Run ID: SRR13837579
Sample name:
Date: 2024-10-05T08:58:09.531356
Number of reads: 597205
Percentage reads mapped: 96.55
Median coverage: 20.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
| 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 | katG | c.1700delT | Assoc w R | High-level resistance |
| 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 |
|---|---|---|---|---|---|---|---|
| katG | 2154411 | c.1700delT | frameshift_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 7949 | c.648G>T | synonymous_variant | 0.96 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8123 | p.Leu274Phe | missense_variant | 0.95 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| gyrA | 9768 | p.Gly823Cys | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| Rv0565c | 657349 | p.Glu41Val | missense_variant | 1.0 | ethionamide | |
| mmaA3 | 738066 | c.84C>T | synonymous_variant | 1.0 | isoniazid | |
| rpoC | 763734 | p.Pro122Leu | missense_variant | 0.91 | rifampicin | |
| Rv1129c | 1253309 | p.His409Pro | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| rrl | 1476640 | n.2983C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| tsnR | 1853566 | c.-40C>T | upstream_gene_variant | 1.0 | linezolid | |
| tlyA | 1918034 | p.Val32Ala | missense_variant | 1.0 | capreomycin | |
| bacA | 2064615 | p.Leu38Phe | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| katG | 2155918 | p.Ala65Val | missense_variant | 1.0 | isoniazid | |
| PPE35 | 2168767 | p.Ser616Gly | missense_variant | 1.0 | pyrazinamide | |
| PPE35 | 2170815 | c.-203C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2222377 | p.Val263Gly | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv2477c | 2783104 | c.939C>A | synonymous_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| ribD | 2986993 | p.Gly52Val | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2752c | 3065787 | c.405G>C | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv3083 | 3448649 | p.Arg49Pro | missense_variant | 1.0 | ethionamide | |
| Rv3236c | 3613067 | p.Val17Gly | missense_variant | 1.0 | pyrazinamide | |
| Rv3236c | 3613315 | c.-199T>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| fbiA | 3640435 | c.-108A>C | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rpoA | 3877743 | c.765T>C | synonymous_variant | 0.32 | rifampicin | Not assoc w R - Interim |
| rpoA | 3878982 | c.-475A>T | upstream_gene_variant | 1.0 | rifampicin | |
| clpC1 | 4039842 | c.862_863insT | frameshift_variant | 1.0 | pyrazinamide | |
| panD | 4044103 | p.Ile60Ser | missense_variant | 1.0 | pyrazinamide | |
| embA | 4245031 | p.Arg600Gln | missense_variant | 1.0 | ethambutol | |
| gid | 4408218 | c.-16G>T | upstream_gene_variant | 1.0 | streptomycin |
