Run ID: SRR25207025
Sample name:
Date: 2025-02-11T17:38:18.913583
Number of reads: 7940269
Percentage reads mapped: 99.6
Median coverage: 264.0
Strain: lineage4.5
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.5 | Euro-American | RD122 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Leu430Pro | Assoc w R | |
p.Ser431Gly | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB | ||
isoniazid | katG | p.Trp149* | Assoc w R | High-level resistance |
ahpC | c.-48G>A | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Met306Ile | Assoc w R | |
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 |
---|---|---|---|---|---|---|---|
rpoB | 761095 | p.Leu430Pro | missense_variant | 0.99 | rifampicin | Assoc w R | |
rpoB | 761097 | p.Ser431Gly | missense_variant | 0.99 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
katG | 2155666 | p.Trp149* | stop_gained | 1.0 | isoniazid | Assoc w R | High-level resistance |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 0.52 | isoniazid | Uncertain significance | Mutation from literature |
embB | 4247431 | p.Met306Ile | missense_variant | 0.97 | ethambutol | 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 | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7892 | c.591G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
ccsA | 620029 | c.139C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
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 |
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 |
PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.39 | isoniazid | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
glpK | 4138933 | p.Gly275Arg | missense_variant | 0.35 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
embC | 4239081 | c.-782G>A | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245131 | c.1899G>A | synonymous_variant | 0.99 | ethambutol | Not assoc w R - Interim |
ethA | 4327959 | c.-486C>A | upstream_gene_variant | 1.0 | ethionamide | |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |