Run ID: ERR2184309
Sample name:
Date: 2024-04-15T13:33:38.974543
Number of reads: 3077070
Percentage reads mapped: 99.79
Median coverage: 106.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Val170Phe | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Asp1024Asn | Uncertain significance | Mutation from literature |
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.754_755dupGC | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 760314 | p.Val170Phe | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
embB | 4249583 | p.Asp1024Asn | missense_variant | 0.11 | ethambutol | Uncertain significance | Mutation from literature |
ethA | 4326718 | c.754_755dupGC | frameshift_variant | 0.64 | ethionamide | 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 | |||||
nusG | 734935 | p.Val228Leu | missense_variant | 0.28 | rifampicin | |
rpoB | 762685 | p.Ala960Glu | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 764817 | p.Val483Ala | missense_variant | 1.0 | rifampicin | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
Rv2680 | 2996096 | c.-9G>A | upstream_gene_variant | 0.53 | capreomycin | |
mtrA | 3627478 | c.-129G>C | upstream_gene_variant | 0.99 | bedaquiline | Uncertain significance |
rifampicin | 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 | |||||
gid | 4407758 | p.Ser149Arg | missense_variant | 1.0 | streptomycin | Uncertain significance |