##fileformat=VCFv4.3
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate==21/11/22
##ALT=<ID=SNP,Description="SNP">
##ALT=<ID=PH_SNPs,Description="Phased SNPs">
##ALT=<ID=INDEL,Description="Insertion-deletion">
##ALT=<ID=COMPLEX,Description="Complex variant, collection of SNPs and indels">
##INFO=<ID=VC,Number=1,Type=String,Description="Type (class) of variant">
##ALT=<ID=SIMPLE,Description="Graph bubble is simple">
##ALT=<ID=NESTED,Description="Variation site was a nested feature in the graph">
##ALT=<ID=TOO_MANY_ALTS,Description="Variation site was a multinested feature with too many alts to include all in the VCF">
##INFO=<ID=GRAPHTYPE,Number=1,Type=String,Description="Type of graph feature">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MEAN_FWD_COVG,Number=R,Type=Integer,Description="Mean forward coverage">
##FORMAT=<ID=MEAN_REV_COVG,Number=R,Type=Integer,Description="Mean reverse coverage">
##FORMAT=<ID=MED_FWD_COVG,Number=R,Type=Integer,Description="Med forward coverage">
##FORMAT=<ID=MED_REV_COVG,Number=R,Type=Integer,Description="Med reverse coverage">
##FORMAT=<ID=SUM_FWD_COVG,Number=R,Type=Integer,Description="Sum forward coverage">
##FORMAT=<ID=SUM_REV_COVG,Number=R,Type=Integer,Description="Sum reverse coverage">
##FORMAT=<ID=GAPS,Number=R,Type=Float,Description="Number of gap bases">
##FORMAT=<ID=LIKELIHOOD,Number=R,Type=Float,Description="Likelihood">
##FORMAT=<ID=GT_CONF,Number=1,Type=Float,Description="Genotype confidence">
##contig=<ID=ahpC>
##contig=<ID=ddn>
##contig=<ID=eis>
##contig=<ID=embA>
##contig=<ID=embB>
##contig=<ID=ethA>
##contig=<ID=fabG1>
##contig=<ID=gid>
##contig=<ID=gyrA>
##contig=<ID=gyrB>
##contig=<ID=inhA>
##contig=<ID=katG>
##contig=<ID=pncA>
##contig=<ID=rplC>
##contig=<ID=rpoB>
##contig=<ID=rpsL>
##contig=<ID=rrs>
##contig=<ID=tlyA>
##FILTER=<ID=ld,Description="Kmer coverage on called allele less than 3">
##FILTER=<ID=sb,Description="A strand on the called allele has less than 1.00% of the coverage for that allele">
##FILTER=<ID=lgc,Description="Genotype confidence score less than 5.0">
##FILTER=<ID=lindel,Description="Indel is longer than 20bp">
##FILTER=<ID=frs,Description="Fraction of read support on called allele is less than 0.51">
##INFO=<ID=VARID,Number=.,Type=String,Description="The identifier for the panel variant(s) the record overlaps with">
##INFO=<ID=PREDICT,Number=.,Type=String,Description="The drug resistance prediction(s) for the corresponding VARID(s), where 'R' = resistant, 'S' = susceptible, 'F' = failed, and 'U' = unknown">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
ahpC 11 89987700 GTG ATG,GTA . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=ahpC_G-88A;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:29,0,0:20,0,0:29,0,0:20,0,0:29,0,0:20,0,0:0,1,1:-16.9127,-417.653,-417.653:400.741
ahpC 19 e808eff0 TCACCTTTGCC TCACCTTGCC,TCACCTTTGCT,TCC . PASS VC=COMPLEX;GRAPHTYPE=SIMPLE;VARID=ahpC_C-72T;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:31,0,9,0:18,0,6,0:29,0,0,0:20,0,0,0:156,0,29,0:90,0,20,0:0.2,1,0.666667,1:-105.19,-486.731,-345.087,-486.731:239.897
ahpC 50 60e6fcf9 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:54,0:35,0:54,0:35,0:54,0:35,0:0,1:-3.42584,-601.86:598.434
ahpC 326 694cacfc G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:21,0:37,0:30,0:54,0:64,0:113,0:0.333333,1:-43.7241,-459.1:415.376
ddn 244 258eeb83 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:54,0:46,0:54,0:46,0:108,0:92,0:0,1:-3.30456,-652.517:649.212
ddn 268 f528388d C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:52,17:46,13:52,0:46,0:104,53:93,39:0,0.666667:-141.388,-549.034:407.646
ddn 349 81b30902 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:43,0:74,0:43,0:74,0:87,0:148,0:0,1:-5.44635,-730.805:725.359
ddn 437 7d7e792e G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:58,0:80,0:57,0:79,0:175,0:240,0:0,1:-11.4641,-827.513:816.049
ddn 588 f8f19ade G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:69,23:34,11:69,0:34,0:139,70:69,34:0,0.666667:-160.062,-567.726:407.663
ddn 627 b1dde0cf CG C . PASS VC=INDEL;GRAPHTYPE=SIMPLE;VARID=ddn_CG527C;PREDICT=u GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:57,31:28,14:57,31:28,14:114,62:57,29:0,0.5:-211.03,-459.168:248.138
eis 55 fa0c40ac A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:37,0:57,0:37,0:57,0:74,0:115,0:0,1:-3.21245,-624.886:621.674
eis 64 7cbe8359 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=eis_G-37T;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:44,0:60,0:44,0:60,0:88,0:121,0:0,1:-3.56638,-670.938:667.371
eis 87 e28b1124 CAC CAT,TAC . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=eis_C-14T,eis_C-12T;PREDICT=.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:50,0,0:59,0,0:50,0,0:59,0,0:101,0,0:118,0,0:0,1,1:-4.10834,-693.964,-693.964:689.855
eis 417 20ad2328 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:60,0:68,0:60,0:68,0:121,0:136,0:0,1:-8.16891,-781.462:773.293
eis 587 76ed6a55 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=eis_V163I;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:54,0:45,0:55,0:46,0:162,0:135,0:0,1:-3.26373,-647.912:644.648
eis 903 f2c215e4 TCA T . PASS VC=INDEL;GRAPHTYPE=SIMPLE;VARID=eis_ACC805C;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:18,0:57,0:18,0:57,0:37,0:114,0:0,1:-5.56429,-537.388:531.823
eis 1116 09822128 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:55,0:48,0:56,0:50,0:222,0:195,0:0,1:-3.48633,-666.333:662.846
embA 58 e55d0a43 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:32,0:35,0:32,0:35,0:64,0:70,0:0,1:-7.92561,-500.546:492.621
embA 69 c6fd392a GC G . PASS VC=INDEL;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:40,8:40,9:42,0:40,0:120,35:120,36:0,0.75:-82.8132,-492.325:409.512
embA 328 898fe58b C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:41,0:59,0:41,0:59,0:83,0:118,0:0,1:-3.30456,-652.517:649.212
embA 409 9c3eceb2 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:37,0:36,0:37,0:36,0:151,0:145,0:0,1:-6.07143,-528.177:522.106
embA 438 04f5218f C G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:41,0:36,0:41,0:36,0:82,0:72,0:0,1:-5.11013,-546.598:541.488
embA 448 88070a19 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:44,0:36,0:44,0:36,0:44,0:36,0:0,1:-4.52527,-560.414:555.888
embA 457 635a24f5 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:44,22:37,18:44,22:37,18:88,44:74,36:0,0.5:-188.562,-444.765:256.203
embA 716 34a0d406 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embA_V206M;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,19:43,20:39,19:43,20:79,39:87,41:0,0.5:-183.799,-450.246:266.447
embA 964 ca2f3ca4 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:30,0:63,0:30,0:63,0:30,0:63,0:0,1:-3.23351,-620.281:617.047
embA 1088 533441e8 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:51,0:33,0:51,0:33,0:102,0:67,0:0,1:-3.9187,-578.834:574.916
embA 1247 33bc1d09 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embA_P383S;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:34,0:31,0:34,0:31,0:69,0:63,0:0,1:-8.65995,-491.336:482.676
embA 1288 40fcbe85 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:36,0:31,0:36,0:31,0:73,0:62,0:0,1:-7.92561,-500.546:492.621
embA 1315 17a9f13f G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:44,0:35,0:44,0:34,0:176,0:142,0:0,1:-4.70759,-555.808:551.101
embA 1503 4d404735 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embA_V468A;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:17,0:63,0:17,0:63,0:35,0:127,0:0,1:-4.52527,-560.414:555.888
embA 1609 9b4dae5c C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:27,0:38,0:27,0:35,0:110,0:153,0:0,1:-8.65995,-491.336:482.676
embA 1826 3ba396e2 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embA_A576T;PREDICT=U GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:0,32:0,32:0,33:0,33:0,97:1,97:1,0:-486.731,-9.04992:477.681
embA 2015 0740371d C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embA_P639S;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:68,0:26,0:68,0:26,0:137,0:52,0:0,1:-3.21245,-624.886:621.674
embA 2086 8f1cff16 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:41,0:30,0:43,0:32,0:124,0:91,0:0,1:-6.633,-518.967:512.334
embA 2137 cd945547 C CCGG . PASS VC=INDEL;GRAPHTYPE=SIMPLE; GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:40,25:40,23:41,41:43,37:200,127:204,118:0,0.4:-225.573,-424.399:198.825
embA 2182 8dadf853 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:46,15:52,18:46,0:52,0:92,45:105,54:0,0.666667:-155.204,-545.738:390.534
embA 2524 c824b15e C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:38,0:30,0:38,0:30,0:38,0:30,0:0,1:-7.58076,-505.152:497.571
embA 2837 f5372fc0 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embA_P913S;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:47,0:33,0:47,0:33,0:47,0:33,0:0,1:-4.52527,-560.414:555.888
embA 3376 a46d4d14 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,0:31,0:39,0:31,0:78,0:63,0:0,1:-6.93467,-514.362:507.427
embA 3419 7214097e A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:13,0:13,0:13,0:13,0:26,0:27,0:0,1:-38.5886,-311.734:273.146
embA 3431 3a327039 TGGGG GGGGT . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:10,0:12,0:11,0:12,0:53,0:60,0:0,1:-44.0555,-293.314:249.258
embA 3452 480c8fd1 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:5,0:5,0:5,0:5,0:15,0:15,0:0.333333,1:-97.4609,-238.052:140.591
embB 95 51f46034 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:4,0:4,0:4,0:4,0:8,0:9,0:0.5,1:-118.09,-228.841:110.752
embB 138 3ae49082 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embB_N13S;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:21,0:19,0:21,0:19,0:42,0:38,0:0,1:-23.7467,-376.207:352.46
embB 150 26e08e43 TGGGG GGGGT . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:22,0:19,0:23,0:19,0:114,0:96,0:0,1:-22.8959,-380.812:357.916
embB 171 30290595 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:18,0:17,0:28,0:25,0:56,0:51,0:0.333333,1:-60.384,-353.181:292.797
embB 451 4418a626 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:46,0:49,0:46,0:49,0:138,0:148,0:0,1:-3.20198,-629.491:626.289
embB 690 f2aa728d C G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:64,13:20,4:64,0:20,0:128,65:41,21:0,0.8:-82.2066,-515.545:433.339
embB 760 0b34acec G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,0:23,0:39,0:23,0:79,0:47,0:0.5,1:-57.8766,-477.521:419.644
embB 836 cf1fbb61 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:65,0:61,0:66,0:61,0:197,0:184,0:0,1:-7.60139,-772.251:764.65
embB 989 e09a227a T G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:49,0:77,0:49,0:77,0:99,0:154,0:0,1:-7.60139,-772.251:764.65
embB 1016 343fe7cc ATG ATA,ATC,CTG,GTG . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=embB_M306K,embB_M306N,embB_M306T,embB_M306I,embB_M306Q,embB_M306H,embB_M306P,embB_M306R,embB_M306E,embB_M306D,embB_M306A,embB_M306G,embB_M306V,embB_M306Y,embB_M306S,embB_M306W,embB_M306C,embB_M306L,embB_M306F;PREDICT=.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:43,0,0,0,0:68,0,0,0,0:43,0,0,0,0:68,0,0,0,0:87,0,0,0,0:137,0,0,0,0:0,1,1,1,1:-4.38966,-703.174,-703.174,-703.174,-703.174:698.784
embB 1082 7ef54c79 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embB_D328Y;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:45,0:68,0:45,0:68,0:45,0:68,0:0,1:-4.70685,-712.384:707.677
embB 1100 eedbaa96 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:36,11:61,21:36,0:64,0:146,35:244,65:0,0.666667:-150.578,-542.2:391.623
embB 1165 f4776303 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:53,0:31,0:53,0:31,0:53,0:31,0:0,1:-3.9187,-578.834:574.916
embB 1233 9945ec50 A C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embB_E378A;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:68,0:37,0:68,0:37,0:136,0:75,0:0,1:-3.65599,-675.543:671.887
embB 1316 dfbff61d GG AG,GC,TG . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=embB_G406D,embB_G406A,embB_G406S,embB_G406C;PREDICT=.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:49,0,0,0:55,0,0,0:49,0,0,0:55,0,0,0:49,0,0,0:55,0,0,0:0,1,1,1:-3.56638,-670.938,-670.938,-670.938:667.371
embB 1407 ba22730b T G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:52,0:50,0:52,0:50,0:158,0:150,0:0,1:-3.41595,-661.727:658.311
embB 1434 614c277e A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:59,0:41,0:58,0:40,0:238,0:165,0:0,1:-3.30456,-652.517:649.212
embB 1590 a11d55fb A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embB_Q497K,embB_Q497R;PREDICT=.,R GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:0,38:0,75:0,38:0,75:0,116:0,225:1,0:-712.384,-4.70685:707.677
embB 1630 9273d502 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:46,0:68,0:46,0:68,0:93,0:137,0:0,1:-4.8787,-716.989:712.111
embB 1642 40ab0b34 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:43,0:70,0:42,0:74,0:129,0:211,0:0,1:-4.70685,-712.384:707.677
embB 2027 50f34919 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:59,0:61,0:59,0:61,0:59,0:61,0:0,1:-6.09061,-744.62:738.53
embB 2467 1bf14052 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:43,0:61,0:43,0:61,0:86,0:122,0:0,1:-3.56638,-670.938:667.371
embB 2712 4fc9446a G T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:54,0:55,0:54,0:55,0:54,0:55,0:0,1:-4.10834,-693.964:689.855
embB 2845 73b4ea86 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,0:31,0:39,0:31,0:39,0:31,0:0,1:-6.93467,-514.362:507.427
embB 2995 8d73f96f G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,0:41,0:39,0:40,0:197,0:205,0:0,1:-4.52527,-560.414:555.888
embB 3181 0ff5fa86 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:21,0:49,0:21,0:49,0:64,0:147,0:0,1:-6.93467,-514.362:507.427
embB 3260 04576d36 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embB_S1054P;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:27,0:37,0:27,0:37,0:54,0:74,0:0,1:-9.04992,-486.731:477.681
embB 3318 d77d941f C A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:35,0:22,0:36,0:23,0:107,0:68,0:0,1:-12.228,-454.495:442.267
embB 3344 e18f8bd8 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=embB_T1082A;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,0:32,0:39,0:32,0:39,0:32,0:0,1:-6.633,-518.967:512.334
ethA 19 4988c25a T C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:16,0:33,0:16,0:33,0:16,0:33,0:0,1:-16.9127,-417.653:400.741
ethA 50 be7c0f44 AGTGTCGACATCTCGTTGACG A . PASS VC=INDEL;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:30,0:46,0:30,0:46,0:247,0:368,0:0,1:-5.33067,-541.993:536.662
ethA 90 b682290a A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:52,0:27,0:51,0:26,0:158,0:82,0:0,1:-4.70759,-555.808:551.101
ethA 191 a38ad7c7 A AGC . PASS VC=INDEL;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:86,0:28,0:86,0:28,0:86,0:28,0:0,1:-4.8787,-716.989:712.111
ethA 330 227669cc A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:34,0:59,0:34,0:59,0:69,0:119,0:0,1:-3.23351,-620.281:617.047
ethA 471 906521eb G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:78,0:42,0:78,0:42,0:156,0:84,0:0,1:-6.09061,-744.62:738.53
ethA 490 19f568fa C CT . PASS VC=INDEL;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:81,0:48,0:81,0:48,0:162,0:97,0:0,1:-8.46437,-786.067:777.603
ethA 522 9bb3b952 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:80,0:46,0:80,0:46,0:160,0:93,0:0,1:-7.60139,-772.251:764.65
ethA 646 a3e4cb53 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:57,0:47,0:57,0:47,0:172,0:142,0:0,1:-3.56638,-670.938:667.371
ethA 674 40458eb5 C A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,0:65,0:39,0:65,0:39,0:65,0:0,1:-3.56638,-670.938:667.371
ethA 835 d81188f4 C G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:74,0:72,0:74,0:72,0:149,0:145,0:0,1:-14.623,-864.355:849.732
ethA 850 fa1199dc C G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:67,0:65,0:67,0:66,0:203,0:197,0:0,1:-9.39686,-799.882:790.486
ethA 898 66a8fb60 C G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:68,0:74,0:68,0:74,0:68,0:74,0:0,1:-12.9874,-845.934:832.947
ethA 942 b83dd277 A C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:70,0:67,0:72,0:69,0:210,0:202,0:0,1:-11.1012,-822.908:811.807
ethA 1108 7ac3b329 CAT CGT,GG . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:50,15,11:61,19,14:49,0,0:61,0,0:250,47,47:308,58,58:0,0.666667,0.75:-276.095,-719.696,-779.645:443.601
ethA 1135 66a05a02 C A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:52,0:69,0:52,0:69,0:104,0:139,0:0,1:-6.32205,-749.226:742.904
ethA 1269 1420f624 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=ethA_S390F;PREDICT=F GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF .:83,0:64,0:83,0:64,0:167,0:129,0:0,1:-15.0491,-868.96:853.911
ethA 1314 cd0b1d7e T C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:64,0:59,0:80,0:72,0:322,0:296,0:0.2,1:-26.0096,-758.436:732.426
ethA 1426 55c924cf G T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:58,0:54,0:58,0:54,0:116,0:108,0:0,1:-4.54381,-707.779:703.235
ethA 1651 32060ac9 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:22,0:30,0:22,0:30,0:22,0:30,0:0,1:-15.0147,-431.469:416.454
fabG1 54 6f09a602 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:40,0:41,0:40,0:41,0:40,0:41,0:0,1:-4.35537,-565.019:560.663
fabG1 93 1090e755 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=fabG1_T-8X;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:38,0:37,0:38,0:37,0:76,0:75,0:0,1:-5.56429,-537.388:531.823
fabG1 427 ff9e4f44 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:45,0:37,0:45,0:37,0:91,0:75,0:0,1:-4.19774,-569.624:565.426
fabG1 709 cbb8fbfb G A . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=fabG1_CTG607CTA,fabG1_CTG607CTC,fabG1_CTG607CTT,fabG1_CTG607TTA,fabG1_CTG607TTG;PREDICT=.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:45,0:33,0:46,0:34,0:136,0:101,0:0,1:-4.90249,-551.203:546.301
fabG1 823 df8e0a8a C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:19,0:36,0:22,0:45,0:76,0:145,0:0.25,1:-37.2883,-445.284:407.996
gid 90 d1c8fdf6 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:56,0:49,0:56,0:49,0:112,0:99,0:0,1:-3.65599,-675.543:671.887
gid 117 271f6fa8 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:60,0:54,0:64,0:58,0:182,0:162,0:0,1:-4.8787,-716.989:712.111
gid 160 20adddfa GC G . PASS VC=INDEL;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:56,0:58,0:56,0:59,0:169,0:175,0:0,1:-4.8787,-716.989:712.111
gid 269 8afce4af G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:48,0:39,0:48,0:39,0:48,0:39,0:0,1:-3.58856,-592.65:589.061
gid 303 6f403cfd T G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gid_ATATCGGTAGCGGAGC200C,gid_ATATCGGTAGCGGAGCC200CC;PREDICT=.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:43,0:46,0:43,0:46,0:130,0:139,0:0,1:-3.42584,-601.86:598.434
gid 330 ffd7f30a TGCCATTGGCGATAGCGCG GGCTACGTCACGCACATTT . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=gid_L79S,gid_L79W,gid_A80P,gid_R83P;PREDICT=.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:44,0:55,0:45,0:51,0:224,0:277,0:0,1:-3.26373,-647.912:644.648
gid 386 efc026e2 C A . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gid_TTCTCCTAGAACCGCTACTGCGCCGCACCGAGTTTCTTCG266G;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:44,0:60,0:44,0:61,0:133,0:182,0:0,1:-3.56638,-670.938:667.371
gid 413 fce1bba1 G GT . PASS VC=INDEL;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:42,0:62,0:42,0:62,0:85,0:125,0:0,1:-3.56638,-670.938:667.371
gid 429 84a4d749 TG T,TT . PASS VC=INDEL;GRAPHTYPE=SIMPLE;VARID=gid_V110G;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:17,0,0:20,0,0:2,0,0:0,0,0:52,0,0:61,0,0:0.666667,1,1:-90.4497,-362.391,-362.391:271.942
gid 455 a58246ff G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:52,0:44,1:52,0:44,1:105,0:89,2:0,1:-7.80715,-629.532:621.725
gid 505 0ee38316 G T . PASS VC=SNP;GRAPHTYPE=NESTED GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:31,0:20,0:31,0:20,0:62,0:40,0:0.5,1:-63.6278,-426.864:363.236
gid 505 99da04ab GTCACGG TTGGGCGGCAGCGACGCT . PASS VC=COMPLEX;GRAPHTYPE=NESTED;VARID=gid_R137P,gid_R137W;PREDICT=.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:43,9:28,6:61,0:40,0:130,58:84,39:0.333333,0.833333:-107.711,-462.401:354.691
gid 520 c84fd8fa CGCG AGCG,CGCA . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:64,0,17:49,0,11:64,1,0:49,0,0:129,3,68:99,0,44:0,1,0.75:-133.652,-841.329,-628.472:494.821
gid 550 a4576265 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:63,20:52,17:63,0:52,0:127,61:105,52:0,0.666667:-175.451,-620.044:444.594
gid 608 eedde426 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gid_G508AAAGGCGAGCGGGCTCACGACG;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:50,0:57,0:50,0:57,0:100,0:114,0:0,1:-3.86356,-684.753:680.89
gid 683 33ae9ca0 TA CA,TAT . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=gid_Y195H;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:53,0,0:61,0,0:53,0,0:61,0,0:106,0,0:122,0,0:0,1,1:-4.8787,-716.989,-716.989:712.111
gid 813 16c891b3 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:31,0:22,0:45,0:28,0:94,0:66,0:0.333333,1:-46.4207,-436.074:389.653
gid 856 96a53b7f C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:26,0:13,0:26,0:13,0:26,0:13,0:0,1:-24.6222,-371.602:346.979
gyrA 21 1e4d2d5c C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF .:5,0:2,0:5,0:2,0:10,0:4,0:0.5,1:-120.575,-224.236:103.661
gyrA 67 e83c41ed C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrA_C-34T;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:35,0:24,0:35,0:24,0:35,0:24,0:0,1:-11.2373,-463.705:452.468
gyrA 259 c46f7b52 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:11,0:17,0:0,0:1,0:34,0:51,1:0.666667,1:-100.088,-320.945:220.857
gyrA 302 3bdda791 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:47,0:59,0:47,0:58,0:236,0:297,0:0,1:-3.75508,-680.148:676.393
gyrA 362 1e66e18d G T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrA_G88N,gyrA_G88A,gyrA_G88C;PREDICT=.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:23,0:34,0:23,0:34,0:92,0:138,0:0.5,1:-60.228,-454.495:394.267
gyrA 414 26586c74 T G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrA_L105R;PREDICT=U GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:0,52:0,43:0,52:0,43:0,104:0,86:1,0:-629.491,-3.20198:626.289
gyrA 433 b4508b14 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:59,0:41,0:59,0:41,0:178,0:124,0:0,1:-3.30456,-652.517:649.212
gyrA 477 789caa3e C A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:63,0:50,0:63,0:50,0:63,0:50,0:0,1:-4.70685,-712.384:707.677
gyrA 561 591b3fa0 C G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:44,0:45,0:44,0:45,0:88,0:90,0:0,1:-3.42584,-601.86:598.434
gyrA 670 375e962c G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:55,0:43,0:55,0:43,0:110,0:87,0:0,1:-3.23296,-643.307:640.074
gyrA 770 6669b5f4 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:38,0:56,0:38,0:56,0:76,0:112,0:0,1:-3.21245,-624.886:621.674
gyrA 839 bb448d43 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrA_G247S;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:58,0:62,0:58,0:62,0:116,0:125,0:0,1:-6.09061,-744.62:738.53
gyrA 855 6319c355 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrA_R252L;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:58,0:56,0:58,0:57,0:174,0:168,0:0,1:-4.8787,-716.989:712.111
gyrA 1084 87cd481c C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:48,0:47,0:48,0:47,0:97,0:94,0:0,1:-3.20198,-629.491:626.289
gyrA 1213 3c387557 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:44,0:65,0:44,0:65,0:89,0:131,0:0,1:-4.10834,-693.964:689.855
gyrA 1251 a6555923 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrA_A384V;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,0:56,0:39,0:56,0:156,0:225,0:0,1:-3.20198,-629.491:626.289
gyrA 1292 5cb81d16 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:49,0:60,0:49,0:60,0:98,0:121,0:0,1:-4.10834,-693.964:689.855
gyrA 1423 b20d5170 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:82,0:32,0:82,0:32,0:164,0:64,0:0,1:-4.8787,-716.989:712.111
gyrA 1487 9d82cf9c G T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrA_A463S;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:75,0:27,0:75,0:27,0:303,0:110,0:0,1:-3.41595,-661.727:658.311
gyrA 1493 a22b2421 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:72,0:27,0:72,0:27,0:145,0:55,0:0,1:-3.26373,-647.912:644.648
gyrA 1540 cc7d9000 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:56,0:38,0:56,0:38,0:113,0:76,0:0,1:-3.21245,-624.886:621.674
gyrA 1747 face782f G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:70,0:64,0:70,0:64,0:140,0:129,0:0,1:-10.0564,-809.093:799.036
gyrA 1846 379e7639 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:74,0:62,0:74,0:62,0:149,0:125,0:0,1:-10.7456,-818.303:807.558
gyrA 1963 6857f776 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:60,0:53,0:60,0:53,0:120,0:107,0:0,1:-4.70685,-712.384:707.677
gyrA 2016 adbad1af A C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:54,17:54,17:54,0:51,0:164,53:162,51:0,0.666667:-160.557,-590.751:430.194
gyrA 2059 04d0fcb6 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:49,0:78,0:49,0:78,0:49,0:78,0:0,1:-7.88123,-776.857:768.975
gyrA 2242 dae1dfae G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:58,0:74,0:58,0:74,0:116,0:148,0:0,1:-9.39686,-799.882:790.486
gyrA 2323 d79c35a3 GG AG,GC . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=gyrA_V742L;PREDICT=U GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 2:0,0,48:0,0,48:0,0,48:0,0,48:0,0,146:0,0,145:1,1,0:-634.096,-634.096,-3.20198:630.894
gyrA 2365 70e4f283 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:25,0:19,0:25,0:18,0:102,0:76,0:0.5,1:-68.486,-394.627:326.142
gyrA 2395 9207d732 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:53,0:41,0:53,0:41,0:107,0:83,0:0,1:-3.21245,-624.886:621.674
gyrA 2640 9a68cf6b C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrA_C2540T;PREDICT=U GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:9,38:12,50:0,39:0,49:37,232:48,300:0.75,0:-522.784,-100.21:422.574
gyrB 64 520aeb35 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:75,0:53,0:75,0:53,0:75,0:53,0:0,1:-8.16891,-781.462:773.293
gyrB 381 1677758f C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrB_P94L;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:55,0:68,0:55,0:68,0:110,0:136,0:0,1:-6.80956,-758.436:751.626
gyrB 613 ed32903b G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:54,0:58,0:54,0:58,0:109,0:116,0:0,1:-4.54381,-707.779:703.235
gyrB 632 e997fc22 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:61,0:59,0:61,0:59,0:122,0:119,0:0,1:-6.09061,-744.62:738.53
gyrB 973 af445e4f G C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrB_M291I;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:76,0:74,0:76,0:74,0:153,0:148,0:0,1:-16.3679,-882.776:866.408
gyrB 985 bb18043b C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:74,0:73,0:74,0:73,0:148,0:146,0:0,1:-15.0491,-868.96:853.911
gyrB 1168 39afddf5 T G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:68,0:66,0:68,0:66,0:68,0:66,0:0,1:-10.0564,-809.093:799.036
gyrB 1267 b472cea1 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:52,0:64,0:52,0:64,0:52,0:64,0:0,1:-5.24852,-726.2:720.951
gyrB 1307 fe5273cd G T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrB_A403S;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:56,0:61,0:56,0:61,0:112,0:122,0:0,1:-5.44635,-730.805:725.359
gyrB 1558 877c7028 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:48,0:54,0:48,0:54,0:48,0:54,0:0,1:-3.41595,-661.727:658.311
gyrB 1582 a6f0a226 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:48,0:56,0:48,0:56,0:97,0:112,0:0,1:-3.56638,-670.938:667.371
gyrB 1596 eb71e2c0 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=gyrB_N499D;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:40,0:51,0:40,0:51,0:40,0:51,0:0,1:-3.30781,-611.07:607.763
gyrB 1659 8350901c G T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:45,0:64,0:45,0:64,0:91,0:129,0:0,1:-4.10834,-693.964:689.855
gyrB 1824 dc89064e G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:62,0:54,0:62,0:54,0:62,0:54,0:0,1:-5.24852,-726.2:720.951
gyrB 2023 6415e5d8 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:51,17:55,18:51,0:55,0:206,52:220,55:0,0.666667:-164.936,-580.532:415.596
gyrB 2083 96bcf94c C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:42,0:43,0:42,0:43,0:84,0:87,0:0,1:-3.79701,-583.439:579.642
gyrB 2129 cc0128e9 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:24,0:30,0:24,0:30,0:24,0:30,0:0,1:-13.8453,-440.679:426.834
gyrB 2223 94cdb9a7 G C . ld;lgc VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF .:0,0:0,0:0,0:0,0:0,0:0,0:1,1:-192,-192:0
inhA 61 4d01de7a C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:3,0:6,0:4,0:7,0:15,0:24,0:0.25,1:-91.7227,-233.447:141.724
inhA 333 a6804c49 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=inhA_V78A;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:18,6:43,14:18,0:43,0:37,20:87,43:0,0.666667:-102.417,-391.964:289.547
inhA 380 21f7b255 T G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=inhA_S94A;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:17,0:50,0:17,0:50,0:17,0:50,0:0,1:-7.92561,-500.546:492.621
inhA 681 9b199a86 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=inhA_I194T;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:40,0:23,0:60,0:33,0:121,0:70,0:0.333333,1:-41.4554,-482.126:440.67
inhA 816 783ad125 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:37,0:38,0:37,0:37,0:148,0:152,0:0,1:-5.56429,-537.388:531.823
katG 187 0df1f533 C A . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=katG_CCGT86T;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:68,0:51,0:68,0:51,0:137,0:102,0:0,1:-5.86746,-740.015:734.148
katG 256 0150fba6 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=katG_AACCCGG151G;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:57,0:40,0:57,0:40,0:57,0:40,0:0,1:-3.21234,-638.702:635.489
katG 357 a16a465a C A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:42,0:45,0:42,0:45,0:85,0:90,0:0,1:-3.58856,-592.65:589.061
katG 480 1ec8a021 A C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:25,0:47,0:25,0:46,0:75,0:141,0:0,1:-6.34532,-523.572:517.227
katG 519 6de9a781 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:29,0:46,0:28,0:46,0:89,0:139,0:0,1:-5.56429,-537.388:531.823
katG 525 dd5c9a6c A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=katG_D142G;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:35,0:45,0:35,0:45,0:70,0:90,0:0,1:-4.52527,-560.414:555.888
katG 600 184f00bf T G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:25,0:27,0:36,0:39,0:75,0:81,0:0.333333,1:-47.0147,-431.469:384.454
katG 709 42fa0f73 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:40,13:57,19:40,0:57,0:80,40:115,59:0,0.666667:-150.578,-542.2:391.623
katG 1044 8118e3ec GC AC,CA,CC . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=katG_S315T;PREDICT=r GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 3:100,0,0,40:70,0,0,49:0,0,0,40:0,0,0,49:0,0,0,120:0,0,0,147:1,1,1,0:-601.86,-601.86,-601.86,-3.42584:598.434
katG 1488 5868c7c4 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=katG_R463L;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:35,0:19,0:50,0:27,0:107,0:58,0:0.333333,1:-45.8453,-440.679:394.834
katG 1538 70e2841c G T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=katG_GCGT1438T,katG_GCGTC1438TC;PREDICT=.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:49,0:33,0:49,0:33,0:98,0:67,0:0,1:-4.19774,-569.624:565.426
katG 1840 dcf54545 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:47,0:49,0:47,0:49,0:47,0:49,0:0,1:-3.20198,-634.096:630.894
katG 1969 b7d9c7c3 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:40,0:64,0:40,0:66,0:120,0:194,0:0,1:-3.56638,-670.938:667.371
katG 2338 1b41370f C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:31,0:2,0:31,0:2,0:63,0:4,0:0,1:-30.431,-343.971:313.54
pncA 156 808fcb6a T G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=pncA_GTGGCTCGCTGGCGGTAACCGGTGGCGC47G,pncA_TGGCTCGCTGGCGGTAACCGGTGGCGCC48C,pncA_L19Q,pncA_L19P,pncA_CTG55CTA,pncA_CTG55CTC,pncA_CTG55CTT,pncA_CTG55TTA,pncA_CTG55TTG;PREDICT=.,.,.,.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:52,0:39,0:65,0:47,0:262,0:196,0:0.2,1:-22.5078,-611.07:588.563
pncA 171 35faad76 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=pncA_GTGGCTCGCTGGCGGTAACCGGTGGCGC47G,pncA_TGGCTCGCTGGCGGTAACCGGTGGCGCC48C,pncA_G24D,pncA_G24V;PREDICT=.,.,R,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:0,55:0,50:0,55:0,50:0,55:1,50:1,0:-675.543,-3.65599:671.887
pncA 180 c4f4afd0 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=pncA_L27Q,pncA_L27P;PREDICT=.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:27,0:24,0:27,0:24,0:54,0:49,0:0.5,1:-63.6278,-426.864:363.236
pncA 269 1763c8cc CACT CACC,GACT,TACT . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=pncA_CGGGTGACCA161A,pncA_H57N,pncA_H57Q,pncA_H57P,pncA_H57R,pncA_H57D,pncA_H57Y,pncA_H57L,pncA_F58I,pncA_F58S,pncA_F58L;PREDICT=.,.,.,.,.,.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,17,17,10:48,18,22,13:52,0,0,0:61,0,0,0:157,52,52,52:194,56,66,66:0.25,0.666667,0.666667,0.8:-474.29,-778.554,-756.372,-860.859:282.082
pncA 292 8d7d1bc6 TTCC TATCT . PASS VC=COMPLEX;GRAPHTYPE=SIMPLE;VARID=pncA_CGGCACACCGGACTATTCCTCGTCG177ACCGGACTATTCCTCGTCG,pncA_ACTATTCCTCGTCG188AG,pncA_Y64D,pncA_TAT190TAA,pncA_TAT190TAG,pncA_TAT190TGA,pncA_S65F,pncA_CTCG195G;PREDICT=.,.,.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:53,0:61,0:53,0:59,0:160,0:184,0:0,1:-4.8787,-716.989:712.111
pncA 326 d679b675 A C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=pncA_AGCGGTACTCCCG220G,pncA_T76I,pncA_T76P,pncA_T76S;PREDICT=.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:57,0:65,0:57,0:65,0:57,0:65,0:0,1:-6.56172,-753.831:747.269
pncA 381 8a02a331 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=pncA_F94S,pncA_F94C,pncA_F94L,pncA_TTC280TTT;PREDICT=.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:37,0:54,0:37,0:54,0:75,0:109,0:0,1:-3.30781,-611.07:607.763
pncA 389 b188b068 G C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=pncA_G97R,pncA_G97D,pncA_G97V,pncA_G97S,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 0:32,0:50,0:32,0:50,0:65,0:100,0:0,1:-4.19774,-569.624:565.426
pncA 441 b30c841a C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=pncA_ACG340ACA,pncA_ACG340ACC,pncA_ACG340ACT,pncA_T114M,pncA_T114P,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 0:61,0:67,0:61,0:67,0:61,0:67,0:0,1:-8.16891,-781.462:773.293
pncA 489 9c43ca29 T TG . PASS VC=INDEL;GRAPHTYPE=SIMPLE;VARID=pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTCGATGAGGTCGGTAT,pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTGGTCGGTAT,pncA_CGATGAGGTCGATGTG375G,pncA_AGGTCGATGT380T,pncA_ATGTGGTCGG386G,pncA_V130E,pncA_V130G;PREDICT=.,.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:61,0:71,0:61,0:71,0:123,0:143,0:0,1:-9.39686,-799.882:790.486
pncA 524 e7eada67 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=pncA_T142K,pncA_ACG424ACA,pncA_ACG424ACC,pncA_ACG424ACT,pncA_T142M,pncA_T142R,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 0:82,21:72,17:82,0:72,0:164,86:144,68:0,0.75:-193.216,-806.719:613.504
pncA 564 579bf745 T G . PASS VC=SNP;GRAPHTYPE=SIMPLE;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 0:62,0:60,0:62,0:60,0:125,0:121,0:0,1:-6.56172,-753.831:747.269
pncA 760 1601d922 GG AG . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:21,0:23,0:21,0:23,0:21,0:23,0:0,1:-20.486,-394.627:374.142
rplC 191 5d0aab32 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:77,0:56,0:77,0:56,0:154,0:112,0:0,1:-9.72286,-804.488:794.765
rplC 467 b0d07614 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:65,0:54,0:65,0:54,0:131,0:108,0:0,1:-5.86746,-740.015:734.148
rpoB 18 c6dd829d A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:29,0:17,0:29,0:17,0:87,0:51,0:0,1:-18.9926,-403.838:384.845
rpoB 40 d4929f45 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=rpoB_C-61T;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:29,9:21,6:29,0:21,0:88,29:65,20:0,0.666667:-85.3379,-349.693:264.355
rpoB 233 a8587584 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:48,0:36,0:48,0:36,0:96,0:73,0:0,1:-3.9187,-578.834:574.916
rpoB 409 5ff13f9f C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:52,0:45,0:52,0:44,0:157,0:135,0:0,1:-3.21234,-638.702:635.489
rpoB 784 20cb2171 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:41,0:53,0:41,0:53,0:41,0:53,0:0,1:-3.21245,-624.886:621.674
rpoB 965 4b4fd520 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:45,0:62,0:45,0:62,0:91,0:125,0:0,1:-3.86356,-684.753:680.89
rpoB 1149 41d19d67 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:64,0:37,0:64,0:37,0:129,0:75,0:0,1:-3.35533,-657.122:653.767
rpoB 1263 3f4712cf C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=rpoB_S388L;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:33,0:42,0:43,0:54,0:133,0:170,0:0.25,1:-29.5643,-537.388:507.823
rpoB 1326 167acc2e A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:43,11:46,12:43,0:46,0:129,44:140,49:0,0.75:-109.345,-524.487:415.142
rpoB 1422 ec5f831b C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=rpoB_GACCAGAACAACCCGCTGTCGGGGTTGACCCACA1303GCCCAGAACAACCCGCTGTCCGGGCCCC;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:15,0:12,0:0,0:0,0:61,0:49,0:0.75,1:-109.32,-316.34:207.019
rpoB 1433 1828fdbd CA AA,CT,GG,TA . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=rpoB_GACCAGAACAACCCGCTGTCGGGGTTGACCCACA1303GCCCAGAACAACCCGCTGTCCGGGCCCC,rpoB_TTGACCCACAA1327TGGCCCCA,rpoB_TGACCCACAA1328GGCCCCA,rpoB_CCCACAAG1331CC;PREDICT=.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:37,0,0,0,0:35,0,0,0,0:55,0,0,0,0:50,0,0,0,0:113,0,0,0,0:105,0,1,0,0:0.333333,1,1,1,1:-38.3453,-523.572,-523.572,-523.572,-523.572:485.227
rpoB 1449 0e1c5bc8 C G,T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=rpoB_ACTGTCGGCG1344A,rpoB_S450W;PREDICT=.,R GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:0,58,0:0,55,0:0,58,0:1,56,0:0,233,0:2,222,0:1,0,1:-712.384,-4.70685,-712.384:707.677
rpoB 1717 a38fdf80 T G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:47,0:69,0:47,0:69,0:47,0:69,0:0,1:-5.24852,-726.2:720.951
rpoB 1783 81051f27 G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:41,0:62,0:41,0:62,0:41,0:62,0:0,1:-3.48633,-666.333:662.846
rpoB 1862 4c02cc64 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:49,0:46,0:49,0:46,0:198,0:185,0:0,1:-3.20198,-629.491:626.289
rpoB 2017 5d85327b A C . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=rpoB_E639D;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:44,0:62,0:44,0:62,0:89,0:124,0:0,1:-3.75508,-680.148:676.393
rpoB 2728 0957c23b T G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:43,0:46,0:43,0:46,0:129,0:140,0:0,1:-3.42584,-601.86:598.434
rpoB 2993 fa4901ab A G . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:35,0:45,0:34,0:43,0:141,0:181,0:0,1:-4.52527,-560.414:555.888
rpoB 3226 f9924683 G T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:55,0:67,0:55,0:67,0:111,0:135,0:0,1:-6.56172,-753.831:747.269
rpoB 3325 d296515b T C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:49,0:53,0:49,0:53,0:49,0:53,0:0,1:-3.41595,-661.727:658.311
rpoB 3574 142bdc49 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:65,0:40,0:65,0:40,0:65,0:40,0:0,1:-3.65599,-675.543:671.887
rpsL 109 63510d26 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:37,0:73,0:37,0:73,0:37,0:73,0:0,1:-4.24448,-698.569:694.324
rpsL 228 5ce2e9da A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=rpsL_K43R;PREDICT=R GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:0,74:0,48:0,73:0,48:0,298:0,193:1,0:-753.831,-6.56172:747.269
rpsL 363 51a3cfdd A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=rpsL_K88M,rpsL_K88Q,rpsL_K88R;PREDICT=.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:55,0:69,0:55,0:69,0:55,0:69,0:0,1:-7.06549,-763.041:755.976
rpsL 478 c13d463c C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:54,0:55,0:50,0:56,0:164,0:165,0:0,1:-4.10834,-693.964:689.855
rrs 363 93e5517b C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:86,0:73,0:86,0:73,0:173,0:146,0:0,1:-20.6783,-924.222:903.544
rrs 592 aac3f350 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=rrs_C492T;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:37,0:72,0:37,0:72,0:74,0:144,0:0,1:-4.10834,-693.964:689.855
rrs 614 b2178722 AGCC AGCT,CGCC . PASS VC=PH_SNPs;GRAPHTYPE=SIMPLE;VARID=rrs_A514C,rrs_A514X,rrs_G515X,rrs_C516X,rrs_C517X,rrs_C517T;PREDICT=.,.,.,.,.,. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:15,0,0:50,1,0:22,0,0:68,1,0:46,0,0:150,2,1:0.333333,1,1:-45.2651,-486.772,-495.941:441.507
rrs 1008 35d9cdc7 A C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:47,0:17,0:48,0:19,0:141,0:53,0:0,1:-9.04992,-486.731:477.681
rrs 1083 78d2c5b5 T C . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:41,12:25,8:41,0:25,0:82,38:51,24:0,0.666667:-100.389,-414.99:314.601
rrs 1128 99b8225d C A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:68,0:27,0:69,0:26,0:206,0:83,0:0,1:-3.20198,-629.491:626.289
rrs 1241 746b10d8 C T . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:47,0:17,0:66,0:26,0:141,0:53,0:0.333333,1:-41.0499,-486.731:445.681
rrs 1501 d7b55751 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=rrs_A1401X;PREDICT=R GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:16,63:17,60:0,66:0,63:50,190:53,181:0.666667,0:-660.867,-158.78:502.087
tlyA 10 61246b7a G A . ld;lgc VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF .:0,0:0,0:0,0:0,0:0,0:0,0:1,1:-192,-192:0
tlyA 43 9e21a60a G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:31,0:38,0:31,0:38,0:63,0:77,0:0,1:-7.25052,-509.757:502.506
tlyA 133 382e6ba7 A G . PASS VC=SNP;GRAPHTYPE=SIMPLE;VARID=tlyA_L11L;PREDICT=. GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:0,41:0,17:0,41:0,17:0,82:0,34:1,0:-459.1,-11.7241:447.376
tlyA 265 938c646b G A . PASS VC=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:39,0:57,0:39,0:57,0:39,0:57,0:0,1:-3.20198,-634.096:630.894