Run ID: SRR998851
Sample name:
Date: 2024-10-04T18:27:30.287399
Number of reads: 1131138
Percentage reads mapped: 92.69
Median coverage: 28.0
Strain: lineage4.1.3
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1.3 | Euro-American | None | 0.79 |
lineage4.1 | Euro-American | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Phe | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | pncA | p.His137Arg | Not assoc w R - Interim | Mutation from literature |
streptomycin | gid | c.102delG | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | p.Met1? | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Phe | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288832 | p.His137Arg | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim | Mutation from literature |
ethA | 4327471 | p.Met1? | start_lost | 1.0 | ethionamide | Assoc w R | |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin | 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 | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
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 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
inhA | 1674102 | c.-100C>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
ethionamide | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.96 | cycloserine | |
lpqB | 3624660 | p.Ala84Gly | missense_variant | 1.0 | rifampicin | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
ubiA | 4269313 | p.Lys174Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |