Run ID: SRR9971051
Sample name:
Date: 04-04-2023 23:08:32
Number of reads: 6084869
Percentage reads mapped: 96.8
Strain: lineage4.3.3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Gly | missense_variant | 1.0 | rifampicin |
rpoB | 761161 | p.Leu452Pro | missense_variant | 1.0 | rifampicin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.14 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.83 | kanamycin, capreomycin, aminoglycosides, amikacin |
rrs | 1473247 | n.1402C>A | non_coding_transcript_exon_variant | 0.16 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673432 | c.-8T>A | upstream_gene_variant | 1.0 | isoniazid |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288785 | c.456dupC | frameshift_variant | 1.0 | pyrazinamide, pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4327484 | c.-11A>G | upstream_gene_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.28 |
rpoB | 763123 | p.Ile1106Thr | missense_variant | 1.0 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472507 | n.662C>G | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472517 | n.672T>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472518 | n.673G>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472690 | n.845C>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473270 | n.1425G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473276 | n.1431A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1473923 | n.266C>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474035 | n.380delG | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474506 | n.849C>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474637 | n.980C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474638 | n.981C>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474677 | n.1020A>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475681 | n.2024C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476056 | n.2399G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476153 | n.2496T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476165 | n.2508T>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476195 | n.2538C>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476204 | n.2547C>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476211 | n.2554G>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476212 | n.2555T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476214 | n.2557G>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476215 | n.2558C>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476227 | n.2570C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476229 | n.2572C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476523 | n.2866T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.1 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.19 |
Rv1979c | 2223051 | p.Glu38Asp | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 |
Rv2752c | 3065824 | p.Pro123Leu | missense_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.55 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.12 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.19 |
embB | 4248324 | p.Ala604Gly | missense_variant | 0.22 |
ubiA | 4269271 | p.Val188Ala | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
gid | 4407912 | c.160_290del | frameshift_variant | 1.0 |