Run ID: SRR1735569
Sample name:
Date: 2024-04-15T00:47:01.314953
Number of reads: 374729
Percentage reads mapped: 98.98
Median coverage: 10.0
Strain: La3
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
La3 | M.orygis | None | 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 | 9143 | c.1842T>C | synonymous_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13441 | p.Thr40Ala | missense_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
fgd1 | 490661 | c.-122_-121insGCGAGC | upstream_gene_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
katG | 2154707 | p.Val469Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
pncA | 2289978 | c.-737T>G | upstream_gene_variant | 1.0 | pyrazinamide | |
Rv2752c | 3067009 | c.-818A>G | upstream_gene_variant | 1.0 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
thyA | 3074494 | c.-81_-24delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
lpqB | 3624350 | c.561G>T | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R | |||||
lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
lpqB | 3624593 | c.318G>A | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R | |||||
fbiB | 3641584 | p.Val17Ala | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247533 | p.Met340Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4328211 | c.-738A>G | upstream_gene_variant | 1.0 | ethionamide |