Run ID: ERR3276249
Sample name:
Date: 2024-04-16T09:40:57.382309
Number of reads: 4328497
Percentage reads mapped: 99.99
Median coverage: 62.5
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 | |||||
| rpoB | 761871 | c.2065C>A | synonymous_variant | 1.0 | rifampicin | |
| rpoC | 765146 | p.Pro593Ser | missense_variant | 1.0 | rifampicin | |
| 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 |
| Rv1129c | 1254565 | c.-31T>G | upstream_gene_variant | 1.0 | moxifloxacin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| fabG1 | 1673162 | c.-278T>C | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2170198 | p.Ala139Thr | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2477c | 2784149 | c.-107C>G | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
| Rv3236c | 3612047 | p.Ala357Val | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| alr | 3840226 | p.Thr399Ala | missense_variant | 1.0 | cycloserine | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4268593 | p.Val82Met | missense_variant | 1.0 | ethambutol | |
| ethA | 4326505 | c.969C>G | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| whiB6 | 4338594 | c.-74delC | upstream_gene_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin |
