Run ID: ERR4811139
Sample name:
Date: 2024-10-03T15:33:37.752249
Number of reads: 11267303
Percentage reads mapped: 99.37
Median coverage: 324.0
Strain: lineage4.4.2;lineage4.5
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.5 | Euro-American | RD122 | 0.44 |
lineage4 | Euro-American | None | 1.0 |
lineage4.4 | Euro-American | None | 0.55 |
lineage4.4.2 | Euro-American | None | 0.54 |
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 |
---|---|---|---|---|---|---|
gyrB | 6766 | c.1527G>A | synonymous_variant | 0.43 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | 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 | 7892 | c.591G>A | synonymous_variant | 0.41 | 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 | 0.45 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
ccsA | 620072 | p.Pro61Leu | missense_variant | 0.43 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
ccsA | 620566 | p.Asp226Asn | missense_variant | 0.41 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
Rv0565c | 657302 | p.Gly57Ser | missense_variant | 0.46 | ethionamide | 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 | 1253847 | p.Ala230Thr | missense_variant | 0.57 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
fbiC | 1304338 | p.Phe470Val | missense_variant | 0.47 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | 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 |
bacA | 2064579 | c.150G>A | synonymous_variant | 0.5 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
PPE35 | 2170568 | p.Ile15Met | missense_variant | 0.44 | pyrazinamide | Not assoc w R |
Rv1979c | 2222124 | c.1041C>T | synonymous_variant | 0.48 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R - Interim | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2681 | 2997738 | p.Pro334Thr | missense_variant | 0.58 | capreomycin | Uncertain significance |
Rv2752c | 3066099 | p.Met31Ile | missense_variant | 0.55 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.56 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
alr | 3840846 | p.Gly192Ala | missense_variant | 0.46 | cycloserine | |
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 0.5 | rifampicin | Not assoc w R |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 0.43 | pyrazinamide | Not assoc w R |
embC | 4238963 | c.-900C>T | upstream_gene_variant | 0.55 | ethambutol | Not assoc w R |
embC | 4240618 | p.Asp252Glu | missense_variant | 0.59 | ethambutol | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4246508 | c.3276G>A | synonymous_variant | 0.53 | ethambutol | Not assoc w R |
embB | 4248189 | p.Arg559Pro | missense_variant | 0.49 | ethambutol | Uncertain significance |
embB | 4248548 | p.Ala679Thr | missense_variant | 0.41 | ethambutol | Uncertain significance |
embB | 4249024 | c.2511C>T | synonymous_variant | 0.42 | ethambutol | Not assoc w R - Interim |
ubiA | 4268928 | c.906C>T | synonymous_variant | 0.52 | ethambutol | Not assoc w R |
ubiA | 4269375 | c.459G>A | synonymous_variant | 0.5 | ethambutol | Not assoc w R |
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 |