Run ID: SRR12199442
Sample name:
Date: 2025-02-11T16:07:28.133835
Number of reads: 607536
Percentage reads mapped: 98.45
Median coverage: 10.0
Strain: lineage1.2.2
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.2.1.2 | Indo-Oceanic | RD239 | 0.51 |
lineage1.2.2 | Indo-Oceanic | RD239 | 0.05 |
lineage1 | Indo-Oceanic | RD239 | 0.89 |
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 | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9260 | c.1959G>C | synonymous_variant | 0.62 | 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 | |||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.82 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.92 | rifampicin | Not assoc w R |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
sigE | 1364463 | c.52_53delGT | frameshift_variant | 0.75 | pyrazinamide | Uncertain significance |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.9 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.8 | isoniazid | |
ribD | 2986898 | c.60G>A | synonymous_variant | 0.8 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.83 | ethionamide | Uncertain significance |
whiB7 | 3568488 | c.191delG | frameshift_variant | 0.83 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
panD | 4044878 | c.-597C>T | upstream_gene_variant | 0.75 | pyrazinamide | |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.83 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.97 | ethambutol | Not assoc w R |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 0.64 | ethambutol | Not assoc w R |