Run ID: SRR15368852
Sample name:
Date: 2024-10-03T18:43:22.866438
Number of reads: 5481462
Percentage reads mapped: 99.42
Median coverage: 166.0
Strain: lineage4.2.2
Spoligotype:
Drug-resistance: MDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.2.2 | Euro-American (Ural) | None | 1.0 |
| lineage4.2 | Euro-American | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Ser450Trp | Assoc w R | |
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | embB | p.Met306Ile | Assoc w R | |
| p.Gly406Ala | Assoc w R | |||
| pyrazinamide | pncA | p.Ser67Pro | Assoc w R | |
| streptomycin | gid | p.Glu103* | Assoc w R | |
| 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 |
|---|---|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin | Assoc w R | |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2289043 | p.Ser67Pro | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
| embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol | Assoc w R | |
| embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol | Assoc w R | |
| gid | 4407896 | p.Glu103* | stop_gained | 1.0 | streptomycin | Assoc w R |
| 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 | 8863 | p.Thr521Ser | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9713 | p.Met804Ile | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| mshA | 576077 | c.730C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| ethionamide | Not assoc w R - Interim | |||||
| nusG | 734624 | p.Arg124Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
| mmaA3 | 737317 | p.Ala278Glu | missense_variant | 1.0 | isoniazid | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 778882 | c.-402C>T | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rplC | 800204 | c.-605T>C | upstream_gene_variant | 1.0 | linezolid | |
| fbiC | 1303746 | c.816T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| 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 |
| bacA | 2063685 | c.1044G>A | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
| capreomycin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R | |||||
| bacA | 2063911 | p.Ile273Thr | missense_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| PPE35 | 2168718 | p.Thr632Met | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2170674 | c.-62T>G | 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 | |||||
| Rv1979c | 2223770 | c.-670_-607delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223770 | c.-669_-607delTGGAAAATTACATCGCCCAGACGCGCGACAAGTTCCTCAGCGCGGCCACATCGTCCACTCCAC | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| thyX | 3067949 | c.-4C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| thyA | 3074232 | p.Trp80* | stop_gained | 1.0 | para-aminosalicylic_acid | |
| ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.99 | cycloserine | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3236c | 3612469 | c.648A>G | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
