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% |
| Coverage at least 4X | 98.12% |
| Coverage at least 10X | 97.81% |
| Coverage at least 20X | 96.06% |
After they successfully extracted DNA from my second saliva sample – the first sample did not qualify – it took much longer than the 50 business days advertised to get results:
15001702301675A.gvcffile (28,139,979,844 bytes) (88 business days after DNA extraction)- A hard disk with raw sequencing reads and more (~150 business days after DNA extraction)
The gVCF file
The genome Variant Call Format (gVCF) file represents the genotype as constructed by the sequencing pipeline. Let's go through the gVCF file line by line:
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1 |
##fileformat=VCFv4.1 |
The string ## at the beginning of the line denotes file meta-information which follows in format key=value. The file format is Variant Call Format (VCF) Version 4.1. The VCF format is maintained and specified by the Global Alliance for Genomics and Health Data Working group file format team / Samtools organization. A gVCF file is a valid VCF 4.1 file that follows a set of gVCF conventions maintained in the gvcftools repository by Chris Saunders (Illumina).
|
1 |
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> |
|
1 |
##FILTER=<ID=LowQual,Description="Low quality"> |
|
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 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 |
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> ##GATKCommandLine=<ID=CombineGVCFs,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"> ##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"> ##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> ##contig=<ID=chrM,length=16571,assembly=hg19> ##contig=<ID=chr1,length=249250621,assembly=hg19> ##contig=<ID=chr2,length=243199373,assembly=hg19> ##contig=<ID=chr3,length=198022430,assembly=hg19> ##contig=<ID=chr4,length=191154276,assembly=hg19> ##contig=<ID=chr5,length=180915260,assembly=hg19> ##contig=<ID=chr6,length=171115067,assembly=hg19> ##contig=<ID=chr7,length=159138663,assembly=hg19> ##contig=<ID=chr8,length=146364022,assembly=hg19> ##contig=<ID=chr9,length=141213431,assembly=hg19> ##contig=<ID=chr10,length=135534747,assembly=hg19> ##contig=<ID=chr11,length=135006516,assembly=hg19> ##contig=<ID=chr12,length=133851895,assembly=hg19> ##contig=<ID=chr13,length=115169878,assembly=hg19> ##contig=<ID=chr14,length=107349540,assembly=hg19> ##contig=<ID=chr15,length=102531392,assembly=hg19> ##contig=<ID=chr16,length=90354753,assembly=hg19> ##contig=<ID=chr17,length=81195210,assembly=hg19> ##contig=<ID=chr18,length=78077248,assembly=hg19> ##contig=<ID=chr19,length=59128983,assembly=hg19> ##contig=<ID=chr20,length=63025520,assembly=hg19> ##contig=<ID=chr21,length=48129895,assembly=hg19> ##contig=<ID=chr22,length=51304566,assembly=hg19> ##contig=<ID=chrX,length=155270560,assembly=hg19> ##contig=<ID=chrY,length=59373566,assembly=hg19> ##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19> ##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19> ##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19> ##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19> ##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19> ##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19> ##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19> ##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19> ##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19> ##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19> ##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19> ##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19> ##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19> ##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19> ##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19> ##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19> ##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19> ##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19> ##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19> ##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19> ##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19> ##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19> ##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19> ##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19> ##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19> ##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19> ##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19> ##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19> ##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19> ##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19> ##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19> ##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19> ##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19> ##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19> ##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19> ##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19> ##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19> ##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19> ##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19> ##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19> ##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19> ##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19> ##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19> ##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19> ##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19> ##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19> ##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19> ##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19> ##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19> ##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19> ##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19> ##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19> ##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19> ##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19> ##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19> ##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19> ##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19> ##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19> ##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19> ##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19> ##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19> ##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19> ##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19> ##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19> ##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19> ##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19> ##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19> ##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19> ##reference=file:///hwfssz1/BC_COM_P0/BC_RD_P1/DNA/DNA_Human_WGS/DNA_Human_WGS_2017b/Database/hg19/hg19.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 15001702301675A-PE100-2 chrM 1 . G <NON_REF> . . END=2 GT:DP:GQ:MIN_DP:PL ./.:10:15:5:0,15,161 chrM 3 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:15:45:15:0,45,430 chrM 4 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:20:60:20:0,60,621 chrM 5 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:25:75:25:0,75,753 chrM 6 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:29:87:29:0,87,993 chrM 7 . A <NON_REF> . . END=71 GT:DP:GQ:MIN_DP:PL ./.:191:99:35:0,105,1112 chrM 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 chrM 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 chrM 74 . T <NON_REF> . . END=92 GT:DP:GQ:MIN_DP:PL ./.:394:99:355:0,120,1800 chrM 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 chrM 94 . G <NON_REF> . . END=149 GT:DP:GQ:MIN_DP:PL ./.:475:99:445:0,120,1800 chrM 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 chrM 151 . C <NON_REF> . . END=194 GT:DP:GQ:MIN_DP:PL ./.:472:99:465:0,120,1800 chrM 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 chrM 196 . T <NON_REF> . . END=301 GT:DP:GQ:MIN_DP:PL ./.:312:99:174:0,120,1800 chrM 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 chrM 304 . C <NON_REF> . . END=310 GT:DP:GQ:MIN_DP:PL ./.:154:99:150:0,120,1800 chrM 311 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:143:0:143:0,0,1913 chrM 312 . C <NON_REF> . . END=317 GT:DP:GQ:MIN_DP:PL ./.:151:99:147:0,120,1800 chrM 318 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:146:0:146:0,0,2262 chrM 319 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:152:99:152:0,120,1800 chrM 320 . T <NON_REF> . . END=321 GT:DP:GQ:MIN_DP:PL ./.:148:0:136:0,0,2475 chrM 322 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:148:99:148:0,120,1800 chrM 323 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:140:0:140:0,0,3054 chrM 324 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:132:31:132:0,32,3123 chrM 325 . G <NON_REF> . . END=327 GT:DP:GQ:MIN_DP:PL ./.:141:99:139:0,120,1800 chrM 328 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:138:0:138:0,0,2492 |
This is work in progress that is published to force myself to improve it. To be continued...