# HG changeset patch # User greg # Date 1587478451 14400 # Node ID ee4ef1fc23c6043269370c33234546f15b91ba7c Uploaded diff -r 000000000000 -r ee4ef1fc23c6 .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,11 @@ +name: vsnp_get_snps +owner: greg +description: | + Contains a tool that collects quality parsimonious SNPs from vcf files and outputs alignment files in fasta format. +homepage_url: https://github.com/USDA-VS/vSNP +long_description: | + Contains a tool that collects quality parsimonious SNPs from vcf files and outputs alignment files in fasta format. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps +type: unrestricted +categories: + - Sequence Analysis diff -r 000000000000 -r ee4ef1fc23c6 test-data/SRR1792272_zc.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR1792272_zc.vcf Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,1058 @@ +##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/SRR1792272/NC_002945v4.fasta +##contig= +##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/SRR1792272/NC_002945v4.fasta /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1792272/SRR1792272-nodup.bam --region NC_002945.4:0-100000 +##filter="QUAL > 20 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR1792272 +NC_002945.4 1057 . A G 8671.65 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=288;CIGAR=1X;DP=289;DPB=289;DPRA=0;EPP=3.04046;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=403.858;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=9688;QR=0;RO=0;RPL=157;RPP=8.10723;RPPR=0;RPR=131;RUN=1;SAF=146;SAP=3.13094;SAR=142;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:289:0,288:0:0:288:9688:-871.673,-86.6966,0 +NC_002945.4 4480 . T C 4873.39 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=163;CIGAR=1X;DP=163;DPB=163;DPRA=0;EPP=3.1302;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=230.571;PAIRED=0.97546;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5469;QR=0;RO=0;RPL=94;RPP=11.3365;RPPR=0;RPR=69;RUN=1;SAF=72;SAP=7.81951;SAR=91;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:163:0,163:0:0:163:5469:-492.275,-49.0679,0 +NC_002945.4 8741 . T C 6443.62 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=221;CIGAR=1X;DP=224;DPB=224;DPRA=0;EPP=24.7152;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=306.56;PAIRED=0.977376;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7233;QR=12;RO=1;RPL=118;RPP=5.22108;RPPR=5.18177;RPR=103;RUN=1;SAF=115;SAP=3.80618;SAR=106;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:224:1,221:1:12:221:7233:-649.748,-65.752,0 +NC_002945.4 29061 . C T 6683.56 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=218;CIGAR=1X;DP=221;DPB=221;DPRA=0;EPP=8.74777;EPPR=7.35324;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=59.5;NS=1;NUMALT=1;ODDS=298.686;PAIRED=0.954128;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7482;QR=24;RO=2;RPL=103;RPP=4.44467;RPPR=7.35324;RPR=115;RUN=1;SAF=108;SAP=3.05014;SAR=110;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:221:2,218:2:24:218:7482:-671.072,-64.0666,0 +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 3844.38 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=137;CIGAR=1X;DP=137;DPB=137;DPRA=0;EPP=5.68898;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=194.527;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4647;QR=0;RO=0;RPL=68;RPP=3.02615;RPPR=0;RPR=69;RUN=1;SAF=131;SAP=250.669;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:137:0,137:0:0:137:4647:-418.367,-41.2411,0 +NC_002945.4 41228 . A C 8160.68 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=279;CIGAR=1X;DP=286;DPB=286;DPRA=0;EPP=12.5445;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=356.696;PAIRED=0.992832;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9191;QR=99;RO=7;RPL=131;RPP=5.2596;RPPR=3.32051;RPR=148;RUN=1;SAF=140;SAP=3.01808;SAR=139;SRF=0;SRP=18.2106;SRR=7;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:286:7,279:7:99:279:9191:-817.976,-77.0432,0 +NC_002945.4 41437 . T C 7833.61 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=256;CIGAR=1X;DP=257;DPB=257;DPRA=0;EPP=3.85853;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=359.497;PAIRED=0.984375;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8761;QR=0;RO=0;RPL=133;RPP=3.85853;RPPR=0;RPR=123;RUN=1;SAF=144;SAP=11.6962;SAR=112;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:257:0,256:0:0:256:8761:-788.305,-77.0637,0 +NC_002945.4 50470 . C T 7146.42 . 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GT ./. +NC_002945.4 624669 . N . . . . GT ./. +NC_002945.4 624670 . N . . . . GT ./. +NC_002945.4 624671 . N . . . . GT ./. +NC_002945.4 624672 . N . . . . GT ./. +NC_002945.4 624673 . N . . . . GT ./. +NC_002945.4 624674 . N . . . . GT ./. +NC_002945.4 624675 . N . . . . GT ./. +NC_002945.4 624676 . N . . . . GT ./. +NC_002945.4 624677 . N . . . . GT ./. +NC_002945.4 624678 . N . . . . GT ./. +NC_002945.4 624679 . N . . . . GT ./. +NC_002945.4 624901 . N . . . . GT ./. +NC_002945.4 624902 . N . . . . GT ./. +NC_002945.4 624903 . N . . . . GT ./. +NC_002945.4 624904 . N . . . . GT ./. +NC_002945.4 624905 . N . . . . GT ./. +NC_002945.4 624906 . N . . . . GT ./. +NC_002945.4 624907 . N . . . . GT ./. +NC_002945.4 624908 . N . . . . GT ./. +NC_002945.4 624909 . N . . . . GT ./. +NC_002945.4 624910 . N . . . . GT ./. +NC_002945.4 624911 . N . . . . GT ./. +NC_002945.4 641896 . A C 6646.66 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=217;CIGAR=1X;DP=217;DPB=217;DPRA=0;EPP=5.26183;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=305.431;PAIRED=0.990783;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7442;QR=0;RO=0;RPL=94;RPP=11.426;RPPR=0;RPR=123;RUN=1;SAF=101;SAP=5.26183;SAR=116;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:217:0,217:0:0:217:7442:-669.755,-65.3235,0 +NC_002945.4 642875 . C G 7980.41 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=255;CIGAR=1X;DP=256;DPB=256;DPRA=0;EPP=4.92631;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=352.807;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8971;QR=14;RO=1;RPL=164;RPP=48.3898;RPPR=5.18177;RPR=91;RUN=1;SAF=125;SAP=3.22319;SAR=130;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:256:1,255:1:14:255:8971:-805.839,-75.6637,0 +NC_002945.4 644245 . C G 5488.97 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=190;CIGAR=1X;DP=192;DPB=192;DPRA=0;EPP=3.05602;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=247.117;PAIRED=0.978947;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=6207;QR=76;RO=2;RPL=95;RPP=3.0103;RPPR=7.35324;RPR=95;RUN=1;SAF=99;SAP=3.74174;SAR=91;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:192:2,190:2:76:190:6207:-551.485,-50.5829,0 +NC_002945.4 649910 . T C 6733.74 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=223;CIGAR=1X;DP=224;DPB=224;DPRA=0;EPP=4.65594;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=313.749;PAIRED=0.986547;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7540;QR=0;RO=0;RPL=127;RPP=12.3681;RPPR=0;RPR=96;RUN=1;SAF=118;SAP=4.65594;SAR=105;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:224:0,223:0:0:223:7540:-678.455,-67.1297,0 +NC_002945.4 652349 . G C 8112.27 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=262;CIGAR=1X;DP=264;DPB=264;DPRA=0;EPP=4.63476;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=367.814;PAIRED=0.996183;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=9069;QR=0;RO=0;RPL=125;RPP=4.20378;RPPR=0;RPR=137;RUN=1;SAF=143;SAP=7.78422;SAR=119;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:264:0,262:0:0:262:9069:-815.907,-78.8699,0 diff -r 000000000000 -r ee4ef1fc23c6 test-data/SRR8073662_zc.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR8073662_zc.vcf Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,1011 @@ +##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/SRR8073662/NC_002945v4.fasta +##contig= +##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/SRR8073662/NC_002945v4.fasta /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR8073662/SRR8073662-nodup.bam --region NC_002945.4:0-100000 +##filter="QUAL > 20 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8073662 +NC_002945.4 1057 . A G 1991.37 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=78;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=4.01252;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=112.736;PAIRED=0.961538;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2256;QR=0;RO=0;RPL=41;RPP=3.45573;RPPR=0;RPR=37;RUN=1;SAF=47;SAP=10.1372;SAR=31;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:80:0,78:0:0:78:2256:-203.125,-23.4803,0 +NC_002945.4 4480 . T C 1266.94 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=48;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=71.1473;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1446;QR=0;RO=0;RPL=26;RPP=3.73412;RPPR=0;RPR=22;RUN=1;SAF=24;SAP=3.0103;SAR=24;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:49:0,48:0:0:48:1446:-130.232,-14.4494,0 +NC_002945.4 8741 . T C 1656.81 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=68;CIGAR=1X;DP=68;DPB=68;DPRA=0;EPP=44.396;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=98.8732;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1927;QR=0;RO=0;RPL=35;RPP=3.13803;RPPR=0;RPR=33;RUN=1;SAF=41;SAP=9.26925;SAR=27;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:68:0,68:0:0:68:1927:-173.649,-20.47,0 +NC_002945.4 29061 . C T 1418.86 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=55;CIGAR=1X;DP=56;DPB=56;DPRA=0;EPP=3.36563;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=59.8909;MQMR=0;NS=1;NUMALT=1;ODDS=80.8514;PAIRED=0.854545;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1614;QR=0;RO=0;RPL=22;RPP=7.78754;RPPR=0;RPR=33;RUN=1;SAF=29;SAP=3.36563;SAR=26;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:56:0,55:0:0:55:1614:-145.339,-16.5567,0 +NC_002945.4 29470 . N . . . . GT ./. +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 . . . . 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AB=0;ABP=0;AC=2;AF=1;AN=2;AO=23;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=7.63648;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=50.7391;MQMR=0;NS=1;NUMALT=1;ODDS=36.4899;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=784;QR=0;RO=0;RPL=13;RPP=3.86001;RPPR=0;RPR=10;RUN=1;SAF=6;SAP=14.4341;SAR=17;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:23:0,23:0:0:23:784:-64.6602,-6.92369,0 +NC_002945.4 103814 . C G 586.81 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=23;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=10.6577;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=50.7391;MQMR=0;NS=1;NUMALT=1;ODDS=36.4899;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=768;QR=0;RO=0;RPL=14;RPP=5.3706;RPPR=0;RPR=9;RUN=1;SAF=6;SAP=14.4341;SAR=17;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:23:0,23:0:0:23:768:-63.1462,-6.92369,0 +NC_002945.4 110198 . C T 2695.05 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=91;CIGAR=1X;DP=94;DPB=94;DPRA=0;EPP=3.60686;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=130.758;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3034;QR=0;RO=0;RPL=44;RPP=3.22506;RPPR=0;RPR=47;RUN=1;SAF=50;SAP=4.94315;SAR=41;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:94:0,91:0:0:91:3034:-273.013,-27.3937,0 +NC_002945.4 114965 . C T 1722.74 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=59;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=9.23028;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=86.3965;PAIRED=0.983051;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1959;QR=0;RO=0;RPL=23;RPP=9.23028;RPPR=0;RPR=36;RUN=1;SAF=27;SAP=3.93042;SAR=32;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:59:0,59:0:0:59:1959:-176.553,-17.7608,0 +NC_002945.4 117800 . C G 1957.8 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=72;CIGAR=1X;DP=73;DPB=73;DPRA=0;EPP=17.6074;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=100.831;PAIRED=0.972222;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2227;QR=12;RO=1;RPL=36;RPP=3.0103;RPPR=5.18177;RPR=36;RUN=1;SAF=37;SAP=3.13094;SAR=35;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:73:1,72:1:12:72:2227:-199.435,-20.7752,0 +NC_002945.4 127447 . G C 1892.36 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=70;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=4.99565;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=101.646;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2137;QR=0;RO=0;RPL=36;RPP=3.13438;RPPR=0;RPR=34;RUN=1;SAF=33;SAP=3.50664;SAR=37;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:70:0,70:0:0:70:2137:-192.56,-21.0721,0 +NC_002945.4 130166 . C T 1493.38 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=52;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=3.17734;EPPR=7.35324;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.1691;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1708;QR=28;RO=2;RPL=25;RPP=3.17734;RPPR=3.0103;RPR=27;RUN=1;SAF=30;SAP=5.68288;SAR=22;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:55:2,52:2:28:52:1708:-151.305,-13.7356,0 +NC_002945.4 130237 . T C 1891.76 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=63;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=3.32051;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=91.9417;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2145;QR=0;RO=0;RPL=24;RPP=10.7656;RPPR=0;RPR=39;RUN=1;SAF=35;SAP=4.69922;SAR=28;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:64:0,63:0:0:63:2145:-193.142,-18.9649,0 +NC_002945.4 132052 . N . . . . GT ./. +NC_002945.4 132620 . N . . . . GT ./. +NC_002945.4 132621 . N . . . . GT ./. +NC_002945.4 132622 . N . . . . GT ./. +NC_002945.4 132623 . N . . . . GT ./. +NC_002945.4 132624 . N . . . . GT ./. +NC_002945.4 132625 . N . . . . GT ./. +NC_002945.4 132626 . N . . . . GT ./. +NC_002945.4 132627 . N . . . . GT ./. +NC_002945.4 132628 . N . . . . GT ./. +NC_002945.4 132629 . N . . . . GT ./. +NC_002945.4 132630 . N . . . . GT ./. +NC_002945.4 132631 . N . . . . GT ./. +NC_002945.4 132632 . N . . . . GT ./. +NC_002945.4 132633 . N . . . . GT ./. +NC_002945.4 132634 . N . . . . GT ./. +NC_002945.4 132635 . N . . . . GT ./. +NC_002945.4 132636 . N . . . . GT ./. +NC_002945.4 132637 . N . . . . GT ./. +NC_002945.4 132638 . N . . . . GT ./. +NC_002945.4 132639 . N . . . . GT ./. +NC_002945.4 132640 . N . . . . GT ./. +NC_002945.4 132641 . N . . . . GT ./. +NC_002945.4 132642 . N . . . . GT ./. +NC_002945.4 132643 . N . . . . GT ./. +NC_002945.4 132644 . N . . . . GT ./. +NC_002945.4 132645 . N . . . . GT ./. +NC_002945.4 132646 . N . . . . GT ./. +NC_002945.4 132647 . N . . . . GT ./. +NC_002945.4 132648 . N . . . . GT ./. +NC_002945.4 132649 . N . . . . GT ./. +NC_002945.4 132650 . N . . . . GT ./. +NC_002945.4 132651 . N . . . . GT ./. +NC_002945.4 132652 . N . . . . GT ./. +NC_002945.4 132653 . N . . . . GT ./. +NC_002945.4 132654 . N . . . . GT ./. +NC_002945.4 132655 . N . . . . GT ./. +NC_002945.4 132656 . N . . . . GT ./. +NC_002945.4 132657 . N . . . . GT ./. +NC_002945.4 132658 . N . . . . GT ./. +NC_002945.4 132659 . N . . . . GT ./. +NC_002945.4 132660 . N . . . . GT ./. +NC_002945.4 132661 . N . . . . GT ./. +NC_002945.4 132662 . N . . . . GT ./. +NC_002945.4 132663 . N . . . . GT ./. +NC_002945.4 132664 . N . . . . GT ./. +NC_002945.4 132665 . N . . . . GT ./. +NC_002945.4 132666 . N . . . . GT ./. +NC_002945.4 132667 . N . . . . GT ./. +NC_002945.4 132668 . N . . . . GT ./. +NC_002945.4 132669 . N . . . . GT ./. +NC_002945.4 132670 . N . . . . GT ./. +NC_002945.4 132671 . N . . . . GT ./. +NC_002945.4 132672 . N . . . . GT ./. +NC_002945.4 132673 . N . . . . GT ./. +NC_002945.4 132674 . N . . . . GT ./. +NC_002945.4 140686 . A G 2969.95 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=110;CIGAR=1X;DP=112;DPB=112;DPRA=0;EPP=4.2737;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=157.098;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3362;QR=0;RO=0;RPL=71;RPP=23.2247;RPPR=0;RPR=39;RUN=1;SAF=52;SAP=3.72096;SAR=58;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:112:0,110:0:0:110:3362:-302.582,-33.1133,0 +NC_002945.4 143799 . T C 2348.79 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=93;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=3.03365;EPPR=7.35324;GTI=0;LEN=1;MEANALT=3;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=124.333;PAIRED=0.989247;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2699;QR=37;RO=2;RPL=57;RPP=13.3073;RPPR=7.35324;RPR=36;RUN=1;SAF=31;SAP=25.4488;SAR=62;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:97:2,93:2:37:93:2699:-239.615,-25.243,0 +NC_002945.4 144992 . G A 1419.32 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=51;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=3.3935;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=75.3062;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1617;QR=0;RO=0;RPL=19;RPP=10.206;RPPR=0;RPR=32;RUN=1;SAF=28;SAP=4.07475;SAR=23;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:52:0,51:0:0:51:1617:-145.649,-15.3525,0 +NC_002945.4 148871 . G A 2283.59 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=78;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=3.45573;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=59.9231;MQMR=0;NS=1;NUMALT=1;ODDS=112.736;PAIRED=0.974359;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2572;QR=0;RO=0;RPL=41;RPP=3.45573;RPPR=0;RPR=37;RUN=1;SAF=42;SAP=4.01252;SAR=36;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:78:0,78:0:0:78:2572:-231.682,-23.4803,0 +NC_002945.4 149955 . N . . . . GT ./. +NC_002945.4 149956 . N . . . . GT ./. +NC_002945.4 149957 . N . . . . GT ./. +NC_002945.4 149958 . N . . . . GT ./. +NC_002945.4 149959 . N . . . . GT ./. +NC_002945.4 149960 . N . . . . GT ./. +NC_002945.4 149961 . N . . . . GT ./. +NC_002945.4 149962 . N . . . . GT ./. +NC_002945.4 149963 . N . . . . GT ./. +NC_002945.4 149964 . N . . . . GT ./. +NC_002945.4 149965 . N . . . . GT ./. +NC_002945.4 149966 . N . . . . GT ./. +NC_002945.4 149967 . N . . . . GT ./. +NC_002945.4 149968 . N . . . . GT ./. +NC_002945.4 149969 . N . . . . GT ./. +NC_002945.4 149970 . N . . . . GT ./. +NC_002945.4 149971 . N . . . . GT ./. +NC_002945.4 149972 . N . . . . GT ./. +NC_002945.4 149973 . N . . . . GT ./. +NC_002945.4 149974 . N . . . . GT ./. +NC_002945.4 149975 . N . . . . GT ./. +NC_002945.4 149976 . N . . . . GT ./. +NC_002945.4 149977 . N . . . . GT ./. +NC_002945.4 149978 . N . . . . GT ./. +NC_002945.4 149979 . N . . . . GT ./. +NC_002945.4 149980 . N . . . . GT ./. +NC_002945.4 149981 . N . . . . GT ./. +NC_002945.4 149982 . N . . . . GT ./. +NC_002945.4 149983 . N . . . . GT ./. +NC_002945.4 149984 . N . . . . GT ./. +NC_002945.4 149985 . N . . . . GT ./. +NC_002945.4 149986 . N . . . . GT ./. +NC_002945.4 149987 . N . . . . GT ./. +NC_002945.4 149988 . N . . . . GT ./. +NC_002945.4 149989 . N . . . . GT ./. +NC_002945.4 149990 . N . . . . GT ./. +NC_002945.4 149991 . N . . . . GT ./. +NC_002945.4 149992 . N . . . . GT ./. +NC_002945.4 149993 . N . . . . GT ./. +NC_002945.4 149994 . N . . . . GT ./. +NC_002945.4 149995 . N . . . . GT ./. +NC_002945.4 149996 . N . . . . GT ./. +NC_002945.4 149997 . N . . . . GT ./. +NC_002945.4 149998 . N . . . . GT ./. +NC_002945.4 149999 . N . . . . GT ./. +NC_002945.4 150000 . N . . . . GT ./. +NC_002945.4 150001 . N . . . . GT ./. +NC_002945.4 150002 . N . . . . GT ./. +NC_002945.4 150003 . N . . . . GT ./. +NC_002945.4 150004 . N . . . . GT ./. +NC_002945.4 150005 . N . . . . GT ./. +NC_002945.4 150006 . N . . . . GT ./. +NC_002945.4 150007 . N . . . . GT ./. +NC_002945.4 150008 . N . . . . GT ./. +NC_002945.4 150009 . N . . . . GT ./. +NC_002945.4 150010 . N . . . . GT ./. +NC_002945.4 150011 . N . . . . GT ./. +NC_002945.4 150012 . N . . . . GT ./. +NC_002945.4 150013 . N . . . . GT ./. +NC_002945.4 150014 . N . . . . GT ./. +NC_002945.4 150015 . N . . . . GT ./. +NC_002945.4 150016 . N . . . . GT ./. +NC_002945.4 150017 . N . . . . GT ./. +NC_002945.4 150018 . N . . . . GT ./. +NC_002945.4 150019 . N . . . . GT ./. +NC_002945.4 150020 . N . . . . GT ./. +NC_002945.4 150021 . N . . . . GT ./. +NC_002945.4 150022 . N . . . . GT ./. +NC_002945.4 150023 . N . . . . GT ./. +NC_002945.4 150024 . N . . . . GT ./. +NC_002945.4 150025 . N . . . . GT ./. +NC_002945.4 150026 . N . . . . GT ./. +NC_002945.4 150027 . N . . . . GT ./. +NC_002945.4 150028 . N . . . . GT ./. +NC_002945.4 150029 . N . . . . GT ./. +NC_002945.4 150030 . N . . . . GT ./. +NC_002945.4 150031 . N . . . . GT ./. +NC_002945.4 150032 . N . . . . GT ./. +NC_002945.4 150033 . N . . . . GT ./. +NC_002945.4 150034 . N . . . . GT ./. +NC_002945.4 150035 . N . . . . GT ./. +NC_002945.4 150036 . N . . . . GT ./. +NC_002945.4 150037 . N . . . . GT ./. +NC_002945.4 150038 . N . . . . GT ./. +NC_002945.4 150039 . N . . . . GT ./. +NC_002945.4 150040 . N . . . . GT ./. +NC_002945.4 150041 . N . . . . GT ./. +NC_002945.4 150042 . N . . . . GT ./. +NC_002945.4 150043 . N . . . . GT ./. +NC_002945.4 150044 . N . . . . GT ./. +NC_002945.4 150045 . N . . . . GT ./. +NC_002945.4 150046 . N . . . . GT ./. +NC_002945.4 150047 . N . . . . GT ./. +NC_002945.4 150048 . N . . . . GT ./. +NC_002945.4 150049 . N . . . . GT ./. +NC_002945.4 150050 . N . . . . GT ./. +NC_002945.4 150051 . N . . . . GT ./. +NC_002945.4 150052 . N . . . . GT ./. +NC_002945.4 150053 . N . . . . GT ./. +NC_002945.4 150054 . N . . . . GT ./. +NC_002945.4 150055 . N . . . . GT ./. +NC_002945.4 150056 . N . . . . GT ./. +NC_002945.4 150057 . N . . . . GT ./. +NC_002945.4 150058 . N . . . . GT ./. +NC_002945.4 150059 . N . . . . GT ./. +NC_002945.4 150060 . N . . . . GT ./. +NC_002945.4 150061 . N . . . . GT ./. +NC_002945.4 150062 . N . . . . GT ./. +NC_002945.4 150063 . N . . . . GT ./. +NC_002945.4 150064 . N . . . . GT ./. +NC_002945.4 150065 . N . . . . GT ./. +NC_002945.4 150066 . N . . . . GT ./. +NC_002945.4 150067 . N . . . . GT ./. +NC_002945.4 150068 . N . . . . GT ./. +NC_002945.4 150069 . N . . . . GT ./. +NC_002945.4 150070 . N . . . . GT ./. +NC_002945.4 150071 . N . . . . GT ./. +NC_002945.4 150072 . N . . . . GT ./. +NC_002945.4 150073 . N . . . . GT ./. +NC_002945.4 150074 . N . . . . GT ./. +NC_002945.4 150075 . N . . . . GT ./. +NC_002945.4 150076 . N . . . . GT ./. +NC_002945.4 150077 . N . . . . GT ./. +NC_002945.4 150078 . N . . . . GT ./. +NC_002945.4 150079 . N . . . . GT ./. +NC_002945.4 150080 . N . . . . GT ./. +NC_002945.4 150081 . N . . . . GT ./. +NC_002945.4 150082 . N . . . . GT ./. +NC_002945.4 150083 . N . . . . GT ./. +NC_002945.4 150084 . N . . . . GT ./. +NC_002945.4 150085 . N . . . . GT ./. +NC_002945.4 150086 . N . . . . GT ./. +NC_002945.4 150087 . N . . . . GT ./. +NC_002945.4 150088 . N . . . . GT ./. +NC_002945.4 150089 . N . . . . GT ./. +NC_002945.4 150090 . N . . . . GT ./. +NC_002945.4 150091 . N . . . . GT ./. +NC_002945.4 150092 . N . . . . GT ./. +NC_002945.4 150093 . N . . . . GT ./. +NC_002945.4 150094 . N . . . . GT ./. +NC_002945.4 150095 . N . . . . GT ./. +NC_002945.4 150096 . N . . . . GT ./. +NC_002945.4 150097 . N . . . . GT ./. +NC_002945.4 150098 . N . . . . GT ./. +NC_002945.4 150099 . N . . . . GT ./. +NC_002945.4 150100 . N . . . . GT ./. +NC_002945.4 150101 . N . . . . GT ./. +NC_002945.4 150102 . N . . . . GT ./. +NC_002945.4 150103 . N . . . . GT ./. +NC_002945.4 150104 . N . . . . GT ./. +NC_002945.4 150105 . N . . . . GT ./. +NC_002945.4 150106 . N . . . . GT ./. +NC_002945.4 150107 . N . . . . GT ./. +NC_002945.4 150108 . N . . . . GT ./. +NC_002945.4 150109 . N . . . . GT ./. +NC_002945.4 150110 . N . . . . GT ./. +NC_002945.4 150111 . N . . . . GT ./. +NC_002945.4 150112 . N . . . . GT ./. +NC_002945.4 150113 . N . . . . GT ./. +NC_002945.4 150114 . N . . . . GT ./. +NC_002945.4 150115 . N . . . . GT ./. +NC_002945.4 150116 . N . . . . GT ./. +NC_002945.4 150117 . N . . . . GT ./. +NC_002945.4 150118 . N . . . . GT ./. +NC_002945.4 150119 . N . . . . GT ./. +NC_002945.4 150120 . N . . . . GT ./. +NC_002945.4 150121 . N . . . . GT ./. +NC_002945.4 150122 . N . . . . GT ./. +NC_002945.4 150123 . N . . . . GT ./. +NC_002945.4 150124 . N . . . . GT ./. +NC_002945.4 150125 . N . . . . GT ./. +NC_002945.4 150126 . N . . . . GT ./. +NC_002945.4 150127 . N . . . . GT ./. +NC_002945.4 150128 . N . . . . GT ./. +NC_002945.4 150129 . N . . . . GT ./. +NC_002945.4 150130 . N . . . . GT ./. +NC_002945.4 150131 . N . . . . GT ./. +NC_002945.4 150132 . N . . . . GT ./. +NC_002945.4 150133 . N . . . . GT ./. +NC_002945.4 150134 . N . . . . GT ./. +NC_002945.4 150135 . N . . . . GT ./. +NC_002945.4 150136 . N . . . . GT ./. +NC_002945.4 150137 . N . . . . GT ./. +NC_002945.4 150138 . N . . . . GT ./. +NC_002945.4 150139 . N . . . . GT ./. +NC_002945.4 150140 . N . . . . GT ./. +NC_002945.4 150141 . N . . . . GT ./. +NC_002945.4 150142 . N . . . . GT ./. +NC_002945.4 150143 . N . . . . GT ./. +NC_002945.4 151022 . N . . . . GT ./. +NC_002945.4 151023 . N . . . . GT ./. +NC_002945.4 151024 . N . . . . GT ./. +NC_002945.4 151025 . N . . . . GT ./. +NC_002945.4 151026 . N . . . . GT ./. +NC_002945.4 151027 . N . . . . GT ./. +NC_002945.4 151028 . N . . . . GT ./. +NC_002945.4 151029 . N . . . . GT ./. +NC_002945.4 151030 . N . . . . GT ./. +NC_002945.4 151031 . N . . . . GT ./. +NC_002945.4 151032 . N . . . . GT ./. +NC_002945.4 151033 . N . . . . GT ./. +NC_002945.4 151034 . N . . . . GT ./. +NC_002945.4 151035 . N . . . . GT ./. +NC_002945.4 151036 . N . . . . GT ./. +NC_002945.4 151037 . N . . . . GT ./. +NC_002945.4 151038 . N . . . . GT ./. +NC_002945.4 151039 . N . . . . GT ./. +NC_002945.4 151040 . N . . . . GT ./. +NC_002945.4 159370 . A G 1749.91 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=62;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=3.15039;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=90.5554;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1998;QR=0;RO=0;RPL=42;RPP=19.9618;RPPR=0;RPR=20;RUN=1;SAF=26;SAP=6.51267;SAR=36;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:62:0,62:0:0:62:1998:-180.043,-18.6639,0 +NC_002945.4 160535 . T C 1804.25 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=74;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=3.12768;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQ=59.8649;MQMR=60;NS=1;NUMALT=1;ODDS=100.699;PAIRED=0.986486;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2050;QR=25;RO=2;RPL=41;RPP=4.88833;RPPR=7.35324;RPR=33;RUN=1;SAF=31;SAP=7.23587;SAR=43;SRF=2;SRP=7.35324;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:76:2,74:2:25:74:2050:-182.337,-20.5033,0 +NC_002945.4 165799 . G A 1394.34 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=48;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.9056;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=71.1473;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1583;QR=0;RO=0;RPL=25;RPP=3.19126;RPPR=0;RPR=23;RUN=1;SAF=25;SAP=3.19126;SAR=23;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:51:0,48:0:0:48:1583:-142.577,-14.4494,0 +NC_002945.4 166696 . A G 1822.75 . 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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 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=193;CIGAR=1X;DP=195;DPB=195;DPRA=0;EPP=10.0423;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=272.16;PAIRED=0.746114;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6714;QR=0;RO=0;RPL=90;RPP=4.91174;RPPR=0;RPR=103;RUN=1;SAF=119;SAP=25.7939;SAR=74;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:195:0,193:0:0:193:6714:-604.088,-58.0988,0 +NC_002945.4 59861 . A G 4760.67 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=153;CIGAR=1X;DP=153;DPB=153;DPRA=0;EPP=11.8807;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=216.708;PAIRED=0.986928;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5376;QR=0;RO=0;RPL=55;RPP=29.2525;RPPR=0;RPR=98;RUN=1;SAF=88;SAP=10.5182;SAR=65;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:153:0,153:0:0:153:5376:-483.917,-46.0576,0 +NC_002945.4 69913 . T C 7603.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=255;CIGAR=1X;DP=257;DPB=257;DPRA=0;EPP=3.70006;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=353.556;PAIRED=0.988235;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8501;QR=12;RO=1;RPL=138;RPP=6.76567;RPPR=5.18177;RPR=117;RUN=1;SAF=127;SAP=3.01882;SAR=128;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:257:1,255:1:12:255:8501:-763.836,-75.9887,0 +NC_002945.4 70082 . G A 5924.16 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=194;CIGAR=1X;DP=197;DPB=197;DPRA=0;EPP=14.4721;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=273.546;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6664;QR=0;RO=0;RPL=117;RPP=20.9194;RPPR=0;RPR=77;RUN=1;SAF=86;SAP=8.42779;SAR=108;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:197:0,194:0:0:194:6664:-599.623,-58.3998,0 +NC_002945.4 70438 . A G 6080.55 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=196;CIGAR=1X;DP=196;DPB=196;DPRA=0;EPP=4.60567;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=276.319;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6801;QR=0;RO=0;RPL=93;RPP=4.11819;RPPR=0;RPR=103;RUN=1;SAF=97;SAP=3.05462;SAR=99;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:196:0,196:0:0:196:6801:-612.063,-59.0019,0 +NC_002945.4 79918 . G A 4959.13 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=161;CIGAR=1X;DP=163;DPB=163;DPRA=0;EPP=21.4746;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=227.799;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5574;QR=0;RO=0;RPL=86;RPP=4.64228;RPPR=0;RPR=75;RUN=1;SAF=79;SAP=3.13169;SAR=82;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:163:0,161:0:0:161:5574:-501.545,-48.4658,0 +NC_002945.4 96244 . G A 2669.63 . 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GT ./. +NC_002945.4 306660 . N . . . . GT ./. +NC_002945.4 306661 . N . . . . GT ./. +NC_002945.4 306662 . N . . . . GT ./. +NC_002945.4 306663 . N . . . . GT ./. +NC_002945.4 306664 . N . . . . GT ./. +NC_002945.4 306665 . N . . . . GT ./. +NC_002945.4 306666 . N . . . . GT ./. +NC_002945.4 306667 . N . . . . GT ./. +NC_002945.4 306668 . N . . . . GT ./. +NC_002945.4 306669 . N . . . . GT ./. +NC_002945.4 306670 . N . . . . GT ./. +NC_002945.4 306671 . N . . . . GT ./. +NC_002945.4 306672 . N . . . . GT ./. +NC_002945.4 306673 . N . . . . GT ./. +NC_002945.4 306674 . N . . . . GT ./. +NC_002945.4 306675 . N . . . . GT ./. +NC_002945.4 306676 . N . . . . GT ./. +NC_002945.4 306677 . N . . . . GT ./. +NC_002945.4 306678 . N . . . . GT ./. +NC_002945.4 306679 . N . . . . GT ./. +NC_002945.4 306680 . N . . . . GT ./. +NC_002945.4 306681 . N . . . . GT ./. +NC_002945.4 306682 . N . . . . GT ./. +NC_002945.4 306683 . N . . . . GT ./. +NC_002945.4 306684 . N . . . . GT ./. +NC_002945.4 306685 . N . . . . GT ./. +NC_002945.4 306686 . N . . . . GT ./. +NC_002945.4 306687 . N . . . . GT ./. +NC_002945.4 306688 . N . . . . GT ./. +NC_002945.4 306689 . N . . . . GT ./. +NC_002945.4 306690 . N . . . . GT ./. +NC_002945.4 306691 . N . . . . GT ./. +NC_002945.4 306692 . N . . . . GT ./. +NC_002945.4 306693 . N . . . . GT ./. +NC_002945.4 306694 . N . . . . GT ./. +NC_002945.4 306695 . N . . . . GT ./. +NC_002945.4 306696 . N . . . . GT ./. +NC_002945.4 306697 . N . . . . GT ./. +NC_002945.4 306698 . N . . . . GT ./. +NC_002945.4 306699 . N . . . . GT ./. +NC_002945.4 306700 . N . . . . GT ./. +NC_002945.4 306701 . N . . . . GT ./. +NC_002945.4 306702 . N . . . . GT ./. +NC_002945.4 306703 . N . . . . GT ./. +NC_002945.4 306704 . N . . . . GT ./. +NC_002945.4 306705 . N . . . . GT ./. +NC_002945.4 306706 . N . . . . GT ./. +NC_002945.4 306707 . N . . . . GT ./. +NC_002945.4 306708 . N . . . . GT ./. +NC_002945.4 306709 . N . . . . GT ./. +NC_002945.4 306710 . N . . . . GT ./. +NC_002945.4 319911 . C T 5117.89 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=173;CIGAR=1X;DP=174;DPB=174;DPRA=0;EPP=3.02285;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=59.815;MQMR=0;NS=1;NUMALT=1;ODDS=244.434;PAIRED=0.99422;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5734;QR=0;RO=0;RPL=95;RPP=6.63779;RPPR=0;RPR=78;RUN=1;SAF=81;SAP=4.52908;SAR=92;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:174:0,173:0:0:173:5734:-515.956,-52.0782,0 +NC_002945.4 332124 . C T 235.47099999999998 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=10;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=6.48466;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=59.1;MQMR=0;NS=1;NUMALT=1;ODDS=18.4681;PAIRED=0.9;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=314;QR=0;RO=0;RPL=10;RPP=24.725;RPPR=0;RPR=0;RUN=1;SAF=7;SAP=6.48466;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:11:0,10:0:0:10:314:-28.4197,-3.0103,0 +NC_002945.4 332128 . C G 201.09 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=10;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=10.8276;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=59.1;MQMR=0;NS=1;NUMALT=1;ODDS=18.4681;PAIRED=0.9;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=284;QR=0;RO=0;RPL=10;RPP=24.725;RPPR=0;RPR=0;RUN=1;SAF=8;SAP=10.8276;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:10:0,10:0:0:10:284:-25.8335,-3.0103,0 +NC_002945.4 332144 . C T 125.417 . 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=196;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 1/1:6:0,6:0:0:6:196:-17.9602,-1.80618,0 +NC_002945.4 332145 . G T 139.142 . 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 . 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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 . . . . 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AB=0;ABP=0;AC=2;AF=1;AN=2;AO=179;CIGAR=1X;DP=179;DPB=179;DPRA=0;EPP=3.02243;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=252.752;PAIRED=0.977654;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6172;QR=0;RO=0;RPL=86;RPP=3.60473;RPPR=0;RPR=93;RUN=1;SAF=92;SAP=3.31358;SAR=87;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:179:0,179:0:0:179:6172:-555.473,-53.8844,0 +NC_002945.4 518522 . C T 5022.35 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=170;CIGAR=1X;DP=175;DPB=175;DPRA=0;EPP=3.8278;EPPR=9.52472;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=222.502;PAIRED=0.994118;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=5690;QR=59;RO=3;RPL=64;RPP=25.5425;RPPR=3.73412;RPR=106;RUN=1;SAF=91;SAP=4.84966;SAR=79;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:175:3,170:3:59:170:5690:-506.649,-46.7265,0 +NC_002945.4 519412 . T C 2988.47 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=100;CIGAR=1X;DP=100;DPB=100;DPRA=0;EPP=4.40004;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=143.235;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3388;QR=0;RO=0;RPL=34;RPP=25.2462;RPPR=0;RPR=66;RUN=1;SAF=58;SAP=8.56927;SAR=42;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:100:0,100:0:0:100:3388:-305.075,-30.103,0 +NC_002945.4 541571 . T C 4690.54 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=154;CIGAR=1X;DP=154;DPB=154;DPRA=0;EPP=15.7007;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=218.095;PAIRED=0.993506;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5283;QR=0;RO=0;RPL=60;RPP=19.3104;RPPR=0;RPR=94;RUN=1;SAF=78;SAP=3.0667;SAR=76;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:154:0,154:0:0:154:5283:-475.539,-46.3586,0 +NC_002945.4 544180 . C T 6381.36 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=214;CIGAR=1X;DP=218;DPB=218;DPRA=0;EPP=4.02501;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=301.272;PAIRED=0.990654;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7162;QR=0;RO=0;RPL=131;RPP=26.3891;RPPR=0;RPR=83;RUN=1;SAF=103;SAP=3.65971;SAR=111;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:218:0,214:0:0:214:7162:-644.439,-64.4204,0 +NC_002945.4 577068 . G T 3066.54 . AB=0.881481;ABP=173.656;AC=1;AF=0.5;AN=2;AO=119;CIGAR=1X;DP=135;DPB=135;DPRA=0;EPP=9.59771;EPPR=4.31318;GTI=0;LEN=1;MEANALT=2;MQ=59.8487;MQMR=60;NS=1;NUMALT=1;ODDS=61.7924;PAIRED=0.991597;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=3865;QR=471;RO=15;RPL=63;RPP=3.90444;RPPR=35.5824;RPR=56;RUN=1;SAF=50;SAP=9.59771;SAR=69;SRF=9;SRP=4.31318;SRR=6;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:135:15,119:15:471:119:3865:-307.53,0,-2.2127 +NC_002945.4 598704 . C G 6668.19 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=222;CIGAR=1X;DP=222;DPB=222;DPRA=0;EPP=27.4638;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=312.363;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7554;QR=0;RO=0;RPL=70;RPP=68.7805;RPPR=0;RPR=152;RUN=1;SAF=112;SAP=3.04943;SAR=110;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:222:0,222:0:0:222:7554:-679.797,-66.8287,0 +NC_002945.4 600207 . T C 6781.53 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=217;CIGAR=1X;DP=217;DPB=217;DPRA=0;EPP=8.30389;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=59.9724;MQMR=0;NS=1;NUMALT=1;ODDS=305.431;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7591;QR=0;RO=0;RPL=96;RPP=9.26454;RPPR=0;RPR=121;RUN=1;SAF=110;SAP=3.10036;SAR=107;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:217:0,217:0:0:217:7591:-683.114,-65.3235,0 +NC_002945.4 608835 . T C 209.35299999999998 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=11;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=19.0002;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=34.8182;MQMR=0;NS=1;NUMALT=1;ODDS=19.8544;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=377;QR=0;RO=0;RPL=1;RPP=19.0002;RPPR=0;RPR=10;RUN=1;SAF=11;SAP=26.8965;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:12:0,11:0:0:11:377:-28.7865,-3.31133,0 +NC_002945.4 611077 . A G 6633.15 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=225;CIGAR=1X;DP=230;DPB=230;DPRA=0;EPP=3.4832;EPPR=7.35324;GTI=0;LEN=1;MEANALT=3;MQ=59.96;MQMR=60;NS=1;NUMALT=1;ODDS=308.327;PAIRED=0.991111;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7440;QR=24;RO=2;RPL=100;RPP=9.04217;RPPR=7.35324;RPR=125;RUN=1;SAF=131;SAP=16.2225;SAR=94;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:230:2,225:2:24:225:7440:-667.303,-66.1738,0 +NC_002945.4 622386 . C G 6094.46 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=199;CIGAR=1X;DP=200;DPB=200;DPRA=0;EPP=3.89417;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=280.478;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6828;QR=0;RO=0;RPL=90;RPP=6.9495;RPPR=0;RPR=109;RUN=1;SAF=112;SAP=9.83025;SAR=87;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:200:0,199:0:0:199:6828:-614.351,-59.905,0 diff -r 000000000000 -r ee4ef1fc23c6 test-data/json_all_vcf.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/json_all_vcf.json Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,1 @@ +{"columns":[ diff -r 000000000000 -r ee4ef1fc23c6 test-data/json_avg_mq_all_vcf.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/json_avg_mq_all_vcf.json Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,1 @@ +{"name":null,"index":[ diff -r 000000000000 -r ee4ef1fc23c6 test-data/output_fasta.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_fasta.fasta Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,4 @@ +>SRR1792272_zc +>SRR8073662_zc +>input_zc_vcf_vcf +>root diff -r 000000000000 -r ee4ef1fc23c6 test-data/output_json_avg_mq.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_json_avg_mq.json Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,1 @@ +{"name":null,"index":["NC_002945 diff -r 000000000000 -r ee4ef1fc23c6 test-data/output_json_snps.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_json_snps.json Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,1 @@ +{"columns":["NC_002945 diff -r 000000000000 -r ee4ef1fc23c6 test-data/output_summary.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_summary.html Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,6 @@ + + +
Number of VCF inputs: 3
Reference: +
Total run time: + + diff -r 000000000000 -r ee4ef1fc23c6 tool-data/vsnp_excel.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/vsnp_excel.loc.sample Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,4 @@ +## vSNP Excel files +#Value Name Path Description +#AF2122 Mbovis_define_filter.xlsx vsnp/AF2122/Mbovis_define_filter.xlsx Excel file for Mycobacterium bovis AF2122/97 +#NC_006932 Bab1_define_filter.xlsx /vsnp/NC_006932/Bab1_define_filter.xlsx Excel file for Brucella abortus bv. 1 str. 9-941 diff -r 000000000000 -r ee4ef1fc23c6 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,7 @@ + + + value, name, path, description + +
+ + diff -r 000000000000 -r ee4ef1fc23c6 vsnp_get_snps.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vsnp_get_snps.py Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,519 @@ +#!/usr/bin/env python + +# Collect quality parsimonious SNPs from vcf files and output alignment files in fasta format. + +import argparse +import multiprocessing +import os +import pandas +import queue +import shutil +import sys +import time +import vcf +from collections import OrderedDict +from datetime import datetime + +ALL_VCFS_DIR = 'all_vcf' +INPUT_VCF_DIR = 'input_vcf_dir' +OUTPUT_JSON_AVG_MQ_DIR = 'output_json_avg_mq_dir' +OUTPUT_JSON_SNPS_DIR = 'output_json_snps_dir' +OUTPUT_SNPS_DIR = 'output_snps_dir' + + +def get_time_stamp(): + return datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H-%M-%S') + + +def set_num_cpus(num_files, processes): + num_cpus = int(multiprocessing.cpu_count()) + if num_files < num_cpus and num_files < processes: + return num_files + if num_cpus < processes: + half_cpus = int(num_cpus / 2) + if num_files < half_cpus: + return num_files + return half_cpus + return processes + + +def setup_all_vcfs(vcf_files, vcf_dirs): + # Create the all_vcfs directory and link + # all input vcf files into it for processing. + os.makedirs(ALL_VCFS_DIR) + vcf_dirs.append(ALL_VCFS_DIR) + for vcf_file in vcf_files: + file_name_base = os.path.basename(vcf_file) + dst_file = os.path.join(ALL_VCFS_DIR, file_name_base) + os.symlink(vcf_file, dst_file) + return vcf_dirs + + +class SnpFinder: + + def __init__(self, num_files, reference, excel_grouper_file, + all_isolates, ac, mq_val, n_threshold, qual_threshold, output_summary): + self.ac = ac + self.all_isolates = all_isolates + self.all_positions = None + # Filter based on the contents of an Excel file. + self.excel_grouper_file = excel_grouper_file + # Use Genbank file + self.groups = [] + # This will be populated from the columns + # in the Excel filter file if it is used. + self.mq_val = mq_val + self.n_threshold = n_threshold + self.qual_threshold = qual_threshold + self.reference = reference + self.start_time = get_time_stamp() + self.summary_str = "" + self.timer_start = datetime.now() + self.num_files = num_files + self.initiate_summary(output_summary) + + def append_to_summary(self, html_str): + self.summary_str = "%s%s" % (self.summary_str, html_str) + + def bin_input_files(self, filename, samples_groups_dict, defining_snps, inverted_defining_snps, found_positions, found_positions_mix): + sample_groups_list = [] + table_name = self.get_base_file_name(filename) + try: + defining_snp = False + # Absolute positions in set union of two lists. + for abs_position in list(defining_snps.keys() & (found_positions.keys() | found_positions_mix.keys())): + group = defining_snps[abs_position] + sample_groups_list.append(group) + self.check_add_group(group) + if len(list(defining_snps.keys() & found_positions_mix.keys())) > 0: + table_name = self.get_base_file_name(filename) + table_name = '%s[[MIXED]]' % table_name + self.copy_file(filename, group) + defining_snp = True + if not set(inverted_defining_snps.keys()).intersection(found_positions.keys() | found_positions_mix.keys()): + for abs_position in list(inverted_defining_snps.keys()): + group = inverted_defining_snps[abs_position] + sample_groups_list.append(group) + self.check_add_group(group) + self.copy_file(filename, group) + defining_snp = True + if defining_snp: + samples_groups_dict[table_name] = sorted(sample_groups_list) + else: + samples_groups_dict[table_name] = ['No defining SNP'] + except TypeError as e: + msg = "
Error processing file %s to generate samples_groups_dict: %s
" % (filename, str(e)) + self.append_to_summary(msg) + samples_groups_dict[table_name] = [msg] + return samples_groups_dict + + def check_add_group(self, group): + if group not in self.groups: + self.groups.append(group) + + def copy_file(self, filename, dir): + if not os.path.exists(dir): + os.makedirs(dir) + shutil.copy(filename, dir) + + def decide_snps(self, filename): + positions_dict = self.all_positions + # Find the SNPs in a vcf file to produce a pandas data + # frame and a dictionary containing sample map qualities. + sample_map_qualities = {} + # Eliminate the path. + file_name_base = self.get_base_file_name(filename) + vcf_reader = vcf.Reader(open(filename, 'r')) + sample_dict = {} + for record in vcf_reader: + alt = str(record.ALT[0]) + record_position = "%s:%s" % (str(record.CHROM), str(record.POS)) + if record_position in positions_dict: + if alt == "None": + sample_dict.update({record_position: "-"}) + else: + # Not sure this is the best place to capture MQM average + # may be faster after parsimony SNPs are decided, but + # then it will require opening the files again. + # On rare occassions MQM gets called "NaN", thus passing + # a string when a number is expected when calculating average. + mq_val = self.get_mq_val(record.INFO, filename) + if str(mq_val).lower() not in ["nan"]: + sample_map_qualities.update({record_position: mq_val}) + # Add parameters here to change what each vcf represents. + # SNP is represented in table, now how will the vcf represent + # the called position alt != "None", which means a deletion + # as alt is not record.FILTER, or rather passed. + len_alt = len(alt) + if len_alt == 1: + qual_val = self.val_as_int(record.QUAL) + ac = record.INFO['AC'][0] + ref = str(record.REF[0]) + if ac == 2 and qual_val > self.n_threshold: + sample_dict.update({record_position: alt}) + elif ac == 1 and qual_val > self.n_threshold: + alt_ref = "%s%s" % (alt, ref) + if alt_ref == "AG": + sample_dict.update({record_position: "R"}) + elif alt_ref == "CT": + sample_dict.update({record_position: "Y"}) + elif alt_ref == "GC": + sample_dict.update({record_position: "S"}) + elif alt_ref == "AT": + sample_dict.update({record_position: "W"}) + elif alt_ref == "GT": + sample_dict.update({record_position: "K"}) + elif alt_ref == "AC": + sample_dict.update({record_position: "M"}) + elif alt_ref == "GA": + sample_dict.update({record_position: "R"}) + elif alt_ref == "TC": + sample_dict.update({record_position: "Y"}) + elif alt_ref == "CG": + sample_dict.update({record_position: "S"}) + elif alt_ref == "TA": + sample_dict.update({record_position: "W"}) + elif alt_ref == "TG": + sample_dict.update({record_position: "K"}) + elif alt_ref == "CA": + sample_dict.update({record_position: "M"}) + else: + sample_dict.update({record_position: "N"}) + # Poor calls + elif qual_val <= 50: + # Do not coerce record.REF[0] to a string! + sample_dict.update({record_position: record.REF[0]}) + elif qual_val <= self.n_threshold: + sample_dict.update({record_position: "N"}) + else: + # Insurance -- Will still report on a possible + # SNP even if missed with above statement + # Do not coerce record.REF[0] to a string! + sample_dict.update({record_position: record.REF[0]}) + # Merge dictionaries and order + merge_dict = {} + # abs_pos:REF + merge_dict.update(positions_dict) + # abs_pos:ALT replacing all_positions, because keys must be unique + merge_dict.update(sample_dict) + sample_df = pandas.DataFrame(merge_dict, index=[file_name_base]) + return sample_df, file_name_base, sample_map_qualities + + def df_to_fasta(self, parsimonious_df, group): + # Generate SNP alignment file from the parsimonious_df + # data frame. + snps_file = os.path.join(OUTPUT_SNPS_DIR, "%s.fasta" % group) + test_duplicates = [] + has_sequence_data = False + for index, row in parsimonious_df.iterrows(): + for pos in row: + if len(pos) > 0: + has_sequence_data = True + break + if has_sequence_data: + with open(snps_file, 'w') as fh: + for index, row in parsimonious_df.iterrows(): + test_duplicates.append(row.name) + if test_duplicates.count(row.name) < 2: + print(f'>{row.name}', file=fh) + for pos in row: + print(pos, end='', file=fh) + print("", file=fh) + return has_sequence_data + + def find_initial_positions(self, filename): + # Find SNP positions in a vcf file. + found_positions = {} + found_positions_mix = {} + try: + vcf_reader = vcf.Reader(open(filename, 'r')) + try: + for record in vcf_reader: + qual_val = self.val_as_int(record.QUAL) + chrom = record.CHROM + position = record.POS + absolute_position = "%s:%s" % (str(chrom), str(position)) + alt = str(record.ALT[0]) + if alt != "None": + mq_val = self.get_mq_val(record.INFO, filename) + ac = record.INFO['AC'][0] + len_ref = len(record.REF) + if ac == self.ac and len_ref == 1 and qual_val > self.qual_threshold and mq_val > self.mq_val: + found_positions.update({absolute_position: record.REF}) + if ac == 1 and len_ref == 1 and qual_val > self.qual_threshold and mq_val > self.mq_val: + found_positions_mix.update({absolute_position: record.REF}) + return found_positions, found_positions_mix + except (ZeroDivisionError, ValueError, UnboundLocalError, TypeError) as e: + self.append_to_summar("
Error parsing record in file %s: %s
" % (filename, str(e))) + return {'': ''}, {'': ''} + except (SyntaxError, AttributeError) as e: + self.append_to_summary("
Error attempting to read file %s: %s
" % (filename, str(e))) + return {'': ''}, {'': ''} + + def gather_and_filter(self, prefilter_df, mq_averages, group_dir): + # Group a data frame of SNPs. + if self.excel_grouper_file is None: + filtered_all_df = prefilter_df + sheet_names = None + else: + # Filter positions to be removed from all. + xl = pandas.ExcelFile(self.excel_grouper_file) + sheet_names = xl.sheet_names + # Use the first column to filter "all" postions. + exclusion_list_all = self.get_position_list(sheet_names, 0) + exclusion_list_group = self.get_position_list(sheet_names, group_dir) + exclusion_list = exclusion_list_all + exclusion_list_group + # Filters for all applied. + filtered_all_df = prefilter_df.drop(columns=exclusion_list, errors='ignore') + json_snps_file = os.path.join(OUTPUT_JSON_SNPS_DIR, "%s.json" % group_dir) + parsimonious_df = self.get_parsimonious_df(filtered_all_df) + samples_number, columns = parsimonious_df.shape + if samples_number >= 4: + has_sequence_data = self.df_to_fasta(parsimonious_df, group_dir) + if has_sequence_data: + json_avg_mq_file = os.path.join(OUTPUT_JSON_AVG_MQ_DIR, "%s.json" % group_dir) + mq_averages.to_json(json_avg_mq_file, orient='split') + parsimonious_df.to_json(json_snps_file, orient='split') + else: + msg = "
No sequence data" + if group_dir is not None: + msg = "%s for group: %s" % (msg, group_dir) + self.append_to_summary("%s
\n" % msg) + else: + msg = "
Too few samples to build tree" + if group_dir is not None: + msg = "%s for group: %s" % (msg, group_dir) + self.append_to_summary("%s
\n" % msg) + + def get_base_file_name(self, file_path): + base_file_name = os.path.basename(file_path) + if base_file_name.find(".") > 0: + # Eliminate the extension. + return os.path.splitext(base_file_name)[0] + elif base_file_name.find("_") > 0: + # The dot extension was likely changed to + # the " character. + items = base_file_name.split("_") + return "_".join(items[0:-1]) + else: + return base_file_name + + def get_mq_val(self, record_info, filename): + # Get the MQ (gatk) or MQM (freebayes) value + # from the record.INFO component of the vcf file. + try: + mq_val = record_info['MQM'] + return self.return_val(mq_val) + except Exception: + try: + mq_val = record_info['MQ'] + return self.return_val(mq_val) + except Exception: + msg = "Invalid or unsupported vcf header %s in file: %s\n" % (str(record_info), filename) + sys.exit(msg) + + def get_parsimonious_df(self, filtered_all_df): + # Get the parsimonious SNPs data frame + # from a data frame of filtered SNPs. + try: + ref_series = filtered_all_df.loc['root'] + # In all_vcf root needs to be removed. + filtered_all_df = filtered_all_df.drop(['root']) + except KeyError: + pass + parsimony = filtered_all_df.loc[:, (filtered_all_df != filtered_all_df.iloc[0]).any()] + parsimony_positions = list(parsimony) + parse_df = filtered_all_df[parsimony_positions] + ref_df = ref_series.to_frame() + ref_df = ref_df.T + parsimonious_df = pandas.concat([parse_df, ref_df], join='inner') + return parsimonious_df + + def get_position_list(self, sheet_names, group): + # Get a list of positions defined by an excel file. + exclusion_list = [] + try: + filter_to_all = pandas.read_excel(self.excel_grouper_file, header=1, usecols=[group]) + for value in filter_to_all.values: + value = str(value[0]) + if "-" not in value.split(":")[-1]: + exclusion_list.append(value) + elif "-" in value: + try: + chrom, sequence_range = value.split(":") + except Exception as e: + sys.exit(str(e)) + value = sequence_range.split("-") + for position in range(int(value[0].replace(',', '')), int(value[1].replace(',', '')) + 1): + exclusion_list.append(chrom + ":" + str(position)) + return exclusion_list + except ValueError: + exclusion_list = [] + return exclusion_list + + def get_snps(self, task_queue, timeout): + while True: + try: + group_dir = task_queue.get(block=True, timeout=timeout) + except queue.Empty: + break + # Parse all vcf files to accumulate SNPs into a + # data frame. + positions_dict = {} + group_files = [] + for file_name in os.listdir(os.path.abspath(group_dir)): + file_path = os.path.abspath(os.path.join(group_dir, file_name)) + group_files.append(file_path) + for file_name in group_files: + try: + found_positions, found_positions_mix = self.find_initial_positions(file_name) + positions_dict.update(found_positions) + except Exception as e: + self.append_to_summary("Error updating the positions_dict dictionary when processing file %s:\n%s\n" % (file_name, str(e))) + # Order before adding to file to match + # with ordering of individual samples. + # all_positions is abs_pos:REF + self.all_positions = OrderedDict(sorted(positions_dict.items())) + ref_positions_df = pandas.DataFrame(self.all_positions, index=['root']) + all_map_qualities = {} + df_list = [] + for file_name in group_files: + sample_df, file_name_base, sample_map_qualities = self.decide_snps(file_name) + df_list.append(sample_df) + all_map_qualities.update({file_name_base: sample_map_qualities}) + all_sample_df = pandas.concat(df_list) + # All positions have now been selected for each sample, + # so select parisomony informative SNPs. This removes + # columns where all fields are the same. + # Add reference to top row. + prefilter_df = pandas.concat([ref_positions_df, all_sample_df], join='inner') + all_mq_df = pandas.DataFrame.from_dict(all_map_qualities) + mq_averages = all_mq_df.mean(axis=1).astype(int) + self.gather_and_filter(prefilter_df, mq_averages, group_dir) + task_queue.task_done() + + def group_vcfs(self, vcf_files): + # Parse an excel file to produce a + # grouping dictionary for filtering SNPs. + xl = pandas.ExcelFile(self.excel_grouper_file) + sheet_names = xl.sheet_names + ws = pandas.read_excel(self.excel_grouper_file, sheet_name=sheet_names[0]) + defining_snps = ws.iloc[0] + defsnp_iterator = iter(defining_snps.iteritems()) + next(defsnp_iterator) + defining_snps = {} + inverted_defining_snps = {} + for abs_pos, group in defsnp_iterator: + if '!' in abs_pos: + inverted_defining_snps[abs_pos.replace('!', '')] = group + else: + defining_snps[abs_pos] = group + samples_groups_dict = {} + for vcf_file in vcf_files: + found_positions, found_positions_mix = self.find_initial_positions(vcf_file) + samples_groups_dict = self.bin_input_files(vcf_file, samples_groups_dict, defining_snps, inverted_defining_snps, found_positions, found_positions_mix) + # Output summary grouping table. + self.append_to_summary('
') + self.append_to_summary('Groupings with %d listed:
\n' % len(samples_groups_dict)) + self.append_to_summary('\n') + for key, value in samples_groups_dict.items(): + self.append_to_summary('\n') + self.append_to_summary('' % key) + for group in value: + self.append_to_summary('\n' % group) + self.append_to_summary('\n') + self.append_to_summary('
Sample Name%s%s

\n') + + def initiate_summary(self, output_summary): + # Output summary file handle. + self.append_to_summary('\n') + self.append_to_summary('\n') + self.append_to_summary('') + self.append_to_summary("Time started: %s
" % str(get_time_stamp())) + self.append_to_summary("Number of VCF inputs: %d
" % self.num_files) + self.append_to_summary("Reference: %s
" % str(self.reference)) + self.append_to_summary("All isolates: %s
" % str(self.all_isolates)) + + def return_val(self, val, index=0): + # Handle element and single-element list values. + if isinstance(val, list): + return val[index] + return val + + def val_as_int(self, val): + # Handle integer value conversion. + try: + return int(val) + except TypeError: + # val is likely None here. + return 0 + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + + parser.add_argument('--all_isolates', action='store', dest='all_isolates', required=False, default="No", help='Create table with all isolates'), + parser.add_argument('--excel_grouper_file', action='store', dest='excel_grouper_file', required=False, default=None, help='Optional Excel filter file'), + parser.add_argument('--output_summary', action='store', dest='output_summary', help='Output summary html file'), + parser.add_argument('--reference', action='store', dest='reference', help='Reference file'), + parser.add_argument('--processes', action='store', dest='processes', type=int, help='User-selected number of processes to use for job splitting') + + args = parser.parse_args() + + # Initializations - TODO: should these be passed in as command line args? + ac = 2 + mq_val = 56 + n_threshold = 50 + qual_threshold = 150 + + # Build the list of sample vcf files for the current run. + vcf_files = [] + for file_name in os.listdir(INPUT_VCF_DIR): + file_path = os.path.abspath(os.path.join(INPUT_VCF_DIR, file_name)) + vcf_files.append(file_path) + + multiprocessing.set_start_method('spawn') + queue1 = multiprocessing.JoinableQueue() + num_files = len(vcf_files) + cpus = set_num_cpus(num_files, args.processes) + # Set a timeout for get()s in the queue. + timeout = 0.05 + + # Initialize the snp_finder object. + snp_finder = SnpFinder(num_files, args.reference, args.excel_grouper_file, args.all_isolates, + ac, mq_val, n_threshold, qual_threshold, args.output_summary) + + # Initialize the set of directories containiing vcf files for analysis. + vcf_dirs = [] + if args.excel_grouper_file is None: + vcf_dirs = setup_all_vcfs(vcf_files, vcf_dirs) + else: + if args.all_isolates.lower() == "yes": + vcf_dirs = setup_all_vcfs(vcf_files, vcf_dirs) + # Parse the Excel file to detemine groups for filtering. + snp_finder.group_vcfs(vcf_files) + # Append the list of group directories created by + # the above call to the set of directories containing + # vcf files for analysis + group_dirs = [d for d in os.listdir(os.getcwd()) if os.path.isdir(d) and d in snp_finder.groups] + vcf_dirs.extend(group_dirs) + + # Populate the queue for job splitting. + for vcf_dir in vcf_dirs: + queue1.put(vcf_dir) + + # Complete the get_snps task. + processes = [multiprocessing.Process(target=snp_finder.get_snps, args=(queue1, timeout, )) for _ in range(cpus)] + for p in processes: + p.start() + for p in processes: + p.join() + queue1.join() + + # Finish summary log. + snp_finder.append_to_summary("
Time finished: %s
\n" % get_time_stamp()) + total_run_time = datetime.now() - snp_finder.timer_start + snp_finder.append_to_summary("
Total run time: %s
\n" % str(total_run_time)) + snp_finder.append_to_summary('\n\n') + with open(args.output_summary, "w") as fh: + fh.write("%s" % snp_finder.summary_str) diff -r 000000000000 -r ee4ef1fc23c6 vsnp_get_snps.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vsnp_get_snps.xml Tue Apr 21 10:14:11 2020 -0400 @@ -0,0 +1,179 @@ + + + + pandas + pyvcf + xlrd + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Accepts a zero-coverage VCF file (or a collection of them) produced by the **vSNP: add zero coverage** tool +along with a collection of VCF files that have been aligned with the same reference. The inputs are analyzed +to discover quality parsimonious SNPs in the zero-coverage VCF file(s). An Excel spreadsheet containing +specified SNPs can optiomally be used to filter desired SNP positions by group. Users can choose whether to +select a locally cached Excel spreadsheet or one from their current history. + +**Required Options** + + * **Choose the category of the files to be analyzed** - select single file or a collection of files, then select the appropriate history item (single VCF item or dataset collection of VCF elements) based on the selected option. + * **Collection of VCF files against which to analyze the zero coverages VCF file(s)** - select a dataset collection from the current history that is associated with the same reference as the selected zero-coverage VCF file(s). + +**Additional Options** + + * **Use Excel file for grouping and filtering?** - select Yes to filter desired SNP positions by group. A cached Excel spreadsheet provides the most widely used SNP positions for grouping, but a custom spreadhseet can be selected from the current history. + * **Job Resource Parameters** - an administrator for the Galaxy instance must configure this tool to display this option, so it may not be available. If it is, you can choose the number of processors to use for tool execution. + * **Number of processes for job splitting** - Select the number of processes for splitting the job to shorten execution time. + + + + @misc{None, + journal = {None}, + author = {1. Stuber T}, + title = {Manuscript in preparation}, + year = {None}, + url = {https://github.com/USDA-VS/vSNP},} + + + +