Run ID: SRR6797399
Sample name:
Date: 2024-04-15T08:16:47.802530
Number of reads: 3854928
Percentage reads mapped: 99.55
Median coverage: 87.0
Strain: lineage1;lineage3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage3 | East-African-Indian | RD750 | 0.93 |
| lineage1 | Indo-Oceanic | RD239 | 0.06 |
| 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 | |||||
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.96 | ethionamide | Not assoc w R - Interim |
| rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.95 | rifampicin | Not assoc w R |
| rpoB | 762434 | c.2628T>G | synonymous_variant | 0.91 | rifampicin | Not assoc w R |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 763884 | p.Ala172Val | missense_variant | 0.16 | rifampicin | Not assoc w R |
| rpoC | 763886 | c.517C>A | synonymous_variant | 0.17 | rifampicin | Not assoc w R |
| rpoC | 766582 | c.3213C>A | synonymous_variant | 0.95 | rifampicin | Not assoc w R |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| 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 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| 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 | 2154362 | p.Phe584Val | missense_variant | 0.12 | isoniazid | Uncertain significance |
| 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 | 2169158 | c.1455G>A | synonymous_variant | 0.9 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| pncA | 2289047 | c.195C>T | synonymous_variant | 0.89 | pyrazinamide | Not assoc w R |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.86 | pyrazinamide | |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.86 | isoniazid | Not assoc w R |
| Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| levofloxacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| rifampicin | 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 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| fbiA | 3640377 | c.-166G>A | upstream_gene_variant | 0.84 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| alr | 3841253 | c.168C>T | synonymous_variant | 0.12 | cycloserine | |
| alr | 3841277 | c.144C>T | synonymous_variant | 0.11 | cycloserine | |
| alr | 3841473 | c.-53G>A | upstream_gene_variant | 0.95 | cycloserine | |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.12 | pyrazinamide | Not assoc w R - Interim |
| panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.95 | pyrazinamide | |
| glpK | 4138622 | c.1134C>T | synonymous_variant | 0.9 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| embC | 4242075 | p.Arg738Gln | missense_variant | 0.85 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243848 | p.Val206Met | missense_variant | 0.11 | ethambutol | Not assoc w R |
| ubiA | 4269606 | c.228T>C | synonymous_variant | 0.15 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
| gid | 4407712 | p.Gly164Val | missense_variant | 0.92 | streptomycin | Uncertain significance |
