Run ID: SRR19304007
Sample name:
Date: 2025-07-26T22:10:42.830865
Number of reads: 6289048
Percentage reads mapped: 99.75
Median coverage: 173.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 100.0 |
| lineage4.8 | Euro-American (mainly T) | RD219 | 100.0 |
| 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 | |||||
| fgd1 | 491695 | c.913C>T | synonymous_variant | 1.0 | clofazimine | Uncertain significance |
| delamanid | Uncertain significance | |||||
| pretomanid | Uncertain significance | |||||
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.24 | ethionamide | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| Rv0565c | 657237 | p.Glu78Asp | missense_variant | 1.0 | ethionamide | Uncertain significance |
| 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 | amikacin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2168428 | c.2184delG | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2168905 | p.Ile570Val | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| 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 | |||||
| folC | 2746275 | p.Val442Phe | missense_variant | 1.0 | para-aminosalicylic_acid | Uncertain significance |
| Rv2680 | 2996169 | p.Glu22Gly | missense_variant | 0.82 | capreomycin | Uncertain significance |
| Rv3083 | 3448507 | c.5_*1407del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
| embC | 4238972 | c.-891C>G | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338594 | c.-75_-73delGCTinsCC | upstream_gene_variant | 0.53 | amikacin | Not assoc w R |
| capreomycin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| whiB6 | 4338594 | c.-75delG | upstream_gene_variant | 0.42 | amikacin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| gid | 4407678 | c.525G>C | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
