Run ID: ERR2517457
Sample name:
Date: 2024-10-03T23:46:02.410624
Number of reads: 2496193
Percentage reads mapped: 48.53
Median coverage: 65.0
Strain: lineage3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage3 | East-African-Indian | RD750 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9422 | c.2121C>T | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9596 | c.2295G>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| Rv0010c | 13277 | c.282T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| clofazimine | Not assoc w R | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| nusG | 734354 | p.Pro34Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| nusG | 734753 | p.Thr167Met | missense_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 762434 | c.2628T>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 762872 | p.Met1022Ile | missense_variant | 0.1 | rifampicin | Uncertain significance |
| rpoB | 762878 | p.Ile1024Met | missense_variant | 0.1 | rifampicin | |
| rpoB | 762879 | p.Met1025Leu | missense_variant | 0.11 | rifampicin | Uncertain significance |
| rpoB | 762887 | c.3081G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| rpoC | 762896 | c.-474G>C | upstream_gene_variant | 0.14 | rifampicin | |
| rpoB | 762917 | c.3111C>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
| rpoB | 762923 | c.3117C>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
| rpoB | 762925 | p.Thr1040Ile | missense_variant | 0.15 | rifampicin | |
| rpoB | 762929 | c.3123G>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
| rpoB | 762939 | p.Met1045Leu | missense_variant | 0.15 | rifampicin | |
| rpoB | 762942 | p.Ile1046Val | missense_variant | 0.13 | rifampicin | Uncertain significance |
| rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.16 | rifampicin | |
| rpoC | 762980 | c.-390T>C | upstream_gene_variant | 0.14 | rifampicin | |
| rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.11 | rifampicin | |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 764181 | p.Asp271Gly | missense_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 764405 | c.1036_1038delAGGinsCGC | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
| rpoC | 764410 | c.1041G>C | synonymous_variant | 0.22 | rifampicin | |
| rpoC | 764428 | c.1059G>C | synonymous_variant | 0.28 | rifampicin | Not assoc w R - Interim |
| rpoC | 764434 | c.1065A>G | synonymous_variant | 0.29 | rifampicin | Not assoc w R - Interim |
| rpoC | 764435 | c.1066A>C | synonymous_variant | 0.29 | rifampicin | Not assoc w R - Interim |
| rpoC | 764446 | p.Asp359Glu | missense_variant | 0.27 | rifampicin | |
| rpoC | 764450 | p.Gly361Arg | missense_variant | 0.27 | rifampicin | |
| rpoC | 764458 | c.1089G>C | synonymous_variant | 0.29 | rifampicin | Not assoc w R - Interim |
| rpoC | 764461 | p.Glu364Asp | missense_variant | 0.29 | rifampicin | |
| rpoC | 764468 | p.Val367Ile | missense_variant | 0.3 | rifampicin | |
| rpoC | 764471 | p.Asn368Arg | missense_variant | 0.3 | rifampicin | |
| rpoC | 764497 | c.1128A>G | synonymous_variant | 0.25 | rifampicin | Not assoc w R - Interim |
| rpoC | 764498 | p.Ser377Ala | missense_variant | 0.23 | rifampicin | |
| rpoC | 764503 | c.1134G>C | synonymous_variant | 0.23 | rifampicin | |
| rpoC | 764509 | c.1140G>C | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
| rpoC | 764611 | c.1242G>C | synonymous_variant | 0.19 | rifampicin | |
| rpoC | 764632 | c.1263T>C | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
| rpoC | 764650 | c.1281G>C | synonymous_variant | 0.24 | rifampicin | |
| rpoC | 764672 | p.Gln435Glu | missense_variant | 0.25 | rifampicin | |
| rpoC | 764677 | c.1308C>G | synonymous_variant | 0.24 | rifampicin | Not assoc w R - Interim |
| rpoC | 764695 | c.1326T>C | synonymous_variant | 0.24 | rifampicin | |
| rpoC | 764705 | p.Leu446Lys | missense_variant | 0.17 | rifampicin | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| Rv1129c | 1254749 | c.-215C>T | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.19 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.48 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.57 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.54 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.54 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.54 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.5 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.49 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.5 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472266 | n.421C>A | non_coding_transcript_exon_variant | 0.48 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472277 | n.432C>G | non_coding_transcript_exon_variant | 0.38 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.13 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>G | non_coding_transcript_exon_variant | 0.21 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.21 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476384 | n.2727G>C | non_coding_transcript_exon_variant | 0.31 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.31 | capreomycin | |
| linezolid | ||||||
| rrl | 1476428 | n.2771C>A | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>G | non_coding_transcript_exon_variant | 0.24 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.21 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2170769 | c.-157C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 | pyrazinamide | |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.99 | isoniazid | Not assoc w R |
| Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| panD | 4044872 | c.-591C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| glpK | 4138622 | c.1134C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244454 | p.Ala408Ser | missense_variant | 0.96 | ethambutol | Uncertain significance |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
