Run ID: SRR2101263
Sample name:
Date: 2024-04-15T22:40:03.185382
Number of reads: 3576398
Percentage reads mapped: 99.56
Median coverage: 82.0
Strain: lineage3;lineage4.4
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.85 |
lineage4 | Euro-American | None | 0.14 |
lineage4.4 | Euro-American | None | 0.14 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
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) |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
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 | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.87 | 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) |
ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
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 | |||||
gyrA | 9596 | c.2295G>T | synonymous_variant | 0.8 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
Rv0010c | 13277 | c.282T>C | synonymous_variant | 0.88 | isoniazid | Not assoc w R |
fgd1 | 491367 | c.585G>A | synonymous_variant | 0.24 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.88 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.88 | ethionamide | Not assoc w R - Interim |
nusG | 734354 | p.Pro34Leu | missense_variant | 0.77 | rifampicin | Not assoc w R |
nusG | 734753 | p.Thr167Met | missense_variant | 0.8 | rifampicin | Not assoc w R |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.85 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.84 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.74 | rifampicin | Not assoc w R |
rpoC | 764181 | p.Asp271Gly | missense_variant | 0.81 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.83 | 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 |
Rv1129c | 1254039 | p.Asn166Asp | missense_variant | 0.83 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.85 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.64 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475357 | n.1700C>T | non_coding_transcript_exon_variant | 0.79 | capreomycin | |
linezolid | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.98 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.82 | isoniazid | Not assoc w R |
katG | 2155351 | p.Arg254Leu | missense_variant | 0.84 | isoniazid | |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.83 | pyrazinamide | Not assoc w R |
PPE35 | 2170769 | c.-157C>T | upstream_gene_variant | 0.85 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 0.86 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.86 | pyrazinamide | |
eis | 2714523 | p.His270Gln | missense_variant | 0.16 | amikacin | Uncertain significance |
kanamycin | Uncertain significance | |||||
eis | 2714879 | p.Asp152Asn | missense_variant | 0.86 | amikacin | Uncertain significance |
kanamycin | Uncertain significance | |||||
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.88 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.82 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv2752c | 3066452 | c.-261T>G | upstream_gene_variant | 0.13 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3087118 | p.Ser100Leu | missense_variant | 0.21 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.84 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.91 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
glpK | 4139528 | p.Asn76Lys | missense_variant | 0.8 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | ||||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4242075 | p.Arg738Gln | missense_variant | 0.9 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247548 | c.1035C>T | synonymous_variant | 0.15 | ethambutol | Not assoc w R - Interim |
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 | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.86 | streptomycin | Not assoc w R |