Run ID: ERR4827580
Sample name:
Date: 2024-10-03T18:04:54.548750
Number of reads: 2836368
Percentage reads mapped: 99.44
Median coverage: 83.0
Strain: lineage4.1.2
Spoligotype:
Drug-resistance: HR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.1 | Euro-American | None | 1.0 |
| lineage4.1.2 | Euro-American | None | 0.98 |
| lineage4 | Euro-American | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | katG | p.Ser315Asn | Assoc w R | High-level resistance |
| ethambutol | ||||
| pyrazinamide | pncA | p.His51Gln | Assoc w R | |
| streptomycin | gid | p.Leu79Ser | Uncertain significance | Mutation from literature |
| 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 |
|---|---|---|---|---|---|---|---|
| katG | 2155168 | p.Ser315Asn | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2289089 | p.His51Gln | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
| gid | 4407967 | p.Leu79Ser | missense_variant | 0.3 | streptomycin | Uncertain significance | Mutation from literature |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 1163 | p.Thr388Ile | missense_variant | 0.41 | isoniazid | 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 | |||||
| mshA | 576766 | c.1419G>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| 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 |
| rpoC | 763555 | c.186C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| 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 | 778134 | c.345_346delAC | frameshift_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| fbiC | 1303434 | p.Asp168Glu | missense_variant | 1.0 | pretomanid | |
| delamanid | Uncertain significance | |||||
| clofazimine | Uncertain significance | |||||
| 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 |
| PPE35 | 2169041 | c.1572G>A | synonymous_variant | 0.44 | pyrazinamide | Not assoc w R - Interim |
| PPE35 | 2169053 | c.1560T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2169059 | c.1554G>A | synonymous_variant | 0.58 | pyrazinamide | |
| PPE35 | 2169063 | p.Met517Thr | missense_variant | 1.0 | pyrazinamide | |
| PPE35 | 2169065 | p.Ala516Ile | missense_variant | 0.58 | pyrazinamide | |
| PPE35 | 2169068 | c.1545G>T | synonymous_variant | 0.59 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| pncA | 2290171 | c.-930G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.13 | capreomycin | Uncertain significance |
| Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.19 | capreomycin | |
| 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 | |||||
| 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 | 4248551 | p.Ala680Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4249357 | c.2844G>A | synonymous_variant | 1.0 | ethambutol | |
| 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 | ||||||
| gid | 4407756 | p.Ser149Arg | missense_variant | 0.47 | streptomycin | Uncertain significance |
| gid | 4407854 | p.Gly117Trp | missense_variant | 0.19 | streptomycin | Uncertain significance |
| gid | 4408082 | p.Val41Ile | missense_variant | 1.0 | streptomycin | Uncertain significance |
