Run ID: ERR4798167
Sample name:
Date: 2024-04-15T11:36:52.971349
Number of reads: 2562158
Percentage reads mapped: 99.61
Median coverage: 72.0
Strain: lineage3.1.2;lineage4.5
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.16 |
lineage4.5 | Euro-American | RD122 | 0.78 |
lineage3.1.2 | East-African-Indian | RD750 | 0.17 |
lineage4 | Euro-American | None | 0.86 |
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 | 7892 | c.591G>A | synonymous_variant | 0.8 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
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 | 0.17 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
ccsA | 620029 | c.139C>T | synonymous_variant | 0.82 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.19 | ethionamide | Not assoc w R - Interim |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.22 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.12 | 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 | 0.15 | 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 | 1254562 | c.-28T>C | upstream_gene_variant | 0.16 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1258c | 1406101 | p.Pro414Ser | missense_variant | 0.83 | streptomycin | Uncertain significance |
isoniazid | Not assoc w R | |||||
pyrazinamide | Not assoc w R - Interim | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1475752 | n.2095C>T | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
tsnR | 1853597 | c.-9G>C | upstream_gene_variant | 0.77 | linezolid | Uncertain significance |
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 |
tlyA | 1918104 | c.165G>A | synonymous_variant | 0.18 | capreomycin | Not assoc w R - Interim |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.14 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.12 | pyrazinamide | Not assoc w R |
PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.16 | pyrazinamide | Not assoc w R |
PPE35 | 2170521 | p.Trp31* | stop_gained | 0.82 | pyrazinamide | Uncertain significance |
PPE35 | 2170568 | p.Ile15Met | missense_variant | 0.81 | pyrazinamide | 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 | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 0.22 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.16 | pyrazinamide | |
kasA | 2519344 | c.1230G>A | synonymous_variant | 0.22 | isoniazid | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.22 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.18 | 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 | 0.26 | cycloserine | |
Rv3236c | 3612666 | p.Val151Met | missense_variant | 0.83 | pyrazinamide | Uncertain significance |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 0.91 | rifampicin | Not assoc w R |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 0.87 | pyrazinamide | Not assoc w R |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.15 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.19 | 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 | 0.14 | 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 | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.21 | streptomycin | Not assoc w R |
gid | 4407961 | p.Ile81Thr | missense_variant | 0.78 | streptomycin | Uncertain significance |
gid | 4408085 | p.Glu40Lys | missense_variant | 0.19 | streptomycin | Uncertain significance |