Run ID: SRR13838003
Sample name:
Date: 2024-10-05T10:19:23.061981
Number of reads: 888896
Percentage reads mapped: 97.82
Median coverage: 29.0
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 |
|---|---|---|---|---|---|---|
| Rv1129c | 1254656 | c.-123dupG | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| rrs | 1472240 | n.395G>A | non_coding_transcript_exon_variant | 0.97 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rpsA | 1833449 | c.-93G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| PPE35 | 2168966 | c.1647G>C | synonymous_variant | 1.0 | pyrazinamide | |
| PPE35 | 2170688 | c.-76G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2222009 | p.Phe386Ile | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| kasA | 2519254 | c.1140_1141insA | frameshift_variant | 1.0 | isoniazid | |
| ahpC | 2726279 | p.Lys29Asn | missense_variant | 1.0 | isoniazid | Uncertain significance |
| Rv2477c | 2783642 | p.Ala134Glu | missense_variant | 0.94 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783761 | c.282G>T | synonymous_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2680 | 2996057 | c.-48A>C | upstream_gene_variant | 1.0 | capreomycin | |
| Rv2681 | 2996557 | c.-182G>A | upstream_gene_variant | 1.0 | capreomycin | |
| Rv2681 | 2997120 | c.383dupG | frameshift_variant | 1.0 | capreomycin | Uncertain significance |
| Rv2681 | 2997593 | c.855C>A | synonymous_variant | 1.0 | capreomycin | |
| thyA | 3074493 | c.-22C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| whiB7 | 3568433 | p.Arg83Cys | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| lpqB | 3624666 | c.244dupG | frameshift_variant | 1.0 | rifampicin | Uncertain significance |
| bedaquiline | ||||||
| clpC1 | 4038485 | c.2220C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| embC | 4239250 | c.-613G>T | upstream_gene_variant | 1.0 | ethambutol | |
| embB | 4248644 | p.Ala711Pro | missense_variant | 1.0 | ethambutol | |
| aftB | 4267225 | p.Ile538Phe | missense_variant | 1.0 | ethambutol | |
| ubiA | 4269050 | p.Tyr262Asp | missense_variant | 1.0 | ethambutol | |
| ethR | 4327699 | p.Ala51Ser | missense_variant | 1.0 | ethionamide | |
| ethA | 4328373 | c.-900A>G | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338847 | c.-326C>A | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
