Run ID: ERR9125142
Sample name:
Date: 2024-10-05T14:12:29.341694
Number of reads: 9869805
Percentage reads mapped: 99.66
Median coverage: 281.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
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 |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 371 | p.Pro124Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
gyrB | 7017 | p.Ala593Val | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rpoC | 766085 | p.Pro906Ala | missense_variant | 1.0 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
atpE | 1460992 | c.-53A>C | upstream_gene_variant | 1.0 | bedaquiline | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2169041 | c.1572G>A | synonymous_variant | 0.31 | pyrazinamide | Not assoc w R - Interim |
PPE35 | 2169044 | c.1569G>C | synonymous_variant | 0.49 | pyrazinamide | Not assoc w R - Interim |
PPE35 | 2169047 | p.Ile522Val | missense_variant | 0.47 | pyrazinamide | Uncertain significance |
PPE35 | 2169053 | c.1560T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2169056 | c.1557A>G | synonymous_variant | 0.47 | pyrazinamide | Not assoc w R - Interim |
PPE35 | 2169059 | c.1554G>A | synonymous_variant | 0.53 | pyrazinamide | |
PPE35 | 2169063 | p.Met517Thr | missense_variant | 1.0 | pyrazinamide | |
PPE35 | 2169065 | p.Ala516Ile | missense_variant | 0.53 | pyrazinamide | |
PPE35 | 2169068 | c.1545G>T | synonymous_variant | 0.56 | pyrazinamide | |
PPE35 | 2169071 | c.1542A>G | synonymous_variant | 0.4 | pyrazinamide | Not assoc w R - Interim |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518051 | c.-64A>G | upstream_gene_variant | 1.0 | isoniazid | |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 1.0 | ethionamide | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
whiB7 | 3568503 | c.177G>T | synonymous_variant | 0.97 | kanamycin | Not assoc w R - Interim |
amikacin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
alr | 3840764 | c.657G>C | synonymous_variant | 1.0 | cycloserine | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247151 | p.Arg213Gln | missense_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R |