Run ID: SRR958201
Sample name:
Date: 2024-10-04T22:28:31.707761
Number of reads: 12369593
Percentage reads mapped: 99.62
Median coverage: 267.0
Strain: lineage4.3.2.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.3 | Euro-American (LAM) | None | 1.0 |
| lineage4.3.2 | Euro-American (LAM) | None | 1.0 |
| lineage4.3.2.1 | Euro-American (LAM) | RD761 | 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 |
|---|---|---|---|---|---|---|
| gyrB | 5520 | p.Pro94Leu | missense_variant | 0.99 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrB | 7222 | c.1983C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7362 | p.Glu21Arg | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| 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 | |||||
| Rv0565c | 656333 | p.Asp380His | missense_variant | 1.0 | ethionamide | |
| rpoB | 760095 | p.Met97Leu | missense_variant | 1.0 | rifampicin | |
| rpoC | 764995 | c.1626C>G | synonymous_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 | |||||
| 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 | ||||||
| rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.99 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R | |||||
| 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 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv2477c | 2784613 | c.-571T>C | upstream_gene_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| thyA | 3073868 | p.Thr202Ala | missense_variant | 0.99 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3236c | 3613071 | p.Ala16Thr | missense_variant | 0.99 | pyrazinamide | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| mtrB | 3627296 | c.-683T>C | upstream_gene_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| 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 | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |
