##fileformat=VCFv4.3 ##FILTER= ##fileDate==05/01/23 ##ALT= ##ALT= ##ALT= ##ALT= ##INFO= ##ALT= ##ALT= ##ALT= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample pncA 1 6c5cbac2 GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT G,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCGGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATATCTT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCCGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACCTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATATCTT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACGACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACTACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCCGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTGTGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT . ld;lgc VC=INDEL;GRAPHTYPE=SIMPLE;VARID=pncA_S66L,pncA_D8Y,pncA_S65F,pncA_V7F,pncA_T-1TC,pncA_G55C,pncA_H51L,pncA_TGC40TAA,pncA_TTG10TAA,pncA_I31N,pncA_D49Y,pncA_TA-1T,pncA_Q10H,pncA_GGT46GGG,pncA_G17D,pncA_GAA109TGA,pncA_K48T,pncA_H57L,pncA_C185CGGACTATTC,pncA_H51D,pncA_Y34D,pncA_A38G,pncA_D12N,pncA_D63A,pncA_Q10E,pncA_CGGGTGACCA161A,pncA_T-1TTC,pncA_P62A,pncA_D63Y,pncA_Q10P,pncA_GA-5A,pncA_GCG112GCT,pncA_TAT190TAG,pncA_G16R,pncA_CTG55CTC,pncA_M1L,pncA_T-1TAC,pncA_Q10R,pncA_CCG184CCA,pncA_ACTATTCCTCGTCG188AG,pncA_Q10L,pncA_T47P,pncA_TGC40TAG,pncA_D49A,pncA_P62S,pncA_P62T,pncA_TTG10TGA,pncA_H57Y,pncA_H42N,pncA_D8V,pncA_AAG142TGA,pncA_V7L,pncA_M1T,pncA_TAT190TAA,pncA_G16V,pncA_D63H,pncA_A36S,pncA_D8H,pncA_F58S,pncA_V21G,pncA_I5N,pncA_T47S,pncA_H57P,pncA_H51N,pncA_A46P,pncA_GAC166GAT,pncA_GAC-5AC,pncA_TCG196TAG,pncA_GCG7GCA,pncA_CTG55TTA,pncA_D49H,pncA_V21A,pncA_GAG43TGA,pncA_D8G,pncA_G23V,pncA_G24V,pncA_D8E,pncA_GCG7GCC,pncA_S59F,pncA_AAG142TAA,pncA_GCA136GCT,pncA_D12G,pncA_P54L,pncA_L35P,pncA_A-11G,pncA_CTG55TTG,pncA_H51Q,pncA_A3E,pncA_I31S,pncA_CTCG195G,pncA_T-1TCT,pncA_TGGCTCGCTGGCGGTAACCGGTGGCGCC48C,pncA_L4F,pncA_C14Y,pncA_T22I,pncA_I6M,pncA_A30S,pncA_V7A,pncA_T-1TT,pncA_T-1TA,pncA_S32N,pncA_P54Q,pncA_TCG196TGA,pncA_I5S,pncA_TAT-1T,pncA_TGC40TGA,pncA_P54T,pncA_GGGTG162TG,pncA_V9G,pncA_GCA136GCG,pncA_AAG142TAG,pncA_A46V,pncA_N11T,pncA_S18T,pncA_L35R,pncA_CGGCACACCGGACTATTCCTCGTCG177ACCGGACTATTCCTCGTCG,pncA_T-1TGA,pncA_D12A,pncA_V21E,pncA_CTG55CTT,pncA_D12H,pncA_T-1TCG,pncA_CTG55CTA,pncA_T-1TAA,pncA_CAG28TGA,pncA_D12E,pncA_T-1TAG,pncA_H42Q,pncA_A46E,pncA_T47A,pncA_T-1TAT,pncA_H51Y,pncA_V7G,pncA_P62Q,pncA_D8N,pncA_F13Y,pncA_G17C,pncA_D63E,pncA_T-1TCC,pncA_I31T,pncA_I6F,pncA_H57Q,pncA_T37GCCAGCGAGCCACCCTCGCAGAAGTCGT,pncA_D8A,pncA_T-1TGT,pncA_Y64D,pncA_P62R,pncA_H57R,pncA_T-12C,pncA_L19P,pncA_GAA109TAG,pncA_I6L,pncA_CAG28TAA,pncA_P54R,pncA_S59P,pncA_TAT190TGA,pncA_F13L,pncA_D49G,pncA_F58L,pncA_I5F,pncA_TAC121TAG,pncA_A36D,pncA_TAC121TAA,pncA_CCG184CCC,pncA_L19Q,pncA_A28S,pncA_R29C,pncA_L27P,pncA_V44G,pncA_S32I,pncA_L27Q,pncA_D49V,pncA_D63G,pncA_GAG43TAA,pncA_GCG112GCA,pncA_A-11C,pncA_L4S,pncA_I31F,pncA_L4W,pncA_T-1TGG,pncA_GATCATCGT12CATCAT,pncA_K48E,pncA_I52T,pncA_GGT46GGA,pncA_GTGGCTCGCTGGCGGTAACCGGTGGCGC47G,pncA_A-11T,pncA_GCGTTGATCAT7AT,pncA_V44D,pncA_T-1TTT,pncA_GAG43TAG,pncA_C14R,pncA_S18L,pncA_GAA109TAA,pncA_F58I,pncA_T-7C,pncA_TCG52TAG,pncA_TCG52TGA,pncA_A30V,pncA_I6T,pncA_T-1TTA,pncA_TTC148TTT,pncA_TCG196TAA,pncA_GGT46GGC,pncA_I5M,pncA_T-1TGC,pncA_T-1TTG,pncA_TAC100TAT,pncA_H51P,pncA_A26V,pncA_A30P,pncA_TCG52TAA,pncA_D49N,pncA_T-1TG,pncA_GCG7GCT,pncA_D49E,pncA_TTG10TAG,pncA_D12Y,pncA_S66P,pncA_H43P,pncA_CCG184CCT,pncA_H57D,pncA_TAC121TAT,pncA_V7D,pncA_P62L,pncA_F13I,pncA_TAC121TGA,pncA_GCA136GCC,pncA_H51R,pncA_G24D,pncA_E15G,pncA_A38S,pncA_CAG28TAG,pncA_H43Q,pncA_T-1TCA,pncA_Y41H,pncA_L4V,pncA_H57N;PREDICT=F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF .:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:1,1,1,1,1,1,1,1,1,1,1:-496,-496,-496,-496,-496,-496,-496,-496,-496,-496,-496:0 pncA 302 af9f6ba6 TGGCC GGGCC,TGGCCACCGCATT . PASS VC=PH_SNPs;GRAPHTYPE=NESTED;PDP=0.643478,0.217391,0.13913;VARID=pncA_W68R,pncA_TGG202TAA,pncA_P69Q,pncA_P69L,pncA_TGG202TGA,pncA_W68C,pncA_W68G,pncA_TGG202TAG,pncA_W68L;PREDICT=.,.,.,.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:70,24,15:78,26,17:92,0,0:103,0,0:282,98,90:314,107,102:0.25,0.75,0.833333:-466.642,-1135.74,-1271.62:669.095 pncA 326 25d5a078 A C . PASS VC=SNP;GRAPHTYPE=SIMPLE;PDP=0.995536,0.00446429;VARID=pncA_T76P,pncA_T76I,pncA_T76S,pncA_AGCGGTACTCCCG220G;PREDICT=.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:107,0:116,1:110,0:118,1:321,0:350,4:0,1:-9.53276,-1517.44:1507.91 pncA 381 5ca6778b T C . PASS VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=pncA_TTC280TTT,pncA_F94C,pncA_F94S,pncA_F94L;PREDICT=.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:130,0:145,0:130,0:145,0:260,0:291,0:0,1:-5.14677,-1762.42:1757.28 pncA 389 28333f21 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=pncA_G97R,pncA_G97V,pncA_G97S,pncA_G97D,pncA_G97C;PREDICT=.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:125,0:143,0:123,0:143,0:376,0:429,0:0,1:-4.50035,-1730.19:1725.69 pncA 441 8eca3735 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=pncA_T114P,pncA_ACG340ACC,pncA_ACG340ACA,pncA_ACG340ACT,pncA_T114M,pncA_T114A;PREDICT=.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:133,0:141,0:133,0:141,0:133,0:141,0:0,1:-5.04343,-1757.82:1752.77 pncA 489 1358054f T TG . PASS VC=INDEL;GRAPHTYPE=SIMPLE;PDP=0.805921,0.194079;VARID=pncA_AGGTCGATGT380T,pncA_CGATGAGGTCGATGTG375G,pncA_ATGTGGTCGG386G,pncA_V130E,pncA_V130G,pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTCGATGAGGTCGGTAT,pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTGGTCGGTAT;PREDICT=.,.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:121,29:124,30:121,0:124,0:242,117:248,120:0,0.75:-275.393,-1421.51:1146.12 pncA 495 6c285c3e G GTATTGCCACCGATCAT . PASS VC=INDEL;GRAPHTYPE=SIMPLE;PDP=0.66756,0.33244;VARID=pncA_ATGTGGTCGG386G,pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTGGTCGGTAT,pncA_G132R,pncA_G132V,pncA_G132S,pncA_GTATTGCCACCGA395A,pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTCGATGAGGTCGGTAT,pncA_G132D,pncA_G132A,pncA_G132C;PREDICT=.,.,.,.,.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:122,61:127,63:124,59:128,60:366,367:382,382:0,0.5:-574.721,-1312.07:737.346 pncA 524 0c0971be A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;PDP=0.79402,0.20598;VARID=pncA_ACG424ACT,pncA_ACG424ACA,pncA_T142R,pncA_T142M,pncA_T142K,pncA_ACG424ACC,pncA_T142A;PREDICT=.,.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:116,29:123,33:115,0:122,0:466,118:493,133:0,0.75:-289.343,-1389.67:1100.33 pncA 564 b8a4a3bb T G . PASS VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=pncA_V155M,pncA_V155E,pncA_V155G;PREDICT=.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:127,0:123,0:130,0:127,0:381,0:370,0:0,1:-3.68805,-1647.29:1643.6 pncA 760 2f7460f5 GG AG . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;PDP=1,0 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:80,0:86,0:80,0:86,0:80,0:86,0:0,1:-18.8362,-1260.46:1241.62