##ALT=<ID=NON_REF,Description=\"Represents any possible alternative allele at this location\"><\/pre>\n##FILTER=<ID=LowQual,Description=\"Low quality\"><\/pre>\n##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description=\"Minimum DP observed within the GVCF block\">\r\n##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification\">\r\n##FORMAT=<ID=SB,Number=4,Type=Integer,Description=\"Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.\">\r\n##GATKCommandLine=<ID=CombineGVCFs,Version=3.3-0-g37228af,Date=\"Fri Mar 09 04:16:18 CST 2018\",Epoch=1520540178356,CommandLineOptions=\"analysis_type=CombineGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=\/hwfssz1\/BC_COM_P0\/BC_RD_P1\/DNA\/DNA_Human_WGS\/DNA_Human_WGS_2017b\/Database\/hg19\/hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=15001702301675A\/15001702301675A.chr10.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant2 source=15001702301675A\/15001702301675A.chr11.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant3 source=15001702301675A\/15001702301675A.chr12.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant4 source=15001702301675A\/15001702301675A.chr13.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant5 source=15001702301675A\/15001702301675A.chr14.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant6 source=15001702301675A\/15001702301675A.chr15.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant7 source=15001702301675A\/15001702301675A.chr16.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant8 source=15001702301675A\/15001702301675A.chr17.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant9 source=15001702301675A\/15001702301675A.chr18.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant10 source=15001702301675A\/15001702301675A.chr19.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant11 source=15001702301675A\/15001702301675A.chr1.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant12 source=15001702301675A\/15001702301675A.chr20.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant13 source=15001702301675A\/15001702301675A.chr21.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant14 source=15001702301675A\/15001702301675A.chr22.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant15 source=15001702301675A\/15001702301675A.chr2.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant16 source=15001702301675A\/15001702301675A.chr3.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant17 source=15001702301675A\/15001702301675A.chr4.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant18 source=15001702301675A\/15001702301675A.chr5.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant19 source=15001702301675A\/15001702301675A.chr6.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant20 source=15001702301675A\/15001702301675A.chr7.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant21 source=15001702301675A\/15001702301675A.chr8.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant22 source=15001702301675A\/15001702301675A.chr9.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant23 source=15001702301675A\/15001702301675A.chrM.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant24 source=15001702301675A\/15001702301675A.chrX.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant25 source=15001702301675A\/15001702301675A.chrY.g.vcf.gz)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub convertToBasePairResolution=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false\">\r\n##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date=\"Thu Feb 08 22:43:49 CST 2018\",Epoch=1518101029456,CommandLineOptions=\"analysis_type=HaplotypeCaller input_file=[\/ldfssz1\/BC_WGS\/auto\/projects\/2018\/1\/31\/15001702301675A_2346\/bam\/chr\/15001702301675A.chr11.realign.recal.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[chr11] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=\/ldfssz1\/BC_WGS\/pipeline\/DNA_Human_WGS_2017b\/Database\/hg19\/hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=false pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false\">\r\n##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive)\r\n##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description=\"Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities\">\r\n##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description=\"Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases\">\r\n##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth; some reads may have been filtered\">\r\n##INFO=<ID=DS,Number=0,Type=Flag,Description=\"Were any of the samples downsampled?\">\r\n##INFO=<ID=END,Number=1,Type=Integer,Description=\"Stop position of the interval\">\r\n##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description=\"Consistency of the site with at most two segregating haplotypes\">\r\n##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description=\"Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation\">\r\n##INFO=<ID=MLEAC,Number=A,Type=Integer,Description=\"Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed\">\r\n##INFO=<ID=MLEAF,Number=A,Type=Float,Description=\"Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed\">\r\n##INFO=<ID=MQ,Number=1,Type=Float,Description=\"RMS Mapping Quality\">\r\n##INFO=<ID=MQ0,Number=1,Type=Integer,Description=\"Total Mapping Quality Zero Reads\">\r\n##INFO=<ID=MQRankSum,Number=1,Type=Float,Description=\"Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities\">\r\n##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description=\"Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias\">\r\n##contig=<ID=chrM,length=16571,assembly=hg19>\r\n##contig=<ID=chr1,length=249250621,assembly=hg19>\r\n##contig=<ID=chr2,length=243199373,assembly=hg19>\r\n##contig=<ID=chr3,length=198022430,assembly=hg19>\r\n##contig=<ID=chr4,length=191154276,assembly=hg19>\r\n##contig=<ID=chr5,length=180915260,assembly=hg19>\r\n##contig=<ID=chr6,length=171115067,assembly=hg19>\r\n##contig=<ID=chr7,length=159138663,assembly=hg19>\r\n##contig=<ID=chr8,length=146364022,assembly=hg19>\r\n##contig=<ID=chr9,length=141213431,assembly=hg19>\r\n##contig=<ID=chr10,length=135534747,assembly=hg19>\r\n##contig=<ID=chr11,length=135006516,assembly=hg19>\r\n##contig=<ID=chr12,length=133851895,assembly=hg19>\r\n##contig=<ID=chr13,length=115169878,assembly=hg19>\r\n##contig=<ID=chr14,length=107349540,assembly=hg19>\r\n##contig=<ID=chr15,length=102531392,assembly=hg19>\r\n##contig=<ID=chr16,length=90354753,assembly=hg19>\r\n##contig=<ID=chr17,length=81195210,assembly=hg19>\r\n##contig=<ID=chr18,length=78077248,assembly=hg19>\r\n##contig=<ID=chr19,length=59128983,assembly=hg19>\r\n##contig=<ID=chr20,length=63025520,assembly=hg19>\r\n##contig=<ID=chr21,length=48129895,assembly=hg19>\r\n##contig=<ID=chr22,length=51304566,assembly=hg19>\r\n##contig=<ID=chrX,length=155270560,assembly=hg19>\r\n##contig=<ID=chrY,length=59373566,assembly=hg19>\r\n##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>\r\n##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>\r\n##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>\r\n##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>\r\n##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>\r\n##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19>\r\n##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19>\r\n##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19>\r\n##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19>\r\n##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19>\r\n##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19>\r\n##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19>\r\n##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>\r\n##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>\r\n##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>\r\n##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>\r\n##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>\r\n##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>\r\n##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>\r\n##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>\r\n##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>\r\n##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>\r\n##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>\r\n##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>\r\n##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>\r\n##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>\r\n##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>\r\n##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>\r\n##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>\r\n##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>\r\n##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>\r\n##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>\r\n##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>\r\n##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>\r\n##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>\r\n##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>\r\n##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>\r\n##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>\r\n##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>\r\n##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>\r\n##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>\r\n##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>\r\n##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>\r\n##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>\r\n##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>\r\n##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>\r\n##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>\r\n##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>\r\n##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>\r\n##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>\r\n##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>\r\n##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>\r\n##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>\r\n##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>\r\n##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>\r\n##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>\r\n##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>\r\n##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>\r\n##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>\r\n##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>\r\n##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>\r\n##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>\r\n##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>\r\n##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>\r\n##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>\r\n##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>\r\n##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>\r\n##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>\r\n##reference=file:\/\/\/hwfssz1\/BC_COM_P0\/BC_RD_P1\/DNA\/DNA_Human_WGS\/DNA_Human_WGS_2017b\/Database\/hg19\/hg19.fasta\r\n#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 15001702301675A-PE100-2\r\nchrM 1 . G <NON_REF> . . END=2 GT:DP:GQ:MIN_DP:PL .\/.:10:15:5:0,15,161\r\nchrM 3 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:15:45:15:0,45,430\r\nchrM 4 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:20:60:20:0,60,621\r\nchrM 5 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:25:75:25:0,75,753\r\nchrM 6 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:29:87:29:0,87,993\r\nchrM 7 . A <NON_REF> . . END=71 GT:DP:GQ:MIN_DP:PL .\/.:191:99:35:0,105,1112\r\nchrM 72 . T C,<NON_REF> . . DP=337;MQ=59.87;MQ0=0 GT:AD:DP:PGT:PID:PL:SB .\/.:0,334,0:334:0|1:72_T_C:15370,1032,0,15370,1032,15370:0,0,163,171\r\nchrM 73 . G A,<NON_REF> . . DP=342;MQ=59.88;MQ0=0 GT:AD:DP:PGT:PID:PL:SB .\/.:0,339,0:339:0|1:72_T_C:15508,1047,0,15508,1047,15508:0,0,166,173\r\nchrM 74 . T <NON_REF> . . END=92 GT:DP:GQ:MIN_DP:PL .\/.:394:99:355:0,120,1800\r\nchrM 93 . A G,<NON_REF> . . DP=431;MQ=59.93;MQ0=0 GT:AD:DP:PGT:PID:PL:SB .\/.:0,426,0:426:0|1:72_T_C:17891,1284,0,17891,1284,17891:0,0,203,223\r\nchrM 94 . G <NON_REF> . . END=149 GT:DP:GQ:MIN_DP:PL .\/.:475:99:445:0,120,1800\r\nchrM 150 . T C,<NON_REF> . . DP=463;MQ=59.97;MQ0=0 GT:AD:DP:PL:SB .\/.:0,457,0:457:14389,1371,0,14389,1371,14389:0,0,198,259\r\nchrM 151 . C <NON_REF> . . END=194 GT:DP:GQ:MIN_DP:PL .\/.:472:99:465:0,120,1800\r\nchrM 195 . C T,<NON_REF> . . BaseQRankSum=0.618;ClippingRankSum=-7.600e-01;DP=472;MQ=60.00;MQ0=0;MQRankSum=-1.344e+00;ReadPosRankSum=0.808 GT:AD:DP:PL:SB .\/.:2,464,0:466:14236,1353,0,14241,1392,14280:0,2,205,259\r\nchrM 196 . T <NON_REF> . . END=301 GT:DP:GQ:MIN_DP:PL .\/.:312:99:174:0,120,1800\r\nchrM 302 . AC A,ACC,ACCC,<NON_REF> . . BaseQRankSum=0.188;ClippingRankSum=1.20;DP=133;MQ=60.00;MQ0=0;MQRankSum=0.444;ReadPosRankSum=0.120 GT:AD:DP:PL:SB .\/.:59,4,27,6,0:96:509,685,2657,0,1368,1339,482,2144,1434,2472,612,2040,1375,1987,1962:17,42,7,20\r\nchrM 304 . C <NON_REF> . . END=310 GT:DP:GQ:MIN_DP:PL .\/.:154:99:150:0,120,1800\r\nchrM 311 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:143:0:143:0,0,1913\r\nchrM 312 . C <NON_REF> . . END=317 GT:DP:GQ:MIN_DP:PL .\/.:151:99:147:0,120,1800\r\nchrM 318 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:146:0:146:0,0,2262\r\nchrM 319 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:152:99:152:0,120,1800\r\nchrM 320 . T <NON_REF> . . END=321 GT:DP:GQ:MIN_DP:PL .\/.:148:0:136:0,0,2475\r\nchrM 322 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:148:99:148:0,120,1800\r\nchrM 323 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:140:0:140:0,0,3054\r\nchrM 324 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:132:31:132:0,32,3123\r\nchrM 325 . G <NON_REF> . . END=327 GT:DP:GQ:MIN_DP:PL .\/.:141:99:139:0,120,1800\r\nchrM 328 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .\/.:138:0:138:0,0,2492\r\n<\/pre>\nThis is work in progress that is published to force myself to improve it. To be continued...<\/p>\n","protected":false},"excerpt":{"rendered":"
I bought whole genome sequencing for myself, with raw sequencing data, from Dante Labs in late 2017. They advertised this level of sequencing quality: Dante Labs Whole Genome Sequencing – Technical Sheet Paired End Reads Length 100 base pairs Mapping Rate 99.22% Unique Rate 96.47% Average Sequencing Depth 37.44 Average Coverage 30X Coverage 99.12% … Continue reading “My personal genome”<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":4253,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5],"tags":[],"_links":{"self":[{"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4218"}],"collection":[{"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=4218"}],"version-history":[{"count":46,"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4218\/revisions"}],"predecessor-version":[{"id":4270,"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4218\/revisions\/4270"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=\/wp\/v2\/media\/4253"}],"wp:attachment":[{"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4218"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4218"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/yehar.com\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4218"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
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