Run ID: SRR13861633
Sample name:
Date: 2024-04-15T05:25:20.424606
Number of reads: 386626
Percentage reads mapped: 7.74
Median coverage: 13.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-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 | ||||
isoniazid | katG | p.Gly234Glu | Uncertain significance | Mutation from literature |
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 |
---|---|---|---|---|---|---|---|
katG | 2155411 | p.Gly234Glu | missense_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
Rv0010c | 13524 | p.Gly12Ala | missense_variant | 1.0 | isoniazid | |
mshA | 576259 | c.912C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R - Interim | |||||
ccsA | 620690 | p.Val267Glu | missense_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
Rv0565c | 657622 | c.-152G>A | upstream_gene_variant | 1.0 | ethionamide | |
rpoB | 759805 | c.-2T>C | upstream_gene_variant | 1.0 | rifampicin | |
rpoB | 761961 | p.Pro719Thr | missense_variant | 1.0 | rifampicin | |
rrl | 1474052 | n.395G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
tlyA | 1918432 | p.Pro165Thr | missense_variant | 1.0 | capreomycin | |
ndh | 2101769 | p.Arg425His | missense_variant | 1.0 | ethionamide | |
delamanid | ||||||
isoniazid | Uncertain significance | |||||
katG | 2155508 | p.Ala202Ser | missense_variant | 1.0 | isoniazid | Uncertain significance |
folC | 2746862 | p.Leu246Arg | missense_variant | 1.0 | para-aminosalicylic_acid | |
folC | 2747268 | p.Asp111His | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv2752c | 3065109 | c.1083A>G | synonymous_variant | 1.0 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
whiB7 | 3568816 | c.-137C>T | upstream_gene_variant | 1.0 | streptomycin | |
amikacin | ||||||
kanamycin | ||||||
whiB7 | 3569222 | c.-543G>A | upstream_gene_variant | 1.0 | streptomycin | |
amikacin | ||||||
kanamycin | ||||||
lpqB | 3624508 | p.Ile135Val | missense_variant | 1.0 | bedaquiline | |
rifampicin | ||||||
mtrB | 3625247 | p.Arg456Pro | missense_variant | 1.0 | bedaquiline | |
rifampicin | ||||||
clpC1 | 4040148 | p.Lys186Ile | missense_variant | 1.0 | pyrazinamide | |
embC | 4240125 | p.Cys88Tyr | missense_variant | 1.0 | ethambutol | |
ethR | 4327643 | p.Thr32Ile | missense_variant | 1.0 | ethionamide |