Run ID: SRR12199427
Sample name:
Date: 2024-10-04T00:26:42.997950
Number of reads: 264624
Percentage reads mapped: 50.69
Median coverage: 6.0
Strain: lineage1.2.1.2.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.2.1.2 | Indo-Oceanic | RD239 | 0.5 |
lineage1 | Indo-Oceanic | RD239 | 1.0 |
lineage1.2.1.2.1 | Indo-Oceanic | RD239 | 0.53 |
lineage1.2.1 | Indo-Oceanic | RD239 | 0.54 |
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 |
---|---|---|---|---|---|---|
rplC | 800357 | c.-452C>A | upstream_gene_variant | 1.0 | linezolid | 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 | |||||
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
pyrazinamide | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 1.0 | bedaquiline | |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.42 | cycloserine | |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |