TB-Profiler result

Run: ERR4811178
Summary

Run ID: ERR4811178

Sample name:

Date: 2025-06-07T12:31:19.279246

Number of reads: 7909046

Percentage reads mapped: 99.39

Median coverage: 232.0

Strain: lineage2.2.1;lineage4.4.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.12
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.12
lineage2.2 East-Asian (Beijing) RD105;RD207 0.12
lineage4 Euro-American None 0.87
lineage4.4 Euro-American None 0.88
lineage4.4.2 Euro-American None 0.88
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
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
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
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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.1 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
ccsA 620625 p.Ile245Met missense_variant 0.16 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.16 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.16 ethionamide Uncertain significance
mmaA3 738057 non_coding_transcript_variant 0.88 isoniazid Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.12 rifampicin Not assoc w R
rpoC 763696 c.327T>A synonymous_variant 0.9 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 0.12 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.13 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.1 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 0.11 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406441 c.899delT frameshift_variant 0.86 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.14 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin 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 1833338 c.-204T>G upstream_gene_variant 0.15 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.1 pyrazinamide Not assoc w R - Interim
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
PPE35 2167926 p.Leu896Ser missense_variant 0.11 pyrazinamide 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
Rv2752c 3066099 p.Met31Ile missense_variant 0.87 ethambutol Not assoc w R
isoniazid Not assoc w R - Interim
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Not assoc w R
Rv2752c 3066221 c.-30T>C upstream_gene_variant 0.87 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.83 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.89 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 0.12 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.9 ethambutol Not assoc w R
embB 4247249 p.Gly246Arg missense_variant 0.91 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.12 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.9 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.87 ethambutol Not assoc w R
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 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 0.15 streptomycin Not assoc w R
gid 4407766 p.Thr146Met missense_variant 0.83 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.12 streptomycin Not assoc w R