Run ID: SRR1217053
Sample name:
Date: 2024-04-14T00:49:12.823415
Number of reads: 4225717
Percentage reads mapped: 99.4
Median coverage: 21.0
Strain: lineage4.1.2.1
Spoligotype:
Drug-resistance: RR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.85 |
lineage4.1.2 | Euro-American | None | 0.85 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.69 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | ||||
ethambutol | embB | p.Gln497Arg | 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 | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
embB | 4248003 | p.Gln497Arg | 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 | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.88 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
rpoB | 760115 | c.309C>T | synonymous_variant | 0.99 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 766740 | p.Val1124Gly | missense_variant | 0.95 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.93 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781276 | c.-284A>C | upstream_gene_variant | 1.0 | streptomycin | |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
inhA | 1674917 | p.Ala239Val | missense_variant | 1.0 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
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 | |||||
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.99 | isoniazid | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626093 | p.Gly174Ala | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Uncertain significance | |||||
alr | 3841001 | p.Glu140Asp | missense_variant | 1.0 | cycloserine | |
embC | 4239298 | c.-565C>T | upstream_gene_variant | 1.0 | ethambutol | 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 |
gid | 4407967 | p.Leu79Trp | missense_variant | 1.0 | streptomycin | Uncertain significance |