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1 ##fileformat=VCFv4.2
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2 ##fileDate=20190125
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3 ##source=freeBayes v1.2.0-dirty
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4 ##reference=/scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1791698/NC_002945v4.fasta
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5 ##contig=<ID=NC_002945.4,length=4349904>
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6 ##phasing=none
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7 ##commandline="freebayes -E -1 -e 1 -u --strict-vcf -f /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1791698/NC_002945v4.fasta /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1791698/SRR1791698-nodup.bam --region NC_002945.4:0-100000
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8 ##filter="QUAL > 20
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9 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR1791698
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10 NC_002945.4 1057 . A G 7624.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=262;CIGAR=1X;DP=265;DPB=265;DPRA=0;EPP=4.20378;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=363.221;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8526;QR=12;RO=1;RPL=140;RPP=5.69563;RPPR=5.18177;RPR=122;RUN=1;SAF=139;SAP=5.13204;SAR=123;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:265:1,262:1:12:262:8526:-766.088,-78.0909,0
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11 NC_002945.4 4480 . T C 4142.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=144;CIGAR=1X;DP=145;DPB=145;DPRA=0;EPP=3.07062;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=204.232;PAIRED=0.993056;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4647;QR=0;RO=0;RPL=79;RPP=5.96592;RPPR=0;RPR=65;RUN=1;SAF=72;SAP=3.0103;SAR=72;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:145:0,144:0:0:144:4647:-418.074,-43.3483,0
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12 NC_002945.4 8741 . T C 5252.19 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=184;CIGAR=1X;DP=186;DPB=186;DPRA=0;EPP=16.6528;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=259.683;PAIRED=0.98913;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5901;QR=0;RO=0;RPL=81;RPP=8.72222;RPPR=0;RPR=103;RUN=1;SAF=98;SAP=4.70971;SAR=86;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:186:0,184:0:0:184:5901:-531.016,-55.3895,0
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13 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
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14 NC_002945.4 29471 . N . . . . GT ./.
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15 NC_002945.4 29472 . N . . . . GT ./.
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16 NC_002945.4 29473 . N . . . . GT ./.
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17 NC_002945.4 29474 . N . . . . GT ./.
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18 NC_002945.4 29475 . N . . . . GT ./.
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19 NC_002945.4 29476 . N . . . . GT ./.
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20 NC_002945.4 29477 . N . . . . GT ./.
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21 NC_002945.4 29478 . N . . . . GT ./.
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22 NC_002945.4 29479 . N . . . . GT ./.
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23 NC_002945.4 29480 . N . . . . GT ./.
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24 NC_002945.4 29481 . N . . . . GT ./.
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25 NC_002945.4 29482 . N . . . . GT ./.
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26 NC_002945.4 29483 . N . . . . GT ./.
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27 NC_002945.4 29484 . N . . . . GT ./.
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28 NC_002945.4 29485 . N . . . . GT ./.
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29 NC_002945.4 29486 . N . . . . GT ./.
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30 NC_002945.4 29487 . N . . . . GT ./.
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31 NC_002945.4 29488 . N . . . . GT ./.
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32 NC_002945.4 29489 . N . . . . GT ./.
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33 NC_002945.4 29490 . N . . . . GT ./.
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34 NC_002945.4 29491 . N . . . . GT ./.
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35 NC_002945.4 29492 . N . . . . GT ./.
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36 NC_002945.4 29493 . N . . . . GT ./.
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37 NC_002945.4 29494 . N . . . . GT ./.
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38 NC_002945.4 29495 . N . . . . GT ./.
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39 NC_002945.4 29496 . N . . . . GT ./.
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40 NC_002945.4 29497 . N . . . . GT ./.
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41 NC_002945.4 29498 . N . . . . GT ./.
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42 NC_002945.4 29499 . N . . . . GT ./.
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43 NC_002945.4 29500 . N . . . . GT ./.
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44 NC_002945.4 29501 . N . . . . GT ./.
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45 NC_002945.4 29502 . N . . . . GT ./.
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46 NC_002945.4 29503 . N . . . . GT ./.
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47 NC_002945.4 29504 . N . . . . GT ./.
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48 NC_002945.4 29505 . N . . . . GT ./.
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49 NC_002945.4 29506 . N . . . . GT ./.
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50 NC_002945.4 29507 . N . . . . GT ./.
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51 NC_002945.4 29508 . N . . . . GT ./.
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52 NC_002945.4 29509 . N . . . . GT ./.
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53 NC_002945.4 29510 . N . . . . GT ./.
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54 NC_002945.4 29511 . N . . . . GT ./.
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55 NC_002945.4 29512 . N . . . . GT ./.
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56 NC_002945.4 29513 . N . . . . GT ./.
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57 NC_002945.4 29514 . N . . . . GT ./.
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58 NC_002945.4 29515 . N . . . . GT ./.
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59 NC_002945.4 29516 . N . . . . GT ./.
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60 NC_002945.4 29517 . N . . . . GT ./.
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61 NC_002945.4 29518 . N . . . . GT ./.
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62 NC_002945.4 29519 . N . . . . GT ./.
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63 NC_002945.4 29520 . N . . . . GT ./.
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64 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
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65 NC_002945.4 334323 . T C 2171.15 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=79;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.23675;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=53.4051;MQMR=0;NS=1;NUMALT=1;ODDS=114.122;PAIRED=0.987342;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2540;QR=0;RO=0;RPL=40;RPP=3.03779;RPPR=0;RPR=39;RUN=1;SAF=45;SAP=6.33623;SAR=34;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:79:0,79:0:0:79:2540:-220.812,-23.7814,0
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66 NC_002945.4 339406 . N . . . . GT ./.
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67 NC_002945.4 339407 . N . . . . GT ./.
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68 NC_002945.4 339408 . N . . . . GT ./.
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69 NC_002945.4 339409 . N . . . . GT ./.
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70 NC_002945.4 339410 . N . . . . GT ./.
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71 NC_002945.4 339411 . N . . . . GT ./.
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72 NC_002945.4 340088 . G A 2525.17 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=81;CIGAR=1X;DP=82;DPB=82;DPRA=0;EPP=17.1919;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=58.5062;MQMR=0;NS=1;NUMALT=1;ODDS=116.895;PAIRED=0.987654;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2863;QR=0;RO=0;RPL=39;RPP=3.25157;RPPR=0;RPR=42;RUN=1;SAF=39;SAP=3.25157;SAR=42;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:82:0,81:0:0:81:2863:-257.146,-24.3834,0
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73 NC_002945.4 340090 . C T 2327.84 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=80;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=18.6449;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=58.4;MQMR=0;NS=1;NUMALT=1;ODDS=115.509;PAIRED=0.9875;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2643;QR=0;RO=0;RPL=40;RPP=3.0103;RPPR=0;RPR=40;RUN=1;SAF=38;SAP=3.44459;SAR=42;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:80:0,80:0:0:80:2643:-237.547,-24.0824,0
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74 NC_002945.4 340091 . G A 2328.64 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=80;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=16.1477;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=58.4;MQMR=0;NS=1;NUMALT=1;ODDS=115.509;PAIRED=0.9875;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2649;QR=0;RO=0;RPL=41;RPP=3.11887;RPPR=0;RPR=39;RUN=1;SAF=38;SAP=3.44459;SAR=42;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:80:0,80:0:0:80:2649:-237.385,-24.0824,0
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75 NC_002945.4 340092 . G C 2407.91 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=79;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=17.5509;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=58.8228;MQMR=0;NS=1;NUMALT=1;ODDS=114.122;PAIRED=0.987342;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2733;QR=0;RO=0;RPL=42;RPP=3.69747;RPPR=0;RPR=37;RUN=1;SAF=37;SAP=3.69747;SAR=42;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:80:0,79:0:0:79:2733:-245.528,-23.7814,0
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76 NC_002945.4 340097 . C G 2471.31 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=83;CIGAR=1X;DP=83;DPB=83;DPRA=0;EPP=16.8502;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=58.4578;MQMR=0;NS=1;NUMALT=1;ODDS=119.668;PAIRED=0.987952;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2802;QR=0;RO=0;RPL=43;RPP=3.24576;RPPR=0;RPR=40;RUN=1;SAF=40;SAP=3.24576;SAR=43;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:83:0,83:0:0:83:2802:-251.74,-24.9855,0
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77 NC_002945.4 362818 . T C 400.106 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=15;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=6.62942;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=58.6667;MQMR=0;NS=1;NUMALT=1;ODDS=25.3996;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=483;QR=0;RO=0;RPL=7;RPP=3.15506;RPPR=0;RPR=8;RUN=1;SAF=3;SAP=14.7363;SAR=12;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:15:0,15:0:0:15:483:-43.6129,-4.51545,0
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78 NC_002945.4 364560 . A G 6594.02 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=209;CIGAR=1X;DP=209;DPB=209;DPRA=0;EPP=14.3248;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=59.9234;MQMR=0;NS=1;NUMALT=1;ODDS=294.341;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7388;QR=0;RO=0;RPL=116;RPP=8.50651;RPPR=0;RPR=93;RUN=1;SAF=103;SAP=3.10381;SAR=106;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:209:0,209:0:0:209:7388:-664.866,-62.9153,0
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79 NC_002945.4 364804 . T C 5622.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=193;CIGAR=1X;DP=193;DPB=193;DPRA=0;EPP=7.97206;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=272.16;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6321;QR=0;RO=0;RPL=119;RPP=25.7939;RPPR=0;RPR=74;RUN=1;SAF=90;SAP=4.91174;SAR=103;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:193:0,193:0:0:193:6321:-568.925,-58.0988,0
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80 NC_002945.4 366022 . T C 4678.56 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=159;CIGAR=1X;DP=159;DPB=159;DPRA=0;EPP=3.35173;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=225.026;PAIRED=0.987421;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5277;QR=0;RO=0;RPL=103;RPP=33.1787;RPPR=0;RPR=56;RUN=1;SAF=89;SAP=7.9405;SAR=70;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:159:0,159:0:0:159:5277:-475.022,-47.8638,0
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81 NC_002945.4 402148 . G T 85.8237 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=40;MQMR=0;NS=1;NUMALT=1;ODDS=10.1503;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=136;QR=0;RO=0;RPL=0;RPP=11.6962;RPPR=0;RPR=4;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:4:0,4:0:0:4:136:-12.1947,-1.20412,0
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82 NC_002945.4 407246 . C G 2433.98 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=91;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=7.04303;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=130.758;PAIRED=0.989011;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2860;QR=0;RO=0;RPL=42;RPP=4.17955;RPPR=0;RPR=49;RUN=1;SAF=14;SAP=97.7199;SAR=77;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:93:0,91:0:0:91:2860:-257.436,-27.3937,0
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