Run ID: ERR4830361
Sample name:
Date: 2024-04-16T12:39:35.555062
Number of reads: 3639510
Percentage reads mapped: 98.39
Median coverage: 89.0
Strain: lineage1.2.1.2.1;lineage2.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.2.1.2 | Indo-Oceanic | RD239 | 0.75 |
lineage2 | East-Asian | RD105 | 0.23 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.22 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.23 |
lineage1 | Indo-Oceanic | RD239 | 0.77 |
lineage1.2.1.2.1 | Indo-Oceanic | RD239 | 0.8 |
lineage1.2.1 | Indo-Oceanic | RD239 | 0.8 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Val170Phe | Assoc w R | |
p.Lys446Gln | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB | ||
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethambutol | embB | p.Asp354Ala | Assoc w R | |
pyrazinamide | pncA | c.-11A>G | Assoc w R | |
streptomycin | rpsL | p.Lys88Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 760314 | p.Val170Phe | missense_variant | 0.22 | rifampicin | Assoc w R | |
rpoB | 761142 | p.Lys446Gln | missense_variant | 0.29 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.24 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.2 | isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethionamide | Assoc w R | Alias fabG1_c.-15C>T | |||||
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 0.27 | pyrazinamide | Assoc w R | |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.27 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1302 | c.1302C>A | synonymous_variant | 0.79 | isoniazid | Not assoc w R |
gyrB | 6112 | p.Met291Ile | missense_variant | 0.8 | 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 | 0.81 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.74 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9260 | c.1959G>C | synonymous_variant | 0.79 | 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 | 0.8 | isoniazid | Not assoc w R |
Rv0010c | 13298 | p.Ile87Met | missense_variant | 0.82 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.88 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575368 | c.21T>C | synonymous_variant | 0.78 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.36 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.16 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.2 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.15 | ethionamide | Uncertain significance |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.78 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.82 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 763531 | c.162G>C | synonymous_variant | 0.79 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.85 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.85 | rifampicin | Not assoc w R |
rpoC | 765846 | p.Asn826Thr | missense_variant | 0.23 | 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 | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.17 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.19 | 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 | 0.73 | linezolid | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 0.79 | streptomycin | Not assoc w R |
isoniazid | Not assoc w R | |||||
pyrazinamide | Not assoc w R | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.2 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.82 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.69 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.74 | ethambutol | |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 0.74 | bedaquiline | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 0.78 | ethionamide | Uncertain significance |
isoniazid | Not assoc w R | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.17 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.91 | 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 | 0.78 | 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 | 1.0 | isoniazid | Not assoc w R |
katG | 2155001 | p.Pro371Ser | missense_variant | 0.23 | isoniazid | |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.81 | 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 | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.8 | isoniazid | |
kasA | 2519048 | p.Gly312Ser | missense_variant | 0.88 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.81 | isoniazid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fbiD | 3339417 | c.300A>G | synonymous_variant | 0.69 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.8 | ethionamide | Uncertain significance |
whiB7 | 3568488 | c.191delG | frameshift_variant | 0.84 | streptomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.22 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.75 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.35 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3640557 | c.15T>C | synonymous_variant | 0.73 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.83 | pyrazinamide | Not assoc w R - Interim |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.77 | 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 | 0.83 | ethambutol | Not assoc w R |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.79 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.15 | ethambutol | Not assoc w R |
embA | 4243580 | c.348G>A | synonymous_variant | 0.76 | ethambutol | Not assoc w R |
embA | 4243694 | c.462T>C | synonymous_variant | 0.14 | ethambutol | |
embA | 4244420 | c.1188G>C | synonymous_variant | 0.93 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.63 | ethambutol | Not assoc w R |
embB | 4247578 | c.1065G>A | synonymous_variant | 0.73 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.88 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.14 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.77 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.75 | ethambutol | Not assoc w R |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 0.81 | ethambutol | Not assoc w R |
ethA | 4327085 | p.Thr130Asn | missense_variant | 0.23 | ethionamide | |
whiB6 | 4338361 | p.Arg54Gln | missense_variant | 0.79 | 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 | 0.79 | 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 | 1.0 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.83 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.18 | streptomycin | Not assoc w R |