Run ID: SRR13837547
Sample name:
Date: 2024-10-05T10:19:12.257708
Number of reads: 587628
Percentage reads mapped: 96.0
Median coverage: 20.0
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.Thr153Asn | Mutation from literature | |
| 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 |
|---|---|---|---|---|---|---|---|
| pncA | 2288784 | p.Thr153Asn | missense_variant | 1.0 | pyrazinamide | Mutation from literature |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 750 | c.750C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| dnaA | 1200 | c.1200C>T | synonymous_variant | 1.0 | isoniazid | |
| gyrA | 9494 | p.Tyr731* | stop_gained | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| fgd1 | 491771 | p.Pro330Leu | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv0565c | 657479 | c.-9A>G | upstream_gene_variant | 1.0 | ethionamide | |
| rpoB | 762948 | p.Gln1048Glu | missense_variant | 1.0 | rifampicin | |
| rpoC | 767026 | c.3657G>C | synonymous_variant | 1.0 | rifampicin | |
| fbiC | 1303155 | c.225G>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1304225 | p.Gly432Asp | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1305046 | p.Ser706Pro | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv1258c | 1406433 | c.907delA | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
| pyrazinamide | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rrs | 1471511 | n.-335C>A | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1474652 | n.995T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| tsnR | 1854352 | p.Cys249Trp | missense_variant | 1.0 | linezolid | |
| bacA | 2063152 | p.Arg526Leu | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| bacA | 2064648 | p.Trp27Cys | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| ndh | 2102315 | p.Ile243Thr | missense_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| katG | 2156722 | c.-611G>A | upstream_gene_variant | 1.0 | isoniazid | |
| kasA | 2518563 | p.Ala150Gly | missense_variant | 1.0 | isoniazid | |
| kasA | 2519015 | p.Ser301Ala | missense_variant | 1.0 | isoniazid | |
| Rv2477c | 2783171 | c.871delT | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| Rv2680 | 2995958 | c.-147G>A | upstream_gene_variant | 1.0 | capreomycin | |
| Rv3236c | 3612913 | p.Leu68Phe | missense_variant | 1.0 | pyrazinamide | |
| lpqB | 3624794 | c.117G>C | synonymous_variant | 0.94 | rifampicin | |
| bedaquiline | ||||||
| glpK | 4138701 | p.Gln352Pro | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| glpK | 4138728 | p.Ala343Gly | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| ethA | 4326245 | p.Asp410Ala | missense_variant | 1.0 | ethionamide | |
| ethA | 4327132 | c.342C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| ethA | 4327893 | c.-420C>A | upstream_gene_variant | 1.0 | ethionamide | |
| gid | 4408070 | p.Trp45Arg | missense_variant | 1.0 | streptomycin | Uncertain significance |
