Run ID: ERR202413
Sample name:
Date: 2024-04-14T11:59:33.345975
Number of reads: 35064322
Percentage reads mapped: 99.43
Median coverage: 725.0
Strain: lineage1.2.1.2;lineage4.5
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.5 | Euro-American | RD122 | 0.87 |
lineage1.2.1.2 | Indo-Oceanic | RD239 | 0.14 |
lineage4 | Euro-American | None | 0.86 |
lineage1 | Indo-Oceanic | RD239 | 0.13 |
lineage1.2.1 | Indo-Oceanic | RD239 | 0.14 |
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 |
---|---|---|---|---|---|---|
dnaA | 1302 | c.1302C>A | synonymous_variant | 0.12 | isoniazid | Not assoc w R |
gyrB | 6112 | p.Met291Ile | missense_variant | 0.13 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7162 | c.-140C>G | upstream_gene_variant | 0.86 | levofloxacin | |
moxifloxacin | ||||||
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 | 0.89 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 8452 | p.Ala384Val | missense_variant | 0.12 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.15 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9260 | c.1959G>C | synonymous_variant | 0.12 | 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 | |||||
Rv0010c | 13175 | c.384T>C | synonymous_variant | 0.13 | isoniazid | Not assoc w R |
Rv0010c | 13298 | p.Ile87Met | missense_variant | 0.14 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.13 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575368 | c.21T>C | synonymous_variant | 0.12 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R | |||||
ccsA | 620029 | c.139C>T | synonymous_variant | 0.87 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.13 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.13 | rifampicin | Not assoc w R |
rpoB | 762002 | c.2196C>T | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R |
rpoC | 763531 | c.162G>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.13 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.13 | rifampicin | Not assoc w R |
rpoC | 764809 | c.1440C>T | synonymous_variant | 0.14 | 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 | 0.13 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776253 | p.Lys743Thr | missense_variant | 0.82 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 779199 | c.-719A>G | upstream_gene_variant | 0.13 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.14 | linezolid | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.15 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
fbiC | 1302821 | c.-110G>A | upstream_gene_variant | 0.13 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 0.13 | streptomycin | Not assoc w R |
isoniazid | Not assoc w R | |||||
pyrazinamide | Not assoc w R | |||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.17 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.13 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.13 | ethambutol | |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 0.13 | bedaquiline | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 0.13 | ethionamide | Uncertain significance |
isoniazid | Not assoc w R | |||||
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.12 | linezolid | Not assoc w R |
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 | 1918232 | p.Glu98Val | missense_variant | 0.88 | capreomycin | |
bacA | 2062922 | p.Ile603Val | missense_variant | 0.13 | streptomycin | Not assoc w R |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.13 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.12 | pyrazinamide | Not assoc w R |
PPE35 | 2170568 | p.Ile15Met | missense_variant | 0.88 | pyrazinamide | Not assoc w R |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.14 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223522 | c.-358A>C | upstream_gene_variant | 0.13 | clofazimine | |
bedaquiline | ||||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.12 | isoniazid | |
kasA | 2519048 | p.Gly312Ser | missense_variant | 0.12 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.15 | isoniazid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.13 | cycloserine | |
fbiD | 3339417 | c.300A>G | synonymous_variant | 0.13 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.16 | ethionamide | Uncertain significance |
whiB7 | 3568488 | c.191delG | frameshift_variant | 0.13 | streptomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.13 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3640557 | c.15T>C | synonymous_variant | 0.15 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 0.9 | rifampicin | Not assoc w R |
rpoA | 3879070 | c.-563G>A | upstream_gene_variant | 0.88 | rifampicin | |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 0.88 | pyrazinamide | Not assoc w R |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.12 | pyrazinamide | Not assoc w R - Interim |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.11 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4240671 | p.Thr270Ile | missense_variant | 0.12 | ethambutol | Not assoc w R |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.14 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243640 | c.408T>C | synonymous_variant | 0.86 | ethambutol | Not assoc w R - Interim |
embA | 4244420 | c.1188G>C | synonymous_variant | 0.12 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.13 | ethambutol | Not assoc w R |
embB | 4247578 | c.1065G>A | synonymous_variant | 0.16 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.15 | ethambutol | Not assoc w R |
embB | 4249065 | p.Gly851Val | missense_variant | 0.14 | ethambutol | Uncertain significance |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.14 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.16 | ethambutol | Not assoc w R |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 0.15 | ethambutol | Not assoc w R |
whiB6 | 4338361 | p.Arg54Gln | missense_variant | 0.12 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | 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 | 4338603 | c.-82C>T | upstream_gene_variant | 0.13 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338646 | c.-125A>G | upstream_gene_variant | 0.88 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.13 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.13 | streptomycin | Not assoc w R |