TB-Profiler result

Run: ERR10748243
Summary

Run ID: ERR10748243

Sample name:

Date: 2024-04-15T06:22:31.981046

Number of reads: 1177335

Percentage reads mapped: 99.86

Median coverage: 49.0

Strain: lineage1.2.2.1;lineage2.2.1.1

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2.1 Indo-Oceanic RD239 0.62
lineage1.2.2 Indo-Oceanic RD239 0.65
lineage2 East-Asian RD105 0.42
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.43
lineage2.2 East-Asian (Beijing) RD105;RD207 0.43
lineage1 Indo-Oceanic RD239 0.59
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.38
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Cys 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
pyrazinamide pncA c.64delA Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761139 p.His445Cys missense_variant 0.63 rifampicin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.35 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.71 isoniazid Assoc w R High-level resistance
katG 2155168 p.Ser315Asn missense_variant 0.29 isoniazid Assoc w R High-level resistance
pncA 2289177 c.64delA frameshift_variant 0.52 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.8 ethambutol Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 237 c.237G>A synonymous_variant 0.57 isoniazid Not assoc w R - Interim
gyrB 5075 c.-165C>T upstream_gene_variant 0.73 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.62 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 0.61 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.59 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 0.62 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.5 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.54 isoniazid Not assoc w R
Rv0010c 13503 p.Gly19Ala missense_variant 0.57 isoniazid Uncertain significance
fgd1 491060 p.Met93Thr missense_variant 0.54 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.3 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.44 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
ccsA 620659 p.Arg257Cys missense_variant 0.57 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.5 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.28 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.62 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.57 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.54 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.57 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.25 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.39 clofazimine
bedaquiline
rpsL 781301 c.-259C>T upstream_gene_variant 0.21 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.71 linezolid Not assoc w R
rplC 800899 p.Ala31Thr missense_variant 0.57 linezolid Uncertain significance
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
embR 1417019 p.Cys110Tyr missense_variant 0.53 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.56 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.54 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471842 n.-4T>G upstream_gene_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpsA 1833284 c.-258C>T upstream_gene_variant 0.66 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.43 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.67 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 0.6 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2101848 c.1195C>T synonymous_variant 0.53 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2154977 p.Ala379Thr missense_variant 0.43 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.7 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.42 clofazimine Uncertain significance
bedaquiline Uncertain significance
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 0.66 isoniazid
eis 2714846 p.Val163Ile missense_variant 0.26 amikacin Not assoc w R
kanamycin Not assoc w R
ahpC 2726051 c.-142G>A upstream_gene_variant 0.66 isoniazid
ribD 2987120 c.282C>T synonymous_variant 0.7 para-aminosalicylic_acid
Rv2680 2996287 c.183A>G synonymous_variant 0.53 capreomycin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.71 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.31 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.46 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 0.22 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.58 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.66 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 0.49 ethambutol Not assoc w R
embC 4240750 c.888C>T synonymous_variant 0.67 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.62 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243225 c.-8C>T upstream_gene_variant 0.38 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.39 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.61 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.73 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.29 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.49 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.73 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.67 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.63 ethionamide Uncertain significance
ethA 4327450 c.24C>T synonymous_variant 0.63 ethionamide Not assoc w R - Interim
ethR 4327602 c.54G>A synonymous_variant 0.59 ethionamide Not assoc w R - Interim
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 0.71 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 0.61 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.42 streptomycin Not assoc w R