Run ID: SRR13861511
Sample name:
Date: 2024-10-04T23:33:19.607783
Number of reads: 2399366
Percentage reads mapped: 48.04
Median coverage: 82.0
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 |
|---|---|---|---|---|---|---|
| dnaA | 497 | p.Thr166Ser | missense_variant | 1.0 | isoniazid | |
| dnaA | 558 | c.558G>T | synonymous_variant | 1.0 | isoniazid | |
| gyrB | 5333 | p.Met32Val | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| ccsA | 620509 | p.Thr207Ser | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| ccsA | 620749 | p.Trp287Arg | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| rpoC | 766954 | c.3586delG | frameshift_variant | 1.0 | rifampicin | |
| mmpL5 | 776080 | p.Ala801Pro | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rplC | 801220 | p.Ser138Gly | missense_variant | 1.0 | linezolid | |
| fbiC | 1303494 | p.Leu188Phe | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rrl | 1476502 | n.2845G>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| inhA | 1673622 | c.-580C>A | upstream_gene_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| inhA | 1673718 | c.-484_-483insT | upstream_gene_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| katG | 2155998 | p.Trp38Cys | missense_variant | 1.0 | isoniazid | |
| katG | 2156285 | c.-174T>G | upstream_gene_variant | 1.0 | isoniazid | |
| ahpC | 2726085 | c.-108G>A | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2477c | 2782501 | c.1542T>C | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
| levofloxacin | Not assoc w R - Interim | |||||
| moxifloxacin | Not assoc w R - Interim | |||||
| streptomycin | ||||||
| rifampicin | Not assoc w R - Interim | |||||
| ethambutol | ||||||
| amikacin | Not assoc w R - Interim | |||||
| ribD | 2987458 | p.Val207Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2681 | 2997953 | c.1215C>G | synonymous_variant | 1.0 | capreomycin | |
| Rv3236c | 3612721 | c.395delT | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| lpqB | 3623213 | p.Trp566Cys | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3625250 | p.Leu455Gln | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrA | 3627307 | p.Ala15Ser | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| alr | 3840445 | p.Leu326Met | missense_variant | 1.0 | cycloserine | |
| alr | 3841156 | p.Leu89Val | missense_variant | 1.0 | cycloserine | |
| rpoA | 3877966 | p.Thr181Asn | missense_variant | 1.0 | rifampicin | |
| panD | 4044216 | c.65_66insT | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| glpK | 4138295 | p.Trp487Cys | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| embB | 4247289 | p.Ala259Gly | missense_variant | 1.0 | ethambutol | |
| embB | 4249154 | p.Gly881Arg | missense_variant | 1.0 | ethambutol | |
| ubiA | 4270024 | c.-191T>G | upstream_gene_variant | 1.0 | ethambutol |
