Run ID: ERR4596934
Sample name:
Date: 2024-10-03T15:29:40.881572
Number of reads: 4645839
Percentage reads mapped: 99.47
Median coverage: 140.0
Strain: lineage1.1.2;lineage3.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.76 |
lineage1.1.2 | Indo-Oceanic | RD239 | 0.23 |
lineage3.1.1 | East-African-Indian | RD750 | 0.79 |
lineage1.1 | Indo-Oceanic | RD239 | 0.21 |
lineage1 | Indo-Oceanic | RD239 | 0.21 |
lineage3.1 | East-African-Indian | RD750 | 0.74 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
p.Leu452Pro | Assoc w R | |||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
p.Ser315Asn | Assoc w R | High-level resistance | ||
ethambutol | embB | p.Met306Val | Assoc w R | |
p.Gln497Arg | Assoc w R | |||
pyrazinamide | pncA | p.Val128Gly | Assoc w R | |
streptomycin | gid | c.471delG | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.1265_1266insT | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.8 | rifampicin | Assoc w R | |
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.21 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.63 | isoniazid | Assoc w R | High-level resistance |
katG | 2155168 | p.Ser315Asn | missense_variant | 0.33 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288859 | p.Val128Gly | missense_variant | 0.84 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 0.16 | ethambutol | Assoc w R | |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.78 | ethambutol | Assoc w R | |
ethA | 4326208 | c.1265_1266insT | frameshift_variant | 0.74 | ethionamide | Assoc w R | |
gid | 4407731 | c.471delG | frameshift_variant | 0.72 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.19 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrB | 6124 | c.885C>T | synonymous_variant | 0.19 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 | 8452 | p.Ala384Val | missense_variant | 0.24 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.25 | 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 | 13298 | p.Ile87Met | missense_variant | 0.22 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.22 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.97 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.81 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.29 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.27 | rifampicin | Not assoc w R |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.75 | rifampicin | Not assoc w R |
rpoB | 761407 | p.Val534Ala | missense_variant | 0.76 | rifampicin | Uncertain significance |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.7 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.97 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.16 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.15 | rifampicin | Not assoc w R |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.21 | rifampicin | Not assoc w R |
rpoC | 765988 | c.2619G>A | synonymous_variant | 0.24 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.99 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.16 | linezolid | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.99 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.25 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.17 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.27 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.22 | linezolid | Not assoc w R |
tsnR | 1854045 | p.Tyr147Cys | missense_variant | 0.2 | 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 |
bacA | 2062922 | p.Ile603Val | missense_variant | 0.24 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.99 | isoniazid | Not assoc w R |
katG | 2155383 | c.729C>T | synonymous_variant | 0.21 | isoniazid | Not assoc w R - Interim |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.97 | pyrazinamide | Not assoc w R |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.2 | pyrazinamide | Uncertain significance |
PPE35 | 2170461 | p.Gly51Glu | missense_variant | 0.77 | pyrazinamide | Not assoc w R |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.21 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223550 | c.-386C>T | upstream_gene_variant | 0.26 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 0.79 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.75 | pyrazinamide | |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.19 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.21 | isoniazid | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.78 | isoniazid | Not assoc w R |
ahpC | 2726468 | c.276G>A | synonymous_variant | 0.31 | isoniazid | Not assoc w R - Interim |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.73 | kanamycin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ribD | 2986645 | c.-194G>A | upstream_gene_variant | 0.23 | para-aminosalicylic_acid | |
Rv2681 | 2996912 | c.174C>T | synonymous_variant | 0.23 | capreomycin | Not assoc w R |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.25 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
Rv2752c | 3065951 | p.His81Tyr | missense_variant | 0.24 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
thyX | 3067491 | p.Ala152Val | missense_variant | 0.2 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.29 | ethionamide | Uncertain significance |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.24 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
fbiA | 3640446 | c.-97A>T | upstream_gene_variant | 0.24 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
clpC1 | 4040036 | c.669C>T | synonymous_variant | 0.22 | pyrazinamide | |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.27 | pyrazinamide | Not assoc w R - Interim |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.81 | pyrazinamide | |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.14 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.78 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
embC | 4240172 | p.Val104Met | missense_variant | 0.72 | ethambutol | Not assoc w R |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.24 | ethambutol | Not assoc w R |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.24 | ethambutol | Not assoc w R |
embC | 4241562 | p.Arg567His | missense_variant | 0.88 | ethambutol | Not assoc w R |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.76 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243323 | p.Val31Ile | missense_variant | 0.77 | ethambutol | Uncertain significance |
embA | 4243848 | p.Val206Met | missense_variant | 0.19 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.27 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.15 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.15 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.18 | ethambutol | Not assoc w R |
ethR | 4328051 | p.Ala168Val | missense_variant | 0.75 | ethionamide | |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.24 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
whiB6 | 4338846 | c.-325T>G | upstream_gene_variant | 0.79 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.99 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.15 | streptomycin | Not assoc w R |