Run ID: SRR11349152
Sample name:
Date: 02-04-2023 20:52:49
Number of reads: 4254779
Percentage reads mapped: 79.75
Strain: lineage4.3.3
Drug-resistance: 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 | 0.99 |
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 | 0.16 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
rrl | 1476471 | n.2814G>T | non_coding_transcript_exon_variant | 0.3 | linezolid |
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 | 0.99 | 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 | 0.31 |
rpoB | 763123 | p.Ile1106Thr | missense_variant | 1.0 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.99 |
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 | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472580 | n.735C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472670 | n.825G>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472673 | n.828T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472675 | n.830T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472677 | n.832C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472681 | n.837_838delTT | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472687 | n.842_843insC | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472690 | n.845C>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472975 | n.1130T>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.27 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476056 | n.2399G>A | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.58 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.56 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.26 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
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 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.22 |
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 | 0.51 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.14 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ubiA | 4269271 | p.Val188Ala | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408042 | p.Val54Ala | missense_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
gid | 4407912 | c.160_290del | frameshift_variant | 1.0 |