Run ID: ERR1035296
Sample name:
Date: 2025-03-08T10:02:55.405925
Number of reads: 10398945
Percentage reads mapped: 99.81
Median coverage: 187.0
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.316dupG | Assoc w R | High-level resistance |
ahpC | c.-81C>T | Uncertain significance | Mutation from literature | |
ethambutol | ||||
pyrazinamide | pncA | p.Ala171Val | Uncertain significance | Mutation from literature |
c.246delT | Assoc w R | |||
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 | 2155795 | c.316dupG | frameshift_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288730 | p.Ala171Val | missense_variant | 0.53 | pyrazinamide | Uncertain significance | Mutation from literature |
pncA | 2288995 | c.246delT | frameshift_variant | 0.38 | pyrazinamide | Assoc w R | |
ahpC | 2726112 | c.-81C>T | upstream_gene_variant | 0.99 | isoniazid | Uncertain significance | Mutation from literature |
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 | |||||
Rv0565c | 656195 | p.Gly426Cys | missense_variant | 1.0 | ethionamide | Uncertain significance |
fbiC | 1303257 | c.327C>T | synonymous_variant | 1.0 | clofazimine | Uncertain significance |
delamanid | Uncertain significance | |||||
pretomanid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | amikacin | Uncertain significance |
capreomycin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
glpK | 4138415 | c.1341G>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R - Interim |
isoniazid | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R - Interim | |||||
moxifloxacin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | amikacin | Not assoc w R |
capreomycin | Not assoc w R | |||||
kanamycin | Not assoc w R |