Run ID: ERR2513456
Sample name:
Date: 2024-10-03T17:41:17.943798
Number of reads: 4621777
Percentage reads mapped: 99.6
Median coverage: 162.0
Strain: lineage4.6.2
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 1.0 |
lineage4.6.2 | Euro-American | RD726 | 0.99 |
lineage4 | Euro-American | 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 |
---|---|---|---|---|---|---|
dnaA | 324 | c.324C>G | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.99 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 778298 | c.183G>A | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R - Interim | |||||
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 | 1853605 | c.-1G>T | upstream_gene_variant | 0.99 | linezolid | |
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 |
bacA | 2063187 | c.1542C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
ndh | 2103304 | c.-262T>G | upstream_gene_variant | 0.99 | isoniazid | |
delamanid | ||||||
ethionamide | ||||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
pncA | 2289427 | c.-186T>C | upstream_gene_variant | 1.0 | pyrazinamide | |
Rv2680 | 2996208 | p.Ala35Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
thyA | 3074425 | p.Thr16Met | missense_variant | 1.0 | para-aminosalicylic_acid | |
rpoA | 3878601 | c.-95delG | upstream_gene_variant | 0.42 | rifampicin | Uncertain significance |
rpoA | 3878613 | c.-113_-107delCAACCCA | upstream_gene_variant | 0.25 | rifampicin | Uncertain significance |
rpoA | 3878654 | c.-147A>G | upstream_gene_variant | 0.96 | rifampicin | Uncertain significance |
embC | 4239917 | p.Val19Met | missense_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242883 | c.3021C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R - Interim |
embA | 4245015 | p.Ile595Val | missense_variant | 0.99 | ethambutol | Uncertain significance |
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 |