Run ID: ERR2228811
Sample name:
Date: 2024-04-15T08:55:46.922181
Number of reads: 831683
Percentage reads mapped: 99.23
Median coverage: 17.0
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 |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
PPE35 | 2167965 | p.Ala883Gly | missense_variant | 0.18 | pyrazinamide | |
PPE35 | 2167967 | c.2646A>C | synonymous_variant | 0.18 | pyrazinamide | |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
PPE35 | 2169287 | c.1326T>C | synonymous_variant | 0.16 | pyrazinamide | |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.34 | pyrazinamide | |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.4 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2519140 | c.1026G>C | synonymous_variant | 0.23 | isoniazid | |
kasA | 2519143 | c.1029G>C | synonymous_variant | 0.24 | isoniazid | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
lpqB | 3623710 | p.Asp401Asn | missense_variant | 0.92 | bedaquiline | |
rifampicin | ||||||
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.2 | cycloserine | |
clpC1 | 4039645 | p.His354Asp | missense_variant | 0.36 | pyrazinamide | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R |