Run ID: ERR11775890
Sample name:
Date: 2024-05-22T13:26:38.328618
Number of reads: 4622696
Percentage reads mapped: 99.51
Median coverage: 149.0
Strain: lineage3.1.1;lineage4.2.2.2
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2.2 | Euro-American (Ural) | None | 0.81 |
lineage3 | East-African-Indian | RD750 | 0.18 |
lineage3.1.1 | East-African-Indian | RD750 | 0.19 |
lineage4.2 | Euro-American | None | 0.83 |
lineage4 | Euro-American | None | 0.8 |
lineage4.2.2.2 | Euro-American (Ural) | None | 0.84 |
lineage3.1 | East-African-Indian | RD750 | 0.23 |
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 | 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 | 8688 | p.Ala463Ser | missense_variant | 0.78 | 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 | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.21 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 576077 | c.730C>T | synonymous_variant | 0.79 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R | |||||
mshA | 576108 | p.Ala254Gly | missense_variant | 0.4 | ethionamide | |
isoniazid | ||||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.23 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657425 | p.Gly16Ser | missense_variant | 0.82 | ethionamide | Uncertain significance |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.29 | rifampicin | Not assoc w R |
rpoB | 761489 | c.1683G>A | synonymous_variant | 0.82 | rifampicin | Not assoc w R |
rpoB | 761907 | p.Cys701Ser | missense_variant | 0.79 | rifampicin | Uncertain significance |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.18 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R |
rpoC | 767094 | p.Ser1242Asn | missense_variant | 0.88 | rifampicin | Uncertain significance |
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 | 0.12 | 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 |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.83 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.21 | 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 | ||||||
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 | 2063685 | c.1044G>A | synonymous_variant | 0.87 | streptomycin | Not assoc w R - Interim |
kanamycin | Not assoc w R - Interim | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 0.76 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.27 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.17 | pyrazinamide | Not assoc w R |
PPE35 | 2168971 | p.Ile548Val | missense_variant | 0.81 | pyrazinamide | Uncertain significance |
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 | 0.19 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.16 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.17 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.27 | 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 | 3066280 | c.-89C>T | upstream_gene_variant | 0.89 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.82 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | 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 | 0.19 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.22 | 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 | 4240172 | p.Val104Met | missense_variant | 0.25 | ethambutol | Not assoc w R |
embC | 4241562 | p.Arg567His | missense_variant | 0.14 | ethambutol | Not assoc w R |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.23 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | 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 | ||||||
whiB6 | 4338846 | c.-325T>G | upstream_gene_variant | 0.21 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.17 | streptomycin | Not assoc w R |