Run ID: ERR4820164
Sample name:
Date: 2024-04-16T07:24:03.346329
Number of reads: 2640786
Percentage reads mapped: 99.59
Median coverage: 59.5
Strain: lineage4.6.2.2;lineage4.8
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 0.71 |
lineage4.6.2 | Euro-American | RD726 | 0.71 |
lineage4.6.2.2 | Euro-American (Cameroon) | RD726 | 0.68 |
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.34 |
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 |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.74 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.63 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 778298 | c.183G>A | synonymous_variant | 0.74 | clofazimine | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
fbiC | 1302966 | c.36G>A | synonymous_variant | 0.27 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.63 | 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 | 0.71 | streptomycin | Not assoc w R - Interim |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.4 | pyrazinamide | Not assoc w R |
PPE35 | 2170917 | c.-305C>A | upstream_gene_variant | 0.75 | pyrazinamide | |
Rv1979c | 2221746 | c.1416_1418dupCCG | disruptive_inframe_insertion | 0.65 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.36 | capreomycin | |
Rv2680 | 2996208 | p.Ala35Asp | missense_variant | 0.8 | capreomycin | Uncertain significance |
Rv2752c | 3064810 | p.Thr461Ser | missense_variant | 0.34 | ethambutol | Uncertain significance |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv3083 | 3448322 | c.-182G>A | upstream_gene_variant | 0.28 | ethionamide | |
Rv3083 | 3448567 | p.His22Asp | missense_variant | 0.97 | ethionamide | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
aftB | 4267272 | p.Lys522Arg | missense_variant | 0.63 | ethambutol | Not assoc w R |
ethA | 4326739 | c.735C>G | synonymous_variant | 0.64 | ethionamide | Not assoc w R - Interim |
ethR | 4328004 | c.456G>A | synonymous_variant | 0.7 | ethionamide | Not assoc w R - Interim |
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 | 0.74 | capreomycin | |
amikacin | ||||||
kanamycin |