Run ID: SRR18715380
Sample name:
Date: 2024-04-15T15:02:29.531819
Number of reads: 2507509
Percentage reads mapped: 99.77
Median coverage: 51.0
Strain: lineage4.3.3;lineage4.8
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.64 |
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.36 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 0.65 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
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 |
---|---|---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 0.6 | isoniazid | Assoc w R | High-level resistance |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 434 | p.His145Arg | missense_variant | 0.43 | isoniazid | Uncertain significance |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.58 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8040 | p.Gly247Ser | missense_variant | 0.7 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.72 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0565c | 656265 | c.1204_1205delAC | frameshift_variant | 0.37 | ethionamide | Uncertain significance |
Rv0565c | 657449 | p.Gly8Ser | missense_variant | 0.63 | ethionamide | Uncertain significance |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.75 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
fbiC | 1303095 | c.165G>A | synonymous_variant | 0.65 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
embR | 1417942 | c.-595G>T | upstream_gene_variant | 0.89 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834836 | p.Met432Thr | missense_variant | 0.66 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.54 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 0.58 | isoniazid | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.45 | pyrazinamide | Not assoc w R |
PPE35 | 2168343 | p.Gly757Val | missense_variant | 0.6 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.76 | isoniazid | |
ahpC | 2726066 | c.-127G>A | upstream_gene_variant | 0.36 | isoniazid | |
folC | 2746340 | p.Ala420Val | missense_variant | 0.64 | para-aminosalicylic_acid | |
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.37 | capreomycin | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.57 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.65 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.67 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.64 | pyrazinamide | Not assoc w R |
clpC1 | 4038968 | c.1737G>A | synonymous_variant | 0.58 | pyrazinamide | Not assoc w R - Interim |
glpK | 4139015 | c.741G>T | synonymous_variant | 0.75 | ethambutol | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4244728 | p.Phe499Cys | missense_variant | 0.34 | ethambutol | Uncertain significance |
embA | 4245131 | c.1899G>A | synonymous_variant | 0.35 | ethambutol | Not assoc w R - Interim |
embB | 4247395 | c.882C>T | synonymous_variant | 0.42 | ethambutol | 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 | 0.6 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408016 | p.Asp63Tyr | missense_variant | 0.71 | streptomycin | Uncertain significance |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.67 | streptomycin | Not assoc w R |