Run ID: SRR22249704
Sample name:
Date: 2024-10-04T22:35:33.227972
Number of reads: 3062116
Percentage reads mapped: 99.73
Median coverage: 90.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.8 | Euro-American (mainly T) | RD219 | 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 | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.47 | isoniazid | |
| ethionamide | ||||||
| mshA | 576347 | p.Thr334Ala | missense_variant | 1.0 | isoniazid | Uncertain significance |
| ethionamide | Uncertain significance | |||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpS5 | 778825 | c.81G>C | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rplC | 801206 | p.Arg133His | missense_variant | 1.0 | linezolid | |
| sigE | 1364904 | c.492C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| inhA | 1673346 | c.-856C>G | upstream_gene_variant | 0.17 | isoniazid | |
| ethionamide | ||||||
| inhA | 1673349 | c.-853G>C | upstream_gene_variant | 0.17 | isoniazid | |
| ethionamide | ||||||
| inhA | 1673357 | c.-845G>A | upstream_gene_variant | 0.12 | isoniazid | |
| ethionamide | ||||||
| inhA | 1673359 | c.-843T>C | upstream_gene_variant | 0.13 | isoniazid | |
| ethionamide | ||||||
| inhA | 1673361 | c.-841C>G | upstream_gene_variant | 0.14 | isoniazid | |
| ethionamide | ||||||
| inhA | 1673380 | c.-822C>G | upstream_gene_variant | 0.21 | isoniazid | |
| ethionamide | ||||||
| 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 | |||||
| Rv1979c | 2223491 | c.-327C>A | upstream_gene_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Not assoc w R | |||||
| mtrB | 3626583 | p.Gly11Cys | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| 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 |
