TB-Profiler result

Run: ERR4830357
Summary

Run ID: ERR4830357

Sample name:

Date: 2025-05-16T13:00:31.561185

Number of reads: 3295260

Percentage reads mapped: 99.57

Median coverage: 72.0

Strain: lineage1.1;lineage2.2.1.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.88
lineage1.1 Indo-Oceanic RD239 0.13
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.9
lineage2.2 East-Asian (Beijing) RD105;RD207 0.85
lineage1 Indo-Oceanic RD239 0.06
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.9
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid folC p.Glu40Gly Mutation from literature
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
rpsL 781687 p.Lys43Arg missense_variant 0.9 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.85 isoniazid Assoc w R High-level resistance
folC 2747480 p.Glu40Gly missense_variant 0.89 para-aminosalicylic_acid Mutation from literature
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
gyrB 6112 p.Met291Ile missense_variant 0.15 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 0.12 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 13275 p.Tyr95Cys missense_variant 0.14 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.16 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.15 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.17 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
mshA 575907 p.Ala187Val missense_variant 0.9 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.94 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.67 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.84 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.15 ethionamide Uncertain significance
mmaA3 738311 c.-162A>G upstream_gene_variant 0.23 isoniazid Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.92 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.92 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
fbiC 1302716 c.-215G>A upstream_gene_variant 0.85 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.88 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.15 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.97 pyrazinamide Not assoc w R - Interim
rpsA 1834319 p.Val260Ile missense_variant 0.11 pyrazinamide 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
bacA 2062922 p.Ile603Val missense_variant 0.16 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Not assoc w R
katG 2154264 c.1848G>A synonymous_variant 0.96 isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.22 pyrazinamide Uncertain significance
PPE35 2169122 c.1491C>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
PPE35 2169125 p.Val496Ile missense_variant 0.13 pyrazinamide Uncertain significance
PPE35 2169131 c.1482C>T synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
PPE35 2169134 c.1479G>A synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14 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
eis 2714846 p.Val163Ile missense_variant 0.89 amikacin Not assoc w R
kanamycin Not assoc w R
ahpC 2726051 c.-142G>A upstream_gene_variant 0.25 isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
ald 3086987 p.Gln56His missense_variant 0.2 cycloserine Uncertain significance
Rv3083 3448714 p.Asp71His missense_variant 0.12 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.95 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625416 p.Pro400Ala missense_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.79 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878630 c.-124delC upstream_gene_variant 0.19 rifampicin Not assoc w R
glpK 4138377 p.Val460Ala missense_variant 0.17 ethambutol Not assoc w R
isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin 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 0.93 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.13 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.89 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.9 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 0.1 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.19 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.17 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.21 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.82 streptomycin Not assoc w R