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insert_size_metrics_test.sam
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insert_size_metrics_test.sam
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@RG ID:62A79.7 PL:ILLUMINA PU:62A79AAXX100907.7 LB:Solexa-41748 DT:2010-09-07T00:00:00-0400 SM:NA12878 CN:BI
@RG ID:62A79.8 PL:ILLUMINA PU:62A79AAXX100907.8 LB:Solexa-41753 DT:2010-09-07T00:00:00-0400 SM:NA12878 CN:BI
@PG ID:GATK IndelRealigner VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/6/Solexa-41748/62A79AAXX.6.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.1 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/3/Solexa-41734/62A79AAXX.3.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.1.1 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/7/Solexa-41748/62A79AAXX.7.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@31884174 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@31884174 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@31884174 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.1.2 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/5/Solexa-41734/62A79AAXX.5.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.1.3 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/1/Solexa-41739/62A79AAXX.1.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.2 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/2/Solexa-41739/62A79AAXX.2.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@2565a3c2 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@2565a3c2 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@2565a3c2 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.3 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/8/Solexa-41753/62A79AAXX.8.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@691e0c13 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@691e0c13 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@691e0c13 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK TableRecalibration VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/6/Solexa-41748/62A79AAXX.6.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@7f92c8d9 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@7f92c8d9 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@7f92c8d9 output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/6/Solexa-41748/62A79AAXX.6.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.1 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/7/Solexa-41748/62A79AAXX.7.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@f9da4fc bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@f9da4fc index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@f9da4fc output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/7/Solexa-41748/62A79AAXX.7.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.1.1 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/5/Solexa-41734/62A79AAXX.5.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5097eded bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5097eded index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5097eded output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/5/Solexa-41734/62A79AAXX.5.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.1.2 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/1/Solexa-41739/62A79AAXX.1.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/1/Solexa-41739/62A79AAXX.1.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.2 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/3/Solexa-41734/62A79AAXX.3.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@77d2b01b bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@77d2b01b index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@77d2b01b output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/3/Solexa-41734/62A79AAXX.3.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.3 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/2/Solexa-41739/62A79AAXX.2.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/2/Solexa-41739/62A79AAXX.2.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.4 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/8/Solexa-41753/62A79AAXX.8.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/8/Solexa-41753/62A79AAXX.8.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
62A79AAXX100907:6:22:12941:18509 163 1 10001 0 36M65S = 10007 41 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTACCAGGAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA :=H;:;>AI=;;>AI><<?@I><<?AI=:887>.**69C54467B634357536=/,;?14245;50367@33247?53347@53357A53347@52237@ RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:IIIIIIIIIIIIIIIIIIIHIIIIIIIIIIHIIIIHHIIHHHGFHIEHBBEEE3C1*<;8=:<<<B<B=@?9@:<@@B@@>BBBBD@BDB@B7?B@AA8@= UQ:i:0
62A79AAXX100907:8:109:17192:16752 99 1 10001 0 36M65S = 10010 44 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC >>I<:;?AI=<;>AI><<?BI?==<BI=:888>.*)69B64468C53458B52258A53358A32357>53357>5335###################### RG:Z:62A79.8 NM:i:0 MQ:i:0 OQ:Z:HIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIHIHGIGIBEHFHHECFEEEDBEBEEC;BBB@@BBB@@B@@@###################### UQ:i:0
62A79AAXX100907:5:4:15479:18365 73 1 10002 0 36M65S = 10002 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC =C?AB@FHCDDAFI?=?AFHDAEAGIDDD@DE=;95@D???<BD<>?:AC=;;<>@8898>@99747<.58############################## RG:Z:62A79.5 NM:i:0 OQ:Z:HHHHHHHHHHHHHHDBDGGGHFHGHHHHHHHHHHHHEHHHHHHHDGHEGGEDDGCB;@B@==?=?8<>2>@############################## UQ:i:0
62A79AAXX100907:5:4:15479:18365 133 1 10002 0 * = 10002 0 CTGCTGTACGGCCAAGGCGGATGTACGGTACAGCAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTG 79;;;>EEC@HADHHII>AI=G@EAB?GCD@C@7=;DDBC<ABB4<><B>>C>CAD>@<@@B=@<A>@=@9A@@=<><>?=<<@??5?>?########### RG:Z:62A79.5 OQ:Z:HHHGFHHHHHGHHHGHHDGH<GEEBGGGCGGGGGFGGGFGACEE-A?AEA@GBGDG@DADCE=C@CAC;C>CCC=A=AA?>A@DB?/?=?###########
62A79AAXX100907:8:73:4240:3224 133 1 10002 0 * = 10002 0 GGGTTAGGGTTAGGGTTAGCCTGGTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGCTAGGGTGAGGGTTAGGG 8@@CH>GCCEI?GCDGIAI<<>CD9=GCBAA6;532B7?<;7=7?::9A7=:;:48=:;:938662=5=:############################### RG:Z:62A79.8 OQ:Z:GEGGGEGEEGGGGEGHHHHHGGDG8BGGGDCAEDE@G@GGE8AAECC9E@CCE>8=??B:91<<<-@<?@###############################
62A79AAXX100907:8:73:4240:3224 73 1 10002 0 36M65S = 10002 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCCAACCCCAACCCTAAACCCAAACCCAAACC >G::;=@I=<<=@I=;=>AI><=>@I:897:A0,+-7?52258A50357?33337############################################## RG:Z:62A79.8 NM:i:0 OQ:Z:HHHHHHHHHHHHHHHGHGHHHGHGGGBDGBGE<EG<AA=?FBDEB<B@AB>@D6A############################################## UQ:i:0
62A79AAXX100907:6:105:5519:16017 99 1 10003 0 36M65S = 10006 38 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCTAAACACAACCAC >:9:<?I=<<==I=;<>@I=<<9AI<9:;<D40-,.B43337?42367@52326?433########################################### RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:HHGHGHGHHHHBHHGHHHHGGG>GGEFGGGHEHHHHH>@E8AA??D=BB@A@0>@;@@########################################### UQ:i:0
62A79AAXX100907:6:51:2857:17932 101 1 10003 0 * = 10003 0 TGGCTTATGGATGCCTGGTAGCTAACCCTAACCCTAACCCTAACCCTAACTCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCT >AB><I@IDEIID@<>DEC@G@>>H><<<<D40--.B54458B54458B55758B54468B54458B53446?41458A43346@513%>310036?322# RG:Z:62A79.6 OQ:Z:HHHHHHHHHHHHHHHHHHBGEGGCCHHHHHHHHHFHHHHHDGGGGGEGGGDHDHGHHHHHGEGGBGGBDGACA>CGBDD>@@>>C@C@+C34976>A<AA#
62A79AAXX100907:8:93:2828:16974 99 1 10003 0 36M65S = 10012 44 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCTAACCCAAACCCACACACA >:8:<?I=<<<@I=;=<AI>==;AI<;8:;C4/,..B53357A32######################################################## RG:Z:62A79.8 NM:i:0 MQ:i:0 OQ:Z:HHGHHHHHHHDHHHEHBHGHHH@HHEGDEDGGGG@EGEEEB@E>C######################################################## UQ:i:0
62A79AAXX100907:6:51:2857:17932 153 1 10003 0 65S36M = 10003 0 GGCTTATGGATGCCTGGTAGCTAACCCTAACCCTAACCCTAACCCTAACTCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA 37>@7@@37@=7<?A45848?7A<<<?7B;<<?7@<<<?7A<<<?7C<@B@8C<==?8B<<=@9C435;7DBCDHAIDEEH@IEDDG@IDDDHAIHCBE=: RG:Z:62A79.6 NM:i:0 OQ:Z:BFBBEBEEEC>EGDGGEDCDDECBGFGEE@GGDBB;GGGEFBGGEEIEIDIGIEIIGDGBGIIIIHGGGGGFIIIIIEIIIGGFGGGGGFGIIIIIIIIII UQ:i:0
62A79AAXX100907:6:117:11919:16423 163 1 10004 0 36M65S = 10009 40 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAGATCGGCAGAGCGTCGTGTAGGG :78;>I=<<=@I=;<<@I>==;?I<=<<9G730//[email protected];53457@5+15-@>:?5:################## RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:BDGGHHHHHHHHGGHEHHHHH@DGDHHG?HHHHEGHHEHHHHHHGD<>GDFC3BCGGB@,EFA@C<GBGD?CG3C?,==8;CA################## UQ:i:0 XT:i:78
62A79AAXX100907:6:13:15155:6154 165 1 10004 0 * = 10004 0 AACCCTCTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA :G:9:=?>A=;IHD?>AI><=?BI><<=?G72/./864469C64469C54468B54469B53468B54468B53353B53347@53347?23469@22+26 RG:Z:62A79.6 OQ:Z:IIIIIIIIIIIIIHIIIIIIHIIIIIIIIIIIIIIIIIIHIIIHIHIIHIIHHHGIHHIHGEHGHGEGGGHGGEEB8EBBB>BBB@B>BA6@===?6?229
62A79AAXX100907:6:13:15155:6154 89 1 10004 0 65S36M = 10004 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA #######################:;=9@:::=7?<::=7A<:8:5;=<<?7B<<<?7B;<<?8B<2384A=@BF>IDEEH@IEDDG@ICCCHAIIDCF?H? RG:Z:62A79.6 NM:i:0 OQ:Z:#######################A=?==9A???@=C@A?C;?>><>?GGGAGBGGGBG@GGGDGBGGGFGBGGGDGEGGGGGDGGGGGEGGIIIIIIIIII UQ:i:0
62A79AAXX100907:6:73:2424:1293 163 1 10005 0 36M65S = 10015 45 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCTGGTAGCTAACCCTAACCCTAACCCTAAACCTAACCCTAACCCTAACCCTAAACCCAACCCCAA :8;>I<<<>AI=<<>AI><<>AI><<<@I:53119,35<<;8>757A53357@53355@50043;)3037@############################## RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:IIIIIIIIIIIIIIIIIIIIGIIIIIDIIHIHGIHDEEID@DB@EBDBBDBBBB@DB<B=<<<8<'<<8;?############################## UQ:i:0
62A79AAXX100907:7:119:15783:6171 163 1 10005 0 36M65S = 10011 41 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTGGAAACTAACCCC :8;>I<<<>AI=;;>AI><<?AI><<>@H:53219+4458C54468A52458C53347B53357@53349@322########################### RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:IIIIIIIIIIIIIIHIIIIIIGIIIIIIGIIHFIIIHIDGIGHHGHFEFHBHIHEE>EEDBD@AA@BD<=A<AA########################### UQ:i:0
62A79AAXX100907:7:63:15400:7094 163 1 10005 0 36M65S = 10006 36 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTAACTACCAGGCTA :8;>I<<<>?I=;;>@I><<>@I><<=@I:52119+4459C44457C44448A52257A54458B32257B3234;7A5.35-?4################ RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:IIIIIIIIIFIIIIIHIIIIHHIIIIGIIIIIIIIHIIFIIFHGFFIFHICDFEFFFEFEHHDDGCCFBBECCB<>??@8@?,@?################ UQ:i:0
62A79AAXX100907:8:69:9249:5472 165 1 10005 0 * = 10005 0 CGCGCCGGCGCAGGCGCAGAGACCTGGTAGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACAGATCGGAAGAGCGTCGT 8;5<=:B@?B>HA?5A?GG?HI><<:<:19344:.*358?32347:5234624+368B53.46?4#################################### RG:Z:62A79.8 OQ:Z:EB<BGGGBGG=G@@4FEEFEGGGGB5;7/97AAC><BBFBCCD>A7=CBA>3?1=GDGDB8>CCA#################################### XT:i:84
62A79AAXX100907:8:69:9249:5472 89 1 10005 0 65S36M = 10005 0 CCCCCCCTCCCCGCCTCCCGCCCGGGGACGGGCGCAGAGCCCTGGTAGCTACCCCTACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC ##########################################################################@<AAE>HFBCF>HACCF=GCCBC=FB= RG:Z:62A79.8 NM:i:0 OQ:Z:##########################################################################@7BBB=C??DDBF@FFF@FEFDBCFFF UQ:i:0 XT:i:84
62A79AAXX100907:6:62:15066:3015 163 1 10006 0 36M65S = 10012 41 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACCAACCCCAACCCCCACCCCACCCCAAACAACCCA :;>H;;<>AI=;<>AI><<=AI><<>AI<8554;,)459A53357B31158?5.337############################################ RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:IIIIHIIIIIIIIIIIHIIEIIIIIHIIIIIHIDIIHBIFEEDBEEC>C@D@@8B8?############################################ UQ:i:0
62A79AAXX100907:6:105:5519:16017 147 1 10006 0 65S36M = 10003 -38 TACGCCCACCCCTAACCCTACCCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC ###########################################>8::=7@<:;=7@6<<?7B=<<40:8;?A9?@CDG@I@EDG@IDCCF=H@CCF>GB@: RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:###########################################A4AAA?==?B@?B1GGGEGDGGGAB;EFB?>;DGGEG@GGGGGAFFFCF@DFFGGGGD UQ:i:0
62A79AAXX100907:7:63:15400:7094 83 1 10006 0 65S36M = 10005 -36 ACCCCGAACCCTACCCCTACCCCTACCCCTACCCCTAACCCTAACCCTTAACCCTAACCCTAACTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACC #######################################################################?7E9BCG>IADDG?IBDCF?IBDDF>HDA> RG:Z:62A79.7 NM:i:5 MQ:i:0 OQ:Z:#######################################################################B?D8DFECF@GGGCGBGGGGGBGGGHHHHH UQ:i:10
62A79AAXX100907:5:27:16532:6367 99 1 10007 0 36M65S = 10013 41 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCCACCCCAAACCCACCC ;?B>@8?EGBDDAGIDEEAGIDEE=GIDDC<BB:989@D???9BD;;;6>A;;;6<?68777<878/9>597############################# RG:Z:62A79.5 NM:i:0 MQ:i:0 OQ:Z:GGGGG@GGGGHHHHHHHHHHHHHHEHHHHHDHHHHHFFHHHHBHHBDD<BDBDD<@@>CA74>;?;)5;7=?############################# UQ:i:0
62A79AAXX100907:6:22:12941:18509 83 1 10007 0 65S36M = 10001 -41 CCCTAACCCCTACCAGGTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC ##########################::=7?<::=7@:::=9><::?7@=<<?8C<<<?7B;<<?.958;A:H?CDG?IEEDG@IEDDF?IFEEH@IDCB? RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:##########################A@@?@;A@A??9AAA=A=AAGAD?DFFDIBGGGBG@GGGEGBGGGDGBGGGDGDGGGGGFGGGGGHIIIIIHIII UQ:i:0
62A79AAXX100907:6:25:3117:6332 165 1 10008 0 * = 10008 0 AATGGAACGCCTGGTAGAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT :FFAAII=>?;=CDD@HII>=;>?I=;9;<C40--.B54468B54256A53458@41457@53357B53458A54347=53367@50347########### RG:Z:62A79.6 OQ:Z:GGGGDFGGBEGGGGEHHHHHHDGDFGGFFGGHHHEHHHHHHHHGHFB>FFEHBHCA>G@BCEBE@EEEBHDDDDGEAE>B@B=@B@<@<@###########
62A79AAXX100907:8:27:12846:20680 165 1 10008 0 * = 10008 0 CCTTTCCTTTATGCTGCTCTACCAGGACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC 88:GH=<>II@ID@>DA>@:A>=IGCI=:887=.+*58B53468B54368B54448B53468B53458B53348B33358:.02/8?4*027>11+46;50 RG:Z:62A79.8 OQ:Z:HHHHHGHHGHHGHHHHHHHHHHHHGEHHHGHEDHGHDHHH@HHHHHHBGGGGGG>HHGBGGEGBBGBDGB@D<GG<D@BD62<;*==:090?;8>27;>=<
62A79AAXX100907:6:25:3117:6332 89 1 10008 0 65S36M = 10008 0 ACCCTAGCCCTAACCCTACCCCTACCCCTAACCCTACCCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT ###############################;:=7;*;7>6@6::=5;;::<6;&:;66B=;:=76558:6E@CCF=D@AAF;GCADF@IDDCG@IDBAC= RG:Z:62A79.6 NM:i:0 OQ:Z:###############################B@?:@.=<=7?0AAA6>:AA:5:+@B8CGAB??:?CFF>?FCFFF:A>BBC>B=BGGGGDGEGGGGGGGG UQ:i:0
62A79AAXX100907:8:27:12846:20680 89 1 10008 0 65S36M = 10008 0 ACCCCAACCCCTACCCCAACCCCAACCCCTACCCCAACCCCAAACCCAACCCCAAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT ###########################################################?/9;>04345;3?1>8B3?6ABE/DEA<F?CD@9B>BB@9B. RG:Z:62A79.8 NM:i:0 OQ:Z:###########################################################?':==2=0B?=8?*=7=3>1==B-;DB>?D:D@<@B;DD>D4 UQ:i:0
62A79AAXX100907:8:107:1555:6623 101 1 10009 0 * = 10009 0 TCCGCCTTCGCAGTACCCCTGGTAGCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCTAC >;9A>;>I?B?GGE@>===?CEDAG>:<>F73/./752245@42247342################################################### RG:Z:62A79.8 OQ:Z:HHHHHHHHHGGGGGGHHHHHDGAGGEEGGGHHGHDGHFF><?AAA<A/A?###################################################
62A79AAXX100907:6:117:11919:16423 83 1 10009 0 65S36M = 10004 -40 CCTGCTGAACCCCTCTTCCGACCTCCCTACCCCTACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ######################################################::=7?;;895=03595?=ACF=IEEEG@IDDDG@IECEH@IFCCE=> RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:######################################################A??:@:B><6;)CA?:A>EFECGDGGGGGEGGGGGGGHHHHHHHHHH UQ:i:0 XT:i:78
62A79AAXX100907:8:107:1555:6623 153 1 10009 0 65S36M = 10009 0 ACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ##############:=09/;9>505;;:2837:345::?7=<:;>6?::;?5976:?7A:;<?79335;7CABCG:HEEEH3GADDG@IDCDH@EECBD<8 RG:Z:62A79.8 NM:i:0 OQ:Z:##############??25(=:=532==>/78>>882ACE@AAAEB;?@CEE<>89AE?E@BGGB>>GGGGGDGGG>FCGGGA?BGGGGGDGGHGBHHHHHH UQ:i:0
62A79AAXX100907:8:109:17192:16752 147 1 10010 0 65S36M = 10001 -44 CCCCCCCCCCAACCCCTCCCCCTACCCCCACCCCTACCCCCCCCCCAACCCAACCCAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA ##########################################################;<<?8B=2385A@ACGAIDDEG@FEDDG@IDCCHAIEDCF>G9 RG:Z:62A79.8 NM:i:0 MQ:i:0 OQ:Z:##########################################################BGGGEGFDIIFIHIIIIIEGGGFGDGGGGGDGGIIIFIIIIII UQ:i:0
62A79AAXX100907:3:113:16808:6267 163 1 10011 0 36M65S = 10012 36 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACACCAGAGATAAGCCTGTTATATTTAGGGTGTCATGTGTGCATTACGAATGCCGC 7;9@C@A??EIABDAGIDEDAGEDDCADGBB?8<=6>+4A>8########################################################### RG:Z:62A79.3 NM:i:0 MQ:i:0 OQ:Z:GGEGGGGEGGHFGHHHHHHHHHDHHGHEGHHHBHGGG28G:@########################################################### UQ:i:0
62A79AAXX100907:7:18:8574:19050 99 1 10011 0 36M65S = 10014 38 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCACCCCCAA ?9<?I=<<>AI<<<>AI><<>BI><<9@I:52119+4458A54448B54447@53357@53226?33257############################### RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:IIIIIIHIIIIGIIIIIIIIGIIHIIBIIIIIIIIIIGFHFHHHCHHGGG>@BB@B@BBBEC0C@A@A?A############################### UQ:i:0
62A79AAXX100907:7:43:12512:9027 99 1 10011 0 36M65S = 10012 36 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAAACCTCACCCTAA >9;>I=<<>@I=;<=@I===?@I>=;>?H962109+3458A53258@51347?31347@53369@43245@42149<,3###################### RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:HHHHHHHHHHHHGHEHHGHHHHHHHGHHHFHDHHFHEHEHFBBFBDBB>B9@@9>B>@A@@B==B;@;49=;;>7=6-@###################### UQ:i:0
62A79AAXX100907:7:119:15783:6171 83 1 10011 0 65S36M = 10005 -41 ACCCCTCACCCTACCCCTAACCCTACCCCTAACCCCACCCCCTGGTACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC ##############################################################@4:161;5<<@9D=AAD=FEDDG?IDCCF@IGEDF>HC> RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:##############################################################?/AA?:A5CBB>B7CCA;AAGGGCGEGGGHHHHHHHHHH UQ:i:0
62A79AAXX100907:3:113:16808:6267 83 1 10012 0 65S36M = 10011 -36 TAACCCTAACCCTACCCCAAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC ###################################################################;4==9<82<@7+<4AC@<;>GGGHFDFGEBCAB< RG:Z:62A79.3 NM:i:0 MQ:i:0 OQ:Z:###################################################################?,??<47(4;8+5+;B@7>>EEECECEEE?E?EE UQ:i:0
62A79AAXX100907:6:62:15066:3015 83 1 10012 0 65S36M = 10006 -41 CCCTAACCCTACCCCTACCCCTAGCCCTAACCCTAACCCTACCCCTACCCCTAACCCTAACCCCTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACC #######################################################################C>I@DDG?IBDEG?ICDDF?IEDDF>HCA= RG:Z:62A79.6 NM:i:5 MQ:i:0 OQ:Z:#######################################################################GGGBGGGDGBGGECGEGGGGGFGGGGGFGG UQ:i:10
62A79AAXX100907:7:43:12512:9027 147 1 10012 0 65S36M = 10011 -36 CTACCCTGGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC #####################::=5@8::=7@<::>5?:::>6@::;?7@<<<?7@<<<?6@<<<4/:8;>C;IADDI?IEEDG@IBCCF>IDDDE?H?A: RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:#####################??@6?4@?A;?;@??9=<???>?7@BD@B=DGDBDBFFGCDBGGGBD@DGGBGBGGIDIDGGGGGBGGGDGEGGGIIBII UQ:i:0
62A79AAXX100907:8:93:2828:16974 147 1 10012 0 65S36M = 10003 -44 CCCCGCCCTACCCCTACCCCTAACCCTAACCCTAACCCTACCCCTCTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC #####################################################?8@;<<?8B;<<5/;:<?C=ICDEI>IG@DG@IDDDF?ICBDF>GA@8 RG:Z:62A79.8 NM:i:0 MQ:i:0 OQ:Z:#####################################################GDDBGGGDGBGGGHHHHHGEGEGHHBHHGGGGGEGGGEGEDGGGGDGG UQ:i:0
62A79AAXX100907:6:90:1828:20961 73 1 10013 0 36M65S = 10013 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCAAACCCCAACCCAAAACCCAACACCCACCCACCCC >=H;;:>>I=<;=@E=<;=;G4999@G;5734;-*)58@13357@412##################################################### RG:Z:62A79.6 NM:i:0 OQ:Z:HHHHHGHDHHHGHG@GGED>B8@B?GDEBE8?@?:GDDB8DBBBBA>A##################################################### UQ:i:0
62A79AAXX100907:6:90:1828:20961 133 1 10013 0 * = 10013 0 GGTTAGGGTTAGGGTTAGGGTTAGCTACCAGGAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTGGGG :@BG>FDDDG<FDDDI@GAD?I@G:;:7*>B;;53################################################################## RG:Z:62A79.6 OQ:Z:GGGGGEGGFD@GGGDGGGBE>GGG>=::0:FE;<C##################################################################
62A79AAXX100907:7:32:5399:2634 101 1 10013 0 * = 10013 0 AGGCGCACAGTCACACGCCACCGGGACAGGAGCGCGGGGGCTACCAGGCTAACCCTAACCCCCAAACCCTAACCCTCACCCCAACCCAAAACCCACCCACA ?EB>A?I=IHF>H>I>C@<I><C@AI;IF<D?33/1::<:############################################################# RG:Z:62A79.7 OQ:Z:IIHIIIHHIIHHGIIIIHIIIIG@BHDIHBFHHGBCCCDC#############################################################
62A79AAXX100907:8:101:5724:10556 101 1 10013 0 * = 10013 0 AACCCTAACCCTAACCTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC >H;::>BI><<>AI><?B?=IIF@>AI=;887>.+*58B53359A53358B53458A53358A53356?33358?53258?50247?43357>50346>43 RG:Z:62A79.8 OQ:Z:IIIIIIIIIIIIIIIIIIIIIIHIGHHHHIIHIHHHFGHFEEEIFEEEEFGDDGEFEDBEEHDBBBBCB>BBBDCB@;BDBB7C>BBA@B@B@@7B>>@:@
62A79AAXX100907:5:27:16532:6367 147 1 10013 0 65S36M = 10007 -41 CACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC ###############?4077$?9899??90<?>@A9<?>@A>@>ADC?C?AEC>E@DDC@C?DDC8<=ADDDHDIIIFIEIIIHIHHHGEGEIIHBECD@7 RG:Z:62A79.5 NM:i:0 MQ:i:0 OQ:Z:###############?8341)=>7<6==>2:?ACC>A?ACCBD@DGGDGBDIGBICGGGFGBGGGDGFGGGGIEIIIGIEIIIIIIGGGGGFIIIGIFIGG UQ:i:0
62A79AAXX100907:7:32:5399:2634 153 1 10013 0 65S36M = 10013 0 GGGACAGGAGCGCGGGGGCTACCAGGCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC ############833337?6=:9536>7>6;<?6>=<<;?7@;<<<?8@<<<?6B<<<?7@<<<?.:78;A<HCDDG@IDDEG?IECCF>IBDDG?HBA@: RG:Z:62A79.7 NM:i:0 OQ:Z:############B=@@@BDCACCB@>BB@2BDEC@AFDEEEB@DGDGDB=GGGCGBDGGBDBGGGEEDIGIEGEGGGGGEGGGDGDFGGCGBGGGGGEGGG UQ:i:0
62A79AAXX100907:8:101:5724:10556 153 1 10013 0 65S36M = 10013 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 98::=3A<;;?7?;<<<8=;;:=3A:::?8?9:;?7B;<<?8A;<<?6B<;<?8B;<<?8B<<<?.968;A<HCDDG@IDEAI?IGDCG?IDDDG?HCAA8 RG:Z:62A79.8 NM:i:0 OQ:Z:<7???8EEEEGBBBGGA=A=BCC8E@?AE=B9CEEAGBGGGDEBGGGCGAEGGDGBGGGDGEGGGBGEGGGDGDGGGEGEGHHDHHGFGGGFGGGGHHHHH UQ:i:0
62A79AAXX100907:8:13:11880:18982 165 1 10014 0 * = 10014 0 GTTTACATTTTACATGGATAAGGCCCTGCCTGGTAGAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 9EHH?=IIIIIA=IIDEII@IIE@<<>C=88:8705BC64468C64469C64469C54469C64459A64469A54359B54469B54468B54357B533 RG:Z:62A79.8 OQ:Z:IIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIGIIHIIIIIHIIHIIIIIIIIIIHIIIIIIHHEIFIHHHIFGGDDIHHHHGIGEHGHHGEGBEBHEED
62A79AAXX100907:7:18:8574:19050 147 1 10014 0 65S36M = 10011 -38 ACCCTACCCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT ##########################:>1;9::=5=6::>9@;<<?5B;<<=6A;<;?8B<<<?87558>:FBCDG@IEEDG?IDBDF?IEDDF@FDAAC: RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:##########################A?3>5?AA<;1?CB=?:DDE<E>GGCCF@FBGDGBGGGGGGGGGGGDGGGGGDGGEFFECGGGGGGGDGDGGGGG UQ:i:0
62A79AAXX100907:8:13:11880:18982 89 1 10014 0 65S36M = 10014 0 GGTAGAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT #######:;=7=::;=7A;;:?79;;<?7B;;;?7A<<<?8B<<<?8B=;<?8B<<<?8B<<<?87558>:FCCCG@IFEEG?IFDDG@IADDG@IBBAC= RG:Z:62A79.8 NM:i:0 OQ:Z:#######AB??@:CECAE;ECEA>=EGGBGBEEE?ECGGGFGEGGGGGDEGGGGEGGGGGEGGGGGDGGGGGGGGGGGGGGGDGGGGGGGBGGGGGEGGGG UQ:i:0
62A79AAXX100907:8:74:13340:18350 73 1 10015 0 36M65S = 10015 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCC >;9:=AI><<>AI><<?BI>==>BI><;<=E4/,-.B53458A53258A32468A50348?50347A53316>1+257@###################### RG:Z:62A79.8 NM:i:0 OQ:Z:IIIIIIIIIIIIIIIIIIIIIIGIIIIIHIIIIIIIGGEIDGD@BFDEFCFHHDFB<ECEBB<D>BDBB@2;;82????###################### UQ:i:0
62A79AAXX100907:8:74:13340:18350 133 1 10015 0 * = 10015 0 TTGTCATTGTAGAAAGTCTGAACCTGGTAGTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGG 9G@F=HIICHAHIIIHI??BII><?DEE?D?7;534C9@==<C8@<<<B8?<<<B8?<<;B8?<<;96?<;7988;:;?6998797<::84359819553: RG:Z:62A79.8 OQ:Z:IIIIIIIIIIIIIIIIIIIIHIIIIIIGIIGBGGGFIIIIIEIHIGGCGEGGGCGFGGGBGFGGGB>>DD=5<=<B?=?;5:;59?@AA6888:;+5688?
62A79AAXX100907:6:73:2424:1293 83 1 10015 0 65S36M = 10005 -45 CCCTACCCCTACCCCTACCCCTAACCCTACCCTGGTAGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ######################################=9@4::=9@4:::9@8::=5@<::=7A234;4A<BCF=ICDEG>IBDDG>IBCDF?IDBBD== RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:######################################?=?.???==/??>=?4AA?<?=ACCAC8EBE?B<GGGBEAEGGBGBGGGDGBGGGFGFGGGGG UQ:i:0