Run ID: SRR12420630
Sample name:
Date: 2024-03-26T19:20:41.985448
Number of reads: 3724340
Percentage reads mapped: 98.24
Median coverage: 71.0
Strain: lineage4.4.2
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.4 | Euro-American | None | 0.97 |
lineage4.4.2 | Euro-American | None | 0.95 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Leu430Pro | Assoc w R | |
p.His445Gln | Assoc w R - Interim | |||
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Leu48Gln | Uncertain significance | Mutation from literature | |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | thyX | c.-16C>T | Mutation from literature | |
thyA | c.-1061_*1080del | Mutation from literature | ||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761095 | p.Leu430Pro | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpoB | 761141 | p.His445Gln | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.96 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.96 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155969 | p.Leu48Gln | missense_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 0.71 | para-aminosalicylic_acid | Mutation from literature | |
thyA | 3072599 | c.-1061_*1080del | transcript_ablation | 0.95 | para-aminosalicylic_acid | Mutation from literature |
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 | |||||
gyrA | 7585 | p.Ser95Thr | missense_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 | |||||
Rv0565c | 656342 | p.Met377Val | missense_variant | 1.0 | ethionamide | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1476758 | n.3101G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518603 | c.489G>A | synonymous_variant | 1.0 | isoniazid | |
Rv2752c | 3066099 | p.Met31Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R - Interim | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
glpK | 4139039 | c.717T>C | synonymous_variant | 0.91 | ethambutol | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4268928 | c.906C>T | synonymous_variant | 0.85 | ethambutol | Not assoc w R |
ubiA | 4269375 | c.459G>A | synonymous_variant | 0.94 | 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 | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |