annotate test-data/02_0585_COA_TX_Fed.vcf @ 4:da20c7c76d06 draft

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author greg
date Thu, 17 Jun 2021 13:23:41 +0000
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1 ##fileformat=VCFv4.2
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2 ##FILTER=<ID=LowQual,Description="Low quality">
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3 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
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5 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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7 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
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8 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.8-0-ge9d806836,Date="Sat Dec 23 17:42:05 CST 2017",Epoch=1514072525658,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/02-0585/02-0585-quality.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/02-0585/NC_002945v4.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 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 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false 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 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false out=/scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/02-0585/02-0585-hapall.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[] excludeAnnotation=[] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 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=false gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=true numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 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 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=true captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 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">
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9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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10 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
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11 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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12 ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
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13 ##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
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14 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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15 ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
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16 ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
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17 ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
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18 ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
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19 ##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">
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20 ##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">
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21 ##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">
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22 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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23 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
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24 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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25 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
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26 ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
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27 ##contig=<ID=NC_002945.4,length=4349904>
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28 ##reference=file:///scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/02-0585/NC_002945v4.fasta
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29 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 02-0585
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30 NC_002945.4 1057 . A G 1996.77 . AC=2;AF=1.00;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.60;SOR=0.976 GT:AD:DP:GQ:PL 1/1:0,78:78:99:2025,229,0
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31 NC_002945.4 8741 . T C 3395.77 . AC=2;AF=1.00;AN=2;DP=123;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.83;SOR=0.726 GT:AD:DP:GQ:PL 1/1:0,122:122:99:3424,360,0
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32 NC_002945.4 33788 . A G 2576.77 . AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.24;SOR=6.091 GT:AD:DP:GQ:PL 1/1:0,64:64:99:2605,192,0
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33 NC_002945.4 41437 . T C 3407.77 . AC=2;AF=1.00;AN=2;DP=117;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.38;SOR=0.728 GT:AD:DP:GQ:PL 1/1:0,116:116:99:3436,343,0
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34 NC_002945.4 67098 . G A 3616.77 . AC=2;AF=1.00;AN=2;DP=128;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.26;SOR=0.724 GT:AD:DP:GQ:PL 1/1:0,128:128:99:3645,381,0
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35 NC_002945.4 69913 . T C 4863.77 . AC=2;AF=1.00;AN=2;DP=167;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.12;SOR=0.805 GT:AD:DP:GQ:PL 1/1:0,167:167:99:4892,494,0
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36 NC_002945.4 72105 . C G 3686.77 . AC=2;AF=1.00;AN=2;DP=114;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.63;SOR=0.784 GT:AD:DP:GQ:PL 1/1:0,113:113:99:3715,337,0
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37 NC_002945.4 79288 . C G 3432.77 . AC=2;AF=1.00;AN=2;DP=133;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.81;SOR=0.802 GT:AD:DP:GQ:PL 1/1:0,133:133:99:3461,391,0
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38 NC_002945.4 103928 . G C 1644.77 . AC=2;AF=1.00;AN=2;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.19;QD=29.09;SOR=3.202 GT:AD:DP:GQ:PL 1/1:0,39:39:99:1673,117,0
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39 NC_002945.4 103931 . G C 1524.77 . AC=2;AF=1.00;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.88;QD=32.93;SOR=3.321 GT:AD:DP:GQ:PL 1/1:0,35:35:99:1553,105,0
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40 NC_002945.4 119328 . G T 3237.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.678;ClippingRankSum=0.000;DP=112;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.91;ReadPosRankSum=1.955;SOR=0.976 GT:AD:DP:GQ:PL 1/1:2,110:112:99:3266,287,0
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41 NC_002945.4 127447 . G C 3007.77 . AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.33;SOR=1.313 GT:AD:DP:GQ:PL 1/1:0,96:96:99:3036,286,0
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42 NC_002945.4 130237 . T C 4147.77 . AC=2;AF=1.00;AN=2;DP=136;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.72;SOR=1.441 GT:AD:DP:GQ:PL 1/1:0,135:135:99:4176,403,0
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43 NC_002945.4 131617 . T C 4973.77 . AC=2;AF=1.00;AN=2;DP=173;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.09;SOR=1.120 GT:AD:DP:GQ:PL 1/1:0,171:171:99:5002,507,0
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44 NC_002945.4 136900 . T G 3085.77 . AC=2;AF=1.00;AN=2;DP=104;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.67;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,104:104:99:3114,310,0
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45 NC_002945.4 139569 . A G 1920.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.626;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.25;ReadPosRankSum=-0.492;SOR=0.288 GT:AD:DP:GQ:PL 1/1:1,67:68:99:1949,191,0
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46 NC_002945.4 149997 . N . . . . GT ./.
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47 NC_002945.4 149998 . N . . . . GT ./.
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48 NC_002945.4 149999 . N . . . . GT ./.
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49 NC_002945.4 150000 . N . . . . GT ./.
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50 NC_002945.4 150001 . N . . . . GT ./.
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51 NC_002945.4 150002 . N . . . . GT ./.
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52 NC_002945.4 150003 . N . . . . GT ./.
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53 NC_002945.4 150004 . N . . . . GT ./.
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54 NC_002945.4 150005 . N . . . . GT ./.
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55 NC_002945.4 150006 . N . . . . GT ./.
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56 NC_002945.4 150007 . N . . . . GT ./.
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57 NC_002945.4 150008 . N . . . . GT ./.
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58 NC_002945.4 150061 . N . . . . GT ./.
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59 NC_002945.4 150062 . N . . . . GT ./.
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60 NC_002945.4 150063 . N . . . . GT ./.
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61 NC_002945.4 150064 . N . . . . GT ./.
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62 NC_002945.4 150065 . N . . . . GT ./.
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63 NC_002945.4 150066 . N . . . . GT ./.
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64 NC_002945.4 150067 . N . . . . GT ./.
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65 NC_002945.4 150068 . N . . . . GT ./.
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66 NC_002945.4 150069 . N . . . . GT ./.
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67 NC_002945.4 150070 . N . . . . GT ./.
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68 NC_002945.4 150071 . N . . . . GT ./.
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69 NC_002945.4 150072 . N . . . . GT ./.
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70 NC_002945.4 150073 . N . . . . GT ./.
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71 NC_002945.4 150074 . N . . . . GT ./.
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72 NC_002945.4 152355 . G T 2756.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=3.008;ClippingRankSum=0.000;DP=108;ExcessHet=3.0103;FS=9.280;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.76;ReadPosRankSum=-1.223;SOR=0.203 GT:AD:DP:GQ:PL 1/1:3,104:107:99:2785,285,0
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73 NC_002945.4 159370 . A G 2799.77 . AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.77;SOR=0.855 GT:AD:DP:GQ:PL 1/1:0,91:91:99:2828,272,0
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74 NC_002945.4 160535 . T C 3002.77 . AC=2;AF=1.00;AN=2;DP=102;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.44;SOR=1.212 GT:AD:DP:GQ:PL 1/1:0,102:102:99:3031,303,0
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75 NC_002945.4 165799 . G A 2597.77 . AC=2;AF=1.00;AN=2;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.52;SOR=0.786 GT:AD:DP:GQ:PL 1/1:0,88:88:99:2626,262,0
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76 NC_002945.4 166696 . A G 3285.77 . AC=2;AF=1.00;AN=2;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.42;SOR=0.892 GT:AD:DP:GQ:PL 1/1:0,108:108:99:3314,321,0
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77 NC_002945.4 175486 . N . . . . GT ./.
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78 NC_002945.4 175487 . N . . . . GT ./.
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79 NC_002945.4 175488 . N . . . . GT ./.
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80 NC_002945.4 175489 . N . . . . GT ./.
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81 NC_002945.4 175490 . N . . . . GT ./.
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82 NC_002945.4 175491 . N . . . . GT ./.
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83 NC_002945.4 175492 . N . . . . GT ./.
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84 NC_002945.4 175493 . N . . . . GT ./.
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85 NC_002945.4 175494 . N . . . . GT ./.
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86 NC_002945.4 175495 . N . . . . GT ./.
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87 NC_002945.4 175496 . N . . . . GT ./.
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da20c7c76d06 Uploaded
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1906 NC_002945.4 841088 . N . . . . GT ./.
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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1913 NC_002945.4 841095 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1914 NC_002945.4 841096 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1915 NC_002945.4 841097 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1916 NC_002945.4 841098 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1917 NC_002945.4 841099 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1918 NC_002945.4 841100 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1919 NC_002945.4 841101 . N . . . . GT ./.
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1920 NC_002945.4 841102 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1921 NC_002945.4 841103 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1922 NC_002945.4 841104 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1923 NC_002945.4 841105 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1924 NC_002945.4 841106 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1925 NC_002945.4 841107 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1926 NC_002945.4 841108 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1927 NC_002945.4 841109 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1928 NC_002945.4 841110 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1929 NC_002945.4 841111 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1930 NC_002945.4 841112 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1931 NC_002945.4 841113 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1932 NC_002945.4 841114 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1933 NC_002945.4 841115 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1934 NC_002945.4 841116 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1935 NC_002945.4 841117 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1936 NC_002945.4 841118 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1937 NC_002945.4 841119 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1938 NC_002945.4 841120 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1939 NC_002945.4 841121 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1940 NC_002945.4 841122 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1941 NC_002945.4 841123 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1942 NC_002945.4 841124 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1943 NC_002945.4 841125 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1944 NC_002945.4 841126 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1945 NC_002945.4 841127 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1946 NC_002945.4 841128 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1947 NC_002945.4 841129 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1948 NC_002945.4 841130 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1949 NC_002945.4 841131 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1950 NC_002945.4 841132 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1951 NC_002945.4 841133 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1952 NC_002945.4 841134 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1953 NC_002945.4 841135 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1954 NC_002945.4 841136 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1955 NC_002945.4 841137 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1956 NC_002945.4 841138 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1957 NC_002945.4 841139 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1958 NC_002945.4 841140 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1959 NC_002945.4 841141 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1960 NC_002945.4 841142 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1961 NC_002945.4 841143 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1962 NC_002945.4 841144 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1963 NC_002945.4 841145 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1964 NC_002945.4 841146 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1965 NC_002945.4 841147 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1966 NC_002945.4 841148 . N . . . . GT ./.
da20c7c76d06 Uploaded
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1967 NC_002945.4 841149 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1968 NC_002945.4 841150 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1969 NC_002945.4 841151 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1970 NC_002945.4 841152 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1971 NC_002945.4 841153 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1972 NC_002945.4 841154 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1973 NC_002945.4 841155 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1974 NC_002945.4 841156 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1975 NC_002945.4 841157 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1976 NC_002945.4 841158 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1977 NC_002945.4 841159 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1978 NC_002945.4 841160 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1979 NC_002945.4 841161 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1980 NC_002945.4 841162 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1981 NC_002945.4 841163 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1982 NC_002945.4 841164 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1983 NC_002945.4 841165 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1984 NC_002945.4 841166 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1985 NC_002945.4 841167 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1986 NC_002945.4 841168 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1987 NC_002945.4 841169 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1988 NC_002945.4 841170 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1989 NC_002945.4 841171 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1990 NC_002945.4 841172 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1991 NC_002945.4 841173 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1992 NC_002945.4 841174 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1993 NC_002945.4 841175 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1994 NC_002945.4 841176 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1995 NC_002945.4 841177 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1996 NC_002945.4 841178 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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1997 NC_002945.4 841179 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1998 NC_002945.4 841180 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1999 NC_002945.4 841181 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2000 NC_002945.4 841182 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2001 NC_002945.4 841183 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2002 NC_002945.4 841184 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2003 NC_002945.4 841185 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
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2004 NC_002945.4 841186 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2005 NC_002945.4 841187 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2006 NC_002945.4 841188 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2007 NC_002945.4 841189 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2008 NC_002945.4 841190 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2009 NC_002945.4 841191 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2010 NC_002945.4 841192 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2011 NC_002945.4 841193 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2012 NC_002945.4 841194 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2013 NC_002945.4 841195 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2014 NC_002945.4 841196 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2015 NC_002945.4 841197 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2016 NC_002945.4 841198 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2017 NC_002945.4 841199 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2018 NC_002945.4 841200 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2019 NC_002945.4 841201 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2020 NC_002945.4 841202 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2021 NC_002945.4 841203 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2022 NC_002945.4 841204 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2023 NC_002945.4 841205 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2024 NC_002945.4 841206 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2025 NC_002945.4 841207 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2026 NC_002945.4 841208 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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2027 NC_002945.4 841209 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
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2028 NC_002945.4 841210 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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da20c7c76d06 Uploaded
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parents:
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2030 NC_002945.4 841212 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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da20c7c76d06 Uploaded
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parents:
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da20c7c76d06 Uploaded
greg
parents:
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da20c7c76d06 Uploaded
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parents:
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da20c7c76d06 Uploaded
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parents:
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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diff changeset
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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diff changeset
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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diff changeset
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da20c7c76d06 Uploaded
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diff changeset
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da20c7c76d06 Uploaded
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diff changeset
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da20c7c76d06 Uploaded
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diff changeset
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da20c7c76d06 Uploaded
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diff changeset
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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diff changeset
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da20c7c76d06 Uploaded
greg
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diff changeset
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da20c7c76d06 Uploaded
greg
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diff changeset
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da20c7c76d06 Uploaded
greg
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diff changeset
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da20c7c76d06 Uploaded
greg
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diff changeset
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da20c7c76d06 Uploaded
greg
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diff changeset
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da20c7c76d06 Uploaded
greg
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diff changeset
2079 NC_002945.4 842340 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2080 NC_002945.4 842341 . N . . . . GT ./.
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da20c7c76d06 Uploaded
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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5373 NC_002945.4 3247623 . C T 2041.77 . AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.59;SOR=1.134 GT:AD:DP:GQ:PL 1/1:0,74:74:99:2070,217,0
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
greg
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da20c7c76d06 Uploaded
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diff changeset
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