Run ID: SRR13837465
Sample name:
Date: 2024-10-05T11:41:39.087226
Number of reads: 881460
Percentage reads mapped: 99.0
Median coverage: 29.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
| 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 | pncA | p.Val7Leu | Assoc w R | |
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | fbiC | c.827dupC | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| fbiC | 1303756 | c.827dupC | frameshift_variant | 1.0 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
| pncA | 2289223 | p.Val7Leu | missense_variant | 1.0 | pyrazinamide | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5850 | c.611_612insA | frameshift_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| mmaA3 | 737500 | p.Ile217Ser | missense_variant | 1.0 | isoniazid | |
| mmaA3 | 738175 | c.-26A>C | upstream_gene_variant | 1.0 | isoniazid | |
| rpoB | 762083 | c.2277T>A | synonymous_variant | 1.0 | rifampicin | |
| rpoC | 766578 | p.Asp1070Val | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 776436 | p.Ala682Gly | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| fbiC | 1304155 | p.Arg409Gly | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| atpE | 1460879 | c.-166C>A | upstream_gene_variant | 1.0 | bedaquiline | |
| ndh | 2102784 | p.Gly87Ser | missense_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| pncA | 2290201 | c.-960G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518058 | c.-57G>A | upstream_gene_variant | 1.0 | isoniazid | |
| eis | 2714947 | p.Phe129Ser | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| pepQ | 2860319 | p.Ser34Thr | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv2752c | 3064817 | p.Asp459Tyr | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| whiB7 | 3568660 | p.Pro7Leu | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | Uncertain significance | |||||
| lpqB | 3623509 | p.Val468Ile | missense_variant | 1.0 | rifampicin | Uncertain significance |
| bedaquiline | ||||||
| mtrA | 3627016 | p.Leu112Val | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| alr | 3841536 | c.-117_-116insT | upstream_gene_variant | 0.96 | cycloserine | |
| ddn | 3986940 | p.Asp33His | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| panD | 4045249 | c.-968C>G | upstream_gene_variant | 0.96 | pyrazinamide | |
| glpK | 4138519 | p.Glu413* | stop_gained | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| embB | 4246529 | p.Ser6Arg | missense_variant | 1.0 | ethambutol |
