Run ID: ERR2229454
Sample name:
Date: 2024-04-16T02:08:40.625458
Number of reads: 1915191
Percentage reads mapped: 99.36
Median coverage: 44.0
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 | |||||
| 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 |
| fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | 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 | 1673346 | c.-94C>G | upstream_gene_variant | 0.17 | ethionamide | |
| isoniazid | ||||||
| fabG1 | 1673349 | c.-91G>C | upstream_gene_variant | 0.22 | ethionamide | |
| isoniazid | ||||||
| fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.17 | ethionamide | |
| isoniazid | ||||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2167965 | p.Ala883Gly | missense_variant | 0.16 | pyrazinamide | |
| PPE35 | 2167967 | c.2646A>C | synonymous_variant | 0.16 | pyrazinamide | |
| PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.23 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.23 | pyrazinamide | |
| PPE35 | 2170147 | p.Ser156Ala | missense_variant | 0.14 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv3083 | 3448497 | c.-6_*1408del | transcript_ablation | 1.0 | ethionamide | Uncertain significance |
| alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.18 | cycloserine | |
| clpC1 | 4039714 | p.Tyr331His | missense_variant | 0.16 | pyrazinamide | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246544 | p.Thr11Pro | missense_variant | 0.38 | ethambutol | Uncertain significance |
| embB | 4246548 | p.Pro12Gln | missense_variant | 0.56 | ethambutol | Uncertain significance |
| embB | 4246555 | c.42G>C | synonymous_variant | 0.69 | ethambutol | |
| embB | 4246556 | p.Ala15Pro | missense_variant | 0.69 | ethambutol | Uncertain significance |
| embB | 4246563 | p.Leu17Trp | missense_variant | 0.6 | ethambutol | Uncertain significance |
| embB | 4246567 | c.54G>T | synonymous_variant | 0.6 | ethambutol | Not assoc w R - Interim |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R |
