Run ID: ERR12328162
Sample name:
Date: 2024-05-20T10:04:53.197022
Number of reads: 3808127
Percentage reads mapped: 99.61
Median coverage: 118.0
Strain: lineage4.5
Spoligotype:
Drug-resistance: Other
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 | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | gid | c.102delG | 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 |
---|---|---|---|---|---|---|---|
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1002 | p.Glu334Asp | missense_variant | 1.0 | isoniazid | Uncertain significance |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
gyrA | 7892 | c.591G>A | synonymous_variant | 1.0 | moxifloxacin | Not assoc w R - Interim |
levofloxacin | Not assoc w R - Interim | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
Rv0010c | 13394 | p.Trp55* | stop_gained | 1.0 | isoniazid | Uncertain significance |
mshA | 576106 | c.759C>G | synonymous_variant | 0.22 | ethionamide | |
isoniazid | ||||||
ccsA | 620029 | c.139C>T | synonymous_variant | 1.0 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 778455 | p.Pro9Leu | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
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 | |
amikacin | ||||||
streptomycin | ||||||
capreomycin | ||||||
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 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
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 |
rpoA | 3879070 | c.-563G>A | upstream_gene_variant | 1.0 | rifampicin | |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
clpC1 | 4039265 | c.1440C>T | synonymous_variant | 1.0 | pyrazinamide | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4248733 | c.2220G>A | synonymous_variant | 1.0 | ethambutol | |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |