Run ID: ERR1465978_ERR1465867
Sample name:
Date: 2024-04-14T06:58:13.772560
Number of reads: 9272589
Percentage reads mapped: 99.69
Median coverage: 168.0
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 |
|---|---|---|---|---|---|---|
| dnaA | 902 | p.Val301Ala | missense_variant | 0.13 | isoniazid | Uncertain significance |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| 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 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.99 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.16 | ethionamide | |
| isoniazid | ||||||
| fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.16 | ethionamide | |
| isoniazid | ||||||
| fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.16 | ethionamide | |
| isoniazid | ||||||
| fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.26 | ethionamide | |
| isoniazid | ||||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.53 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.54 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| pncA | 2289461 | c.-220T>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
| thyX | 3067570 | p.Ala126Thr | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv3083 | 3448497 | c.-6_*1408del | transcript_ablation | 1.0 | ethionamide | Uncertain significance |
| whiB7 | 3568417 | p.Lys88Thr | missense_variant | 1.0 | streptomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | ||||||
| Rv3236c | 3613379 | c.-263T>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246544 | p.Thr11Pro | missense_variant | 0.22 | ethambutol | Uncertain significance |
| embB | 4246555 | c.42G>C | synonymous_variant | 0.28 | ethambutol | |
| embB | 4246556 | p.Ala15Pro | missense_variant | 0.28 | 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 |
