Run ID: ERR10680031
Sample name:
Date: 2024-03-27T00:25:27.017707
Number of reads: 4405900
Percentage reads mapped: 99.49
Median coverage: 135.0
Strain: lineage4.1.3
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1.3 | Euro-American | None | 1.0 |
lineage4.1 | Euro-American | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Tyr | Assoc w R | |
p.Leu452Met | Assoc w R - Interim | |||
isoniazid | katG | p.Ser315Ile | Assoc w R - Interim | High-level resistance |
ethambutol | embB | p.Met306Ile | Assoc w R | |
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 |
---|---|---|---|---|---|---|---|
rpoB | 761109 | p.Asp435Tyr | missense_variant | 0.99 | rifampicin | Assoc w R | |
rpoB | 761160 | p.Leu452Met | missense_variant | 0.11 | rifampicin | Assoc w R - Interim | |
katG | 2155168 | p.Ser315Ile | missense_variant | 1.0 | isoniazid | Assoc w R - Interim | High-level resistance |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R |
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 | 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 | |||||
Rv0010c | 13627 | c.-69A>G | upstream_gene_variant | 0.63 | isoniazid | Uncertain significance |
mshA | 576403 | c.1056C>T | synonymous_variant | 0.61 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R - Interim | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpR5 | 779048 | p.Val20Ala | missense_variant | 0.64 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rpsL | 781421 | c.-139C>A | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
fbiC | 1304610 | c.1680C>T | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
lpqB | 3624660 | p.Ala84Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269308 | p.Phe176Leu | missense_variant | 0.2 | ethambutol | Uncertain significance |
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 | ||||||
gid | 4408072 | p.Leu44Gln | missense_variant | 0.13 | streptomycin | Uncertain significance |
gid | 4408180 | p.Ala8Glu | missense_variant | 1.0 | streptomycin | Uncertain significance |