Run ID: ERR6358870
Sample name:
Date: 2024-10-05T08:45:39.045497
Number of reads: 6210632
Percentage reads mapped: 99.63
Median coverage: 180.0
Strain: lineage4.6.1.1
Spoligotype:
Drug-resistance: RR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.6 | Euro-American | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.6.1.1 | Euro-American | RD724 | 1.0 |
| lineage4.6.1 | Euro-American (Uganda) | RD724 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.His445Arg | Assoc w R | |
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | gid | p.Ala134Glu | Assoc w R | |
| 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 |
|---|---|---|---|---|---|---|---|
| rpoB | 761140 | p.His445Arg | missense_variant | 1.0 | rifampicin | Assoc w R | |
| gid | 4407802 | p.Ala134Glu | missense_variant | 0.99 | streptomycin | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7539 | p.Thr80Ala | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.18 | isoniazid | |
| ethionamide | ||||||
| hadA | 732265 | c.336G>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| rpoB | 761265 | p.Asn487His | missense_variant | 0.93 | rifampicin | Uncertain significance |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1253754 | p.Thr261Pro | missense_variant | 0.99 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| katG | 2154620 | p.Arg498Cys | missense_variant | 1.0 | isoniazid | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| pncA | 2289000 | p.Phe81Ser | missense_variant | 0.99 | pyrazinamide | Uncertain significance |
| folC | 2747195 | p.Asp135Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2681 | 2996876 | c.138A>C | synonymous_variant | 0.99 | capreomycin | Not assoc w R |
| Rv2752c | 3064257 | c.754_*257del | stop_lost&conservative_inframe_deletion&splice_region_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| thyA | 3074218 | p.Ser85Ile | missense_variant | 1.0 | para-aminosalicylic_acid | |
| whiB7 | 3569029 | c.-350A>G | upstream_gene_variant | 0.99 | kanamycin | Not assoc w R |
| amikacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| glpK | 4139670 | p.Cys29Tyr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243217 | c.-16C>A | upstream_gene_variant | 0.97 | ethambutol | Uncertain significance |
| embB | 4248150 | p.Thr546Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
| ethA | 4328329 | c.-856C>G | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338595 | c.-75_-74insA | upstream_gene_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338599 | c.-79_-78delTAinsC | upstream_gene_variant | 0.99 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338602 | c.-81A>T | upstream_gene_variant | 0.98 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
