Run ID: SRR11972438
Sample name:
Date: 03-04-2023 05:42:25
Number of reads: 534071
Percentage reads mapped: 71.63
Strain: lineage1.1.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 0.92 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.95 |
lineage1.1.1 | Indo-Oceanic | EAI4;EAI5 | RD239 | 0.93 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 0.27 | isoniazid |
pncA | 2289095 | p.Asp49Glu | missense_variant | 0.33 | pyrazinamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.9 |
gyrA | 6853 | c.-449A>G | upstream_gene_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
ccsA | 620748 | c.858T>G | synonymous_variant | 0.45 |
rpoB | 760386 | p.His194Tyr | missense_variant | 1.0 |
rpoB | 760796 | c.990A>G | synonymous_variant | 0.15 |
rpoB | 761152 | p.Leu449Gln | missense_variant | 0.22 |
rpoB | 762144 | p.Glu780Lys | missense_variant | 0.11 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.73 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.73 |
rpoC | 764326 | c.957G>C | synonymous_variant | 0.18 |
rpoC | 764341 | c.972G>T | synonymous_variant | 0.2 |
rpoC | 764359 | c.990C>A | synonymous_variant | 0.13 |
rpoC | 764368 | c.999C>A | synonymous_variant | 0.12 |
rpoC | 764371 | c.1002G>C | synonymous_variant | 0.12 |
rpoC | 764383 | c.1014C>G | synonymous_variant | 0.12 |
rpoC | 764387 | c.1018T>C | synonymous_variant | 0.13 |
rpoC | 764395 | c.1026C>T | synonymous_variant | 0.14 |
rpoC | 764405 | c.1036_1038delAGGinsCGC | synonymous_variant | 0.14 |
rpoC | 764410 | c.1041G>T | synonymous_variant | 0.15 |
rpoC | 764413 | c.1044C>T | synonymous_variant | 0.18 |
rpoC | 764419 | c.1050C>G | synonymous_variant | 0.22 |
rpoC | 765121 | c.1752G>A | synonymous_variant | 0.18 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.75 |
rpoC | 765383 | p.Met672Val | missense_variant | 0.82 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 778116 | p.His122Arg | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303819 | p.Ala297Thr | missense_variant | 0.14 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.88 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472400 | n.555C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472953 | n.1108_1109insA | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472975 | n.1130T>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472986 | n.1142delG | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472992 | n.1147_1148insT | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473053 | n.1208T>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473070 | n.1225G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473226 | n.1381C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474199 | n.542G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474201 | n.544T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474202 | n.545T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474218 | n.561T>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474228 | n.571T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1474782 | n.1125G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474790 | n.1133C>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1474794 | n.1137C>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474798 | n.1141C>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1474804 | n.1147C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1474806 | n.1149A>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.48 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.55 |
rrl | 1474830 | n.1173A>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474831 | n.1174A>C | non_coding_transcript_exon_variant | 0.55 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.46 |
rrl | 1474864 | n.1207C>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.52 |
rrl | 1474896 | n.1239A>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1474902 | n.1245T>C | non_coding_transcript_exon_variant | 0.36 |
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1474913 | n.1256T>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1474920 | n.1263G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475574 | n.1917C>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475696 | n.2039T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475703 | n.2046A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475707 | n.2050T>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475716 | n.2059A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475751 | n.2094C>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475752 | n.2095C>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475753 | n.2096C>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475756 | n.2100_2101insGGGGAA | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475761 | n.2106_2113delCAAGGGTG | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475775 | n.2118G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475776 | n.2119G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475777 | n.2120A>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475783 | n.2126T>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.3 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.3 |
rrl | 1475843 | n.2186G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475849 | n.2192G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475853 | n.2196C>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476297 | n.2640C>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.36 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.36 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.36 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.56 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.14 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.13 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.2 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.13 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.21 |
inhA | 1674260 | p.Ser20Leu | missense_variant | 0.12 |
inhA | 1674958 | c.759delC | frameshift_variant | 0.25 |
rpsA | 1834319 | p.Val260Ile | missense_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154206 | p.Ala636Thr | missense_variant | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155553 | p.Arg187Trp | missense_variant | 0.15 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.14 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.14 |
PPE35 | 2170454 | c.159C>G | synonymous_variant | 0.11 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.86 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.87 |
kasA | 2518949 | p.Ala279Ser | missense_variant | 0.14 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726070 | c.-123G>A | upstream_gene_variant | 1.0 |
pepQ | 2860580 | c.-162G>T | upstream_gene_variant | 0.14 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.73 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.85 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.88 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.83 |
fprA | 3475302 | c.1296C>T | synonymous_variant | 0.92 |
fbiB | 3642457 | p.Arg308Leu | missense_variant | 0.15 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.14 |
rpoA | 3878549 | c.-42A>G | upstream_gene_variant | 0.75 |
rpoA | 3878630 | c.-124delC | upstream_gene_variant | 1.0 |
clpC1 | 4039508 | c.1197G>C | synonymous_variant | 0.13 |
clpC1 | 4039526 | c.1179G>C | synonymous_variant | 0.14 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4239925 | c.63C>T | synonymous_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4244096 | c.864C>T | synonymous_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.92 |
embB | 4246514 | c.1A>G | start_lost | 0.13 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.2 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.2 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.22 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.22 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.2 |
embB | 4247238 | c.727delG | frameshift_variant | 0.13 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249266 | p.Pro918His | missense_variant | 0.17 |
ubiA | 4269152 | p.Ala228Ser | missense_variant | 0.94 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.94 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4327483 | c.-10G>A | upstream_gene_variant | 0.89 |
ethA | 4328055 | c.-582A>G | upstream_gene_variant | 1.0 |
whiB6 | 4338242 | p.Gln94Glu | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.91 |