTAC 5ECACCC?;CD?BBCD=A>=:?9==?AA@D=DDBHHGHHHFHHHHHHHHHHHHHHHHEH UQ:i:0 +20GAVAAXX100126:8:25:1734:195910 99 chr1 10003819 60 101M = 10004149 430 TGGCCAGCTAATTTTTGTATTTTTAGTATTTTTGTATTTTTGTTTCGCCATGTTGGTTGGGCTGGTCTCCAACTCCTGGCCTCAAGTGATCCACCCACCTC CBC@CCCCDCDCDDDDBBBCDDDAACBCCDDD@@ABCDDDA@AA@=;BBCCBBDBCCDBCCBDBCCBDBBCDADBBDBCBBDBCDCCCDC@CC:CCDBAED MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHGGHHHHGGHHHHHHHGGGGHHHHGGGGGEHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHIHHHFHHBHHHHFHH UQ:i:0 +20GAVAAXX100126:8:26:5030:62604 147 chr1 10003851 60 101M = 10003529 -422 TGTATTTTTGTTTCGCCATGTTGGTTGGGCTGGTCTCCAACTCCTGGCCTCAAGTGATCCACCCACCTCAGCCTACCAAAATGCTCGGATTACAAGTGTGG C@B;)?9)8=@BAC@C?CB?=7ABCCBCC@C@@CDA>?=DCB3BBA6BBCBDBCCCBDBCCCCCBCC;DACDCABAB?@@BD@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@<=AA?AA@@@;2A?ABAABAB?BBBB9?@BBB4BBB6BBABBBBCB@CBBCCBBBCBCCCBCCBCCCCCCCCB UQ:i:0 +20GAVAAXX100126:8:45:3960:5771 83 chr1 10003872 60 101M = 10003525 -447 TGGTTGGGCTGGTCTCCAACTCCTGGCCTCAAGTGATCCACCCACCTCAGCCTACCAAAATGCTCGGATTACAAGTGTGGCCCCTTGTAATAAAAATTTAA EA?A,@CCCCCADCDCBDCCDCCCBBCADBDDACBCDCBACCBBCCDBDBCCCBCBDDDCCBCD;BBCDCBBDDACACBBCCCCDCABABCDDDDCDBCDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HFFD.CHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHFHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:4:16802:116090 611 chr1 10003895 60 101M = 10004234 439 TGGCCTCAAGTGATCCACCCACCTCAGCCTACCAAAATGCTCGGATTACAAGTGTGGCCCCTTGTAATAAAAATTTAATTTTTTGGAATATGACTCTTGGA 1.)4=???3/>@,=<<30+->;>6<<<:;>:+:6;;;<<:9*31=;;99=97=:<@>:==AA7=<9::9:>765198:9+=;:5:A/<>:::86<9@=:.B MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:5..54544/.44+55473+0B@BBBCB;8@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBCBCCBB@BBBBCCBBAABBBBBBB@BBBBB>AABBBBBBBBBBB@BAB@B=@BAAABB@A@@@@??<;1= UQ:i:0 +20GAVAAXX100126:8:47:13004:90024 147 chr1 10003910 60 60S41M = 10003567 -383 TTGTATTTTTGTTTCGCCATGTTGGTTGGGCTGGCATCCAACTCCTGGCCTCAAGTAATCCACCCACCTCAGCCTACCAAAATGCTCGGATTACAAGTGTG #############################################################>:;6=5@6BB7;;A8(@CCC>;AAC;>?A=AB>A@B@ MD:Z:41 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:#############################################################@>><>9>5A@6:6A1,>BBB=7A?BBAA?;B7=?B@@BAB UQ:i:0 +20GAVAAXX100126:8:2:13260:81311 163 chr1 10003923 60 90M11S = 10004222 399 CTACCAAAATGCTCGGATTACAAGTGTGGCCCCTTGTAATAAAAATTTAATTTTTTGGAATATGACTCTTGGAGTTTTTCTTTTTCTTTTTTTACTTTTGG @C4:97@:CB>??>9=;<@:??2?-4?BACACC:<=6:<:16>@9BAD9@889:?BBB3?96>;?=;BDB:?4877?(?;C?D>78D6@############ MD:Z:90 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:B@4;66=7@A?=@A@=79=9@<.;'1:A?B@BA7>@6>?>47><B?0<;7><<<=BA@;<0755>);;B>B<53@4@############ UQ:i:0 +20GAVAAXX100126:8:1:17413:63912 1187 chr1 10003958 60 101M = 10004229 371 GTAATAAAAATTTAATTTTTTGGAATATGACTCTTGGAGATTTTCTTTTTATTCTTTTACTTTTGGACTCTGTTGGACTTCAGTTGTTTTTCTTTAATGGC @BBCBACCCCCCCADCCCCCCBCCDCCCCCADBDB?*34->CCC6DDCCB&:C/CDCD4;8C6BB@0@EB*CC2>$8?5>4 MD:Z:39T10C2T26G20 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:4 SM:i:37 MQ:i:60 OQ:Z:BABBBBBBBABBBBBBBBBBBBBBBBBBBABBBBBA355-@BBA:BABB?';@.>BBB3;7A4BA>/ABA)BA1=(6>B:(0B1;B?7-869?6??991:2 UQ:i:38 +20GAVAAXX100126:8:7:11540:56171 163 chr1 10003958 60 101M = 10004229 371 GTAATAAAAATTTAATTTTTTGGAATATGACTCTTGGAGTTTTTCTTTTTCTTTTTTTACTTTTGGACTCTGTTGGACTTGAGTTGTTTTTCTTTAATGGC @ABCBACCCCCCCAACCCCCCBCBCCACCBADBDBAAD=ABBA?CA@C? MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:ABBBBBBBBBBBBB?BBBBBCBB?ABABB@BBBBBBB>B?BBBBAAAAAA@BABBAA@AAAA@?AA?ABA?A>?@?B8>>@@<>>< UQ:i:0 +20GAVAAXX100126:8:7:11542:56193 1187 chr1 10003958 60 101M = 10004229 371 GTAATAAAAATTTAATTTTTTGGAATATGACTCTTGGAGTTTTTCTTTTTCTTTTTTTACTTTTGGACTCTGTTGGACTTGAGTTGTTTTTCTTTAATGGC @ABBBACCCCCCCACCCCCCCBCBBCACCBADBDBAA7AEABCCAAA=9DBA>C?ACB@>B@=ABB?CA?D# MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBABBBBAABBBBABBBBBCBB?@BABB@BBABBBB9B>BABBABBAA@?A@BBAAAA?B@?@@@>?B?AA>@A@<;A@A>=?<<@?>><>?# UQ:i:0 +20GAVAAXX100126:8:25:18450:91287 83 chr1 10003979 60 101M = 10003652 -427 GGAATATGACTCTTGGAGTTTTTCTTTTTCTTTTTTTACTTTTGGACTCTGTTGGACTTGAGTTGTTTTTCTTTAATGGCTTTATTGAGGTATATTTTATG >DABA><0*(?BC:BCA;B9(BDCBCCBC@6;96ADC?DD7+>65=8'=D@C################ MD:Z:86 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:B@6=AA:@CB00)?BA6>B<>B/)=BBAABBB>679:?BB@BB6+=9-;8(=B?A################ UQ:i:0 +20GAVAAXX100126:8:44:17629:79062 1107 chr1 10004001 60 101M = 10003678 -423 TCTTTTTCTTTTTTTACTTTTGGACTCTGTTGGACTTGAGTTGTTTTTCTTTAATGGCTTTATTGAGGTATATTTTATGTACCATAAAATGCACCTAAGTG =::6<=<<=BBB@<=>A@@B;@?ABA@:ABA@B:=:9<<=AC>ABAABABAAAABAA@@C@??@B>???=====<><=;?AA@<<>< MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:?><:>DGGB5444445554DCFGGGGFGF UQ:i:0 +20GAVAAXX100126:8:25:9891:26690 99 chr1 10004020 60 101M = 10004321 387 TTGGACTCTGTTGGACTTGAGTTGTTTTTCTTTAATGGCTTTATTGAGGTATATTTTATGTACCATAAAATGCACCTAAGTGTACAATTTGATAATTTCTA CDBADADBDBCDBCDADDBDCBDBBDDA@@C@@ADCBCBCDDCCDBCCCBCCCCDDDCCBCCACCCCDDDCBBCABDCDCABCCACDCDDCDCCDCDDCED MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:21:17746:177127 163 chr1 10004141 60 101M = 10004479 438 AACCATTCCTACAATCCAGTTTCAGAACAAGTCAATCACTCCAAAAAGTTCCCTAGAGACCATGTGCTGACAACTATTATTTTATAGGCTTTTCTTTTTCT @DAB@A@BCDCACBDCDDCACCCDCCEACCCBBDC@=B@@@CBDBD?CAC?CDBD:CCCABCBABC8DCC?BB>CBBBB>BAD@BBDB=CAAC>D@CCBCD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCCCCCCCCCCCCCCCCBBCCCCCCCBBACBBCBCCBBCCBCBBC:BABABCBC4BCBBBBABBBCBBBB>>@BBBA@>BB@@A@BBB=@BB=ABB?A@A UQ:i:0 +20GAVAAXX100126:8:21:17763:177132 1187 chr1 10004141 60 101M = 10004479 438 AACCATTCCTACAATCCAGTTTCAGAACAAGTCAATCACTCCAAAAAGTTCCCTAGAGACCATGTGCTGACAACTATTATTTTATAGGATTTTTTTTTTCT >C>A@AB?@D9:@BA?CC?*;CBBCAC8@B)=6B4@BC;=:<@=7CC@CCC?BB@AB=>;71BD MD:Z:88C4C7 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:2 SM:i:37 MQ:i:60 OQ:Z:=A@@?CB?=C;9A?CB)7A@CB?B4@@)@@>CAACBB:@?BC=872;=?>C?<(A7AA)BA@B<CEABCABCAA@BAACCACCA@CCBDABBCDCBE@D@?DBDCAACBCB@A>??ADDCDDDDDDDEDBCDEECCDBDDCBCCBABACD@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:B??A>A?@>>6<:;AB@@AA@BA?@@@@B?BBA@BBABBBB@BBBABBBCABBCBBBBBBBBBCBCCCBCCBBBCCCCCBCBCCCCBCCCBCBCCCBCBBB UQ:i:0 +20GAVAAXX100126:8:42:7969:44162 1187 chr1 10004170 60 101M = 10004491 421 AGTCAATCACTCCAAAAAGTTCCCTAGAGACCATGTGCTGACAACTATTATTTTATAGGCTTTTCTTTTTCTTTTTCTTTTTTTTCTATTTCTGTTTGAGA @CAA@ABBCADCCAEEEECBBCDDDCDCCCBBC?@>AACAA@CD:DCDCC;CCACDCCCCCC?BBD@CCC@DDABCABCBBBBABCDB>CAADABBDCBB> MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@CBCCCCBBCCCCCCCCCC@@CCCBBCBCBCAA>A@BBBBACBBCBBBBBCBBBBBBBBBBB=BBAAB@BA?BBBABB@BAA=BBB@ABB@BBA:@@A@<: UQ:i:0 +20GAVAAXX100126:8:42:7986:44148 163 chr1 10004170 60 101M = 10004491 421 AGTCAATCACTCCAAAAAGTTCCCTAGAGACCATGTGCTGACAACTATTATTTTATAGGCTTTTCTTTTTCTTTTTCTTTTTTTTCTATTTCTGTTTGAGA @CAA@ABBCADCCBEEEDCBCCDDECCCCCBCCCB>=AC>AACD?DCDCBACCACDBCCCCCCBBD@CDC@EDABB?BCBBADABCE=>CBAD@CBCC5B; MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCBCCCCCBCCCCBCCCBCACCCCCBBBBBCBBBB@CBBCABBBBBBCBABBBBBBABBBBBBBABBBBBBBBBBB?BB@BBBBBBB=BBA@A??AB?1<6 UQ:i:0 +20GAVAAXX100126:8:28:13507:25203 99 chr1 10004176 60 101M = 10004453 376 TCACTCCAAAAAGTTCCCTAGAGACCATGTGCTGACAACTATTATTTTATAGGCTTTTCTTTTTCTTTTTCTTTTTTTTCTATTTCTGTTTGAGACAGAGT CBC?DBCCDDDDCBDBBBDCCDCDABCCBBBBCBDACDACCCDCCDDABCCCCBDDDDBDAAAA@CA@@@@C@@@AA@@@C MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHGHHHHHHHHHHHHHHHHHHHHHHHA UQ:i:0 +20GAVAAXX100126:8:2:13260:81311 83 chr1 10004222 60 101M = 10003923 -399 TTATAGGCTTTTCTTTTTCTTTTTCTTTTTTTTCTATTTCTGTTTGAGACAGAGTCTCTTTCTGTCACCCAGGGTGGAGTGGAGTGGCACAATCTCAGCTC ?<@AC>C>@AA>>@@A;<;?=?@>>A??9DDADCBC?AAACADDCB=;>==B?A-CD=DADC??DBB=C>DBBAC=BDA@BBDACBBBCB@CDCD@D@>DC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBEGFBHCCCCCCCCC@@@A@CCCCCCC5HHGHHGHEGEGHHHHHH????@HDH.HHEHGHHEGHHHEHCHHHHHDHHHEHHHHHHHHHHFHHHHGHHFHH UQ:i:0 +20GAVAAXX100126:8:45:4354:79437 99 chr1 10004223 60 101M = 10004540 414 TATAGGCTTTTCTTTTTCTTTTTCTTTTTTTTCTATTTCTGTTTGAGACAGAGTCTCTTTCTGTCACCCAGGGTGGAGTGGAGTGGCACAATCTCAGCTCA CCBACCCDDDDBDAAAAACAAAAB=ACC?9C??C?=>@ABC6>>BB@C?:@C6A@?C? MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:B@@BCBBCCCBCCBCCCCCABCCCCCCBBBBBBBBBAA@A:A:@@:>;@@@A5>>@@A?89>=-29?>2<=;>< UQ:i:0 +20GAVAAXX100126:8:44:5789:104432 163 chr1 10004228 60 101M = 10004558 430 GCTTTTCTTTTTCTTTTTCTTTTTTTTCTATTTCTGTTTGAGACAGAGTCTCTTTCTGTCACCCAGGGTGGAGTGGAGTGGCACAATCTCAGCTCACTGCA @BCB??ACCBBBBBBBBBBECCCCCCCCECDBBCBA?B>ACCCA@CCB@DC@@B?ABAA@D@CDCAACA>=BB@AD@?C MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCBCCBCBCCCCCCCCCBCCCCCCCCCCCCCCCCBBBCBBBBBCA>AABCBBBBBBBBBBBBBA:BA>B@AB?@B>A=A@BBAB@@AABA<:@@BA@?:A UQ:i:0 +20GAVAAXX100126:8:1:17413:63912 1107 chr1 10004229 60 101M = 10003958 -371 CTTTTCTTTTTCTTTTTCTTTTTTTTCTATTTCTGTTTGAGACAGAGTCTCTTTCTGTCACCCAGGGTGGAGTGGAGTGGCACAATCTCAGCTCACTGCAA @@@@CAAAAACAAAABBAAABADDDDCCCDDDCCADDCBDBCBDBDADCDCDDDCCADBBCCBCBBACBBDACBBDACBBBCBDCDCDBDBCDCCCC@BDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GGGGGGGGGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:7:11540:56171 83 chr1 10004229 60 101M = 10003958 -371 CTTTTCTTTTTCTTTTTCTTTTTTTTCTATTTCTGTTTGAGACAGAGTCTCTTTCTGTCACCCAGGGTGGAGTGGAGTGGCACAATCTCAGCTCACTGCAA @@@@CAAAAACAAAABBAAABADDDDCCCDDDCCADDCBDBCBDBDADCDCDDDCCADBBCCBCBBACBBDACBBDACBBBCBDCDCDBDBCDCCCC@BDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GGGGGGGGGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:7:11542:56193 1107 chr1 10004229 60 101M = 10003958 -371 CTTTTCTTTTTCTTTTTCTTTTTTTTCTATTTCTGTTTGAGACAGAGTCTCTTTCTGTCACCCAGGGTGGAGTGGAGTGGCACAATCTCAGCTCACTGCAA @@@@CAAAAACAAAABBAAABADDADCCCDDDCCADDCBDBCBDBDADCDCDDDCCADBBCCBCBBACBBDACBBDACBBBCBDCDCDBDBCDCCCC@BDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GGGGGGGGGGGGGGGGGGGGGGHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:4:16802:116090 659 chr1 10004234 60 101M = 10003895 -439 CTTTTTCTTTATCTTTTTTTTCTATTACTGTTTGAGACAGAGTCTCTTTCTGTCACCCAGGGTGGAGTGGAGTGGCTCAATCTCAGCTCACTGCAACCTCT CEAB?%B*A<&A>)D?;@9<9<@;43,@B(=9C>8AA3<85?;*A47?CC>3)@*6,44BA:@?71B@@;>4B=A9; MD:Z:10T15T49A24 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:3 SM:i:37 MQ:i:60 OQ:Z:BB>;8%=)<;'3:7C>;42)@?)=5A>9?==B+A84ACCA=,A<008ABABBC?8?;;@@*?13@AB*3+01A>9=A8+C>?9;-A;@37 UQ:i:24 +20GAVAAXX100126:8:25:13133:61877 147 chr1 10004291 60 101M = 10003984 -407 CAGGGTGGAGTGGAGTGGCACAATCTCAGCTCACTGCACCCTCTGTCTCCTGGGTTCAAGGGATTCTCCTGCCTCAGCTTCCCAAGTAGCTGGGATTACAG BBA>AAC9A:2>?@@=>=A7<><9>9@;?B7=@>=?B>,=ABAC=4@>B?;CB@C=8A?AB<;?0:ACBCBCCCBDBCDCCCCCEACCBCCCBBBBA@BD@ MD:Z:38A62 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:A:?8A??6<:/9@=?7<<<5<=96>6?:<>6:8=?>A>/=A?@@=/>:<@?@B?BBB=BB?B@>CCC>BC=A@@DCCBC?CBD@BBB5BBCDACDCCCCCBCEDABCCAB;BDCACBBBA@:B@ MD:Z:87 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:###############?67<7<97>::????AAB@35??@==>>>>B=B@>A==9?5<=> MD:Z:85 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:#################A??>552449>;9A3455544515<8<><55440455554445555554<=@9=A>CCC89CCC54455AGDGFAFAD@DDDDD UQ:i:0 +20GAVAAXX100126:8:8:8310:17522 147 chr1 10004327 60 17S84M = 10003989 -421 ACAATCTCAGCTCACTGCAACCTCTGTCTCCTGGGTTCAAGGGATTCTCCTGCCTCAGCTTCCCAAGTAGCTGGGATTACAGGCACTTGCCACCACGCGCA ##################B<@AA@>147?874@C8BB>CAAB?@CCA9ABACBCCB=CB?C@@A?C@CDBBCCCB?DBBBCCBBBCDBBCBBCB@9A:BB@ MD:Z:84 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:##################?6?@=A@>:>ABBABAB?BB?BAABABBBBAABBBB>BAAAABBBABBBBBBABBBBBBBBB UQ:i:0 +20GAVAAXX100126:8:21:4413:182078 99 chr1 10004409 60 101M = 10004700 382 CAGCTAATTTTTGCATTTTGAGTAGACAGGGGGTTTCACCATGTTGGCAAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCCCACCTTGGCCTGCTG CCB@DCDCDDDDBBCCDDDBDCBCCDACCCCCCADDBCABCCBBDBCBCDCCBDBCBBDB;DD@DBBDBCABDBCCCA@DCBDCBCCCACDDCD?CDCCED MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:23 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHIHHHHHHIHHHHHIHHHHHHHGGHHHHHHHHHHHHHHHEHHHHHH UQ:i:0 +20GAVAAXX100126:8:1:11745:83846 163 chr1 10004442 37 101M = 10004719 377 TTTCACCATGTTGGCAAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCCCACCTTGGCCTGCTGGAGGTATGTGACAAACTGATGGCAAATGGATTA @BAA@?BBCBACBBCCDCCCDBC@BBB;CDADBCC;7@ACBCBC;BD?BD=BC@?BBCCAABBCAC@B8A?C?;:>A;C>BAC?@BA;?C=;C>=A;?AA; MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:37 MQ:i:29 OQ:Z:BCCCCCCCBCBBBBCBBCBCBBB:B@BBABBBABB>@A6=9=?:??B??B=?;:?@=CB;7?97@:8 UQ:i:0 +20GAVAAXX100126:8:45:9158:12274 633 chr1 10004442 0 62S39M = 10004442 0 CTGGGATTACAGGTGCCCACCACCACACTTGGCTAAGTTTTGTATTTTTAGTAGAGTCGGGGTTTCACCATGTTGGCAAGGCTGGTCTCGAACTCCTGACC ###############################################################>>=;+<<=9;<:9=;?;;?=<<=?<6==?@>9@>5>*1 MD:Z:39 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:0 OQ:Z:###############################################################AA?51544555455545545544455544445455515 UQ:i:0 +20GAVAAXX100126:8:45:9158:12274 693 chr1 10004442 0 * = 10004442 0 CAAGAATTTCAGTTGCAGTCAGTACTCGGTTCAGGAACACTCCACCCAGGTTTGTAGCTTAGGAGCAATAGACTTTTTCCTATGCAATGTAGGTGTGTGGT ##################################################################?1AC5516*B*C'BA*A&@-<-0;4;6B.@)41@< PG:Z:BWA RG:Z:20GAV.8 OQ:Z:##################################################################@/@A30-2)@*A*A@*?'?-8,29074A,@*02A8 +20GAVAAXX100126:8:28:13507:25203 147 chr1 10004453 60 1S100M = 10004176 -376 TTGGCAAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCCCACCTTGGCCTGCTGGAGGTATGTGACAAACTGATGGCAAATGGATTATGCCCCCAAT ##A:AAC?:?@C:CBB1@B>A>@A@A=ABC@CC@@BBBBB@AAC>BC@CC?CBCCC=CBA5>ABA@BBBCCCBCCBCBCBBCCCCCCBCCCCBCBBAABC@ MD:Z:100 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:##@4=?<=6=?A=@==4B=;@==A?B8A@?AABAAA@AA@A@@A8@AA@BAAAABB@AB@7ABBBBBBABBBABBBB@BBBBCBBBCBBBBBBBBBBBBCB UQ:i:0 +20GAVAAXX100126:8:21:17746:177127 83 chr1 10004479 60 101M = 10004141 -438 CCTCAGGTGATCTGCCCACCTTGGCCTGCTGGAGGTATGTGACAAACTGATGGCAAATGGATTATGCCCCCAATGGACAGTGTTCTCAAACCGTGATCTGA DDDCAC?DCCDCCBCCBCCAD;BBCCCBCCABDBACCCACBCBDDBCCBCCBBBDDCCBBCDCCCBCCCABDCCBBBBCACADDCDBDDBC;ACBCDACBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHDHGHHHHIHHHHHHHGHBHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:21:17763:177132 1107 chr1 10004479 60 101M = 10004141 -438 CCTCAGGTGATCTGCCCACCTTGGCCTGCTGGAGGTATGTGACAAACTGATGGCAAATGGATTATGCCCCCAATGGACAGTGTTCTCAAACCGTGATCTGA BACCDC=D@CD??>?@;45::@A>B?B>>DDA=A:@@B@BADCCBBCDCCC@CCCCBDCCBB@BCCCB>BB=?AABBBABABBA@?BABBB@BBA@A@A@AA@CBA>ABBABA@CA?ABC<>>8@@@AAC@BBBB@AABCA@@?BB@>BBBB=AB>A@:AB?B?AB@C@A@AB9@BABCAC@CA@?BB:@@:==< MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:5GGDG;GCEGGGEGGGGGGGGGGGGGCAC9CGGEGGGGGGGGGGGGGGCDGGECGGGGEGGAGGCGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGG UQ:i:0 +20GAVAAXX100126:8:42:7986:44148 83 chr1 10004491 60 101M = 10004170 -421 TGCCCACCTTGGCCTGCTGGAGGTATGTGACAAACTGATGGCAAATGGATTATGCCCCCAATGGACAGTGTTCTCAAACCGTGATCTGAGGACCCGGGGAT 89A4@9@BCB@C@@>B>BBAABB=?B7>CBABB@BCBBCD>:C=CBDCB@;BDB>=BBCCCCDCCACCCCCACBDBCCBCBDBCBCCCBBABC@ MD:Z:98 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:####?>778?6=9>??A???>??@@@@@@=>:@>BAAA@A@BA@B?B@@B@ABBAAAABBB@@BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBCBB UQ:i:0 +20GAVAAXX100126:8:2:15114:83430 147 chr1 10004542 60 101M = 10004220 -422 ATGCCCCCAATGGACAGTGTTCTCAAACCGTGATCTGAGGACCCGGGGATCCCGAGACCTTTTAAGGGTATCTGTGAGATCAAAGCTATTTTCATAATAAT >D=@B<=ACAAC?BCD@BABBBDAB@=A;BABDC?CBCC>;CC;CCC?DC@C;CDB>BBCCBABBBBACCCCCACBDCCCCCCDBCCBCDDCBBB?@ABC@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:;?;8AABABBBABBBB>:BABBBAABBAABBBB@@BBBBBBBBBBBBBBBBBBBCBBCBBBBBBBBBCBBCBCCCBCB UQ:i:0 +20GAVAAXX100126:8:4:5529:91628 83 chr1 10004550 60 101M = 10004227 -423 AATGGACAGTGTTCTCAAACCGTGATCTGAGGACCCGGGGATCCCGAGACCTTTTAAGGGTATCTGTGAGATCAAAGCTATTTTCATAATAATCCTGAGAT EDDCCCCDAC@DDCDBDDBC;ACBCDCCBDBBBCC;CCBBCDC>;BDBBCCDDDCDCBBACCDCCACBCBCDBDDDBACCDDDDBCCDCCDCDCCCBBBCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHIHHHHHHHGHHHHHHHHHHHHHIHHHHHHHHHHEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:44:5789:104432 83 chr1 10004558 60 101M = 10004228 -430 GTGTTCTCAAACCGTGATCTGAGGACCCGGGGATCCCGAGACCTTTTAAGGGTATCTGTGAGATCAAAGCTATTTTCATAATAATCCTGAGATGATATTTG ?EBEDCCCDDCC;ACBCDCCBBBB@CC;BBBBCDCC8BDBBCCDDDCDDBBACCDCCACBDB@DBDDCBCCCDDDDBCCDCCDCDCCCBDBCCBCCCBDCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GHHHHHFHHHHHHHHHHHHHHGHHEHHHHHHHHHHHFHHHIHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:25:3804:30880 163 chr1 10004579 60 101M = 10004891 412 AGGACCCGGGGATCCCGAGACCTTTTAAGGGTATCTGTGAGATCAAAGCTATTTTCATAATAATCCTGAGATGATATTTGCTCTTCATTCTCTCTCTCTCA @CCB?AB:CCCCCACC;CCCACDCCCCDCCCACCACA>AB@CCCADDCBDACCADCCDBDBCCBACABDCADBABAB@?AABCCCCDB>:AAD?D?DBBD@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:ABBBBBBBBBBBBBBBBBBBBBBBBBBBBBB;BBBBB@BBCBBBBBBBBBBBBBBCBBCBBBABCABBBB@BCBBAB?;AB@BA@BBB>4??BB?B@@@A< UQ:i:0 +20GAVAAXX100126:8:42:4321:53069 99 chr1 10004580 60 101M = 10004795 315 GGACCCGGGGATCCCGAGACCTTTTAAGGGTATCTGTGAGATCAAAGCTATTTTCATAATAATCCTGAGATGATATTTGCTCTTCATTCTCTCTCTCTCAT CCC?CC;ACCDCBBB;DCDABDDDDCDCCCBCCBCBB@DCDCBCDDCBCCCDDDBCCCDCCDCBCDBACDCBDC=CDDBBDBDDBCCD@DADCDCDCDCED MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHDHHHHHHDHHHHHHHHHHHHHGHGHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:41:10214:75276 163 chr1 10004590 60 101M = 10004899 409 ATCCCGAGACCTTTTAAGGGTATCTGTGAGATCAAAGCTATTTTCATAATAATCCTGAGATGATATTTGCTCTTCATTCTCTCTCTCTCATGAGCATATGG @CBBA8BBCACDB@CCDCDCBCCCDBBCCCCCBCCCAACBCCCC@CDCCDABD@CEBDCCBBCBCD@CCBBCEAABAAAC@BBBADCC?C@AC@BAC@ACD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCCBCBBBBBCCCBBBCCB@BBCBBABABBBBBBBBBBBBBBBBBBBBBBABBBBBABBBBBBBBAABAABBBBBAB@B@B@B@ABB@@BA@B@?@<@@B UQ:i:0 +20GAVAAXX100126:8:5:7628:108971 99 chr1 10004623 60 101M = 10004891 362 AAAGCTATTTTCATAATAATCCTGAGATGATATTTGCTCTTCATTCTCTCTCTCTCATGAGCATATGGGAGTTTTCCAGAGACTTCCTGCCAGGCCACATC CDDACDCCDDDBCCCDCCDCBBCBDCDCBDCCCDDBBCBCDBCCDBCBCBCBDBDBCCBDCBCCCCBCCACBDDDBBCCDCDADDBCDCACCCDCCDBDDD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:5:7649:108990 1123 chr1 10004623 60 101M = 10004910 362 GAAGCTATTTTCATAATAATCCTGAGATGATATTTGCTCTTCATTCTCTCTCTCTCATGAGCATATGGGAGTTTTCCAGAGACTTCCTGCCAGGCCACATC *DDACBCADBD?ACBCC?ACBABBDCDCBDCCADBBBCBCDBCCDBCBC?CBDBDBCCBDCBCC>CBCBACBDDDABC@DCDADDBCDCA@CADCCD?DDD MD:Z:0A100 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:8HHHHGHIHIHIIHGIHFGHHGIHHHHHHHHHIHIHHHHHHHHHHHHHHFHHHHHHHHHHHHHHCHHHGDHHHHHGHHGHHHHHHHHHHGFHFHHHHGHHH UQ:i:9 +20GAVAAXX100126:8:42:11066:118124 163 chr1 10004633 60 101M = 10004938 405 TCATAATAATCCTGAGATGATATTTGCTCTTCATTCTCTCTCTCTCATGAGCATATGGGAGTTTTCCAGAGACTTCCTGCCAGGCCACATCACAACTGACC @CBB@ABBDCBCDACCCCCCCCDCCBBDBDCBCCBABACACBDCBBCDBDABCABDBDCCBACACB@CCCACABC@BBB@ABBB?CC@@C?B?>D?DCBBA MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCCCCCCCBCCCCBCBBCBBBCCCBBBBBBBBBBBBBBBBBBBBBBBBBBBBBABBBAAB?A@BAABBAB@AAA@BA@?@A?A>A@A@@@@><@??@@@> UQ:i:0 +20GAVAAXX100126:8:66:6823:31942 83 chr1 10004641 37 20S81M = 10004294 -427 TCAAAGCTATTTTTATAATAATCCTGAGATGATATTTGCTCTTCATTCTCTCTCTCTCATGAGCATATGGGAGTTTTCCAGAGACTTCCTGCCAGGCCACA #####################<>6=><99:26:>@=<:=<=;,<<<+5<;9=<=<===BB?B??AAB8AA>@A@=CBAAB9CACBAB@AC@CDABA?C@CB?@AA@CCBCBBCACADC=CADDCDBCADBABCCBA?CBD@ MD:Z:92 PG:Z:BWA RG:Z:20GAV.8 AM:i:23 NM:i:0 SM:i:23 MQ:i:60 OQ:Z:##########?364??8@9-<>;>@AA8;;?=@>@B>A?A6A@?A:@A@ABBBAABAA@BBAABBABBB@BABBB@BB:B@BCBBBBCBBBCCBBBCCBBB UQ:i:0 +20GAVAAXX100126:8:1:11745:83846 83 chr1 10004719 29 101M = 10004442 -377 ACATCACAACTGACCTGACCCAGAAGTACATCTGAGAATTCAGCTGTCTTCTATTAAGCCAGACATTAAAGAGATTTGCAAAAATGTCAAACAAGGCCACT DDCBCCCDCCCBCCCCBCCCBDBDDACBBCDCCBDBDCDDBDBCCADCDDCCCDCDCBCBDBBBCDCDDCBDBCDDCBBDDDDCCADBDDCBDDCCC@BCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:0 MQ:i:37 OQ:Z:HHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:26:5797:83894 99 chr1 10004750 60 101M = 10005102 425 CTGAGAATTCAGCTGTCTTCTATTAAGCCAGACATTAAAGAGATTTGCAAAAATGTCAAACAAGGCCACTCTGCATGTAATAGGCTTATCTTAAAAATGAA CDBBCDDCDBCCBDBBBDDBDCCDCDCBBCCCABCDCDDCDCDCDDBBCADDDCBBBCDDACDCCBBCADBDBBCCBCCBCC>CBADC@BDDCDB?>BAC6 MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHIHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHEHHEHHEHHHHHFBBFFF5 UQ:i:0 +20GAVAAXX100126:8:43:4132:159191 675 chr1 10004784 29 95M6S = 10005128 377 TTAAATAGATTTGCAAAAATGTCAAACAAGGCCACTCTGCATGTAATAGGCTTATCTTAAAAATGAATTAATATGTCTCTTGGTTGCCGTTTCTAATCAAA <*89B,AA=@4@)(@@CCB=6/C>CB5>B6)7C<>7A;@?.7DA>CCB8BBABA####### MD:Z:5G89 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:1 SM:i:29 MQ:i:29 OQ:Z:8):5@,@;B:AA7@7>A=B?27;ABA7A<+A=>:BAC@78==:7B9:@==8?))<>ACC:6-A?B?6=>4(1B==/A9==.4B?CCBBCCBCCCCBCCCBCCCBCBCCCB UQ:i:0 +20GAVAAXX100126:8:27:3628:73265 611 chr1 10004826 60 35M66S = 10005114 346 GTAATAGGCTTATCTTAAAAATGAATTAATATGTCTCTTGGTTGCCGTTTCTAATACAATCCATCTGCCTCAGACTCCCAAAGTCCTAAGATTATAGGTAT 1405==>9;?<+?>@==<<>>=<=############################################################################# MD:Z:35 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:51155455555,44444554??>?############################################################################# UQ:i:0 +20GAVAAXX100126:8:21:16295:166486 163 chr1 10004833 60 101M = 10005120 387 GCTTATCTTAAAAATGAATTAATATGTCTCTTGGTTGCCGTTTCTAATACAATCCATCTGCCTCGGCCTCCCAAAGTCCTGAGATTATAGGTATGAGCCGC @BCBAAACACDDDBCCCDDCCDDCCBBBDBDCBC@BA?A:@BCCBCDDCAACD@CDBBCB@AC@:C=ACA@DCABA?@BA@;B@ACAB@@?@8@>?@?@>@?;?@>?>??>? UQ:i:0 +20GAVAAXX100126:8:63:6148:94882 675 chr1 10004865 37 73M28S = 10005252 421 GGTTGCCGTTTCTAATACAATCCATCTGCCTCGGCCTCCCAAAGTCCTGAGATTATAGGTATGAGCCGCTGCACCCGACCTAGCCTTTTCATATGGAGTCT @?5??AB6>A;A71DC;@CABB9?C;CA60790,%=7/=?>BC=?8;;=665D=77:;483A:24A.0;73B############################# MD:Z:73 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:37 MQ:i:29 OQ:Z:B=4=?BB>7?;@62BB:AB?AB5;B9A@3.2650(?;0@C?AB9A975>175B?32945/5@80/?/5811@############################# UQ:i:0 +20GAVAAXX100126:8:42:16609:191180 163 chr1 10004875 60 101M = 10005207 432 TCTAATACAATCCATCTGCCTCGGCCTCCCAAAGTCCTGAGATTATAGGTATGAGCCGCTGCACCCGGCCTAGCCTTTTCATATGGAGTCTCAGACAGTGA @CCAAAA@BDCCCACCDCCDDC;CCDEBCDDDDC@A>CABBBCCACCCCBACCACBC;BCABB?CB5CBCBBC@ACBBCAAABBACAB:BBA:AD?BD@DD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCBCCCCCCCCCCCBCBCCCBCBBCCCBBCCBBBABCBBBBABBBBBBB?BBBBBABBBABAAAB@@BABAAAB@AAA@B@B@A@@CCBDBC;BCCBB@CC;BBCCCCBCCDDDDBCCCCBBDADCDBDBBBDACBDDCDDBDADCDCCACCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:#HHHHHHHHHAGHHHHHHFHHHHHHIHHHHHHHDHHHHHHHHHHHHEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:5:7628:108971 147 chr1 10004891 60 6S95M = 10004623 -362 TCCATCTGCCTCGGCCTCCCAAAGTCCTGAGATTATAGGTATGAGCCGCTGCACCCGGCCTAGCCTTTTCATATGGAGTCTCAGACAGTGAAATTCAGTCA #######@B>25;8@8/:A;>B<>9;;>C@B;?@?????@;BBABAB@BABBBBBBBBBBBBBCBBBBBBBCBCBBBBBCBBBCCCBCB UQ:i:0 +20GAVAAXX100126:8:41:10214:75276 83 chr1 10004899 60 101M = 10004590 -409 CCTCCCAAAGTCCTGAGATTATAGGTATGAGCCGCTGCACCCGGCCTAGCCTTTTCATATGGAGTCTCAGACAGTGAAATTCAGTCAATATATTTATAATG DDCDDCDDDADCCCBDBADCCCDCACCCBDBC;BCCBBBCC;BBCCCDBCCDDDDBCCCCBBDADCDBCBBBDACBDDCDDBDADBDCCCCCDDCCCBBCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHFHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:5:7649:108990 1171 chr1 10004910 60 25S76M = 10004623 -362 TCCATCTGCCTCGGCCTCCCAAAGTCCTGAGATTATAGGTATGAGCCGCTGCACCCGGCCTAGCCTTTTCATATGGAGTCTCAGACAGTGAAATTCAGTCA ##########################B7:B8;C<88@A740B@C=D:?C?ACDCCCCDCDCDACCCBDCBBD@CCCBCCBAB@CB@ MD:Z:76 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:##########################A56<99@<<6ACBBBBBBCBCCBBBCBBBCABBBBCBCBCBBBCBBB UQ:i:0 +20GAVAAXX100126:8:42:11066:118124 83 chr1 10004938 60 101M = 10004633 -405 CCCGGCCTAGCCTTTTCATATGGAGTCTCAGACAGTGAAATTCAGTCAATATATTTATAATGAATACTTTTTTTTTTGAGATGGAGTCTTGCTCTTGTCAC DE;AADCCDCCCDDDCBCCCCCBDADCDADBCBDAC>ADBBCBCACADCBCACCC?CADBC?D@C;=>AAADDDDDCBCBCCBBDADCDCBCDCDCABBCC MD:Z:70A30 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:IHHGGHHHHHHHHHHGHHHHHHHHHHHHIHHHHHHHCGHIGGHGHGGHHIGIHIIFHGHGHGHFHCEEGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:32 +20GAVAAXX100126:8:25:19700:154119 147 chr1 10004969 60 101M = 10004642 -427 ACAGTGAAATTCAGTCAATATATTTATAATGAATACTTTTTTTTTTGAGATGGAGTCTTGCTCTTGTCACCCAGGCTGGAGTGCAATGGCGTGATCTTGGC BD?@C@D@CCAC??DCCAC@<@DBABAADD@CDC>AA>BCACCCEDBCCDCDBDCCBDCBB;ACBC@@ABCC@ MD:Z:39A61 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:?B;BBCBBBBCBBCCBCBBBBCBBCCBCCCCABCBC>BBBCCBCBCCBCCCCCCCCCCCCCBCCCCCCB UQ:i:35 +20GAVAAXX100126:8:48:10519:110723 99 chr1 10004994 60 101M = 10005311 417 ATAATGAATACTTTTTTTTTTGAGATGGAGTCTTGCTCTTGTCACCCAGGCTGGAGTGCAATGGCGTGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGC CCCBCCCDCCADDDDDD;>:?>:C@<<7:==;=;=???A@>BBBABBCCCB@BC8CCB?@BC>B:5<:7;9<9;5BCCDDE@ MD:Z:14A86 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:HHHHHHGHHHHHHHHHHBCBCC=HD4555445444EDFFFEHHGHGHHHHHEHH:HHHCDGHCGB=<@;>54445H=HHHEEHEHHHHHHHHHHDHHHHHE UQ:i:35 +20GAVAAXX100126:8:68:18251:192056 147 chr1 10005081 60 27S74M = 10004792 -362 ATGTCGTGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGCTCAAGCGATTCTCCTGTCTCAGCCTCCTGAGTAGCTGGAATTACAGGCATGGGCCACCAC ############################B99A@9?9BBA;=@@BB@@CACBDCBACC>@AABBABA@BBC@ MD:Z:74 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:############################?;;?<6???:@??<6?????;A?A?>A?B@@@A;@AA?A?:A@@=?B>>BABABB@@ABAA?AABABB>AB@B UQ:i:0 +20GAVAAXX100126:8:1:6636:49601 99 chr1 10005102 29 101M = 10005477 440 ATTCTCCTGTCTCAGCCTCCTGAGTAGCTGGAATTACAGGCATGGGCCACCACGCCCGGCTAATTTTTGTGTATTTAGTAGAGATGGGGGTTTCACTATGT CCC@DBCDBCBDBCCBBDBBDBDCBCCBDBCDDCDCACCCBCCBCCBBCABCA;BBB;CBDCDCDDDDB@ABCCDDCCCCCDCDCBCCCC?DDCDADD@DD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:0 SM:i:29 MQ:i:29 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEGHHHHHHHHHHHHHHHHHHHAHHHHHHHDHH UQ:i:0 +20GAVAAXX100126:8:26:5797:83894 147 chr1 10005102 60 27S74M = 10004750 -425 GCAACATCCGCCTCCCAGGCTCAAGCCATTCTCCTGTCTCAGCCTCCTGAGTAGCTGGAATTACAGGCATGGGCCACCACGCCCGGCTAATTTTTGTGTAT ############################B865235A?;>>C;9A:>@)?C7<=@>C899CC28)5B??:CB@CA<8/B>8B;@8@>B:CC?CCCB?@@BC@ MD:Z:74 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:############################?161316B;;<=B99=6<;*;A<9<>:B;6:BB58)8BA>9BA>B@942B9>B;><>>A?BB?BBCBB?BBBB UQ:i:0 +20GAVAAXX100126:8:27:3628:73265 659 chr1 10005114 60 42S59M = 10004826 -346 CATCCAAGCACCCACTCCAAGGCTCAAGCAATTCTCCTGTCTCAGGCTCCTGAGTAGCTGCAATTACAGGCATGGGCCACCACGCCCGGCTAATTTTTGTG ###########################################C@3=3<=>C<&><@C@*'8B9;:'>@8?:BCBBC<,0CA;C9&0/1>9C.CB?@?9A? MD:Z:3C14G40 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:2 SM:i:37 MQ:i:60 OQ:Z:###########################################?>172:>@B:(;;BA@,';B;@9';>6>9?BABB9)3CBCC9)204;;B,BC??><=> UQ:i:24 +20GAVAAXX100126:8:21:16295:166486 83 chr1 10005120 60 101M = 10004833 -387 CCTGAGTAGCTGGAATTACAGGCATGGGCCACCACGCCCGGCTAATTTTTGTGTATTTAGTAGAGATGGGGGTTTCACTATGTTGGCCAGGCTGGTCTCGA DDDCDACDCCCCBDCDCCCDBBBCCBBBCBCCBC;BCC;BBCCDBBDDDCACACCDDCCACCBCBCCBBBBADDDBBCCCCADCBBCBDBBCCCADCB:BC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:43:4132:159191 595 chr1 10005128 29 66S34M1S = 10004784 -377 GTCTGGGCTCACTGCAACCTCCGCCTCCCAGGATCAAGCGATTCTCCTGTCTCAGCCTCCTGAGTAGCGGGAATTAAAGGCATGGGCCCCCACGCCCGGCG ###################################################################################################4. MD:Z:2T7C11A11 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:3 SM:i:29 MQ:i:29 OQ:Z:###################################################################################################A7 UQ:i:6 +20GAVAAXX100126:8:48:2299:12648 99 chr1 10005135 60 101M = 10005519 438 TTACAGGCATGGGCCACCACGCCCGGCTAATTTTTGTGTATTTAGTAGAGATGGGGGTTTCACTATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCATG 9DC?CCCCCCBCABBCABCA;BBB;CBDCDCDDDDBA@?CCD@CCBCC@:DC@CCCC9@DBCADCCBC@:==;;=BABA;:>?:69A9A=?=AC:A=?BAD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:IHHHHHHHHHHHIHHGHHHHHHHHHHHHHHHHHHHHGGEHHHFHHHHHDBHHFHHHHBFHHHHHHHHHD@BABBAGGFFB;DA@D:D@DAA?GGBF>DDGH UQ:i:0 +20GAVAAXX100126:8:42:16609:191180 83 chr1 10005207 60 101M = 10004875 -432 CAGGCTGGTCTCGAACTCCTGACCTCATGATCCACCTGCCTCAGCCTCCCAAAGTGCTGGAATTACAGGCGTGAGCCACTGTGCCTGGCCTATAATGAATA DBC?CDCADCD;BDBCACCB@9CCDB?B=7=>-A9;:<<;7:===:7=<<<:<:7<<,99=>>?>=>?5>;1 MD:Z:61 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:0 SM:i:29 MQ:i:29 OQ:Z:#########################################A=A9A:AA/F=@===444444444544454555/5444/55=9:=CF5AA4454444555 UQ:i:0 +20GAVAAXX100126:8:48:10519:110723 147 chr1 10005311 60 101M = 10004994 -417 TTTAATATTCTCTTTGTTTCTGTCCACAGCAAGAATCTTTATTTCCTGAGACCTTTTGTAGCAGATTATTTTCCCTCAGTTTCTTGCCCTTAAGAGTCTTC DE?BC@ABCA?A=CDAC?A@B@CB:9BACC@CCB>BABCCBDDDCBD:CB:DBDBDABBABACA>A?CDDDCCCDCBDAAECCCDCC8BDCBCBC??BCB@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BAB<@B=AA@>==@BA@=;?BA@A:3B@BA@AB@@?@BBBBBBBB@CC@B-A2A(;A3;9B*ACB8A8;B+A&;>B>81:=/852?97481CB=2=4+*)A)CBC/++@)%>.?''8C3C@######################### MD:Z:16A25T22T11 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:3 SM:i:37 MQ:i:29 OQ:Z:*((?<-?/?(:@4=6@*>C@4@37@*>(8;@;7/9@1<72@;81<1@?>/?1*)(<)@B@/*+@))@.:'(1@2A?######################### UQ:i:35 +20GAVAAXX100126:8:43:10736:78356 611 chr1 10005394 60 35M66S = 10005705 411 TTGCCCTTAAGAGTCTTCGGTTCTCCACAGATAAGAGATTTGCTTTTGATATTTCCTCGACCTGCTCATAAGGATTTCATTATAACTTCTGGGTGCAATCT ?################################################################################################ MD:Z:35 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:AA7>A################################################################################################ UQ:i:0 +20GAVAAXX100126:8:61:2951:38254 163 chr1 10005434 60 96M5S = 10005758 424 TGCTTTTGATATTTCCTCGACCTGCTCATAAGGATTTCATTATAACTTCTGGGTGCAATCTTTAGGAGAGTTTGCAAAACAGTCTTTTTTTTTTTTGTAAT @BBC??@ACCBCB@CDEC;CBDDCCDCCDCDCCCBBAABBBACCBBDCBD@CD>CCCDCB=CC;CD@ACC@DD?ABBBC@@ACACCDCADBCD@D###### MD:Z:96 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCCCCCCBBBCCCCCCCCBCCBCCBCBCBBCBBBBBBBBBCBBBCBBBBBBB?BBBBBBCBB=BBB@AB@BB@BBA@@B?B?AB@AAAAAAABA###### UQ:i:0 +20GAVAAXX100126:8:21:9990:22806 163 chr1 10005457 60 72M29S = 10005782 425 GCTCATAAGGATTTCATTATAACTTCTGGGTGCAATCTTTAGGAGAGTTTGCAAAACAGTCTTTTTTTTTTTGTAATGGAGTTTCGCTCCGTCACCCAGGC @CCAABBCBCCCB@CCDBCCCDADCBECCCBCBCAB@C>BBCCDACCBCC@BC@CC?DCBADCBCC@CDCA############################## MD:Z:72 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCBCBBBBBCBBCCCBCCBBBBBBCBCBBBABBBABBBCBBBBBBBB?BABBBA@ACBBBBBBBBBBBBBB############################## UQ:i:0 +20GAVAAXX100126:8:6:21370:119926 99 chr1 10005465 60 97M4S = 10005757 389 GGATTTCATTATAACTTCTGGGTGCAATCTTTAGGAGAGTTTGCAAAACAGTCTTTTTTTTTTTTGTAATGGAGTTTCGCTCAGTCACCCAGGCTGAAGTT >743?@CCBDADD?DBC=?BBCDC?DDDCCCCA>=?DDB>>????>;;2>:=4A>@?D56>B2:>98@/DBD?##### UQ:i:25 +20GAVAAXX100126:8:1:6636:49601 147 chr1 10005477 29 35S66M = 10005102 -440 ATGATTCCTCGGGCTGCGCATAAGGATCTCCTTTGAACTTCTGGGTGGAATCTTTAAGAGAGTCCTCAAAACAGTCTTTTTTTTTTTTGTAATGGAGTTTC ###############################BC*89BA>=(29CACC?:+8'%BC54@21,-6%5'85=CB?<7%0>EEEEEEEEEEAACBCCBAA?CCB@ MD:Z:12C8G6T0T0G35 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:5 SM:i:29 MQ:i:29 OQ:Z:###############################?@);6@A<;(.8BB@AA5+:'%?B54>/1+08,:(:4=BDCBCCCBDDA;BABC6BBCABBCACB=@BBA;A?;?CCCCBCCDCCDD@D@. MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHGHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHGGGGGGGGEAGHGHHGHGHHIHHEHHEGHHHHHHGHH=GFFFCFDBDHHHHIHHHHHHHGHG2 UQ:i:0 +20GAVAAXX100126:8:48:2299:12648 147 chr1 10005519 60 46S55M = 10005135 -438 TTTAAACTTTGGGGTTAAACTTTTAGGAGAGTTTGCAAAAAATTCTTTTTTTTTTTTGTAATGGAGTTTCGCTCCGTCACCCAGGCTGAAGTGCAGTGGTG ###############################################ACCBDCDDDA=3>C9A?<@CDC;ABCC;=BBBBC?EDAABABD=CB?B?A@=C? MD:Z:55 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:###############################################B@BBBBBBBB<5?B;BA@BBBBBAAABB=@A@AB=CCA@ACCC?CC@CAB??B? UQ:i:0 +20GAVAAXX100126:8:48:13575:23805 163 chr1 10005529 60 83M18S = 10005856 427 TGTAATGGAGTTTCGCTCCGTCACCCAGGCTGAAGTGCAGTGGTGCAATCTTGGCTCACTGCAACCTCCGCCTCCAGGGTTCAAGGGATTCTTGTGCCCCA @BABBBACCBACC>;BDBC;BABACABACBDCCDB;A<ACA@BCBBA>?B@BC@C?BA@A=?B>@B9>CC?>A@9<####################################################################################### PG:Z:BWA RG:Z:20GAV.8 OQ:Z:*@+ABCBAA=47;?####################################################################################### +20GAVAAXX100126:8:46:11003:55063 99 chr1 10005652 60 101M = 10005971 396 CAGGCGCCCGCCACCACACCTGGCTAATTGTTGTATTTTTAGTAGAGATGGGGTTTTACCATGTTGCCCAGGCTGATCTCAACTCCTTTTTTTTTGAGACA CCBAC;CCB;BBCABCACABDBCBDCDCDBB@@@ACDDD@BCBCADCCCBCBC@ADDCABCCBCDBBBBCCBADBBCBCBCDAD@CDDDDDD?@@?D@DBE MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGFGHHHHGGHHHGHHGHHHGHFGHHHHHHHHHHHHHHHHGGHHFHHIHHHHHFHHHHHHHEGGCHDHHH UQ:i:0 +20GAVAAXX100126:8:43:10736:78356 659 chr1 10005705 60 101M = 10005394 -411 GTTTACCATGTTGCCCAGGGTGATCTCAACTCCTGTTTTTTTGAGACAGAGTCTCGCTCTGTTGCCCAGGCTGGAGTATAGTGGCATGATCTCGGCTCACT =@BA::A=C648=BD96>C'@4:(1?5:CD@CCA'3;*@?=C@=>C2<=>8BCD5>?B8@/9@/2@<+@?>CBAB=ACA79B@?@B=69A899BA?@4,?< MD:Z:0T18C14T66 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:3 SM:i:37 MQ:i:60 OQ:Z:=9@>2:>;B512BAB32=>C@5=?-=9=>>BB8>A>9@2=75@BA@>1';9 UQ:i:40 +20GAVAAXX100126:8:43:10431:27195 99 chr1 10005733 60 101M = 10006098 428 ACTCCTTTTTTTTTGAGACAGAGTCTCGCTCTGTTGCCCAGGCTGGAGTATAGTGGCATGATCTCGGCTCACTGCAACCTCTGCCTCCCGGGTTCAAGCGA CAC@CDDDDDDAAAADCCACCDCBBDB;AABCB@DBBBBACCBCBCAC@CCCCBBCBCCBC@@DB9CBBBB:@@@ADA@DBCCBCDBCC9??;?=>?<;6B MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHGGGGHHGHHHHHHHHHHGFHHHFHHHHHFHHHHHHFHFHHHHGHHHHHHGEFHHIHHGHFBDGFFHHFHHIHHHHHHHGDDA;6A8BAACAEA7BBA9<>9>8:@@A6@@=8;1BB;CCA@CA:;->C4@A7>ABBB7A?@:9?;:39A>>6:0A??BB>ACA>8(:@0A@7=BBAB6BBC@:=C>BCB?@@BC@CACCBCA>1@@1>@*@AA< UQ:i:12 +20GAVAAXX100126:8:61:2951:38254 83 chr1 10005758 60 101M = 10005434 -424 TCGCTCTGTTGCCCAGGCTGGAGTATAGTGGCATGATCTCGGCTCACTGCAACCTCTGCCTCCCGGGTTCAAGCGATTCTCTTGCCTTGGCCTCCTGAGTA BC>CC;BBA@DBDDB;>CDDCDCDCBBCDCBBCCDCCCBDACDBCCBBBBCCB;BBBBCCCCCABCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GHGHHHHHHHG=HHHHHHHHHHHHHHIHHHHHHHDHCHHHHHHEHHHHHHEHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:67:2948:89942 147 chr1 10005805 60 20S81M = 10005484 -401 GTGGCATGATCTCGGCTCCCTGCAACCTCTGCCTCCCGGGTTCAAGCGATTCTCTTGCCTTGGCCTCCTGAGTAGCTGGGACTACGGGCACATGCCATCAT #####################@A=;@>=BB@AA5<@:@CA>=@ABC:CBCBC@@B?BDACBBB@CCB@>CB;CCABBBCCBBABBBC@ MD:Z:81 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:#####################?=<6?==@>A?=4?>?@BB?:?=?B=??B@BAB?B?AAABB?AAAAA=BBBB?BA=BBB<C@CBCD?BBAACA8=BBADE MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:37 MQ:i:29 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHIHHHHHFHHHGHHHHHHHHHHHHHHHHHHHHEHH UQ:i:0 +20GAVAAXX100126:8:46:11003:55063 147 chr1 10005971 60 23S78M = 10005652 -396 TGATCTCCTGACCTCGTGATCTGTCTGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCTCACCCAGCCAAGTTAGTATGTGTTTAAAGAT ########################@=@=8><>?C96A88@=?<*;;BAB67C;>;4?:2;B<7=A95C;B@,BCBCCCACDBDCEBCBCACADCA??CBC@ MD:Z:78 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:########################?;@>36>9>;<(:6>B@6:A=672A89>B@9@B<1B9?@)@BBACB@BBCBBCCBBBCCCCCCCCCBCB UQ:i:0 +20GAVAAXX100126:8:26:2983:65747 99 chr1 10005981 29 79M22S = 10006359 410 CCTCCCAAAGGGCTGGGATTACAGGCGTGAGCCACCTCACCCAGCCAAGTTAGTATGTGTTAAAAGATCACACTTGTAATCCTAGAACTTTGGGAGGCTGA 64911=?>?@*:=?>?@A@@:9==8'6==<=::<:@9>>=>>63;;<;<;<:<29@?6?:A;;:;:;??=3>>=;####################### MD:Z:10T50T17 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:2 SM:i:29 MQ:i:29 OQ:Z:=9==84454404455FFFFF55445+444444554C:CAC??;7?55555555.5CC3CCG4@GA44455CCC8AA??####################### UQ:i:35 +20GAVAAXX100126:8:61:18274:143796 163 chr1 10006062 60 92M9S = 10006396 429 CTAGCACTTTGGGAGGCTGATGTAGGAGGATCACTTGAAGCCAGGGGTTTGAGCCCAGCCTGGGCAACATAAAGATTACAGGCGTTAGCCACTAAGCCTGG >A:@?@?A?C?/>9A:AB;??:-7@@A<;B91'8C.>>B;C7=A%?>@@B9(8C<;:?@@A/A8::57::=0,C1%%?>:C@########## MD:Z:53A31G6 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:2 SM:i:37 MQ:i:60 OQ:Z:;>;@CC@@7;>7'5>??8:@79B79@2)?B<>8A4><>;@9==(99>;A8'5B=96@A;@0:4:737;9<.0A5%%<<5@A>@>=<==<@<>7?=>=>=977=;<=:<;:;<<9:=;:::@A=??;<<=<<;99<=7:65>A5:@:617/8>?;><=3?9<>?5>8B MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:23 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:FFDDFCACA>55544=<9<><<=CCCCC444444555445544C98>C>>7A<4@C9AACC;CA8>>@9A8C@@34BBBB@CCC?CD?7A:CA:@;B?BCBBBBABABBB@ MD:Z:64 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:######################################@74@16@AA@A@:;=>4@<@>A:@AA94B@AA@BBA>BB>0@6BA?A9BABBB?BBBBBBBAB UQ:i:0 +20GAVAAXX100126:8:3:10732:109401 163 chr1 10006103 60 101M = 10006447 444 CAGGGGTTTGAGACCAGCCTGGGCAACATAAAGATTACAGGCGTGAGCCACTGAGCCTGGACCCTTCCCTCTCTTAATCTGTTCAGGCTGCTATAACATAA @BBBABBAABCBA@CCCBCABBCACDADCCDDCCBAA;;BCB9@7>CCCC?AC@CCADCAB>BBB@?CBD:E@@@BBAACD;D= MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BABBBBACCBBAABBBBBB>BAB@BBBCBBBBBBBAB@>BBBA;9=ABBBB@BAABCBB@A?AB?=BB?BCB>??BB@@ABBC58CAABAD@C51BCACBBEDA906>;8=AB9@B:CCB@<;@9BC##################### MD:Z:81 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:<0@@@??AA9A;5>B@?B?B?B60@ABBAACB@608C@;@ABA;?BABB>>=A729=8A>ABB>;;?9AA##################### UQ:i:0 +20GAVAAXX100126:8:46:19844:141004 99 chr1 10006137 60 95M6S = 10006468 401 TTACAGGCGTGAGCCACTGAGCCTGGACCCTTCCCTCTCTTAATCTGTTCAGGCTGCTATAACATAATACTGTAGGCTGGCTACAGAGGTTTTAAAATTTG CDC?CCCA;CBDCBBCADBDCBBD@=><=<@;B34;82ABB>DCBEC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:11 NM:i:0 SM:i:11 MQ:i:11 OQ:Z:BBBBBBBBBBBBABABBBBBBBBABBBBBBBBBBBABCBBBBBBABBBBBBBBBBAABAA?A@AB?@A?5<941,8'3<@@1=>>:>32280=@?;@>A@B UQ:i:0 +20GAVAAXX100126:8:45:17313:6715 83 chr1 10006154 60 101M = 10005854 -400 TGAGCCTGGACCCTTCCCTCTCTTAATCTGTTCAGGCTGCTATAACATAATACTGTAGGCTGGCTACAGAGTTTTTAAAATTAGTATTTTTTTTTTTTTTG <>A@??BA@B?CCD>CCCACDCDCDCDCCADA@DBB;CBAB@CDCAC?DCC@CCAC?B@C@@A@?=@;??>DDDDCDDDCDBA<:;?>>??>>>DDDBDCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BACBDACCABAB><;;7?@@A?C<=;;8>+665DC:0?<@:>35;@@B9@@A?=@A;?#################### UQ:i:0 +20GAVAAXX100126:8:22:5084:77687 163 chr1 10006173 60 81M20S = 10006497 424 CTCTTAATCTGTTCAGGCTGCTATAACATAATACTGTAGGCTGGCTACAGAGTTTTTAAAATTAGTATTTTTTTTTTTTTTGAGACGGAGGCTTGCTCTGT @DBC?ACCBDBBCACCCBDB?BCAACACCCDBCA??>=?<@=;C5;@@983<::DDC;AA>A>3813ADBACC<@BBABC##################### MD:Z:81 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCCCBBBBBBABBBBBBBB>?B@@ABBBBBABB@AA@A?A==B::>@832<4CBCD?AB?;BB6?C:9ACB?@7@=AA?B<>73 MD:Z:15C85 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:1 SM:i:0 MQ:i:37 OQ:Z:BBABBBB>BBBB@CC?C=CBCBBBBBABBABBABAABBABBAA?BBBBAAB>AAAAB>AA>BAAAB@A;BBBB?AB=;@B==A39>A??=9=;>>@>4=26 UQ:i:32 +20GAVAAXX100126:8:43:16553:40365 147 chr1 10006358 29 66S35M = 10005967 -425 GTGGTGTGAGCGCGGTTCACTGCAAGCCCCACCCCCCAGGTTCCCACCATCCCCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCAC #############################################################################BA:8:8::2B420@B@ABA@BBC@ MD:Z:35 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:0 MQ:i:37 OQ:Z:#############################################################################@@727537.@8<.@A>ABB>BB@B UQ:i:0 +20GAVAAXX100126:8:26:2983:65747 147 chr1 10006359 29 68S33M = 10005981 -410 AGGTGCTTGAGCCCGCCCACATGCACGCTCCACATCCCGGTTGCACACCGTACCCCTCCCTCAGCATTCCGAGTAGCTGGGACTACAGGCGCCTGCCACCA ############################################################################################BB@?;7=@? MD:Z:33 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:0 SM:i:29 MQ:i:29 OQ:Z:############################################################################################BB@@70>=> UQ:i:0 +20GAVAAXX100126:8:62:16536:90438 147 chr1 10006385 60 66S35M = 10006082 -337 CCCTCCTCCCAGCTTCACTCCTTTCTCCTCCCTCAGCCTCCCGAGTAGATGGGACTACAGGCGCCTGCCACCACGCCGGGCTAATTTTTTTATTTTAGTAG #####################################################################B4,B3?$6;63ACC@9@DBDA;9?8C5?1:D@ MD:Z:35 PG:Z:BWA RG:Z:20GAV.8 AM:i:23 NM:i:0 SM:i:23 MQ:i:60 OQ:Z:#####################################################################?5+@5>(:742@BB>6>BBC?=6<5B6;1;CB UQ:i:0 +20GAVAAXX100126:8:61:18274:143796 83 chr1 10006396 60 5S96M = 10006062 -429 ACGCCGGGCTAATTTTTTTATTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCTGCCGGCCTCGGCCTCC ######?9AB><<<=@<>@==B@B4;59*:@AB?A8;;;=>?@A>7.=,;2;=88<:4;<6<<=:;95:=:8>A?>>==;/7=/:@<7>BAB>GDG@=@FDFFD5/5.57@A@845554;?2=4555044555 UQ:i:0 +20GAVAAXX100126:8:23:12774:197414 99 chr1 10006420 60 101M = 10006790 437 AGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCTGCCGGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA CCC?;CCCCDDBCABCCBBDCCBBCCCDCBCBBCB;CCBCBBCBDABDB;BBDCBDBBB;CBBDB;CBBDBBBCDDCABBDB>CDCDCACCCC;CCDDCDA MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:23 NM:i:0 SM:i:23 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHEHHHHHHHHHHHHHHHHHG UQ:i:0 +20GAVAAXX100126:8:67:19765:57485 83 chr1 10006437 11 1S18M3I77M2S = 10006149 -382 CGTTGGCCAGGATGCTCTCGTGGATCTCTTGACCTCGTAATCCGCCCACCTCCGCCTCCCAAAATGCTGGGGTTACAGGCATGAGCCACTGTGCCCGGCTT HHFEHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:456 +20GAVAAXX100126:8:3:10732:109401 83 chr1 10006447 60 101M = 10006103 -444 ATGGTCTCGATCTCCTGACCTCGTGATCTGCCGGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCCTAAAATTAGTATGTT =ECBDC=4@=B;5>>=B@CCB9AC@BDCCBC;BBCCD;BBCCACBBDDDACBCBBBBCACBBDBB;?CBCBCBBCBB;BCC;BBCCCDDDCDCDACCA@DC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@HHHHHCBFBD?9AA?HDHHEGHHGGHHHHHHHHHHHHHHHHEHGHHHHHHHHGHHHHGHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:46:19844:141004 147 chr1 10006468 60 30S71M = 10006137 -401 TGAGCCAGGTTGGTCTCGATCTCATGACTGCGTGATCTGCCGGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCCTAAAAT ###############################?9<'@A<:=9>8@:>;7C632<83.1;A=;000-8*?;&9A>>BA9>>86>?CA;B@A>@ MD:Z:71 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:###############################@4<&>0032;+==?@0=907A;6(9@6=BB@A@8=;=B@=@?@;@ UQ:i:0 +20GAVAAXX100126:8:48:11905:175240 83 chr1 10006478 60 101M = 10006103 -475 CGGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCCTAAAATTAGTATGTTTTTTGTTGTACTTGTTTTTGTTTTTGTTTTT /8,)09:AABA<>B>ADDACBACCB>AD>BBBBB9ACBDB>B@CBA;B@C;BB@BCD@DCDCDAC??<>??DDBADCACB>?@?DCCCBDCC@D>C;ABBCBCBCCBB9BCC;BBCCCDDDCDCDACBB?ABADDCADCAC9@@B?A@@AB@AAAAB?AAAADDDDDCBDBB;BBDADBCBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:5HEHHHHGHHHGHEHHHGHGHHHHHHHGHHHHHHHHHHHHHHHHHHGGGGGGHHHHHHHHBGGGGGGGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:22:5084:77687 83 chr1 10006497 60 101M = 10006173 -424 GGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCCTAAAATTAGTATGTTTTTTGTTGTACTTGTTTTTGTTTTTGTTTTTTTTTTGAGGCGGAGTTTCA *@DBCCCCDCCCDCC;ACBDBCBC@BB;A@@:BACCC?DDCDCDACBB?ABADDCADCACB@@B?A@@AB@AAAAB?AAAADDDDDCBDBB;BBDADBCBC MD:Z:0T100 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:2GHGHHHHHHHHHHHHHHHHHHHHFHHHFFFIHGHHHEHHHHHHHHGGGGGGHHHHHHHHHGGGGGGGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHH UQ:i:9 +20GAVAAXX100126:8:21:11247:101401 147 chr1 10006514 60 12S89M = 10006257 -345 GGATTACAGGCGTGAGCCACCACGCCCGGCCTAAAATTAGTATGTTTTTTGTTGTACTTGTTTTTGTTTTTGTTTTTTTTTTGAGGCGGAGTTTCACTCTT #############@@A6@A@>@;@@A:A@C>B@?@AB=@>A>BAABBA@@AB@ABA=ABBABBA1AABBB?BBB@BBBCBBBBCBBCCCCCCBCCBBCBCBCCB@CBBCB UQ:i:0 +20GAVAAXX100126:8:46:8850:165700 83 chr1 10006624 37 101M = 10006281 -443 TGGCGTGATCTTGGTTCACCACGACCTCTGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAAGCATGCACCACCATG EDC;ADCCDADBA@ACB@CBC;BACCDCCBCCDCC;CCADDBDDB;?CDDCDCCCBCCDBDBCCDCCCBCACDBCCBBBBCCBBDDBBCCBBCCCCC@BCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:37 MQ:i:29 OQ:Z:HHHHHHHHHGHGGGGFHDHHHHHFHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:22:6227:26566 163 chr1 10006730 60 83M18S = 10006988 358 CTAATTTTGTATTTTTAGTAGAGACAGAGTTTCTCCATATTGGTCAGGCTGGTCTCGAACTCCCGACATCACGTGATCCACCTGCCTCAACGTCCATAAGG @DBC@?BBBBCCBBCCCCADCCCCBCBCCBCCBDABAB9BBA?@?@@?A??=;7=?39@?81AA886:?>:>3687':A@?A################### MD:Z:83 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCBCCBBCACBCBBBBB;CBBBACBABB?BBBBBBBB>BBA@;A?<=A:A>2:6;83>?7/?A=5<9<<:;5/55(:=?@?################### UQ:i:0 +20GAVAAXX100126:8:2:2951:16973 99 chr1 10006763 60 101M = 10007005 342 TCCATATTGGTCAGGCTGGTCTCGAACTCCCGACATCACGTGATCCACCTGCCTCAACCTCCAAAAGGGCTGGGATTACAGGTGCGAGCCACCTCGCCTGA <<>7ABBCBCDABDBBADDD>:BBDB@CCCD@AACCC=B4BCBCCACDC;CCDCDBC<6 MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHCHFEHHHHHHHEHHHHHHHHHHHDFHFHHHHHHHEHHHHHHHHHHHFHHHECHHHHFHGHHFHEHHHEHBFHHHHHHHHHHHHHHHH@5 UQ:i:0 +20GAVAAXX100126:8:23:12774:197414 147 chr1 10006790 60 33S68M = 10006420 -437 AGTTTCTCCATATGGGTCAGGCTGGTCTCGAACTCCCGACATCACGTGATCCACCTGCCTCAACCTCCAAAAGTGCTGGGATTACAGGTGCGAGCCACCTC ##################################'@@3DB:?CA@@A9BA=BBCCCDACABACCABDABACC<BBAB UQ:i:0 +20GAVAAXX100126:8:21:7822:20748 163 chr1 10006812 60 83M18S = 10007120 408 TGCCTCAACCTCCAAAAGTGCTGGGATTACAGGTGCGAGCCACCTCGCCTGACCAAGTTAGTATGTGTTTAAAGATCACACTTGTAATCCCAGCACTTTGG @=5AA>>A:AA>=7:C?4@A@A>CC?;A:;A@;=7<+77:>C?C@5.A:B(4@.+**@@><;BA<61ADC8:@;A7;AA<@A################### MD:Z:83 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@86@??:@9?@;BB;8?7;?><88@59;>?BAAA50@9>(3@/)()6>=>7AA9-0BBA:3<;?5CCCC?ABDBCCCCCCACCB@BC;CCB@B=BCA9ACD@CACACA@C@CCCDBAAACBBD@ACA4CA?@@B@BA@AB@@CCA?@AAA@C*ACA:A MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBBB>ABBB@BBBBBBABBBBBBAB@=A?A@>>@@@?@??=?@-<=A4< UQ:i:0 +20GAVAAXX100126:8:1:4286:192808 99 chr1 10006849 60 101M = 10007174 425 AGCCACCTCGCCTGACCAAGTTAGTATGTGTTTAAAGATCACACTTGTAATCCCAGCACTTTGGGAGGCTGATGTAGGAGGATCGCTTGAGGCCAGGTGTT <<;:A:??BDBBCDC=BAC?BCA?DDB>>?ABABBACBB>><:=CDCB;@ADCDC?@CDA=;?A5 MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GGEGGEDHHEHHHHHEGCGDGGCGEHHHHHHHHGHBF9FF=CDGGHHGHHHEHGHEHHHDHHHEECGGGGHEHHHAA?=AHHHHHEEHHHHDEHHGBBGG4 UQ:i:0 +20GAVAAXX100126:8:63:5666:148033 163 chr1 10006932 60 101M = 10007256 424 CGCTTGAGGCCAGGTGTTTGAGACCAGCCTGGGCAACATAGGGAGACCCTGTCTCTACAAAAAATACAAAAATTAGTTGGGTGTGATGGTTCATGCCTGTA @;BCAABBCBCCBBABABCBCCABCCBCCCBCCBBC?BBBBBCCA?ACCC@>BACD>ACBBBCBBA>BDCACBB@B:BBB;9A>ADCA@C?AC?B?CD@B@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBBBBBBBBBB;BBCBABB>CBBABBAAAABBBBBBBBABAB>AAB?B=?ABA>BA@A@AAA@B@A@@@@A@A7A@A<3>9@AA@A>>?A>@B@>@9? UQ:i:0 +20GAVAAXX100126:8:62:2555:107007 99 chr1 10006969 60 101M = 10007301 421 ATAGGGAGACCCTGTCTCTACAAAAAATACAAAAATTAGTTGGGTGTGATGGTTCATGCCTGTAGTCTCAGCTACTCAGGAAGCTGAGGTGGGAGGATTAC CCCACCDCDABBDBBBDBDCACDDDAABA?CDDD@BDCCBDBCC@B@BDCBCBDBC@BBBDBCCCCBDBCCBDCADBCCCCDCBDBDAC=CC?DCD?BAC1@9?A8@C1CB@4?<@%1:<9@@7?>CCACCC*BB9C?;;0BC@@A?799>#7)6ACBBA66CBDC<(-A?B=AB96<;BBAAAA@@C@ MD:Z:0T22C39A37 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:3 SM:i:37 MQ:i:60 OQ:Z:#?219@>1;9>>8>A.@A;2><<%/;=7@97;9A?BAB=BAABB*=?AB@CAA=BBA UQ:i:8 +20GAVAAXX100126:8:46:18774:97831 163 chr1 10007015 60 79M22S = 10007344 429 TGATGGTTCATGCCTGTAGTCTCAGCTACTCAGGAAGCTGAGGTGGGAGGATTACTTGGGCCCAGGAGGTCGGGGCTGCAGTGAGCCAGTGACCATGCCAG @CCB?B@BBCCBBBDBBCCBBDBCCBCCADBBBC?AAA@A?AC=?CCACC=?C==CB@;A>AB=AA6@B8>;?<>@??####################### MD:Z:79 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCBBCBBBBBBBBCBBABBABBBBBBABBBBAAB@ABBAB@AB6ABA=BA??@@;?@<;@?@A=@?7?@4??==>?=?####################### UQ:i:0 +20GAVAAXX100126:8:24:7834:75053 163 chr1 10007028 60 64M37S = 10007352 424 CTGTAGTCTCAGCTACTCAGGAAGCTGAGGTGGGAGGATTACTTGGGCCCAGGAGGTCGGGGCTGCCGTGAGCCAGTGACCATGCCAGTATACTCCAGCCC @DB@AA@ADACCBCC>CAABCBCBADBBCC@?BB7BB:CB9<80:C@###################################### MD:Z:64 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBBBABABBBBB@AA?AB@AAABB@BB6@BB@BB;A@AAA@:=B??A@A?3=B?###################################### UQ:i:0 +20GAVAAXX100126:8:68:8790:55871 163 chr1 10007049 60 96M5S = 10007343 394 AAGCTGAGGCGGGAGGATTACTTGGGCCCAGGAGGTCGGGGCTGCAGTGAGCCAGTGACCATGCCAGTATACTCCAGTCCTGATTACAGAACAAACCCCTA >=<1?;B>:&0B1'253=B8>=3:5A<3=*?.>=15255%><;=78;CB<6&?@@B<59B<855(C;D?@1;;5/5@;+@>;9;77@B75(;A(-B>C;A>A6BA###### UQ:i:24 +20GAVAAXX100126:8:68:20656:34221 83 chr1 10007102 60 101M = 10006818 -384 AGTGACCATGCCAGTATACTCCAGCCCTGATTACAGAACAAACCCCTATCTCAAACAAACAAACAAGTACATAAATGAAAGAAAGTTTGTGTTCCTACCAC =BDCCDCCCCCAB?@>@ACDCBDBCCCCBCDCC@D@DCBDDACCCCCCDCD@ADBA@DBBDDBBDCACBBCCDDCC@ADD@DDDADDCACAADCCCCABCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:>HHHHHHHHHHFFFFBFFHHHHHHHHHHHHHHHGHFHHHHHFHHHHHHHHHGGHHGGHHHHHHHHHHHHHHHHHHHGGHHGHHHHHHHHHHGHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:21:7822:20748 83 chr1 10007120 60 101M = 10006812 -408 CTCCAGCCCTGATTACAGAACAAACCCCTATCTCAAACAAACAAACAAGTACATAAATGAAAGAAAGTTTGTGTTCCTACCACAGGTGTGTCCAGTGAGAA >)49;7%9;<;0:?9@B9>A?990555;8:945;8?@:;AA><<:=;7;?9=<;<;;49;>;1@>A>?:<>;=>:??5<<=A?=A>9;7==< MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:C+5554.=>=>36@@EB6FDFF?FFFC?B@=ACAB;ADDADBACADDADDB@BBACCBC@CBACBC@B=?@9>3?### UQ:i:0 +20GAVAAXX100126:8:3:4050:181815 163 chr1 10007126 60 101M = 10007427 401 CCCTGATTACAGAACAAACCCCTATCTCAAACAAACAAACAAGTACATAAATGAAAGAAAGTTTGTGTTCCTACCACAGGTGTGTCCAGTGAGAAGAGTGT @CCCABBABACCCBADDDBDCCDCDCDCDDEACDC@ABB@BCBBAACDCD>CCADDCCDBBBCBCC?BDBAEC?BB@@BBB@CABCDB>C77B@A>1C?D? MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCCBBBCBBBBBCBCBBCCBBBBCCBCCBCBBBBBBBBBBBB@BBBBBB@BBBBBB@B@B@BBBAB@BBBBBBBAB?CB@@AB@BBAB@C4@>;;-?9>5BA<@:@;=CC@61>>CC=9BCCADC?<:428>=;?;?4'8=7=6?@9<<<:@BB<11?>@@=3;A@<=6>A?@B<:3*?>;=?3BAEEAA=<<26:35//C029A0A&4::A9CC@B;>?59=672-B444A-=+-49=/:,))@?9:'(?3?BC@?)9?CBC**?)A@:CB<3@########## UQ:i:21 +20GAVAAXX100126:8:48:10108:181079 163 chr1 10007155 60 101M = 10007444 389 AACAAACAAACAAGTACATAAATGAAAGAAAGTTTGTGTTCCTACCACAGGTGTGTCCAGTGAGAAGAGTGTGATGTTGCAGATGAGAGGGGATAAATGCT @D@BBA@BCDACCAACACDCDDCCCDDCCDDCBC@A>A@BBCDC?CCACC@AB>CBBCCC@BBBCD?AC?@CC@BA?BBA@ABABCBB?C@AB?BBCB@DA MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCBBBCBCBCBCBCBBBBCBBBBCBBBBABBB@BCBABBBBBBBBBBBBBA@A?BABBBB@B@B@AA?B8B>A?AA>@@B?B>@A???@@?@>>@@?>@A> UQ:i:0 +20GAVAAXX100126:8:48:10118:181094 1187 chr1 10007155 60 101M = 10007444 389 AACAAACAAACAAGTACATAAATGAAAGAAAGTTTGTGTTCCTACCACAGGTGTGTCCAGTGAGAAGAGTGTGATGTTGCAGATGAGAGGGGATAAATGCT @D@BBB@BCCACCABCACCCDDCBCDDCCCDCACBA>A@BBCDC=BCABC@CBBCCC?BABB?@@C@@CCABABBCA@ABABBA<@B@A>A@<=C@CB MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCBBBBBBBBBBBB?BBBBBBBBBBBBBAABBBBBBABBBBBBBAABBABA8B@BABBAB?B?B?;B>A;B>B@BB@@BA?A>@A>>8A?@?9@=87??@? UQ:i:0 +20GAVAAXX100126:8:1:4286:192808 147 chr1 10007174 60 101M = 10006849 -425 AAATGAAAGAAAGTTTGTGTTCCTACAACAGGTGTGTCCAGTGAGAAGAGTGTGATGTTGCAGATGAGAGGGGATAAATGCTGGACCAAAGTCCTTGAGAA =DADBADAB+@D8CDC:.;>6A?3:>'?@DA@;;@ACBBD9BBE@DE?A@AAACDC:DCBB@A@>?BCDB5=ADCBCBB@@CCC?CC?BDACA?CBACB<@ MD:Z:26C74 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z::?AAA?BBB+?@;BB?:+8=5@;37>(><@AA6A?B>ABBBB@ACDCC?CC@CCADCBB@CBBC=ABCBCC?@ABBA;ABCB?8CCACAAA>BB@CAD@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBBABBBBBBBCCBCCCBBBCB@B?BABBBB@BAB@ABAB>B@BBBBBBBB@B?BB@B>BB@A?@A@AAB@>BABA;@B?A;3?BAA?@;<>A6@>@= UQ:i:0 +20GAVAAXX100126:8:7:7502:151389 1187 chr1 10007181 60 101M = 10007491 410 AGAAAGTTTGTGTTCCTACCACAGGTGTGTCCAGTGAGAAGAGTGTGATGTTGCAGATGAGAGGGGATAAATGCTGGACCAAAGTCCTTGAGAAGGTGAGA @CACB?8AABABA@CDECBDCACCC@B?CBCCCC;A7=:+;;9??;C@CC?CB=DCCDCC?5ABCA6>BC?@B;8=<9@BBBDB?C@;@B9B>1ABCC?>@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCCB@.@CCAABCCCCBCCBBBCBA@?:@<4<=C@BAB@A:A;6@?7A9.@;6< UQ:i:0 +20GAVAAXX100126:8:24:17458:9144 163 chr1 10007190 60 101M = 10007539 449 GTGTTCCTACCACAGGTGTGTCCAGTGAGAAGAGTGTGATGTTGCAGATGAGAGGGGATAAATGCTGGACCAAAGTCCTTGAGAAGGTGAGAGAGAAAGGA @AB@A@BCBACCABCCBBBBBCDBCABCCCDCB?9A;@@@B@@A@ACC@A>BCACBBCACBBA?AC=@DA;CCBB>A@D92=BA@BA8?C>@A?CBCD@CA MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBCBBBBBCBBBB@B@BACCAB?BABBBB@=7B?AAAB@@@B@BA@@@A@BA@A@@BB@@@?@@?BB<@@AA:A?@9/;@?=@>5@?====@?>@>>> UQ:i:0 +20GAVAAXX100126:8:45:16821:90529 1187 chr1 10007194 60 101M = 10007535 436 TCCTACCACAGGTGTGTCCAGTGAGAAGAGTGTGATGTTGCAGATGAGAGGGGATAAATGCTGGACCAAAGTCCTTGAGAAGGTGAGAGAGAAAGGAGAGA @BCCA?BBACCC?ABC?BDCCBBCCCDC>C9CBC?B>=7ABBB=ABACBC9=A@@CD??>AC@8CA;CBD?C@&=B@BABBA>;:D MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCBBCBCCBBC@C?CCBCBBABBBBBC9C5B@B@BA>;BBAB9BB=BAB=>>AB>B?>=':B@A=:@@=/683=?:@<(<=A<663B UQ:i:0 +20GAVAAXX100126:8:45:16833:90513 163 chr1 10007194 60 101M = 10007530 436 TCCTACCACAGGTGTGTCCAGTGAGAAGAGTGTGATGTTGCAGATGAGAGGGGATAAATGCTGGACCAAAGTCCTTGAGAAGGTGAGAGAGAAAGGAGAGA @CCC@?BBACCC=AABABDCC@BCCCDCCCBCACBBA@@?BBB@?BCC@BABB@?@=B?AA>CDDAC@+>BABC?>AC8=>@2BBBBBCBB+;BAAB>=A@5;7;/=?B@AAC>A=C>ABC=CABA##### MD:Z:97 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCBBBCBBB@BBB>BA;AABBBBBBAB8B?BABBAABBAB@AB?A?BBAA?@AA@@A@?@@B?@B?=?9B=A<;@9A@8@>=:A?=@##### UQ:i:0 +20GAVAAXX100126:8:27:21458:11536 629 chr1 10007225 0 * = 10007225 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNAAANTGTTAANNNNNNNNNNNNNNNNNNNNNAGTN ##################################################################################################### PG:Z:BWA RG:Z:20GAV.8 OQ:Z:##################################################################################################### +20GAVAAXX100126:8:27:21458:11536 697 chr1 10007225 37 16S85M = 10007225 0 GTCCAGTGAGAAGAGTGTGATGTTGCAGATGAGAGGGGATAAATGCTGGACCAAAGTCCTTGAGAAGGTGAGAGAGAAAGGAGAGAAAGGAATCCAGAGTC #################BAA=@D@2@;974/A@B:3'2>7@CBC=>D>::73?BB87=28?A=AAC>7:8@BC@D=CCCCCD?BACBBB>CCCBAAACAC@ MD:Z:85 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:37 OQ:Z:#################A=@>@=1'0=8@AA@<9B@56<.??=;8<19@B?BBB@884>BA>B;BCABCB>?AACCB?;=@C>;B4=>2@A?C=9C>:>?>=?A8-8ACBDAD@CCCA?D@E=BBCBBCCBCABAC@C@ MD:Z:69 PG:Z:BWA RG:Z:20GAV.8 AM:i:0 NM:i:0 SM:i:37 OQ:Z:#################################@7/03=?<;?@=6>59=7=@;??;B?;?A@@AA:-6?AAB@B@BB@?=B@C@CA?==?@C?83A<5@?7669-@BBCC5AABDBABBBBA?AABBCCCB;CADCABDD@C?ACEEAACDBCCA@?CBB@ MD:Z:20G69 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:############??=5686>@A@?<<>??:9/=:8>;524:+:=<=ABBB@@@ABAB@BABBABBBBBABABBBBBBABCAB9789;<8::;985;:8:298648:==<@>;:;;;:6C@@C<:;>=<=:6=?A??@?>5<<9<;;:>?=???>AAB<=?<@<<==<>:@?=<@?=>B5?:< MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:A44445544455555555554:9<>=DDDD>@==@<;GFFG54444?<>8>55554ADDFAGAGFGDDADF??A>>>@C?>DFAADGAGDG UQ:i:0 +20GAVAAXX100126:8:46:18774:97831 83 chr1 10007344 60 101M = 10007015 -429 ATAACAGCACATCCTTACGGTTGTAGGTGGCTTTGTAGATCTAAGAAGATCAGGAAGATTGCTGGCTCTAGTTTTGTAGATTATCAGGAAGATTATCAGAA ?DDCCBCCCCCDCCDCC;CADCACDBACBBCDDCACDBCDCCDDBDDBCDBCBBDCBCDCBCCBBCDCCCADDDCACDBCDCCDBDBBDDBCDCCDCBBDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BHHHHEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:24:7834:75053 83 chr1 10007352 60 101M = 10007028 -424 ACATCCTTACGGTTGTAGGTGGCTTTGTAGATCTAAGAAGATCAGGAAGATTGCTGGCTCTAGTTTTGTAGATTATCAGGAAGATTATCAGAAAAACATAT C?CDDCDCC;CADCACDCACBBCDDCACDBCDCCDDBDDBCDBDBBDDBCDCBCCBBCDCCCADDDCACCBCDCCDBDBBDDBCDCCDAC@ADDDCCACCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:FGHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:3:4038:181802 1107 chr1 10007427 60 101M = 10007126 -401 TCAGGAAGATTATCAGAAAAACATATCTTAACCTGGTGAGCTCTCTATGCTCTGGCACTTGAATAAAAGCTATCCTAAAATATTACAAATTCTAGAATTTA EDDCCDDCCDC@DACA@DDDCBCCCDCDCDCCCCBACBDBBDCDCCCCBCDCCBBBBCDC@@CCDDDCBCCCDCCCDDDCCCDCBBDDCDDCCDBDCBDCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHEHGGGGHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:3:4050:181815 83 chr1 10007427 60 101M = 10007126 -401 TCAGGAAGATTATCAGAAAAACATATCTTAACCTGGTGAGCTCTCTATGCTCTGGCACTTGAATAAAAGCTATCCTAAAATATTACAAATTCTAGAATTTA BDDCCDDCCDBCDACA@DDDCBCCCDCDCDCCCCBACBDBCDCDCCCCBCDCCBBBBCDC@@CCDDDCBCCCDCCCDDDCCCDCBBDDCDDCCDBDCBDCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GHHHHHHHIHIHHGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:48:10108:181079 83 chr1 10007444 60 101M = 10007155 -389 AAAACATATCTTAACCTGGTGAGCTCTCTATGCTCTGGCACTTGAATAAAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTT EEDCCCCCDCDCDCCCCCACBDBCDCBCCCCBCDCCCBBCCDC@ACCDDDCBCCCDCCCDDDCCCDCBBDDCDDCCDBDCDDCBCCDDABBDDDDCCBDDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHIHHHHHIHHHHHHHHHGHHHIHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:48:10118:181094 1107 chr1 10007444 60 101M = 10007155 -389 AAAACATATCTTAACCTGGTGAGCTCTCTATGCTCTGGCACTTGAATAAAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTT EEDC@CCCDCBCABCCBCABBDBCDCDCCCCBC?CCDDDC@CCCDCCCDDDCACDABBDDCDDCCDBDCDDCBCCDD@;BAAAA@@7>=< MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHGHHHHHFHGGHHGHHGHHHHHHHHHHHHHBHHHHHGHGHEEHHHHHHFHHHHHHHHHHHGHHGHHHHHHHHHHHHHHHHHHHHHCCHGGGGFGDGGG UQ:i:0 +20GAVAAXX100126:8:43:20013:129172 83 chr1 10007463 60 101M = 10007196 -367 TGAGCTCTCTATGCTCTGGCACTTGAATAAAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTTTCATTAACTAGGAGGCTTT DDDCCCCDCCCCCCDCCCBBCBDC@ACCDDDDA>CCDCCCDDDBCCD>BBDDCDDCCCBDCDDCBCCDD@@BDDDDACDDDDDBCDCDCCCDBBDC@A>DC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:IHHHHGIHHHHHHHHHHHHHHIHHGGHHHHHHFEHHHHHHHHHGHHHEHHHHHHHHHHHHHHHHHHHHHGEHHHHHIHHHHHHHHHHHHHHHHHHHGHGHH UQ:i:0 +20GAVAAXX100126:8:42:6558:108923 163 chr1 10007468 60 101M = 10007800 432 TCTCTATGCTCTGGCACTTGAATAAAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTT @BCABABBBDBDBBBCBDCBCDDCEDDCCDCCBCCBBBBBBCCC:CDCCC@DDADCCDCC@CDBBC>BDCBD@BBCBBCBBBCB@ECB=D@ABBDBCDAAC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCCBBBBBBBBBBBBCBCBCBCBCBBBBBCBBBBBBBBBBBBB@BBABBBBCBBABBBBBBBBABBAAABA@B@A@ABABAB@BBAB>A@@A?@@?@?;B UQ:i:0 +20GAVAAXX100126:8:45:3840:54807 163 chr1 10007468 60 101M = 10007795 427 TCTCTATGCTCTGGCACTTGAATAAAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTT @CCAA@BABDBBB?DABDBB7B?9A=BAC:@D??@??AB=;ADCBDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCBCCBCBBC?B@>ABBBCCBCBBCCB?ABCB:B@BCBC<=BCCC>@CBB>BBBBCBBB=BCBBBA6B>C@CBBBCBA<>ACBBA95>A?@BB UQ:i:0 +20GAVAAXX100126:8:61:17876:93642 99 chr1 10007468 29 101M = 10007872 438 TCTCTATGCTCTGGCACTTGAATAAAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTT CBC@DCCCBDBDBCBCADDBDDCCDDAABDCCBBCCDDDCCCDCACDDCDBDCCDDCDDCABDDBCACDDDA?DDDDDBCCDCDADCCCDCCCDDADDD@@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:0 SM:i:29 MQ:i:29 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHGHHHGG UQ:i:0 +20GAVAAXX100126:8:67:10895:75253 147 chr1 10007475 60 101M = 10007283 -292 GCTCTGGCACTTGAATAAAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTTTTGGATA ;DBCCAB@CAAC?BCBCCDB=ABA>BB?DDACAC@BBACCBCCCCECADBBCADCC@C@BBBBB:BACDCCCCDCCACCDDBDCBBDBCDCDDCB@@ACC@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:9@?@@>@@?@@@A@A@@A@@>@A@=AB@BBBB@BAA?ABBBAABBBBBBABB@BBAAB@BBBBB>BAABAABBBBBBBBBCBBBBABBBBBCCBCCCBBCB UQ:i:0 +20GAVAAXX100126:8:68:20495:7123 99 chr1 10007491 60 101M = 10007858 412 AAAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTTTTGGATACGGAGTCTTGCTCTGT CDDBCCDCCBBDCDDDCCCDCACDDCDBDACDDCDDCABCDBCACDDDA?CDDDDBCCDCDADCCCDCCBDDDDDDA@@@ACDCCA;CDCCCDDCCDCDDD MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:25 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHHHIHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:3:11681:100672 83 chr1 10007491 60 101M = 10007181 -410 AAAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTTTTGGATACGGAGTCTTGCTCTGT DDDDBADDDDDB>DCD@==6@<=BB6AAAADDDDDCBBCCB;BBDADCDCCCDACAC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@@DDCDDC>@BDCDDC=BAAB@:BDDDDBC?DDDDBC>ADBCCCBBBBBAAAAADDDDDCBBC@B;BBDADCDCCCDACAC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:AHHHHHHEEHHHHHHHBCBDDGHHHHHHEEHHHHHH?GGFFGBHHHHHHHDHHHHHHEGHHHHHHHIHHGGGGGHHHHHHHHHIHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:3:9830:12196 163 chr1 10007492 60 83M18S = 10007808 416 AAAGCTATCCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTTTTGGATACGGAGTCTTGCTCTGTC @DCBAAABBCDCCBDDCDCCACDDCCBDCCCDDCBB?BCB@CACBBDDADACCACDCDBD;D@BCC=CCCBDCABC@8.67A################### MD:Z:83 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBCCCBCCBBBBCBCCBBBBBBCBBCBBBCBBBBBBBABBBB@BBBBBBBBBBBBABCB@BA@@AB@AB@@@A?8-49?################### UQ:i:0 +20GAVAAXX100126:8:4:4481:73051 163 chr1 10007500 60 101M = 10007790 390 CCTAAAATATTACAAATTCTAGAATTTACCTTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTTTTGGATACGGAGTCTTGCTCTGTCCTCCAGGC @DCAAABBBCBCA>DDCBCEDCCEDCCCBDEBBD?@?B@B@B@CACCCAC;BB;DC@DCCADCB@C>?DCABDAB>;6>98-CC@>@C=D@BB@D@?D=B< MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCCCCCCBCCCCABBBCCCCCCCCCCCCCCCBCCCCBCBBCCCBBCBCCCCCCCC?BBABBBBCB@CBBB=B@B>=><76(AA>90))?(*CD################################################ MD:Z:32T21 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:A7445*?)))@*+4@?)?A*.->:BA8?@2))?(+BA################################################ UQ:i:7 +20GAVAAXX100126:8:45:16833:90513 83 chr1 10007530 60 101M = 10007194 -436 TTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTTTTGGATACGGAGTCTTGCTCTGTCCTCCAGGCTGGAGTGCAGTGGCACCATCTAGGCTAACT AE>;CDDDDBC?DADB@CDCDCC>DB@@=B>?CBCDCCDCCCCBBCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:EHCBHHHHHGHEHGHEGHHHHHHDHHGEEHEBEEEHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHGHHHHGGGEDHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:45:16821:90529 1107 chr1 10007535 60 5S96M = 10007194 -436 TTCACAAAAACTTTTTCATTAACTAGGAGGCTTTTTTTTTTGGATACGGAGTCTTGCTCTGTCCTCCAGGCTGGAGTGCAGTGGCACCATCTAGGCTAACT ######<<=965DDDDBADCDC>=?BBB=B4=A?ADAADDCBBCCB;BBDADCDCBCDCCADCCDCBCBBCCBBDACBBDACBBB@CBCDCCDCCCCBBCC MD:Z:96 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:######@@@:89HHHHHFHHHHDAAHHFEH6>GEGHGFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:24:17458:9144 83 chr1 10007539 60 101M = 10007190 -449 ACTTTTTCATTAACTAGGAGGCTTTTTTTTTTGGATACGGAGTCTTGCTCTGTCCTCCAGGCTGGAGTGCAGTGGCACCATCTAGGCTAACTGCAACCTCT D@E@EEDCCDCDBCCDCBDCB=A?AADDAADCBBCCC;ABDADADCBCDBCADCCDCBCBBCABBCACBBDACBBB@CBCDCCDBBCCDBCCBCDCCACCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HGHEHHHHHHHHGHHHHHHHHEGEGGHHGGHHHHHHHHIHHHHGHHHHHIHHHHHHHHHHHHFHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:63:6242:80411 163 chr1 10007707 60 101M = 10007988 381 CCACACCCAGCTAATTTTTGTATTTTTAGTGGAGACGGGGTTTCACCATACTGGCCAGGCTGGTCTGGAACTCCTGACCTCAGGTGATCTGCCCGGTGAGG @CB@A?BBCBBDBBCCCBCCBCDCCCCCCBCCCCA@9@BCB@ACCBC>CC@BCBBC<4A@9;-2B<@7@<-<::7-88AA7<9=75A MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBBCBBBBBBBBBBCBC@BCCCCBBB@BBBBABBA?B?ABAABBAABAABA?AA@A;1;A1=;?@7;<6?@59,3@:?4;<(5586*67=@8;/44/? UQ:i:0 +20GAVAAXX100126:8:7:17495:193398 99 chr1 10007724 60 101M = 10007961 337 TTGTATTTTTAGTGGAGACGGGGTTTCACCATACTGGCCAGGCTGGTCTGGAACTCCTGACCTCAGGTGATCTGCCCGGTGAGGCATAACTTTTATTTCAG <<=:AAAAA;;A=AB?@C@:=?=9@A@B?AB?A?A@BAABA?A@;73;718;;9=8><<>?@@>?AB:@AA>=5A<=7;:?CB@A?@A?@A>==:>@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GGGGGGGGGBBGAGGDFGGGDCDCGGGGGGGCGGFFGGGGGCGC=5/582555559D=?CCCCCCGGCGEFC?;G@?D?4BD@DDGGFGGAGEGGBBB>CG UQ:i:0 +20GAVAAXX100126:8:68:12222:58992 99 chr1 10007740 60 101M = 10008056 416 GACGGGGTTTCACCATACTGGCCAGGCTGGTCTGGAACTCCTGACCTCAGGTGATCTGCCCGGTGAGGCATAACTTTTATTTCAGTCTCACATTTCAGTTT CD@9CCCCDDBCABCCCADBCBBCCCADBC;BCBCDD?DBBCBAABCBCC?BBACBDBBBB;BCBDCCBCCCDADDDD>C?A@CCCBDBCACCDDCADBEE MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHIHHHCHHHHHHGHHHHHFHHHHHHFGHFHHHHHHHHGHHHHHHHHHHHHHHHDHEGGHHHHHHHHIHHHHEHFHH UQ:i:0 +20GAVAAXX100126:8:44:5440:118213 163 chr1 10007743 60 101M = 10008043 400 GGGGTTTCACCATACTGGCCAGGCTGGTCTGGAACTCCTGACCTCAGGTGATCTGCCCGGTGAGGCATAACTTTTATTTCAGTCTCACATTTCAGTTTGTT @CCBA?BBCACCCABDCCCDCBCCA@A9B;?C;C7;>@3:;8CA@=@B5A:9@;A@CC:@6=:?A=:@:AD@AA MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBACBBBCCBBBCBCBCCBABC>?@4B8>B8A<=<:=<>=BB?>3<7?96:3<@@7> UQ:i:0 +20GAVAAXX100126:8:4:4481:73051 83 chr1 10007790 60 101M = 10007500 -390 GTGATCTGCCCGGTGAGGCATAACTTTTATTTCAGTCTCACATTTCAGTTTGTTCTGTGGTCTCCTCCTTTATTTGTTGCTAGGTAAAAAACATTTTTTTT BECCDCDCCC;CACBDCBCCCDCAAADACDDDBDADCDBCBCDDDBDADACADDCCACBADCDCCDC@ADCCDDCADCBCCDBABAADDDCBBAADDBDDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHGGGHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHGGGHHHHHGGGHHHHHH UQ:i:0 +20GAVAAXX100126:8:45:3840:54807 83 chr1 10007795 60 101M = 10007468 -427 CTGCCCGGTGAGGCATAACTTTTATTTCAGTCTCACATTTCAGTTTGTTCTGTGGTCTCCTCCTTTATTTGTTGCTAGGTAAAAAACATTTTTTTTTTTTT @A@??:A?BACAA>BB@A<=>AABAAB@B?CAB>A?BAACAC@AAC?@C>C<@A<<<<;<;@@:>=< MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GGGECGGGGGGGGCGGGGBBBGGGGGGGGGGFFEFEGGGGGGGGGGGCGEGEEGEE69*<5<@@GGADGFEGEGCD?EE4@BGGGGG?BBBBBBBGGGGGG UQ:i:0 +20GAVAAXX100126:8:42:6558:108923 83 chr1 10007800 60 101M = 10007468 -432 CGGTGAGGCATAACTTTTATTTCAGTCTCACATTTCAGTTTGTTCTGTGGTCTCCTCCTTTATTTGTTGCTAGGTAAAAAACATTTTTTTTTTTTTTTTTT 8D>DCD?A?=?;C>@=D>9DD9:<896::67?DADB=28<>/>@7<37@;701+.4=3<@=+;;<1>=;7:@?>1<;AAAA=:????>>??>>>>DDBDDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:GHGHHHDFDBDBHCC@HE=HH55544;=<6;EHGHH?6;@A3AD9>8:C?6022/3A7;:??=BBBAB89:1:::,9:D>D=DBB?@B==:8=:<=88CAC>>AB3AAC8?CB:C?BA:=@DD>@=1>AAAAAAAAAAAADDDDDCCCC@@DC MD:Z:0C100 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:#CBFFB<@CD@BDCBDCABCBACBBA################### MD:Z:83 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCBBBBCBBBBBCCBBBCBCBBBBBBBABB@BBBBBBBBBABBBBBAABBBABB@@@@AA@?@BAB@AAAB@B@A@B@BAB################### UQ:i:0 +20GAVAAXX100126:8:3:8873:24347 163 chr1 10007819 60 83M18S = 10008145 426 TTTCAGTCTCACATTTCAGTTTGTTCTGTGGTCTCCTCCTTTATTTGTTGCTAGGTAAAAAACATTTTTTTTTTTTTTTTTTTTTTGGTTTCCAGGGAATT @BAAAA@BDBCACABBBCCACCBACBDCBCCBBDABBAACBCBCACCBCC@DAADC@DBCBB??BD@CDCACDBBBBBC?BA################### MD:Z:83 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BCCBBBBCBBBBBCCCBBCBCCBBBBBBABBABBBBBBBBBBBBBABABBBB@BB?@A@AA@@?AAAABAB@AA@BAAB>AB################### UQ:i:0 +20GAVAAXX100126:8:3:12227:40820 659 chr1 10007841 60 51S50M = 10007513 -377 GTGAGCTGCGACGTGAGGCATAACTTTTATTTCAGTCTCTCATTTCAGTTTGTTCTGTGGTCTCCTCATTTATTTGTTGCTAGGTAAAAAACCTTTTTTTT ####################################################@9B@-3A='&77,''&9=@6%343A>4A.43<2B456B;A'4C76:>D@ MD:Z:16C24A8 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:2 SM:i:37 MQ:i:60 OQ:Z:####################################################?5@?//A@''9<-'''78@4%.12?:3@-02;1@277@7@'1B627=BB UQ:i:11 +20GAVAAXX100126:8:63:18841:113901 595 chr1 10007842 60 66S35M = 10007517 -359 ACTCCTGACCTCAGGTGATCTGCCCGCTGAGGCATAACTTTTATTTCAGTATCACATTTCAGTTTGTTCTGTGGTCTGCTCCTTTATTTGTTGCTAGGTAA ##################################################################################################### MD:Z:11C23 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:1 SM:i:37 MQ:i:60 OQ:Z:##################################################################################################### UQ:i:2 +20GAVAAXX100126:8:68:20495:7123 147 chr1 10007858 60 55S46M = 10007491 -412 TGAGGCATAACTTTTATTTCAGTCTCACATTTCAGTTTGTTCTGTGGTCTCCTCCTTTTTTTGTTGCTAGGTAAAAAACATTTTTTTTTTTTTTTTTTTTG ########################################################@B);C9,?33277?85ACCCC92(ADDDDDDBCDCCCCCBBCCC@ MD:Z:3A40G0C0 PG:Z:BWA RG:Z:20GAV.8 AM:i:25 NM:i:3 SM:i:25 MQ:i:60 OQ:Z:########################################################A?)BCCB5.(>BBBBBBBBBBBBBBBBBBBB UQ:i:73 +20GAVAAXX100126:8:64:7784:120262 163 chr1 10007860 60 42M59S = 10008147 387 TATTTGTTGCTAGGTAAAAAACATTTTTTTTTTTTTTTTTTTTCTGGTTTCCGGGAATTTTAAAAAATAACTAAAGGCCCGTTTCTTTGGAGTTTCTCAGG @CBB?A@BBBDCBABCDDDDD@BCCCCCCCCCCCBBABBB?############################################################ MD:Z:42 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBCBCBBBBCBBCC@BBBBBBAABCCBBBBBBBBBBBBBB@############################################################ UQ:i:0 +20GAVAAXX100126:8:61:17876:93642 147 chr1 10007872 29 66S35M = 10007468 -438 GGATTAACTTTTTTTTCATCTTCACTTTCAGGTTTGTCTTGTGGTCCCCCCTTTTTTTTTTTCCAGGGAAAAAAAATTTTTTTTTTTTTTTTTTTTGCTGG #####################################################################ACCCA-')CEEEEEDEDDBCDCCCCCBABBC@ MD:Z:2T6C0A24 PG:Z:BWA RG:Z:20GAV.8 AM:i:29 NM:i:3 SM:i:29 MQ:i:29 OQ:Z:#####################################################################?BBB?-''ACCCCCBCBBBBCBBBBBBBBBBB UQ:i:16 +20GAVAAXX100126:8:62:20479:199378 99 chr1 10007875 60 8M1D78M15S = 10008195 420 AAAAAACATTTTTTTTTTTTTTTTTTGCTGGTTTCCAGGTAATTCTAAGAACTAACTAAGGTCCTGTTGCTTGGTGGTTACTAAGGGGGGCAGACAGAGTA CDDBDDABBDDDDDAAAAAAAAAA@3+36;;@@@?A?@@;:=:<.6;;09;BFFFFGCGF=><=?/34504FDDGF34555HBHCF54445555531-425FBDBF################ UQ:i:16 +20GAVAAXX100126:8:7:17495:193398 147 chr1 10007961 60 101M = 10007724 -337 GGAGGCAGACAGAGTATTTTGCACCATCCAAAGGAGGTAATGTAATGCTTAAATGGAAGAAACTGAACCAAACAACGAAAATATGGGCTATGTATTACAAA CD<4A<8)A9:C9%5?-ADA6@AA=@48=4A<>A<:;4?1;89@>AC:AA?;;B?C>>@<;@BBBBBB>5<>>A>>=:>BB8=>A?A?ABBCCCC?CACCCCBCCBB@B;ABBB UQ:i:0 +20GAVAAXX100126:8:63:6242:80411 83 chr1 10007988 60 101M = 10007707 -381 CCAAAGGAGGTAATGTAATGCTTAAATGGAAGAAACTGAACCAAACAACGAAAATATGGGCTATGTATTACAAACAACTCTGACACACTGTTATTTATGAT DDDDDCCDCACDCCACDCCBCDCDDCCBBDDBDDBCCBDCCBDDCBDB;BDDDCCCCBBBCCCCACCDCBBDDBBDBCDCCBBBBBBCCADCCDDCCABCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:44:5440:118213 83 chr1 10008043 60 101M = 10007743 -400 ATGGGCTATGTATTACAAACAACTCTGACACACTGTTATTTATGATATTATAGGAAAGCTTCTCCCAAGGAAAGTGGTGGAAACTCCATCACTTAGACAAG DECCCCCCCACCDCCBDDCBDCCDCCBBBBBCCCADCCDDCCCBCCCDCCCCBBDDCBCDDCDCCBDCBBDDDACBACBBDDBCDCBCDBCCDCDBC@CDC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:4:14239:56438 611 chr1 10008048 60 35M66S = 10008306 358 CTATGTATTACAAACAACTCTGACACACTGTTATTTATGATATTATAGGAAAGCTTCTCCCAAGGAAAGTGGTGGAAGATCCATCACTTAGACAAGTTAGA ##################################################################################################### MD:Z:35 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:##################################################################################################### UQ:i:0 +20GAVAAXX100126:8:68:12222:58992 147 chr1 10008056 60 101M = 10007740 -416 TACAAACAACTCTGACACACTGTTATTTATGATATTATAGGAAAGCTTCTCCCAAGGAAAGTGGTGGAAACTCCATCACTTAGACAAGTTAGAACACAACT BA:CD@CBCAAC@ACCBACAB@DAACCADD:CCC?CCBDC@CAD@CD@CCADBCDD@CCD@BA>>@@CCBCCCCCCCACEDECACBD@DCDBCAA@?@AC@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:A77=AAB>AABCC?DCCCD@CABDCCDACBCBBCC?D@B?CD?CAA?BBBA@@@ECC?D@BAACACC@DC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBCBBBCBBBBBBBBBBBBBBBBCBBBBBBBBB@BB@BAABABBBBBBBBABBBBBBAAB@ABB@B@@AAABAB???@A@7@ABAA?A?A@A?@@@ UQ:i:0 +20GAVAAXX100126:8:45:11956:153764 1699 chr1 10008108 29 56M1D3M1I41M = 10008497 423 CAAGGAAAGTGGTGGACACTCCATCACTTAGACAAGTTAGCACACCCGTGTAAAGGACTCATTTAGTGTCTCAGTGACATTTCTACTGTAATAGCCACTGG >:5=A7=C?A?8+5<:-+76;A86)B12C9>C45);641+&B2/?+4%,775+)A4,B+1))8A/)@1A28')<''(0>AA))A2)7*BB,BBB7(-)B2*(@<(.1)4@B@ACCDD@DBCCCACACCBCCAC?B;AA@?BAC=BCACB=BC@CB?AACB@C?CC:AABACBABAB@DA@@DAACDABAC>4CBCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBABBB@BB?BBBBBABBBBBABBABABABA@B?ABA@ABBAAABAA?BAAA@;@BAB>A?@A<@:AA@@A@@@?A@?@A@@@??<@@;>??>2@@>A UQ:i:0 +20GAVAAXX100126:8:3:8864:24332 1107 chr1 10008145 60 101M = 10007819 -426 TAGAACACAACTGTAAAGGTACTAAAAAGTGTATTAGAGAGATTCATCCTGTAAAAGACCCTGGGGGCTGAGTGTGGTGGCTCATGCCTGTAACCCTAACA DECDBCCCDCCCACDDDCACCCCDDDDDACACCDCDBDBDBCDDBCDCCCACDDDCBBCCCCBBBBBCCBDACACBACBBCDBCCBCCCACDCCCCCBBBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:3:8873:24347 83 chr1 10008145 60 101M = 10007819 -426 TAGAACACAACTGTAAAGGTACTAAAAAGTGTATTAGAGAGATTCATCCTGTAAAAGACCCTGGGGGCTGAGTGTGGTGGCTCATGCCTGTAACCCTAACA DECDCCCCDCCCACDDDCACCCCDDDDDACACCDCDBDBDBCDDBCDCCCACDDDCBACCCCBBBBBCCBDACACBACBBCDBCCBCCCACDCCCCCBBBC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:64:7784:120262 83 chr1 10008147 60 101M = 10007860 -387 GAACACAACTGTAAAGGTACTAAAAAGTGTATTAGAGAGATTCATCCTGTAAAAGACCCTGGGGGCTGAGTGTGGTGGCTCATGCCTGTAACCCTAACACT DECCCCDCCCACDDDCACCCCDDDDDACACCDCDBDBDBCDDBCDCCCACDDDDBACCCCBBBBBCCBCACACBACBBCDBCCBCCCACDCCCCCDC@BCC MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH UQ:i:0 +20GAVAAXX100126:8:4:10255:86573 99 chr1 10008172 60 101M = 10008499 427 AGTGTATTAGAGAGATTCATCCTGTAAAAGACCCTGGGGGCTGAGTGTGGTGGCTCATGCCTGTAACCCTAACACTTTGGGAGGGTGAAGCAGAAGGATCA CCB@CCCDCCDCDCDCDBCCBBCBBCDDDCDABBCBCCCCBCBDCBBBBCBBCBDBCCBBBDBCCD=BBDCDACADDDBCCDCCB7)(=DB@@B MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:@AB?BCCBCBABCCCCCCCCCCCCCCCBBCCCBCA?BBABBCBBBBBBBBBBCA:@B>B34B7.8.3::%=859B=5:3(':@>>8C UQ:i:0 +20GAVAAXX100126:8:5:20728:120252 163 chr1 10008188 60 93M8S = 10008458 370 TCATCCTGTAAAAGACCCTGGGGGCTGAGTGTGGTGGCTCATGCCTGTAACCCTAACACTTTGGGAGGGTGAAGCAGAAGGATCACTTGAGTCCAGGAGTT @BBBAABBABCDCABACCDBCCCCABBBC@CBBC::7<=<>>;?==B?>?7@C9AC???CBC@?A5?@B=<>B<:A==27=6;=@@>B77:B######### MD:Z:93 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BBBBBBCBBBBBBB?BBBBBBBBBA@B?B=B?BA9==?????==@6?<:?=<.6=45==@6@519?######### UQ:i:0 +20GAVAAXX100126:8:62:20479:199378 147 chr1 10008195 60 101M = 10007875 -420 GTAAAAGACCCTGGGGGCTGAGTGTGGTGGCTCATGCCTGTAACCCTAACACTTTGGGAGGGTGAAGCAGAAGGATCACTTGAGTCCAGGAGTTTGAGACC ADB;@BB?C:AC@BDC7AD@C@D?BA@ABBACBB@?CBC@BC@D9CCAB?>CCDCCACCBB@?AAC@CDCBECBCCCBCEDCEBCCCBCCDADCA@AAAC@ MD:Z:101 PG:Z:BWA RG:Z:20GAV.8 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 OQ:Z:BA@4;??