Run ID: SRR5818682
Sample name:
Date: 2024-10-04T19:41:52.502894
Number of reads: 1509006
Percentage reads mapped: 99.44
Median coverage: 29.0
Strain: lineage4.1.2
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.1 | Euro-American | None | 0.99 |
| lineage4.1.2 | Euro-American | None | 1.0 |
| lineage4 | Euro-American | None | 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 | 7323 | p.Pro8Ala | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| 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 | 491591 | p.Lys270Met | missense_variant | 1.0 | pretomanid | |
| delamanid | Uncertain significance | |||||
| clofazimine | Not assoc w R | |||||
| Rv0565c | 656832 | c.639G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
| rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 763249 | p.Asp1148Gly | missense_variant | 1.0 | rifampicin | |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 776659 | p.Asp608Asn | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| inhA | 1673346 | c.-856C>G | upstream_gene_variant | 0.17 | isoniazid | |
| ethionamide | ||||||
| inhA | 1673349 | c.-853G>C | upstream_gene_variant | 0.18 | isoniazid | |
| ethionamide | ||||||
| inhA | 1673361 | c.-841C>G | upstream_gene_variant | 0.14 | isoniazid | |
| ethionamide | ||||||
| inhA | 1673380 | c.-822C>G | upstream_gene_variant | 0.2 | isoniazid | |
| ethionamide | ||||||
| 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 |
| PPE35 | 2168501 | p.Phe704Leu | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.55 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.52 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.21 | capreomycin | Uncertain significance |
| 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 | |||||
| mtrB | 3625581 | c.1033C>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| fbiA | 3641258 | p.Pro239Gln | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiB | 3642365 | c.831G>A | synonymous_variant | 0.96 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247121 | p.Ser203Leu | missense_variant | 0.94 | 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 |
