Mercurial > repos > john-mccallum > pcr_markers

annotate test-data/freebayes_out.vcf @ 6:f201e8c6e004 draft default tip

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author ben-warren
date Mon, 07 Jul 2014 19:28:17 -0400
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1 ##fileformat=VCFv4.1
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2 ##fileDate=20140410
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3 ##source=freeBayes version 0.9.6
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4 ##reference=localref.fa
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5 ##phasing=none
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6 ##commandline="freebayes --bam localbam_0.bam --fasta-reference localref.fa --vcf /data/galaxy/galaxy-dist/database/files/000/dataset_31.dat"
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7 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
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8 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
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9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
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10 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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11 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
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12 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observations">
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13 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations">
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14 ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
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15 ##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
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16 ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
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17 ##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
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18 ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
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19 ##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
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20 ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
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21 ##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
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22 ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
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23 ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">
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24 ##INFO=<ID=XRM,Number=1,Type=Float,Description="Reference allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads supporting the reference allele.">
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25 ##INFO=<ID=XRS,Number=1,Type=Float,Description="Reference allele read SNP rate: The rate of per-base mismatches (SNPs + MNPs) in reads supporting the reference allele.">
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26 ##INFO=<ID=XRI,Number=1,Type=Float,Description="Reference allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the reference allele.">
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27 ##INFO=<ID=XAM,Number=A,Type=Float,Description="Alternate allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads supporting the alternate allele, excluding the called variant.">
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28 ##INFO=<ID=XAS,Number=A,Type=Float,Description="Alternate allele read SNP rate: The rate of per-base mismatches (SNPs + MNPs) in reads supporting the alternate allele, excluding the called variant.">
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29 ##INFO=<ID=XAI,Number=A,Type=Float,Description="Alternate allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the alternate allele, excluding the called variant.">
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30 ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
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31 ##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous).">
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32 ##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)">
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33 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
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34 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
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35 ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
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36 ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
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37 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Phred-scaled discrete HWE prior probability of the genotyping across all samples.">
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38 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
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39 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
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40 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
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41 ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
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42 ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
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43 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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44 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
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45 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
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46 ##FORMAT=<ID=GLE,Number=1,Type=String,Description="Genotype Likelihood Explicit, same as GL, but with tags to indicate the specific genotype. For instance, 0^-75.22|1^-223.42|0/0^-323.03|1/0^-99.29|1/1^-802.53 represents both haploid and diploid genotype likilehoods in a biallelic context">
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47 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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48 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
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49 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
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50 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
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51 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
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52 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
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53 Chr1 106 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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54 Chr1 200 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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55 Chr1 217 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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56 Chr1 249 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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57 Chr1 586 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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58 Chr1 669 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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59 Chr1 682 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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60 Chr1 1007 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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61 Chr1 1012 . TGT AGA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0309278;XAS=0.0309278;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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62 Chr1 1056 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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63 Chr1 1067 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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64 Chr1 1257 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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65 Chr1 1305 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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66 Chr1 1319 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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67 Chr1 1330 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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68 Chr1 1441 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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69 Chr1 1451 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
70 Chr1 1460 . CTCTG ATCTC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0421053;XAS=0.0421053;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
71 Chr1 1480 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
72 Chr1 1525 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
73 Chr1 1670 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
74 Chr1 1673 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
75 Chr1 1700 . GC TG 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
76 Chr1 1711 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
77 Chr1 2117 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
78 Chr1 2154 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
79 Chr1 2485 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
80 Chr1 2490 . AAA CAC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
81 Chr1 2906 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
82 Chr1 2925 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
83 Chr1 3371 . CCCTT GCCTA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0105263;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
84 Chr1 3389 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0105263;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
85 Chr1 3431 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
86 Chr1 3464 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
87 Chr1 3746 . C CT 46.0861 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0204082;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0
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diff changeset
88 Chr1 3766 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
89 Chr1 3790 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
90 Chr1 3855 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
91 Chr1 5718 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
92 Chr1 5754 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
93 Chr1 5782 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
94 Chr1 5792 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
95 Chr1 6194 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
96 Chr1 6212 . G A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
97 Chr1 6265 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
98 Chr1 6482 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
99 Chr1 6515 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
100 Chr1 6520 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
101 Chr1 6534 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
102 Chr1 6602 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
103 Chr1 6853 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
104 Chr1 7015 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
105 Chr1 7406 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
106 Chr1 7422 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
107 Chr1 7452 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
108 Chr1 7460 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
109 Chr1 7476 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
110 Chr1 7843 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
111 Chr1 7906 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
112 Chr1 8214 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
113 Chr1 8262 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
114 Chr1 8279 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
115 Chr1 8285 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
116 Chr1 8288 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
117 Chr1 8298 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
118 Chr1 8305 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
119 Chr1 8329 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
120 Chr1 8509 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
121 Chr1 8547 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
122 Chr1 8633 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
123 Chr1 8657 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
124 Chr1 8894 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
125 Chr1 8958 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
126 Chr1 8968 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
127 Chr1 9070 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
128 Chr1 9100 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
129 Chr1 9488 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
130 Chr1 9514 . GTTT CTTG 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=34;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
131 Chr1 9532 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=34;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
132 Chr1 10064 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
133 Chr1 10072 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
134 Chr1 10082 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
135 Chr1 10099 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
136 Chr1 10499 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
137 Chr1 11126 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
138 Chr1 11134 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
139 Chr1 11141 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
140 Chr1 11159 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
141 Chr1 11169 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=40;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
142 Chr1 11208 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
143 Chr1 11418 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
144 Chr1 11547 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
145 Chr1 11567 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
146 Chr1 11582 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
147 Chr1 13312 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
148 Chr1 13336 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
149 Chr1 13352 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
150 Chr1 13652 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
151 Chr1 13666 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
152 Chr1 13728 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
153 Chr1 14087 . ATGAAA GTGAGC 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X3M2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=6;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
154 Chr1 14103 . AGT GGC 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X1M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=3;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
155 Chr1 14119 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
156 Chr1 14126 . A G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
157 Chr1 14131 . GGAGTG TGGGTT 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X1M1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=6;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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parents:
diff changeset
158 Chr1 14141 . TCA CCC 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X1M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=3;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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parents:
diff changeset
159 Chr1 14159 . G A 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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ben-warren
parents:
diff changeset
160 Chr1 14165 . T G 7.01833 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=2;MQM=18;MQMR=0;NS=1;NUMALT=1;ODDS=0;PAIRED=0;PAIREDR=1;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0.0487805;XRM=0.109756;XRS=0.0609756;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:0.628068:3:1:17:1:17:-3.23,-2.00103,-3.23
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parents:
diff changeset
161 Chr1 14167 . A T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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parents:
diff changeset
162 Chr1 14182 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
163 Chr1 14201 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
164 Chr1 14210 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
165 Chr1 14230 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
166 Chr1 14240 . C T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
167 Chr1 14247 . G A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
168 Chr1 14256 . A G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
169 Chr1 14262 . TT CC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0222222;XAM=0.122222;XAS=0.1;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
170 Chr1 14292 . TCTG CCTA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X2M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=4;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.133333;XAS=0.122222;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
171 Chr1 14306 . AC TT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0222222;XAM=0.122222;XAS=0.1;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
172 Chr1 14312 . CG TA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0222222;XAM=0.122222;XAS=0.1;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
173 Chr1 14320 . TCTTT TCCCTA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I1M1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.133333;XAS=0.122222;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
174 Chr1 14327 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
175 Chr1 14595 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
176 Chr1 14624 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
177 Chr1 14629 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
178 Chr1 14724 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
179 Chr1 15170 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
180 Chr1 15183 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.0103093;XRM=0.0206186;XRS=0.0103093;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
181 Chr1 15199 . CAA AAT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
182 Chr1 15209 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
183 Chr1 15599 . TGG GGC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
184 Chr1 15624 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=40;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
185 Chr1 15625 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0103093;XRM=0.0206186;XRS=0.0103093;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
186 Chr1 15670 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0103093;XRM=0.0206186;XRS=0.0103093;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
187 Chr1 15685 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
188 Chr1 15696 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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189 Chr1 15981 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
190 Chr1 16021 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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191 Chr1 16050 . CTGGG ATGGC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0315789;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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192 Chr1 16059 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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193 Chr1 16085 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
194 Chr1 16287 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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195 Chr1 16502 . GCA CCT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0108696;XAM=0.0217391;XAS=0.0108696;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
196 Chr1 16512 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0217391;XAM=0.0217391;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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197 Chr1 16519 . TGTGT GGTGG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0108696;XAM=0.0217391;XAS=0.0108696;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
198 Chr1 17672 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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199 Chr1 17738 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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200 Chr1 17849 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
201 Chr1 17873 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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202 Chr1 17878 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
203 Chr1 18083 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
204 Chr1 18090 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
205 Chr1 18099 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
206 Chr1 18205 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
207 Chr1 18275 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
208 Chr1 18285 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
209 Chr1 18320 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
210 Chr1 18370 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
211 Chr1 18416 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
212 Chr1 20586 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=27;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
213 Chr1 20604 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=27;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
214 Chr1 20625 . G T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=13.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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parents:
diff changeset
215 Chr1 20692 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
216 Chr1 20702 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
217 Chr1 20720 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
218 Chr1 20891 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
219 Chr1 20922 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
220 Chr1 20967 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
221 Chr1 20998 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
222 Chr1 21007 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
223 Chr1 21042 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
224 Chr1 21055 . G A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=21;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
225 Chr1 21080 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=21;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
226 Chr1 21165 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0104167;XAM=0.0104167;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
227 Chr1 21189 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=25;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.0104167;XRM=0.0208333;XRS=0.0104167;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
228 Chr1 21202 . ACCT CCCA,TCCT 20.1741 . AB=0.5,0.5;ABP=3.0103,3.0103;AC=1,1;AF=0.5,0.5;AN=2;AO=1,1;CIGAR=1X2M1X,1X3M;DP=2;DPRA=0,0;EPP=5.18177,5.18177;EPPR=0;HWE=-0;LEN=4,1;MEANALT=2,2;MQM=25,42;MQMR=0;NS=1;NUMALT=2;ODDS=0.00237165;PAIRED=0,0;PAIREDR=0;RO=0;RPP=5.18177,5.18177;RPPR=0;RUN=1,1;SAP=5.18177,5.18177;SRP=0;TYPE=complex,snp;XAI=0,0;XAM=0.0104167,0.02;XAS=0.0104167,0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/2:1.71537:2:0:0:1,1:17,17:-3.23,-2.00103,-1.7,-2.00103,-0.30103,-1.7
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parents:
diff changeset
229 Chr1 21322 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
230 Chr1 21342 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
231 Chr1 21359 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
232 Chr1 21584 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
233 Chr1 21615 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
234 Chr1 21821 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
235 Chr1 21936 . TGT AGA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
236 Chr1 21955 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
237 Chr1 22337 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
238 Chr1 22345 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
239 Chr1 22415 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0104167;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
240 Chr1 22429 . ATTG CTTT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X2M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0104167;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
241 Chr1 22520 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
242 Chr1 22539 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
243 Chr1 22742 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
244 Chr1 22801 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
245 Chr1 22888 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
246 Chr1 22919 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
247 Chr1 23346 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
248 Chr1 23360 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
249 Chr1 23390 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
250 Chr1 23432 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
251 Chr1 23687 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
252 Chr1 23716 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
253 Chr1 23745 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
254 Chr1 23812 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
255 Chr1 23829 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
256 Chr1 23959 . TC AG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0104167;XAM=0.0104167;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
257 Chr1 23989 . ATCT CTCA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X2M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=4;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
258 Chr1 24095 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=26;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
259 Chr1 24350 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
260 Chr1 24377 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
261 Chr1 24395 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0104167;XRM=0.03125;XRS=0.0208333;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
262 Chr1 24413 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0104167;XRM=0.03125;XRS=0.0208333;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
263 Chr1 24416 . GAGT TAGA 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=4;MEANALT=1;MQM=0;MQMR=40;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
264 Chr1 24467 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
265 Chr1 24477 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
266 Chr1 24846 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
267 Chr1 24889 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
268 Chr1 24923 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
269 Chr1 24964 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
270 Chr1 25174 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
271 Chr1 25301 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
272 Chr1 25320 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
273 Chr1 25345 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
274 Chr1 25355 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
275 Chr1 25550 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
276 Chr1 25580 . A T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=20;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.015625;XRS=0.0104167 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
277 Chr1 25584 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=12.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
278 Chr1 25626 . GCAC TCAG 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=4;MEANALT=1;MQM=40;MQMR=33.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0.00526316;XRM=0.0205263;XRS=0.0152632 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
279 Chr1 25644 . A C 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=34.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0.00526316;XRM=0.0155263;XRS=0.0102632 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
280 Chr1 25687 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=27;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0105263;XAM=0.0105263;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
281 Chr1 25696 . ACTCA GCTCT,GCTCA 20.1741 . AB=0.5,0.5;ABP=3.0103,3.0103;AC=1,1;AF=0.5,0.5;AN=2;AO=1,1;CIGAR=1X3M1X,1X4M;DP=2;DPRA=0,0;EPP=5.18177,5.18177;EPPR=0;HWE=-0;LEN=5,1;MEANALT=2,2;MQM=42,27;MQMR=0;NS=1;NUMALT=2;ODDS=0.00237165;PAIRED=0,0;PAIREDR=0;RO=0;RPP=5.18177,5.18177;RPPR=0;RUN=1,1;SAP=5.18177,5.18177;SRP=0;TYPE=complex,snp;XAI=0,0;XAM=0.0105263,0.01;XAS=0.0105263,0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/2:1.71537:2:0:0:1,1:17,17:-3.23,-2.00103,-1.7,-2.00103,-0.30103,-1.7
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diff changeset
282 Chr1 25944 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
283 Chr1 25972 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
284 Chr1 25981 . G T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
285 Chr1 25983 . AA TT 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
286 Chr1 26001 . G C 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
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diff changeset
287 Chr1 26364 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
288 Chr1 26420 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
289 Chr1 27175 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
290 Chr1 27431 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
291 Chr1 27472 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
292 Chr1 27556 . A AT 46.0861 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0102041;XAS=0.0102041;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0
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diff changeset
293 Chr1 27610 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0102041;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
294 Chr1 27909 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
295 Chr1 28614 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
296 Chr1 28993 . TGGG GGGC 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
297 Chr1 29022 . T A 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.015625;XRS=0.0104167 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
298 Chr1 29026 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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parents:
diff changeset
299 Chr1 29032 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
300 Chr1 29080 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
301 Chr1 29218 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
302 Chr1 29342 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
303 Chr1 29463 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
304 Chr1 29516 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
305 Chr1 29528 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
306 Chr1 29575 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
307 Chr1 29580 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
308 Chr1 30681 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
309 Chr1 30735 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
310 Chr1 30766 . CTATT GTATA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0210526;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
311 Chr1 31019 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
312 Chr1 31054 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
313 Chr1 31101 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
314 Chr1 31400 . GT CG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
315 Chr1 31422 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
316 Chr1 32027 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
317 Chr1 32060 . C T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
318 Chr1 32166 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
319 Chr1 32226 . AA CC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
320 Chr1 32480 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
321 Chr1 32491 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
322 Chr1 32651 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
323 Chr1 32934 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
324 Chr1 33054 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
325 Chr1 33109 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
326 Chr1 33143 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
327 Chr1 33245 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
328 Chr1 33274 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
329 Chr1 33377 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
330 Chr1 33392 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
331 Chr1 33417 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
332 Chr1 33713 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
333 Chr1 33746 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
334 Chr1 35247 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
335 Chr1 35679 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
336 Chr1 36145 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
337 Chr1 36591 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
338 Chr1 37260 . AT CA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
339 Chr1 37270 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
340 Chr1 37283 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
341 Chr1 37284 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
342 Chr1 37295 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
343 Chr1 37321 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
344 Chr1 37610 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
345 Chr1 37673 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
346 Chr1 38268 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
347 Chr1 38656 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
348 Chr1 39013 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
349 Chr1 39023 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
350 Chr1 39460 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
351 Chr1 39480 . GA TC 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=mnp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
352 Chr1 39501 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
353 Chr1 39508 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
354 Chr1 41835 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
355 Chr1 41885 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
356 Chr1 42284 . AGTTT TGTTG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
357 Chr1 42628 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.0222222;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
358 Chr1 42637 . ATTCC CTTCG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.0222222;XAS=0.0111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
359 Chr1 42652 . TTTGT ATTGA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.0222222;XAS=0.0111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
360 Chr1 43145 . GG CC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
361 Chr1 43164 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
362 Chr1 43173 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
363 Chr1 43219 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
364 Chr1 43437 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
365 Chr1 44980 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
366 Chr1 45144 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
367 Chr1 45166 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
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diff changeset
368 Chr1 45311 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
369 Chr1 45333 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
370 Chr1 45385 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
371 Chr1 45419 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
372 Chr1 45427 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
373 Chr1 45663 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
374 Chr1 45685 . AG CT 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
375 Chr1 46052 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
376 Chr1 46117 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
377 Chr1 46251 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
378 Chr1 46261 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
379 Chr1 47385 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
380 Chr1 47414 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
381 Chr1 48446 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
382 Chr1 48526 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
383 Chr1 48789 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
384 Chr1 48796 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
385 Chr1 48811 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
386 Chr1 48831 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
387 Chr1 48838 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
388 Chr1 48852 . A T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=3;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
389 Chr1 48907 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
390 Chr1 48936 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
391 Chr1 49044 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
392 Chr1 49059 . A C 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=20;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0310417;XRS=0.0258333 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
393 Chr1 49086 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
394 Chr1 49088 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=20;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0310417;XRS=0.0258333 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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parents:
diff changeset
395 Chr1 49091 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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parents:
diff changeset
396 Chr1 49099 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
397 Chr1 49124 . AAAC TAAA 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=4;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=complex;XAI=0;XAM=0.0416667;XAS=0.0416667;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
398 Chr1 49134 . C A 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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parents:
diff changeset
399 Chr1 49493 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
400 Chr1 49543 . TGCAA GGCAT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0315789;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
401 Chr1 49553 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
402 Chr1 49583 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
403 Chr1 50222 . ACAAAGA CCCACTC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X1M3X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=7;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
404 Chr1 50557 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
405 Chr1 50574 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
406 Chr1 50603 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
407 Chr1 50790 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
408 Chr1 50828 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
409 Chr1 50843 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
410 Chr1 50958 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
411 Chr1 51330 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=35;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
412 Chr1 51606 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
413 Chr1 51681 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
414 Chr1 51984 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
415 Chr1 51996 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
416 Chr1 52061 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
417 Chr1 53145 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
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diff changeset
418 Chr1 53423 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
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diff changeset
419 Chr1 53442 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
420 Chr1 54071 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
421 Chr1 54472 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
422 Chr1 54525 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
423 Chr1 54562 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
424 Chr1 55358 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
425 Chr1 55372 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
426 Chr1 55415 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
427 Chr1 55460 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
428 Chr1 55491 . AA CC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
429 Chr1 55917 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
430 Chr1 56372 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
431 Chr1 56383 . G T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=41;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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diff changeset
432 Chr1 56399 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
433 Chr1 56430 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
434 Chr1 56448 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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diff changeset
435 Chr1 56477 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
436 Chr1 56586 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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diff changeset
437 Chr1 56642 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
438 Chr1 56672 . T TA 46.0861 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0204082;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0
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parents:
diff changeset
439 Chr1 56708 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
440 Chr1 56728 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
441 Chr1 56743 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
442 Chr1 56750 . G C 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=3.73412;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
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parents:
diff changeset
443 Chr1 56756 . A T 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=3.73412;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
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ben-warren
parents:
diff changeset
444 Chr1 56769 . A T 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.0266667;XRS=0.0266667 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
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ben-warren
parents:
diff changeset
445 Chr1 56792 . A T 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
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ben-warren
parents:
diff changeset
446 Chr1 56800 . A T 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
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ben-warren
parents:
diff changeset
447 Chr1 56803 . C G 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=9.52472;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=9.52472;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76
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ben-warren
parents:
diff changeset
448 Chr1 56822 . A T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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ben-warren
parents:
diff changeset
449 Chr1 57075 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
450 Chr1 57129 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
451 Chr1 57130 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
452 Chr1 57164 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
453 Chr1 57166 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
454 Chr1 57533 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
455 Chr1 57543 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
456 Chr1 57561 . TTCGA ATCGC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0210526;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
457 Chr1 57885 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
458 Chr1 57929 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
459 Chr1 58372 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
460 Chr1 58383 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
461 Chr1 58391 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
462 Chr1 58399 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
463 Chr1 58807 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
464 Chr1 58825 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
465 Chr1 58844 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
466 Chr1 58862 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
467 Chr1 59508 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0306122;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
468 Chr1 59524 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0306122;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
469 Chr1 59546 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0306122;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
470 Chr1 59554 . C CG 46.0861 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0306122;XAS=0.0306122;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0
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ben-warren
parents:
diff changeset
471 Chr1 61378 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
472 Chr1 61387 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
473 Chr1 61599 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
474 Chr1 61652 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
475 Chr1 61882 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
476 Chr1 61904 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
477 Chr1 61913 . AGG TGC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0309278;XAS=0.0309278;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
478 Chr1 61957 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
479 Chr1 62010 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
480 Chr1 62056 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
481 Chr1 62168 . CCGCC GCGCG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
482 Chr1 62290 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
483 Chr1 62446 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0152083;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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ben-warren
parents:
diff changeset
484 Chr1 62447 . CTAG ATAC 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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ben-warren
parents:
diff changeset
485 Chr1 62462 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0152083;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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ben-warren
parents:
diff changeset
486 Chr1 62478 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0152083;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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ben-warren
parents:
diff changeset
487 Chr1 62514 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
488 Chr1 62598 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
489 Chr1 62634 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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parents:
diff changeset
490 Chr1 62658 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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ben-warren
parents:
diff changeset
491 Chr1 62665 . G C 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23
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ben-warren
parents:
diff changeset
492 Chr1 62686 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
493 Chr1 62697 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
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ben-warren
parents:
diff changeset
494 Chr1 62758 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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parents:
diff changeset
495 Chr1 62769 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
496 Chr1 62841 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
497 Chr1 62852 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
498 Chr1 62929 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
499 Chr1 63049 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0
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ben-warren
parents:
diff changeset
500 Chr1 63120 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7