Run ID: SRR1232999
Sample name:
Date: 2024-03-26T12:20:45.357076
Number of reads: 852452
Percentage reads mapped: 98.7
Median coverage: 4.0
Strain: lineage4.1.2.1;lineage4.9
Spoligotype:
Drug-resistance: RR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.38 |
lineage4.1.2 | Euro-American | None | 0.22 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.23 |
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.88 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
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 |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 766740 | p.Val1124Gly | missense_variant | 0.86 | rifampicin | Uncertain significance |
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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
inhA | 1674917 | p.Ala239Val | missense_variant | 0.99 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | 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 | 1.0 | isoniazid | |
gid | 4407967 | p.Leu79Trp | missense_variant | 1.0 | streptomycin | Uncertain significance |