Mercurial > repos > greg > vsnp_get_snps
view test-data/input_zc_vcf.vcf @ 0:ee4ef1fc23c6 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 21 Apr 2020 10:14:11 -0400 |
| parents | |
| children | da20c7c76d06 |
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##fileformat=VCFv4.2 ##fileDate=20190125 ##source=freeBayes v1.2.0-dirty ##reference=/scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1791698/NC_002945v4.fasta ##contig=<ID=NC_002945.4,length=4349904> ##phasing=none ##commandline="freebayes -E -1 -e 1 -u --strict-vcf -f /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1791698/NC_002945v4.fasta /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1791698/SRR1791698-nodup.bam --region NC_002945.4:0-100000 ##filter="QUAL > 20 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> ##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> ##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> ##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> ##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"> ##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"> ##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"> ##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"> ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> ##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"> ##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"> ##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> ##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> ##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"> ##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"> ##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."> ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> ##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."> ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> ##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> ##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> ##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> ##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"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR1791698 NC_002945.4 1057 . A G 7624.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=262;CIGAR=1X;DP=265;DPB=265;DPRA=0;EPP=4.20378;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=363.221;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8526;QR=12;RO=1;RPL=140;RPP=5.69563;RPPR=5.18177;RPR=122;RUN=1;SAF=139;SAP=5.13204;SAR=123;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:265:1,262:1:12:262:8526:-766.088,-78.0909,0 NC_002945.4 4480 . T C 4142.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=144;CIGAR=1X;DP=145;DPB=145;DPRA=0;EPP=3.07062;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=204.232;PAIRED=0.993056;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4647;QR=0;RO=0;RPL=79;RPP=5.96592;RPPR=0;RPR=65;RUN=1;SAF=72;SAP=3.0103;SAR=72;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:145:0,144:0:0:144:4647:-418.074,-43.3483,0 NC_002945.4 8741 . T C 5252.19 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=184;CIGAR=1X;DP=186;DPB=186;DPRA=0;EPP=16.6528;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=259.683;PAIRED=0.98913;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5901;QR=0;RO=0;RPL=81;RPP=8.72222;RPPR=0;RPR=103;RUN=1;SAF=98;SAP=4.70971;SAR=86;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:186:0,184:0:0:184:5901:-531.016,-55.3895,0 NC_002945.4 29061 . C T 4714.63 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=163;CIGAR=1X;DP=164;DPB=164;DPRA=0;EPP=3.1302;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=230.571;PAIRED=0.969325;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5311;QR=0;RO=0;RPL=59;RPP=29.9872;RPPR=0;RPR=104;RUN=1;SAF=83;SAP=3.1302;SAR=80;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:164:0,163:0:0:163:5311:-477.817,-49.0679,0 NC_002945.4 29471 . N . . . . GT ./. NC_002945.4 29472 . N . . . . GT ./. NC_002945.4 29473 . N . . . . GT ./. NC_002945.4 29474 . N . . . . GT ./. NC_002945.4 29475 . N . . . . GT ./. NC_002945.4 29476 . N . . . . GT ./. NC_002945.4 29477 . N . . . . GT ./. NC_002945.4 29478 . N . . . . GT ./. NC_002945.4 29479 . N . . . . GT ./. NC_002945.4 29480 . N . . . . GT ./. NC_002945.4 29481 . N . . . . GT ./. NC_002945.4 29482 . N . . . . GT ./. NC_002945.4 29483 . N . . . . GT ./. NC_002945.4 29484 . N . . . . GT ./. NC_002945.4 29485 . N . . . . GT ./. NC_002945.4 29486 . N . . . . GT ./. NC_002945.4 29487 . N . . . . GT ./. NC_002945.4 29488 . N . . . . GT ./. NC_002945.4 29489 . N . . . . GT ./. NC_002945.4 29490 . N . . . . GT ./. NC_002945.4 29491 . N . . . . GT ./. NC_002945.4 29492 . N . . . . GT ./. NC_002945.4 29493 . N . . . . GT ./. NC_002945.4 29494 . N . . . . GT ./. NC_002945.4 29495 . N . . . . GT ./. NC_002945.4 29496 . N . . . . GT ./. NC_002945.4 29497 . N . . . . GT ./. NC_002945.4 29498 . N . . . . GT ./. NC_002945.4 29499 . N . . . . GT ./. NC_002945.4 29500 . N . . . . GT ./. NC_002945.4 29501 . N . . . . GT ./. NC_002945.4 29502 . N . . . . GT ./. NC_002945.4 29503 . N . . . . GT ./. NC_002945.4 29504 . N . . . . GT ./. NC_002945.4 29505 . N . . . . GT ./. NC_002945.4 29506 . N . . . . GT ./. NC_002945.4 29507 . N . . . . GT ./. NC_002945.4 29508 . N . . . . GT ./. NC_002945.4 29509 . N . . . . GT ./. NC_002945.4 29510 . N . . . . GT ./. NC_002945.4 29511 . N . . . . GT ./. NC_002945.4 29512 . N . . . . GT ./. NC_002945.4 29513 . N . . . . GT ./. NC_002945.4 29514 . N . . . . GT ./. NC_002945.4 29515 . N . . . . GT ./. NC_002945.4 29516 . N . . . . GT ./. NC_002945.4 29517 . N . . . . GT ./. NC_002945.4 29518 . N . . . . GT ./. NC_002945.4 29519 . N . . . . GT ./. NC_002945.4 29520 . N . . . . GT ./. NC_002945.4 29521 . N . . . . GT ./. NC_002945.4 29522 . N . . . . GT ./. NC_002945.4 29523 . N . . . . GT ./. NC_002945.4 29524 . N . . . . GT ./. NC_002945.4 29525 . N . . . . GT ./. NC_002945.4 29526 . N . . . . GT ./. NC_002945.4 29527 . N . . . . GT ./. NC_002945.4 29528 . N . . . . GT ./. NC_002945.4 29529 . N . . . . GT ./. NC_002945.4 29530 . N . . . . GT ./. NC_002945.4 29531 . N . . . . GT ./. NC_002945.4 29532 . N . . . . GT ./. NC_002945.4 29533 . N . . . . GT ./. NC_002945.4 29534 . N . . . . GT ./. NC_002945.4 29535 . N . . . . GT ./. NC_002945.4 29536 . N . . . . GT ./. NC_002945.4 29537 . N . . . . GT ./. NC_002945.4 29538 . N . . . . GT ./. NC_002945.4 29539 . N . . . . GT ./. NC_002945.4 29540 . N . . . . GT ./. NC_002945.4 29541 . N . . . . GT ./. NC_002945.4 29542 . N . . . . GT ./. NC_002945.4 29543 . N . . . . GT ./. NC_002945.4 29544 . N . . . . GT ./. NC_002945.4 29545 . N . . . . GT ./. NC_002945.4 29546 . N . . . . GT ./. NC_002945.4 29547 . N . . . . GT ./. NC_002945.4 29548 . N . . . . GT ./. NC_002945.4 29549 . N . . . . GT ./. NC_002945.4 29550 . N . . . . GT ./. NC_002945.4 29551 . N . . . . GT ./. NC_002945.4 29552 . N . . . . GT ./. NC_002945.4 29553 . N . . . . GT ./. NC_002945.4 29554 . N . . . . GT ./. NC_002945.4 29555 . N . . . . GT ./. NC_002945.4 29556 . N . . . . GT ./. NC_002945.4 29557 . N . . . . GT ./. NC_002945.4 29558 . N . . . . GT ./. NC_002945.4 29559 . N . . . . GT ./. NC_002945.4 29560 . N . . . . GT ./. NC_002945.4 29561 . N . . . . GT ./. NC_002945.4 29562 . N . . . . GT ./. NC_002945.4 29563 . N . . . . GT ./. NC_002945.4 29564 . N . . . . GT ./. NC_002945.4 29565 . N . . . . GT ./. NC_002945.4 29566 . N . . . . GT ./. NC_002945.4 29567 . N . . . . GT ./. NC_002945.4 29568 . N . . . . GT ./. NC_002945.4 29569 . N . . . . GT ./. NC_002945.4 29570 . N . . . . GT ./. NC_002945.4 29571 . N . . . . GT ./. NC_002945.4 29572 . N . . . . GT ./. NC_002945.4 29573 . N . . . . GT ./. NC_002945.4 29574 . N . . . . GT ./. NC_002945.4 29575 . N . . . . GT ./. NC_002945.4 29576 . N . . . . GT ./. NC_002945.4 29577 . N . . . . GT ./. NC_002945.4 29578 . N . . . . GT ./. NC_002945.4 29579 . N . . . . GT ./. NC_002945.4 29580 . N . . . . GT ./. NC_002945.4 29581 . N . . . . GT ./. NC_002945.4 29582 . N . . . . GT ./. NC_002945.4 29583 . N . . . . GT ./. NC_002945.4 29584 . N . . . . GT ./. NC_002945.4 29585 . N . . . . GT ./. NC_002945.4 29586 . N . . . . GT ./. NC_002945.4 29587 . N . . . . GT ./. NC_002945.4 29588 . N . . . . GT ./. NC_002945.4 29589 . N . . . . GT ./. NC_002945.4 29590 . N . . . . GT ./. NC_002945.4 29591 . N . . . . GT ./. NC_002945.4 29592 . N . . . . GT ./. NC_002945.4 29593 . N . . . . GT ./. NC_002945.4 29594 . N . . . . GT ./. NC_002945.4 29595 . N . . . . GT ./. NC_002945.4 29596 . N . . . . GT ./. NC_002945.4 29597 . N . . . . GT ./. NC_002945.4 29598 . N . . . . GT ./. NC_002945.4 29599 . N . . . . GT ./. NC_002945.4 29600 . N . . . . GT ./. NC_002945.4 29601 . N . . . . GT ./. NC_002945.4 29602 . N . . . . GT ./. NC_002945.4 29603 . N . . . . GT ./. NC_002945.4 29604 . N . . . . GT ./. NC_002945.4 29605 . N . . . . GT ./. NC_002945.4 29606 . N . . . . GT ./. NC_002945.4 29607 . N . . . . GT ./. NC_002945.4 29608 . N . . . . GT ./. NC_002945.4 29609 . N . . . . GT ./. NC_002945.4 29610 . N . . . . GT ./. NC_002945.4 29611 . N . . . . GT ./. NC_002945.4 29612 . N . . . . GT ./. NC_002945.4 29613 . N . . . . GT ./. NC_002945.4 29614 . N . . . . GT ./. NC_002945.4 29615 . N . . . . GT ./. NC_002945.4 29616 . N . . . . GT ./. NC_002945.4 29617 . N . . . . GT ./. NC_002945.4 29618 . N . . . . GT ./. NC_002945.4 29619 . N . . . . GT ./. NC_002945.4 29620 . N . . . . GT ./. NC_002945.4 29621 . N . . . . GT ./. NC_002945.4 29622 . N . . . . GT ./. NC_002945.4 29623 . N . . . . GT ./. NC_002945.4 29624 . N . . . . GT ./. NC_002945.4 29625 . N . . . . GT ./. NC_002945.4 29626 . N . . . . GT ./. NC_002945.4 29627 . N . . . . GT ./. NC_002945.4 29628 . N . . . . GT ./. NC_002945.4 29629 . N . . . . GT ./. NC_002945.4 29630 . N . . . . GT ./. NC_002945.4 29631 . N . . . . GT ./. NC_002945.4 29632 . N . . . . GT ./. NC_002945.4 29633 . N . . . . GT ./. NC_002945.4 29634 . N . . . . GT ./. NC_002945.4 29635 . N . . . . GT ./. NC_002945.4 29636 . N . . . . GT ./. NC_002945.4 29637 . N . . . . GT ./. NC_002945.4 29638 . N . . . . GT ./. NC_002945.4 29639 . N . . . . GT ./. NC_002945.4 29640 . N . . . . GT ./. NC_002945.4 29641 . N . . . . GT ./. NC_002945.4 29642 . N . . . . GT ./. NC_002945.4 29643 . N . . . . GT ./. NC_002945.4 29644 . N . . . . GT ./. NC_002945.4 29645 . N . . . . GT ./. NC_002945.4 29646 . N . . . . GT ./. NC_002945.4 29647 . N . . . . GT ./. NC_002945.4 29648 . N . . . . GT ./. NC_002945.4 29649 . N . . . . GT ./. NC_002945.4 29650 . N . . . . GT ./. NC_002945.4 29651 . N . . . . GT ./. NC_002945.4 29652 . N . . . . GT ./. NC_002945.4 29653 . N . . . . GT ./. NC_002945.4 29654 . N . . . . GT ./. NC_002945.4 29655 . N . . . . GT ./. NC_002945.4 29656 . N . . . . GT ./. NC_002945.4 29657 . N . . . . GT ./. NC_002945.4 29658 . N . . . . GT ./. NC_002945.4 29659 . N . . . . GT ./. NC_002945.4 29660 . N . . . . GT ./. NC_002945.4 29661 . N . . . . GT ./. NC_002945.4 29662 . N . . . . GT ./. NC_002945.4 29663 . N . . . . GT ./. NC_002945.4 29664 . N . . . . GT ./. NC_002945.4 29665 . N . . . . GT ./. NC_002945.4 29666 . N . . . . GT ./. NC_002945.4 29667 . N . . . . GT ./. NC_002945.4 29668 . N . . . . GT ./. NC_002945.4 29669 . N . . . . GT ./. NC_002945.4 29670 . N . . . . GT ./. NC_002945.4 29671 . N . . . . GT ./. NC_002945.4 29672 . N . . . . GT ./. NC_002945.4 29673 . N . . . . GT ./. NC_002945.4 29674 . N . . . . GT ./. NC_002945.4 29675 . N . . . . GT ./. NC_002945.4 29676 . N . . . . GT ./. NC_002945.4 29677 . N . . . . GT ./. NC_002945.4 29678 . N . . . . GT ./. NC_002945.4 29679 . N . . . . GT ./. NC_002945.4 29680 . N . . . . GT ./. NC_002945.4 29681 . N . . . . GT ./. NC_002945.4 29682 . N . . . . GT ./. NC_002945.4 29683 . N . . . . GT ./. NC_002945.4 29684 . N . . . . GT ./. NC_002945.4 29685 . N . . . . GT ./. NC_002945.4 29686 . N . . . . GT ./. NC_002945.4 29687 . N . . . . GT ./. NC_002945.4 29688 . N . . . . GT ./. NC_002945.4 29689 . N . . . . GT ./. NC_002945.4 29690 . N . . . . GT ./. NC_002945.4 29691 . N . . . . GT ./. NC_002945.4 29692 . N . . . . GT ./. NC_002945.4 29693 . N . . . . GT ./. NC_002945.4 29694 . N . . . . GT ./. NC_002945.4 29695 . N . . . . GT ./. NC_002945.4 29696 . N . . . . GT ./. NC_002945.4 29697 . N . . . . GT ./. NC_002945.4 29698 . N . . . . GT ./. NC_002945.4 29699 . N . . . . GT ./. NC_002945.4 29700 . N . . . . GT ./. NC_002945.4 29701 . N . . . . GT ./. NC_002945.4 29702 . N . . . . GT ./. NC_002945.4 29703 . N . . . . GT ./. NC_002945.4 29704 . N . . . . GT ./. NC_002945.4 29705 . N . . . . GT ./. NC_002945.4 29706 . N . . . . GT ./. NC_002945.4 29707 . N . . . . GT ./. NC_002945.4 29708 . N . . . . GT ./. NC_002945.4 29709 . N . . . . GT ./. NC_002945.4 29710 . N . . . . GT ./. NC_002945.4 29711 . N . . . . GT ./. NC_002945.4 29712 . N . . . . GT ./. NC_002945.4 29713 . N . . . . GT ./. NC_002945.4 29714 . N . . . . GT ./. NC_002945.4 29715 . N . . . . GT ./. NC_002945.4 29716 . N . . . . GT ./. NC_002945.4 29717 . N . . . . GT ./. NC_002945.4 29718 . N . . . . GT ./. NC_002945.4 29719 . N . . . . GT ./. NC_002945.4 29720 . N . . . . GT ./. NC_002945.4 29721 . N . . . . GT ./. NC_002945.4 29722 . N . . . . GT ./. NC_002945.4 29723 . N . . . . GT ./. NC_002945.4 29724 . N . . . . GT ./. NC_002945.4 29725 . N . . . . GT ./. NC_002945.4 29726 . N . . . . GT ./. NC_002945.4 29727 . N . . . . GT ./. NC_002945.4 29728 . N . . . . GT ./. NC_002945.4 29729 . N . . . . GT ./. NC_002945.4 29730 . N . . . . GT ./. NC_002945.4 29731 . N . . . . GT ./. NC_002945.4 29732 . N . . . . GT ./. NC_002945.4 29733 . N . . . . GT ./. NC_002945.4 29734 . N . . . . GT ./. NC_002945.4 29735 . N . . . . GT ./. NC_002945.4 29736 . N . . . . GT ./. NC_002945.4 29737 . N . . . . GT ./. NC_002945.4 29738 . N . . . . GT ./. NC_002945.4 29739 . N . . . . GT ./. NC_002945.4 29740 . N . . . . GT ./. NC_002945.4 29741 . N . . . . GT ./. NC_002945.4 29742 . N . . . . GT ./. NC_002945.4 29743 . N . . . . GT ./. NC_002945.4 29744 . N . . . . GT ./. NC_002945.4 29745 . N . . . . GT ./. NC_002945.4 29746 . N . . . . GT ./. NC_002945.4 29747 . N . . . . GT ./. NC_002945.4 29748 . N . . . . GT ./. NC_002945.4 29749 . N . . . . GT ./. NC_002945.4 29750 . N . . . . GT ./. NC_002945.4 29751 . N . . . . GT ./. NC_002945.4 29752 . N . . . . GT ./. NC_002945.4 29753 . N . . . . GT ./. NC_002945.4 29754 . N . . . . GT ./. NC_002945.4 29755 . N . . . . GT ./. NC_002945.4 29756 . N . . . . GT ./. NC_002945.4 29757 . N . . . . GT ./. NC_002945.4 29758 . N . . . . GT ./. NC_002945.4 29759 . N . . . . GT ./. NC_002945.4 29760 . N . . . . GT ./. NC_002945.4 29761 . N . . . . GT ./. NC_002945.4 29762 . N . . . . GT ./. NC_002945.4 29763 . N . . . . GT ./. NC_002945.4 29764 . N . . . . GT ./. NC_002945.4 29765 . N . . . . GT ./. NC_002945.4 29766 . N . . . . GT ./. NC_002945.4 29767 . N . . . . GT ./. NC_002945.4 29768 . N . . . . GT ./. NC_002945.4 29769 . N . . . . GT ./. NC_002945.4 29770 . N . . . . GT ./. NC_002945.4 29771 . N . . . . GT ./. NC_002945.4 29772 . N . . . . GT ./. NC_002945.4 29773 . N . . . . GT ./. NC_002945.4 29774 . N . . . . GT ./. NC_002945.4 29775 . N . . . . GT ./. NC_002945.4 29776 . N . . . . GT ./. NC_002945.4 29777 . N . . . . GT ./. NC_002945.4 29778 . N . . . . GT ./. NC_002945.4 29779 . N . . . . GT ./. NC_002945.4 29780 . N . . . . GT ./. NC_002945.4 29781 . N . . . . GT ./. NC_002945.4 29782 . N . . . . GT ./. NC_002945.4 29783 . N . . . . GT ./. NC_002945.4 29784 . N . . . . GT ./. NC_002945.4 29785 . N . . . . GT ./. NC_002945.4 29786 . N . . . . GT ./. NC_002945.4 29787 . N . . . . GT ./. NC_002945.4 29788 . N . . . . GT ./. NC_002945.4 29789 . N . . . . GT ./. NC_002945.4 29790 . N . . . . GT ./. NC_002945.4 29791 . N . . . . GT ./. NC_002945.4 29792 . N . . . . GT ./. NC_002945.4 29793 . N . . . . GT ./. NC_002945.4 29794 . N . . . . GT ./. NC_002945.4 29795 . N . . . . GT ./. NC_002945.4 29796 . N . . . . GT ./. NC_002945.4 29797 . N . . . . GT ./. NC_002945.4 29798 . N . . . . GT ./. NC_002945.4 29799 . N . . . . GT ./. NC_002945.4 29800 . N . . . . GT ./. NC_002945.4 29801 . N . . . . GT ./. NC_002945.4 29802 . N . . . . GT ./. NC_002945.4 29803 . N . . . . GT ./. NC_002945.4 29804 . N . . . . GT ./. NC_002945.4 29805 . N . . . . GT ./. NC_002945.4 29806 . N . . . . GT ./. NC_002945.4 29807 . N . . . . GT ./. NC_002945.4 29808 . N . . . . GT ./. NC_002945.4 29809 . N . . . . GT ./. NC_002945.4 29810 . N . . . . GT ./. NC_002945.4 29811 . N . . . . GT ./. NC_002945.4 29812 . N . . . . GT ./. NC_002945.4 29813 . N . . . . GT ./. NC_002945.4 29814 . N . . . . GT ./. NC_002945.4 29815 . N . . . . GT ./. NC_002945.4 29816 . N . . . . GT ./. NC_002945.4 29817 . N . . . . GT ./. NC_002945.4 29818 . N . . . . GT ./. NC_002945.4 29819 . N . . . . GT ./. NC_002945.4 29820 . N . . . . GT ./. NC_002945.4 29821 . N . . . . GT ./. NC_002945.4 29822 . N . . . . GT ./. NC_002945.4 29823 . N . . . . GT ./. NC_002945.4 29824 . N . . . . GT ./. NC_002945.4 29825 . N . . . . GT ./. NC_002945.4 29826 . N . . . . GT ./. NC_002945.4 29827 . N . . . . GT ./. NC_002945.4 29828 . N . . . . GT ./. NC_002945.4 29829 . N . . . . GT ./. NC_002945.4 29830 . N . . . . GT ./. NC_002945.4 29831 . N . . . . GT ./. NC_002945.4 29832 . N . . . . GT ./. NC_002945.4 29833 . N . . . . GT ./. NC_002945.4 29834 . N . . . . GT ./. NC_002945.4 29835 . N . . . . GT ./. NC_002945.4 29836 . N . . . . GT ./. NC_002945.4 29837 . N . . . . GT ./. NC_002945.4 29838 . N . . . . GT ./. NC_002945.4 29839 . N . . . . GT ./. NC_002945.4 29840 . N . . . . GT ./. NC_002945.4 29841 . N . . . . GT ./. NC_002945.4 29842 . N . . . . GT ./. NC_002945.4 29843 . N . . . . GT ./. NC_002945.4 29844 . N . . . . GT ./. NC_002945.4 29845 . N . . . . GT ./. NC_002945.4 29846 . N . . . . GT ./. NC_002945.4 29847 . N . . . . GT ./. NC_002945.4 29848 . N . . . . GT ./. NC_002945.4 29849 . N . . . . GT ./. NC_002945.4 29850 . N . . . . GT ./. NC_002945.4 29851 . N . . . . GT ./. NC_002945.4 29852 . N . . . . GT ./. NC_002945.4 29853 . N . . . . GT ./. NC_002945.4 29854 . N . . . . GT ./. NC_002945.4 29855 . N . . . . GT ./. NC_002945.4 29856 . N . . . . GT ./. NC_002945.4 29857 . N . . . . GT ./. NC_002945.4 29858 . N . . . . GT ./. NC_002945.4 29859 . N . . . . GT ./. NC_002945.4 29860 . N . . . . GT ./. NC_002945.4 29861 . N . . . . GT ./. NC_002945.4 29862 . N . . . . GT ./. NC_002945.4 29863 . N . . . . GT ./. NC_002945.4 29864 . N . . . . GT ./. NC_002945.4 29865 . N . . . . GT ./. NC_002945.4 29866 . N . . . . GT ./. NC_002945.4 29867 . N . . . . GT ./. NC_002945.4 29868 . N . . . . GT ./. NC_002945.4 29869 . N . . . . GT ./. NC_002945.4 29870 . N . . . . GT ./. NC_002945.4 29871 . N . . . . GT ./. NC_002945.4 29872 . N . . . . GT ./. NC_002945.4 29873 . N . . . . GT ./. NC_002945.4 29874 . N . . . . GT ./. NC_002945.4 29875 . N . . . . GT ./. NC_002945.4 29876 . N . . . . GT ./. NC_002945.4 29877 . N . . . . GT ./. NC_002945.4 29878 . N . . . . GT ./. NC_002945.4 29879 . N . . . . GT ./. NC_002945.4 29880 . N . . . . GT ./. NC_002945.4 29881 . N . . . . GT ./. NC_002945.4 29882 . N . . . . GT ./. NC_002945.4 29883 . N . . . . GT ./. NC_002945.4 29884 . N . . . . GT ./. NC_002945.4 29885 . N . . . . GT ./. NC_002945.4 29886 . N . . . . GT ./. NC_002945.4 29887 . N . . . . GT ./. NC_002945.4 29888 . N . . . . GT ./. NC_002945.4 29889 . N . . . . GT ./. NC_002945.4 29890 . N . . . . GT ./. NC_002945.4 29891 . N . . . . GT ./. NC_002945.4 29892 . N . . . . GT ./. NC_002945.4 29893 . N . . . . GT ./. NC_002945.4 29894 . N . . . . GT ./. NC_002945.4 29895 . N . . . . GT ./. NC_002945.4 29896 . N . . . . GT ./. NC_002945.4 29897 . N . . . . GT ./. NC_002945.4 29898 . N . . . . GT ./. NC_002945.4 29899 . N . . . . GT ./. NC_002945.4 29900 . N . . . . GT ./. NC_002945.4 29901 . N . . . . GT ./. NC_002945.4 29902 . N . . . . GT ./. NC_002945.4 29903 . N . . . . GT ./. NC_002945.4 29904 . N . . . . GT ./. NC_002945.4 29905 . N . . . . GT ./. NC_002945.4 29906 . N . . . . GT ./. NC_002945.4 29907 . N . . . . GT ./. NC_002945.4 29908 . N . . . . GT ./. NC_002945.4 29909 . N . . . . GT ./. NC_002945.4 29910 . N . . . . GT ./. NC_002945.4 29911 . N . . . . GT ./. NC_002945.4 29912 . N . . . . GT ./. NC_002945.4 29913 . N . . . . GT ./. NC_002945.4 29914 . N . . . . GT ./. NC_002945.4 29915 . N . . . . GT ./. NC_002945.4 29916 . N . . . . GT ./. NC_002945.4 29917 . N . . . . GT ./. NC_002945.4 29918 . N . . . . GT ./. NC_002945.4 29919 . N . . . . GT ./. NC_002945.4 29920 . N . . . . GT ./. NC_002945.4 29921 . N . . . . GT ./. NC_002945.4 29922 . N . . . . GT ./. NC_002945.4 29923 . N . . . . GT ./. NC_002945.4 29924 . N . . . . GT ./. NC_002945.4 29925 . N . . . . GT ./. NC_002945.4 29926 . N . . . . GT ./. NC_002945.4 29927 . N . . . . GT ./. NC_002945.4 29928 . N . . . . GT ./. NC_002945.4 29929 . N . . . . GT ./. NC_002945.4 29930 . N . . . . GT ./. NC_002945.4 29931 . N . . . . GT ./. NC_002945.4 29932 . N . . . . GT ./. NC_002945.4 29933 . N . . . . GT ./. NC_002945.4 29934 . N . . . . GT ./. NC_002945.4 29935 . N . . . . GT ./. NC_002945.4 29936 . N . . . . GT ./. NC_002945.4 29937 . N . . . . GT ./. NC_002945.4 29938 . N . . . . GT ./. NC_002945.4 29939 . N . . . . GT ./. NC_002945.4 29940 . N . . . . GT ./. NC_002945.4 29941 . N . . . . GT ./. NC_002945.4 29942 . N . . . . GT ./. NC_002945.4 29943 . N . . . . GT ./. NC_002945.4 29944 . N . . . . GT ./. NC_002945.4 29945 . N . . . . GT ./. NC_002945.4 29946 . N . . . . GT ./. NC_002945.4 29947 . N . . . . GT ./. NC_002945.4 29948 . N . . . . GT ./. NC_002945.4 29949 . N . . . . GT ./. NC_002945.4 29950 . N . . . . GT ./. NC_002945.4 29951 . N . . . . GT ./. NC_002945.4 29952 . N . . . . GT ./. NC_002945.4 29953 . N . . . . GT ./. NC_002945.4 29954 . N . . . . GT ./. NC_002945.4 29955 . N . . . . GT ./. NC_002945.4 29956 . N . . . . GT ./. NC_002945.4 29957 . N . . . . GT ./. NC_002945.4 29958 . N . . . . GT ./. NC_002945.4 29959 . N . . . . GT ./. NC_002945.4 29960 . N . . . . GT ./. NC_002945.4 29961 . N . . . . GT ./. NC_002945.4 29962 . N . . . . GT ./. NC_002945.4 29963 . N . . . . GT ./. NC_002945.4 29964 . N . . . . GT ./. NC_002945.4 29965 . N . . . . GT ./. NC_002945.4 29966 . N . . . . GT ./. NC_002945.4 29967 . N . . . . GT ./. NC_002945.4 29968 . N . . . . GT ./. NC_002945.4 29969 . N . . . . GT ./. NC_002945.4 29970 . N . . . . GT ./. NC_002945.4 29971 . N . . . . GT ./. NC_002945.4 29972 . N . . . . GT ./. NC_002945.4 29973 . N . . . . GT ./. NC_002945.4 29974 . N . . . . GT ./. NC_002945.4 29975 . N . . . . GT ./. NC_002945.4 29976 . N . . . . GT ./. NC_002945.4 29977 . N . . . . GT ./. NC_002945.4 29978 . N . . . . GT ./. NC_002945.4 29979 . N . . . . GT ./. NC_002945.4 29980 . N . . . . GT ./. NC_002945.4 29981 . N . . . . GT ./. NC_002945.4 29982 . N . . . . GT ./. NC_002945.4 29983 . N . . . . GT ./. NC_002945.4 29984 . N . . . . GT ./. NC_002945.4 29985 . N . . . . GT ./. NC_002945.4 29986 . N . . . . GT ./. NC_002945.4 29987 . N . . . . GT ./. NC_002945.4 29988 . N . . . . GT ./. NC_002945.4 29989 . N . . . . GT ./. NC_002945.4 29990 . N . . . . GT ./. NC_002945.4 29991 . N . . . . GT ./. NC_002945.4 29992 . N . . . . GT ./. NC_002945.4 29993 . N . . . . GT ./. NC_002945.4 29994 . N . . . . GT ./. NC_002945.4 29995 . N . . . . GT ./. NC_002945.4 29996 . N . . . . GT ./. NC_002945.4 29997 . N . . . . GT ./. NC_002945.4 29998 . N . . . . GT ./. NC_002945.4 29999 . N . . . . GT ./. NC_002945.4 30000 . N . . . . GT ./. NC_002945.4 30001 . N . . . . GT ./. NC_002945.4 30002 . N . . . . GT ./. NC_002945.4 30003 . N . . . . GT ./. NC_002945.4 30004 . N . . . . GT ./. NC_002945.4 30005 . N . . . . GT ./. NC_002945.4 30006 . N . . . . GT ./. NC_002945.4 30007 . N . . . . GT ./. NC_002945.4 30008 . N . . . . GT ./. NC_002945.4 30009 . N . . . . GT ./. NC_002945.4 30010 . N . . . . GT ./. NC_002945.4 30011 . N . . . . GT ./. NC_002945.4 30012 . N . . . . GT ./. NC_002945.4 30013 . N . . . . GT ./. NC_002945.4 30014 . N . . . . GT ./. NC_002945.4 30015 . N . . . . GT ./. NC_002945.4 30016 . N . . . . GT ./. NC_002945.4 30017 . N . . . . GT ./. NC_002945.4 30018 . N . . . . GT ./. NC_002945.4 30019 . N . . . . GT ./. NC_002945.4 30020 . N . . . . GT ./. NC_002945.4 30021 . N . . . . GT ./. NC_002945.4 30022 . N . . . . GT ./. NC_002945.4 30023 . N . . . . GT ./. NC_002945.4 30024 . N . . . . GT ./. NC_002945.4 30025 . N . . . . GT ./. NC_002945.4 30026 . N . . . . GT ./. NC_002945.4 30027 . N . . . . GT ./. NC_002945.4 30028 . N . . . . GT ./. NC_002945.4 30029 . N . . . . GT ./. NC_002945.4 30030 . N . . . . GT ./. NC_002945.4 30031 . N . . . . GT ./. NC_002945.4 30032 . N . . . . GT ./. NC_002945.4 30033 . N . . . . GT ./. NC_002945.4 30034 . N . . . . GT ./. NC_002945.4 30035 . N . . . . GT ./. NC_002945.4 30036 . N . . . . GT ./. NC_002945.4 30037 . N . . . . GT ./. NC_002945.4 30038 . N . . . . GT ./. NC_002945.4 30039 . N . . . . GT ./. NC_002945.4 30040 . N . . . . GT ./. NC_002945.4 30041 . N . . . . GT ./. NC_002945.4 30042 . N . . . . GT ./. NC_002945.4 30043 . N . . . . GT ./. NC_002945.4 30044 . N . . . . GT ./. NC_002945.4 30045 . N . . . . GT ./. NC_002945.4 30046 . N . . . . GT ./. NC_002945.4 30047 . N . . . . GT ./. NC_002945.4 30048 . N . . . . GT ./. NC_002945.4 30049 . N . . . . GT ./. NC_002945.4 30050 . N . . . . GT ./. NC_002945.4 30051 . N . . . . GT ./. NC_002945.4 30052 . N . . . . GT ./. NC_002945.4 30053 . N . . . . GT ./. NC_002945.4 30054 . N . . . . GT ./. NC_002945.4 30055 . N . . . . GT ./. NC_002945.4 30056 . N . . . . GT ./. NC_002945.4 30057 . N . . . . GT ./. NC_002945.4 30058 . N . . . . GT ./. NC_002945.4 30059 . N . . . . GT ./. NC_002945.4 30060 . N . . . . GT ./. NC_002945.4 30061 . N . . . . GT ./. NC_002945.4 30062 . N . . . . GT ./. NC_002945.4 30063 . N . . . . GT ./. NC_002945.4 30064 . N . . . . GT ./. NC_002945.4 30065 . N . . . . GT ./. NC_002945.4 30066 . N . . . . GT ./. NC_002945.4 30067 . N . . . . GT ./. NC_002945.4 30068 . N . . . . GT ./. NC_002945.4 30069 . N . . . . GT ./. NC_002945.4 30070 . N . . . . GT ./. NC_002945.4 30071 . N . . . . GT ./. NC_002945.4 30072 . N . . . . GT ./. NC_002945.4 30073 . N . . . . GT ./. NC_002945.4 30074 . N . . . . GT ./. NC_002945.4 30075 . N . . . . GT ./. NC_002945.4 30076 . N . . . . GT ./. NC_002945.4 30077 . N . . . . GT ./. NC_002945.4 30078 . N . . . . GT ./. NC_002945.4 30079 . N . . . . GT ./. NC_002945.4 30080 . N . . . . GT ./. NC_002945.4 30081 . N . . . . GT ./. NC_002945.4 30082 . N . . . . GT ./. NC_002945.4 33788 . A G 2948.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=104;CIGAR=1X;DP=105;DPB=105;DPRA=0;EPP=11.3621;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=144.138;PAIRED=0.990385;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=3576;QR=15;RO=1;RPL=47;RPP=5.09825;RPPR=5.18177;RPR=57;RUN=1;SAF=99;SAP=187.502;SAR=5;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:105:1,104:1:15:104:3576:-320.525,-30.1082,0 NC_002945.4 41228 . A C 5830.59 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=198;CIGAR=1X;DP=205;DPB=205;DPRA=0;EPP=15.6882;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=254.088;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=6570;QR=98;RO=7;RPL=91;RPP=5.81786;RPPR=18.2106;RPR=107;RUN=1;SAF=107;SAP=5.81786;SAR=91;SRF=0;SRP=18.2106;SRR=7;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:205:7,198:7:98:198:6570:-582.305,-52.7512,0 NC_002945.4 41437 . T C 6677.87 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=220;CIGAR=1X;DP=221;DPB=221;DPRA=0;EPP=3.642;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=309.59;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7473;QR=0;RO=0;RPL=124;RPP=10.7486;RPPR=0;RPR=96;RUN=1;SAF=112;SAP=3.16823;SAR=108;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:221:0,220:0:0:220:7473:-672.448,-66.2266,0 NC_002945.4 50470 . C T 5971.85 . 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AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=16.0391;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=12.9229;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=211;QR=0;RO=0;RPL=6;RPP=16.0391;RPPR=0;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:6:0,6:0:0:6:211:-19.3328,-1.80618,0 NC_002945.4 332154 . G C 126.29799999999999 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=16.0391;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=12.9229;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=197;QR=0;RO=0;RPL=6;RPP=16.0391;RPPR=0;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:6:0,6:0:0:6:197:-18.0484,-1.80618,0 NC_002945.4 332160 . N . . . . GT ./. NC_002945.4 332161 . N . . . . GT ./. NC_002945.4 332162 . N . . . . GT ./. NC_002945.4 332163 . N . . . . GT ./. NC_002945.4 332164 . N . . . . GT ./. NC_002945.4 332165 . N . . . . GT ./. NC_002945.4 332166 . N . . . . GT ./. NC_002945.4 332167 . N . . . . GT ./. NC_002945.4 332168 . N . . . . GT ./. NC_002945.4 332169 . N . . . . GT ./. NC_002945.4 332170 . N . . . . GT ./. NC_002945.4 332171 . N . . . . GT ./. NC_002945.4 332172 . N . . . . GT ./. NC_002945.4 332173 . N . . . . GT ./. NC_002945.4 332174 . N . . . . GT ./. NC_002945.4 332175 . N . . . . GT ./. NC_002945.4 332176 . N . . . . GT ./. NC_002945.4 332177 . N . . . . GT ./. NC_002945.4 332178 . N . . . . GT ./. NC_002945.4 332179 . N . . . . GT ./. NC_002945.4 332180 . N . . . . GT ./. NC_002945.4 332181 . N . . . . GT ./. NC_002945.4 332182 . N . . . . GT ./. NC_002945.4 332183 . N . . . . GT ./. NC_002945.4 332184 . N . . . . GT ./. NC_002945.4 332185 . N . . . . GT ./. NC_002945.4 332186 . N . . . . GT ./. NC_002945.4 332187 . N . . . . GT ./. NC_002945.4 332188 . N . . . . GT ./. NC_002945.4 332189 . N . . . . GT ./. NC_002945.4 332190 . N . . . . GT ./. NC_002945.4 332191 . N . . . . GT ./. NC_002945.4 332192 . N . . . . GT ./. NC_002945.4 332193 . N . . . . GT ./. NC_002945.4 332215 . C G 379.908 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=17;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=39.9253;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=57.1176;MQMR=0;NS=1;NUMALT=1;ODDS=28.1722;PAIRED=0.882353;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=596;QR=0;RO=0;RPL=0;RPP=39.9253;RPPR=0;RPR=17;RUN=1;SAF=17;SAP=39.9253;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:17:0,17:0:0:17:596:-53.3433,-5.11751,0 NC_002945.4 332218 . A G 439.338 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=19;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=44.2683;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=57.4211;MQMR=0;NS=1;NUMALT=1;ODDS=30.9448;PAIRED=0.894737;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=681;QR=0;RO=0;RPL=0;RPP=44.2683;RPPR=0;RPR=19;RUN=1;SAF=19;SAP=44.2683;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:19:0,19:0:0:19:681:-61.0925,-5.71957,0 NC_002945.4 333010 . T G 2567.13 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=84;CIGAR=1X;DP=84;DPB=84;DPRA=0;EPP=8.07707;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=121.054;PAIRED=0.964286;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2912;QR=0;RO=0;RPL=51;RPP=11.386;RPPR=0;RPR=33;RUN=1;SAF=52;SAP=13.3506;SAR=32;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:84:0,84:0:0:84:2912:-262.265,-25.2865,0 NC_002945.4 333486 . N . . . . GT ./. NC_002945.4 333487 . N . . . . GT ./. NC_002945.4 333488 . N . . . . GT ./. NC_002945.4 333489 . N . . . . GT ./. NC_002945.4 333490 . N . . . . GT ./. NC_002945.4 333491 . N . . . . GT ./. NC_002945.4 333492 . N . . . . GT ./. NC_002945.4 333493 . N . . . . GT ./. NC_002945.4 333494 . N . . . . GT ./. NC_002945.4 333495 . N . . . . GT ./. NC_002945.4 333496 . N . . . . GT ./. NC_002945.4 333497 . N . . . . GT ./. NC_002945.4 333498 . N . . . . GT ./. NC_002945.4 333499 . N . . . . GT ./. NC_002945.4 333500 . N . . . . GT ./. NC_002945.4 333501 . N . . . . GT ./. NC_002945.4 333502 . N . . . . GT ./. NC_002945.4 333503 . N . . . . GT ./. NC_002945.4 333504 . N . . . . GT ./. NC_002945.4 333505 . N . . . . GT ./. NC_002945.4 333506 . N . . . . GT ./. NC_002945.4 333507 . N . . . . GT ./. NC_002945.4 333508 . N . . . . GT ./. NC_002945.4 333509 . N . . . . GT ./. NC_002945.4 333510 . N . . . . GT ./. NC_002945.4 333511 . N . . . . GT ./. NC_002945.4 333512 . N . . . . GT ./. NC_002945.4 333513 . N . . . . GT ./. NC_002945.4 333514 . N . . . . GT ./. NC_002945.4 333515 . N . . . . GT ./. NC_002945.4 333516 . N . . . . GT ./. NC_002945.4 333517 . N . . . . GT ./. NC_002945.4 333518 . N . . . . GT ./. NC_002945.4 333519 . N . . . . GT ./. NC_002945.4 333520 . N . . . . GT ./. NC_002945.4 333521 . N . . . . GT ./. NC_002945.4 333522 . N . . . . GT ./. NC_002945.4 333523 . N . . . . GT ./. NC_002945.4 333524 . N . . . . GT ./. NC_002945.4 333525 . N . . . . GT ./. NC_002945.4 333526 . N . . . . GT ./. NC_002945.4 333527 . N . . . . GT ./. NC_002945.4 333528 . N . . . . GT ./. NC_002945.4 333529 . N . . . . GT ./. NC_002945.4 333530 . N . . . . GT ./. NC_002945.4 333531 . N . . . . GT ./. NC_002945.4 333532 . N . . . . GT ./. NC_002945.4 333533 . N . . . . GT ./. NC_002945.4 333534 . N . . . . GT ./. NC_002945.4 333535 . N . . . . GT ./. NC_002945.4 333536 . N . . . . GT ./. NC_002945.4 333537 . N . . . . GT ./. NC_002945.4 333538 . N . . . . GT ./. NC_002945.4 333539 . N . . . . GT ./. NC_002945.4 333540 . N . . . . GT ./. NC_002945.4 333541 . N . . . . GT ./. NC_002945.4 333542 . N . . . . GT ./. NC_002945.4 333543 . N . . . . GT ./. NC_002945.4 333544 . N . . . . GT ./. NC_002945.4 333545 . N . . . . GT ./. NC_002945.4 333546 . N . . . . GT ./. NC_002945.4 333547 . N . . . . GT ./. NC_002945.4 333548 . N . . . . GT ./. NC_002945.4 333549 . N . . . . GT ./. NC_002945.4 333550 . N . . . . GT ./. NC_002945.4 333551 . N . . . . GT ./. NC_002945.4 333552 . N . . . . GT ./. NC_002945.4 333553 . N . . . . GT ./. NC_002945.4 333590 . N . . . . GT ./. NC_002945.4 333591 . N . . . . GT ./. NC_002945.4 333592 . N . . . . GT ./. NC_002945.4 333593 . N . . . . GT ./. NC_002945.4 333594 . N . . . . GT ./. NC_002945.4 333595 . N . . . . GT ./. NC_002945.4 333596 . N . . . . GT ./. NC_002945.4 333597 . N . . . . GT ./. NC_002945.4 333598 . N . . . . GT ./. NC_002945.4 333599 . N . . . . GT ./. NC_002945.4 333600 . N . . . . GT ./. NC_002945.4 333601 . N . . . . GT ./. NC_002945.4 333602 . N . . . . GT ./. NC_002945.4 333603 . N . . . . GT ./. NC_002945.4 333604 . N . . . . GT ./. NC_002945.4 333605 . N . . . . GT ./. NC_002945.4 333606 . N . . . . GT ./. NC_002945.4 333607 . N . . . . GT ./. NC_002945.4 333608 . N . . . . GT ./. NC_002945.4 333609 . N . . . . GT ./. NC_002945.4 333610 . N . . . . GT ./. NC_002945.4 333611 . N . . . . GT ./. NC_002945.4 333612 . N . . . . GT ./. NC_002945.4 333613 . N . . . . GT ./. NC_002945.4 333614 . N . . . . GT ./. NC_002945.4 333615 . N . . . . GT ./. NC_002945.4 333616 . N . . . . GT ./. NC_002945.4 333617 . N . . . . GT ./. NC_002945.4 333618 . N . . . . GT ./. NC_002945.4 333619 . N . . . . GT ./. NC_002945.4 333620 . N . . . . GT ./. NC_002945.4 333621 . N . . . . GT ./. NC_002945.4 333622 . N . . . . GT ./. NC_002945.4 333623 . N . . . . GT ./. NC_002945.4 333624 . N . . . . GT ./. NC_002945.4 333625 . N . . . . GT ./. NC_002945.4 333626 . N . . . . GT ./. NC_002945.4 333627 . N . . . . GT ./. NC_002945.4 333628 . N . . . . GT ./. NC_002945.4 333629 . N . . . . GT ./. NC_002945.4 333630 . N . . . . GT ./. NC_002945.4 333631 . N . . . . GT ./. NC_002945.4 333632 . N . . . . GT ./. NC_002945.4 333633 . N . . . . GT ./. NC_002945.4 333634 . N . . . . GT ./. NC_002945.4 334320 . T C 2194.66 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=79;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=3.69747;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=53.4051;MQMR=0;NS=1;NUMALT=1;ODDS=114.122;PAIRED=0.987342;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2577;QR=0;RO=0;RPL=41;RPP=3.25768;RPPR=0;RPR=38;RUN=1;SAF=46;SAP=7.6556;SAR=33;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:80:0,79:0:0:79:2577:-223.164,-23.7814,0 NC_002945.4 334323 . T C 2171.15 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=79;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.23675;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=53.4051;MQMR=0;NS=1;NUMALT=1;ODDS=114.122;PAIRED=0.987342;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2540;QR=0;RO=0;RPL=40;RPP=3.03779;RPPR=0;RPR=39;RUN=1;SAF=45;SAP=6.33623;SAR=34;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:79:0,79:0:0:79:2540:-220.812,-23.7814,0 NC_002945.4 336477 . N . . . . GT ./. NC_002945.4 336478 . N . . . . GT ./. NC_002945.4 336479 . N . . . . GT ./. NC_002945.4 336480 . N . . . . GT ./. NC_002945.4 336481 . N . . . . GT ./. NC_002945.4 336482 . N . . . . GT ./. NC_002945.4 336483 . N . . . . GT ./. NC_002945.4 336484 . N . . . . GT ./. NC_002945.4 336485 . N . . . . GT ./. NC_002945.4 336486 . N . . . . GT ./. NC_002945.4 336487 . N . . . . GT ./. NC_002945.4 336488 . N . . . . GT ./. NC_002945.4 336489 . N . . . . GT ./. NC_002945.4 336590 . N . . . . GT ./. NC_002945.4 336591 . N . . . . GT ./. NC_002945.4 336592 . N . . . . GT ./. NC_002945.4 336593 . N . . . . GT ./. NC_002945.4 336594 . N . . . . GT ./. NC_002945.4 336595 . N . . . . GT ./. NC_002945.4 336596 . N . . . . GT ./. NC_002945.4 336597 . N . . . . GT ./. NC_002945.4 336598 . N . . . . GT ./. NC_002945.4 336599 . N . . . . GT ./. NC_002945.4 336600 . N . . . . GT ./. NC_002945.4 336601 . N . . . . GT ./. NC_002945.4 336602 . N . . . . GT ./. NC_002945.4 336603 . N . . . . GT ./. NC_002945.4 336604 . N . . . . GT ./. NC_002945.4 336605 . N . . . . GT ./. NC_002945.4 336606 . N . . . . GT ./. NC_002945.4 336607 . N . . . . GT ./. NC_002945.4 336608 . N . . . . GT ./. NC_002945.4 336609 . N . . . . GT ./. NC_002945.4 336610 . N . . . . GT ./. NC_002945.4 336611 . N . . . . GT ./. NC_002945.4 336612 . N . . . . GT ./. NC_002945.4 336613 . N . . . . GT ./. NC_002945.4 336614 . N . . . . GT ./. NC_002945.4 336615 . N . . . . GT ./. NC_002945.4 336616 . N . . . . GT ./. NC_002945.4 336617 . N . . . . GT ./. NC_002945.4 336618 . N . . . . GT ./. NC_002945.4 336619 . N . . . . GT ./. NC_002945.4 336620 . N . . . . GT ./. NC_002945.4 336621 . N . . . . GT ./. NC_002945.4 336622 . N . . . . GT ./. NC_002945.4 336623 . N . . . . GT ./. NC_002945.4 336624 . N . . . . GT ./. NC_002945.4 336625 . N . . . . GT ./. NC_002945.4 336626 . N . . . . GT ./. NC_002945.4 336627 . N . . . . GT ./. NC_002945.4 336628 . N . . . . GT ./. NC_002945.4 336629 . N . . . . GT ./. NC_002945.4 336630 . N . . . . GT ./. NC_002945.4 336631 . N . . . . GT ./. NC_002945.4 336632 . N . . . . GT ./. NC_002945.4 336633 . N . . . . GT ./. NC_002945.4 336634 . N . . . . GT ./. NC_002945.4 336635 . N . . . . GT ./. NC_002945.4 336636 . N . . . . GT ./. NC_002945.4 336637 . N . . . . GT ./. NC_002945.4 336638 . N . . . . GT ./. NC_002945.4 336639 . N . . . . GT ./. NC_002945.4 339369 . N . . . . GT ./. NC_002945.4 339370 . N . . . . GT ./. NC_002945.4 339371 . N . . . . GT ./. NC_002945.4 339372 . N . . . . GT ./. NC_002945.4 339373 . N . . . . GT ./. NC_002945.4 339374 . N . . . . GT ./. NC_002945.4 339375 . N . . . . GT ./. NC_002945.4 339376 . N . . . . GT ./. NC_002945.4 339377 . N . . . . GT ./. NC_002945.4 339378 . N . . . . GT ./. NC_002945.4 339379 . N . . . . GT ./. NC_002945.4 339380 . N . . . . GT ./. NC_002945.4 339381 . N . . . . GT ./. NC_002945.4 339382 . N . . . . GT ./. NC_002945.4 339383 . N . . . . GT ./. NC_002945.4 339384 . N . . . . GT ./. NC_002945.4 339385 . N . . . . GT ./. NC_002945.4 339386 . N . . . . GT ./. NC_002945.4 339387 . N . . . . GT ./. NC_002945.4 339388 . N . . . . GT ./. NC_002945.4 339389 . N . . . . GT ./. NC_002945.4 339390 . N . . . . GT ./. NC_002945.4 339391 . N . . . . GT ./. NC_002945.4 339392 . N . . . . GT ./. NC_002945.4 339393 . N . . . . GT ./. NC_002945.4 339394 . N . . . . GT ./. NC_002945.4 339395 . N . . . . GT ./. NC_002945.4 339396 . N . . . . GT ./. NC_002945.4 339397 . N . . . . GT ./. NC_002945.4 339398 . N . . . . GT ./. NC_002945.4 339399 . N . . . . GT ./. NC_002945.4 339400 . N . . . . GT ./. NC_002945.4 339401 . N . . . . GT ./. NC_002945.4 339402 . N . . . . GT ./. NC_002945.4 339403 . N . . . . GT ./. NC_002945.4 339404 . N . . . . GT ./. NC_002945.4 339405 . N . . . . GT ./. NC_002945.4 339406 . N . . . . GT ./. NC_002945.4 339407 . N . . . . GT ./. NC_002945.4 339408 . N . . . . GT ./. NC_002945.4 339409 . N . . . . GT ./. NC_002945.4 339410 . N . . . . GT ./. NC_002945.4 339411 . N . . . . GT ./. NC_002945.4 340088 . G A 2525.17 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=81;CIGAR=1X;DP=82;DPB=82;DPRA=0;EPP=17.1919;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=58.5062;MQMR=0;NS=1;NUMALT=1;ODDS=116.895;PAIRED=0.987654;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2863;QR=0;RO=0;RPL=39;RPP=3.25157;RPPR=0;RPR=42;RUN=1;SAF=39;SAP=3.25157;SAR=42;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:82:0,81:0:0:81:2863:-257.146,-24.3834,0 NC_002945.4 340090 . C T 2327.84 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=80;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=18.6449;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=58.4;MQMR=0;NS=1;NUMALT=1;ODDS=115.509;PAIRED=0.9875;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2643;QR=0;RO=0;RPL=40;RPP=3.0103;RPPR=0;RPR=40;RUN=1;SAF=38;SAP=3.44459;SAR=42;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:80:0,80:0:0:80:2643:-237.547,-24.0824,0 NC_002945.4 340091 . G A 2328.64 . 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