Run ID: SRR25827511
Sample name:
Date: 2024-04-14T01:50:44.871386
Number of reads: 8346451
Percentage reads mapped: 99.17
Median coverage: 258.0
Strain: lineage2.2.1;lineage3.1.2;lineage4.9
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.79 |
lineage3.1.2 | East-African-Indian | RD750 | 0.77 |
lineage2 | East-Asian | RD105 | 0.07 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.09 |
lineage4 | Euro-American | None | 0.08 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.06 |
lineage3.1 | East-African-Indian | RD750 | 0.74 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
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 |
---|---|---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 0.14 | isoniazid | Assoc w R | High-level resistance |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.93 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.93 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.89 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.92 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.91 | ethionamide | Not assoc w R - Interim |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.83 | rifampicin | Not assoc w R |
rpoB | 761231 | c.1425C>T | synonymous_variant | 0.76 | rifampicin | Not assoc w R - Interim |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.82 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.93 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.95 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.93 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.93 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.92 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1258c | 1406242 | p.Ala367Thr | missense_variant | 0.7 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.95 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.95 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.93 | capreomycin | Not assoc w R |
tlyA | 1918104 | c.165G>A | synonymous_variant | 0.81 | capreomycin | Not assoc w R - Interim |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.92 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.94 | pyrazinamide | Not assoc w R |
PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.77 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.94 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 0.79 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.74 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.84 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.79 | 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 | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.92 | cycloserine | |
whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.14 | streptomycin | |
amikacin | ||||||
kanamycin | ||||||
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.94 | 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 | 0.74 | 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 | |||||
embC | 4242075 | p.Arg738Gln | missense_variant | 0.78 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 0.96 | ethambutol | Not assoc w R |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.19 | ethambutol | |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 0.93 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 0.91 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.96 | streptomycin | Not assoc w R |