Run ID: SRR11972394
Sample name:
Date: 03-04-2023 05:40:06
Number of reads: 951278
Percentage reads mapped: 88.93
Strain: lineage2.2.1.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoC | 764841 | p.Ile491Thr | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.42 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
embB | 4247729 | p.Gly406Cys | missense_variant | 1.0 | ethambutol |
ethA | 4326589 | c.884delT | frameshift_variant | 0.29 | ethionamide, ethionamide |
ethA | 4326882 | c.587_591delACTCG | frameshift_variant | 0.88 | ethionamide |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
pncA | 2277357 | c.-1108_*11323del | transcript_ablation | 1.0 | pyrazinamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576751 | p.Lys468Asn | missense_variant | 0.33 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 761658 | p.Pro618Thr | missense_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472507 | n.662C>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472517 | n.672T>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472518 | n.673G>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472544 | n.699C>G | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472669 | n.824_825insTAG | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472676 | n.832_840delCTTCCTTGG | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472689 | n.844C>G | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472690 | n.845_846insCCTTA | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472697 | n.852T>A | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472700 | n.855C>T | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472705 | n.860G>A | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472779 | n.934G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473053 | n.1208T>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473080 | n.1235C>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473081 | n.1236C>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473097 | n.1252G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473099 | n.1254T>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473122 | n.1277T>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473123 | n.1278A>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473130 | n.1285G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473131 | n.1286G>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473147 | n.1302G>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473150 | n.1305T>G | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473161 | n.1316A>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473164 | n.1319C>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473172 | n.1327T>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473179 | n.1334C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1474527 | n.870T>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474528 | n.871T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474530 | n.873G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474537 | n.880G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474539 | n.882C>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474542 | n.885A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474552 | n.895C>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474570 | n.913G>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474578 | n.921A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474584 | n.927C>G | non_coding_transcript_exon_variant | 0.26 |
rrl | 1474586 | n.929T>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1474587 | n.930G>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475696 | n.2039T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475703 | n.2046A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1475713 | n.2056C>G | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475716 | n.2059A>G | non_coding_transcript_exon_variant | 0.32 |
rrl | 1475722 | n.2065G>A | non_coding_transcript_exon_variant | 0.35 |
rrl | 1475751 | n.2094C>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475752 | n.2095C>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475753 | n.2096C>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475758 | n.2101A>T | non_coding_transcript_exon_variant | 0.34 |
rrl | 1475762 | n.2105G>T | non_coding_transcript_exon_variant | 0.34 |
rrl | 1475763 | n.2106C>T | non_coding_transcript_exon_variant | 0.34 |
rrl | 1475765 | n.2108A>C | non_coding_transcript_exon_variant | 0.35 |
rrl | 1475769 | n.2112T>A | non_coding_transcript_exon_variant | 0.34 |
rrl | 1475775 | n.2118G>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475776 | n.2119G>C | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475777 | n.2120A>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475783 | n.2126T>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.3 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.3 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.31 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475869 | n.2212C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476141 | n.2484A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476153 | n.2496T>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476164 | n.2507A>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476165 | n.2508T>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476195 | n.2538C>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476196 | n.2539C>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476204 | n.2547C>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476210 | n.2553G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476211 | n.2554G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476212 | n.2555T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476215 | n.2558C>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476221 | n.2564T>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476229 | n.2572C>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.49 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476572 | n.2915G>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476573 | n.2916A>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476603 | n.2946G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476607 | n.2950C>T | non_coding_transcript_exon_variant | 0.13 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.24 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.29 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714846 | p.Val163Ile | missense_variant | 1.0 |
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.21 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474379 | p.Ala125Thr | missense_variant | 0.13 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4248115 | c.1602C>T | synonymous_variant | 1.0 |
embB | 4249329 | p.Met939Arg | missense_variant | 0.18 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |