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All_snps_clean.vcf.gz
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All_snps_clean.vcf.gz
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=R,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=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##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=GenomicsDBImport,CommandLine="GenomicsDBImport --genomicsdb-workspace-path All_db --batch-size 50 --sample-name-map cohort.sample_map --reader-threads 5 --intervals NC_013716.1:1-5346659 --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --consolidate false --validate-sample-name-map false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.2.1,Date="January 15, 2020 5:39:34 PM GMT-05:00">
##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs --output All_calls.vcf.gz --variant gendb://All_db --reference ../reference/Citrobacter_rodentium_ICC168.fasta --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --annotation-group StandardAnnotation --disable-tool-default-annotations false --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.2.1,Date="January 15, 2020 6:21:37 PM GMT-05:00">
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --emit-ref-confidence GVCF --output ICC180.g.vcf --input ICC180.analysis.ready.bam --reference Citrobacter_rodentium_ICC168.fasta --annotation-group StandardAnnotation --annotation-group StandardHCAnnotation --disable-tool-default-annotations false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --genotyping-mode DISCOVERY --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20",Version=4.0.2.1,Date="November 25, 2019 11:05:02 AM GMT-05:00">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##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=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##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=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##contig=<ID=NC_013716.1,length=5346659>
##source=GenomicsDBImport
##source=GenotypeGVCFs
##source=HaplotypeCaller
##bcftools_viewVersion=1.9+htslib-1.9
##bcftools_viewCommand=view -m 2 -M 2 -v snps All_calls_thinned.recode.vcf; Date=Thu Apr 16 19:03:06 2020
##bcftools_viewCommand=view -i %QUAL>=100 All_calls_biallelic.vcf.gz; Date=Thu Apr 16 19:04:16 2020
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ICC180 N1P1 N1P10 N1P11 N1P12 N1P13 N1P14 N1P15 N1P16 N1P17 N1P18 N1P19 N1P2 N1P20 N1P21 N1P22 N1P3 N1P4 N1P5 N1P6 N1P7 N1P8 N1P9 N2P1 N2P10 N2P11 N2P12 N2P13 N2P14 N2P15 N2P16 N2P17 N2P18 N2P19 N2P2 N2P20 N2P21 N2P22 N2P3 N2P4 N2P6 N2P7 N2P8 N2P9 N3P1 N3P10 N3P11 N3P12 N3P13 N3P14 N3P15 N3P16 N3P17 N3P18 N3P19 N3P2 N3P21 N3P22 N3P3 N3P4 N3P5 N3P6 N3P7 N3P8 N3P9 N4P1 N4P10 N4P11 N4P12 N4P13 N4P14 N4P15 N4P16 N4P17 N4P18 N4P19 N4P2 N4P20 N4P20SD1 N4P20SD2 N4P20SW1 N4P20SW2 N4P20SWND N4P21 N4P22 N4P3 N4P4 N4P5 N4P6 N4P7 N4P8 N4P9 N5P1 N5P10 N5P11 N5P12 N5P13 N5P14 N5P16 N5P17 N5P18 N5P19 N5P2 N5P20 N5P21 N5P22 N5P3 N5P4 N5P5 N5P6 N5P8 N5P9 W1P1 W1P10 W1P11 W1P12 W1P13 W1P14 W1P15 W1P16 W1P17 W1P18 W1P19 W1P2 W1P20 W1P21 W1P22 W1P3 W1P4 W1P5 W1P6 W1P7 W1P8 W1P9 W2P1 W2P10 W2P11 W2P12 W2P13 W2P14 W2P15 W2P16 W2P17 W2P18 W2P19 W2P2 W2P20 W2P21 W2P22 W2P3 W2P4 W2P5 W2P7 W2P8 W2P9 W3P1 W3P10 W3P11 W3P12 W3P13 W3P14 W3P15 W3P16 W3P17 W3P18 W3P19 W3P2 W3P20 W3P21 W3P22 W3P4 W3P5 W3P6 W3P8 W3P9 W4P1 W4P10 W4P11 W4P12 W4P13 W4P14 W4P15 W4P16 W4P17 W4P2 W4P20 W4P3 W4P4 W4P5 W4P6 W4P8 W4P9 W5P1 W5P10 W5P11 W5P12 W5P13 W5P14 W5P15 W5P16 W5P17 W5P18 W5P19 W5P2 W5P20 W5P21 W5P22 W5P22SD1 W5P22SD2 W5P22SW1 W5P22SW2 W5P22SWND W5P4 W5P5 W5P6 W5P7 W5P8
NC_013716.1 13105 . C T 18835.9 . . 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0/0:52,0:52:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:30,0:30:90:0,90,1127 0/0:53,0:53:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:53,0:53:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:52,0:52:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:53,0:53:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:74,0:74:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:52,0:52:99:0,119,1800 0/0:50,0:50:99:0,120,1800 0/0:52,0:52:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:51,0:51:99:0,120,1800 0/0:50,0:50:99:0,120,1800 0/0:51,0:51:99:0,120,1800 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NC_013716.1 586227 . C T 2731.55 . . 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NC_013716.1 910217 . C T 438.93 . . 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NC_013716.1 919017 . G T 16939.9 . . 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NC_013716.1 937620 . A C 362117 . . 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NC_013716.1 953497 . T G 322.9 . . 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NC_013716.1 1030249 . A G 360.47 . . 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NC_013716.1 1031065 . A G 1467.67 . . 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NC_013716.1 1031178 . G C 318.07 . . 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NC_013716.1 1031335 . C T 337.28 . . 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NC_013716.1 1031758 . A C 516.05 . . 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NC_013716.1 1172320 . G T 2013.89 . . 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NC_013716.1 1593102 . C A 2015.96 . . 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NC_013716.1 1681092 . C T 10900 . . 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NC_013716.1 1749372 . T C 229811 . . 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NC_013716.1 1832190 . T G 1048.96 . . 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NC_013716.1 1896011 . C T 498100 . . 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NC_013716.1 1935661 . C T 2357.87 . . 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NC_013716.1 2475260 . G A 2852.89 . . 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NC_013716.1 2885287 . A C 1341.1 . . 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NC_013716.1 3146917 . A G 1279.99 . . 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NC_013716.1 3163564 . C A 578.93 . . 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NC_013716.1 3180427 . T C 1155.2 . . 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NC_013716.1 3836711 . C T 11739 . . 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NC_013716.1 4609181 . G T 108.79 . . 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NC_013716.1 4623423 . T G 260025 . . 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NC_013716.1 4813783 . C T 5248.89 . . 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NC_013716.1 5042450 . G C 3425.89 . . 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NC_013716.1 5107485 . G T 3503.89 . . 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NC_013716.1 5212274 . A T 10533 . . 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NC_013716.1 5238254 . C T 1841.89 . . 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