Run ID: SRR13837678
Sample name:
Date: 2024-04-15T12:34:46.933692
Number of reads: 2951512
Percentage reads mapped: 96.44
Median coverage: 99.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | None | 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 | 9502 | p.Arg734His | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| Rv0010c | 13527 | p.Ser11* | stop_gained | 1.0 | isoniazid | Uncertain significance |
| rpoB | 759681 | c.-126C>T | upstream_gene_variant | 1.0 | rifampicin | |
| rpoB | 761239 | p.Cys478Tyr | missense_variant | 0.99 | rifampicin | |
| mmpL5 | 776185 | p.Lys766Glu | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 779400 | c.-920C>A | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| embR | 1417986 | c.-639T>A | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1472865 | n.1020C>G | non_coding_transcript_exon_variant | 0.99 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| tlyA | 1918063 | p.Pro42Ala | missense_variant | 1.0 | capreomycin | |
| ndh | 2102985 | p.Ile20Val | missense_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| katG | 2155856 | p.Thr86Ser | missense_variant | 1.0 | isoniazid | |
| PPE35 | 2169233 | c.1379delT | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv2752c | 3065376 | c.815delT | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| Rv2752c | 3066351 | c.-160G>T | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| thyX | 3067731 | p.Val72Ala | missense_variant | 0.97 | para-aminosalicylic_acid | |
| thyX | 3067825 | p.Arg41Gly | missense_variant | 0.99 | para-aminosalicylic_acid | |
| fbiD | 3338949 | c.-169_-168insT | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| Rv3083 | 3448707 | c.204G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| Rv3083 | 3449768 | p.Thr422Lys | missense_variant | 1.0 | ethionamide | |
| lpqB | 3623219 | c.1692A>G | synonymous_variant | 0.99 | bedaquiline | |
| rifampicin | ||||||
| mtrA | 3627790 | c.-441A>G | upstream_gene_variant | 0.99 | bedaquiline | |
| rifampicin | ||||||
| fbiB | 3641403 | c.-132C>T | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| alr | 3841257 | p.His55Leu | missense_variant | 1.0 | cycloserine | |
| rpoA | 3877601 | p.Gln303* | stop_gained | 1.0 | rifampicin | |
| ddn | 3986668 | c.-176T>C | upstream_gene_variant | 1.0 | delamanid | |
| pretomanid | ||||||
| embC | 4239401 | c.-462A>C | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4241864 | p.Leu668Met | missense_variant | 1.0 | ethambutol | |
| embB | 4245557 | c.-957G>A | upstream_gene_variant | 1.0 | ethambutol | |
| ethA | 4327092 | p.Ala128Pro | missense_variant | 1.0 | ethionamide | |
| gid | 4408151 | p.Leu18Val | missense_variant | 0.99 | streptomycin |
