Run ID: ERR11068923
Sample name:
Date: 2024-04-15T23:13:17.831485
Number of reads: 3800462
Percentage reads mapped: 99.83
Median coverage: 121.0
Strain: lineage4.4.1.2
Spoligotype:
Drug-resistance: HR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.4.1.2 | Euro-American | None | 1.0 |
| lineage4.4.1 | Euro-American (S-type) | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.4 | Euro-American | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | rpsL | p.Lys88Arg | Assoc w R | |
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | fbiC | c.592_594delTGGinsCC | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
| fbiC | 1303522 | c.592_594delTGGinsCC | frameshift_variant&missense_variant | 1.0 | pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| 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 | |||||
| Rv0010c | 13568 | c.-10T>G | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.21 | ethionamide | |
| isoniazid | ||||||
| rpoC | 763513 | c.144C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| mmpL5 | 775639 | p.Ile948Val | 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 |
| rplC | 800233 | c.-576G>A | upstream_gene_variant | 1.0 | linezolid | |
| fbiC | 1303519 | p.Ser197Tyr | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1303529 | p.Glu200Val | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1303531 | p.Met201Leu | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1303534 | p.Ser202Ala | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1303538 | p.Arg203Leu | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| 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 |
| ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 | ethionamide | Uncertain significance |
| delamanid | Uncertain significance | |||||
| isoniazid | Not assoc w R | |||||
| PPE35 | 2167770 | p.Ser948Ile | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223290 | c.-126A>C | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2477c | 2784401 | c.-359G>A | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| pepQ | 2860213 | p.Pro69Leu | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 | cycloserine | |
| Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| glpK | 4139386 | p.Ser124Ala | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embC | 4238963 | c.-900C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4249012 | c.2499G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338504 | c.17delC | frameshift_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| 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 | 4408471 | c.-269G>A | upstream_gene_variant | 1.0 | streptomycin |
