Run ID: ERR551569_ERR551568
Sample name:
Date: 2024-03-24T19:10:43.633625
Number of reads: 1449711
Percentage reads mapped: 99.78
Median coverage: 67.0
Strain: lineage4.1
Spoligotype:
Drug-resistance: MDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.1 | Euro-American | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Leu430Pro | Assoc w R | |
| isoniazid | ahpC | c.-57C>T | Uncertain significance | Mutation from literature |
| ethambutol | ||||
| pyrazinamide | pncA | c.-11A>G | Assoc w R | |
| streptomycin | gid | c.102delG | 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 | 761095 | p.Leu430Pro | missense_variant | 1.0 | rifampicin | Assoc w R | |
| pncA | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide | Assoc w R | |
| ahpC | 2726136 | c.-57C>T | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
| gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 1456 | p.Glu486Lys | missense_variant | 1.0 | isoniazid | Uncertain significance |
| gyrB | 6507 | p.Ala423Val | 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 | |||||
| gyrA | 9656 | c.2355C>G | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 765187 | c.1818C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoC | 766012 | c.2643C>G | 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 | |||||
| mmpL5 | 775973 | p.Leu836Phe | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| mmpL5 | 776411 | c.2070T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rpsL | 781421 | c.-139C>A | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| Rv1129c | 1253498 | p.Ser346Leu | missense_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| 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 | 2156007 | c.105C>T | synonymous_variant | 0.99 | isoniazid | Not assoc w R - Interim |
| katG | 2156428 | c.-317C>T | upstream_gene_variant | 0.73 | isoniazid | |
| PPE35 | 2170748 | c.-136C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| 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 | |||||
| mtrA | 3627293 | c.57G>A | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| rifampicin | Not assoc w R - Interim | |||||
| panD | 4044051 | c.231C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| 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 |
| embA | 4245311 | c.2079C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embB | 4248758 | c.2245C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| ubiA | 4269361 | p.Leu158Ser | missense_variant | 1.0 | ethambutol | 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 |
