TB-Profiler result

Run: ERR181785
Summary

Run ID: ERR181785

Sample name:

Date: 2025-05-27T18:24:40.598991

Number of reads: 5397030

Percentage reads mapped: 99.68

Median coverage: 115.5

Strain: lineage3;lineage4.1.2;lineage4.6.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.06
lineage4.6 Euro-American None 0.78
lineage4.1.2 Euro-American None 0.08
lineage4.6.1.2 Euro-American RD724 0.79
lineage4 Euro-American None 0.88
lineage4.6.1 Euro-American (Uganda) RD724 0.79
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
dnaA 1214 p.Asp405Gly missense_variant 0.14 isoniazid Uncertain significance
gyrB 6501 p.Arg421His missense_variant 0.7 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.77 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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 0.13 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.13 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.12 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 0.17 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.13 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
embR 1416410 p.Leu313Arg missense_variant 0.79 ethambutol Uncertain significance
embR 1417140 p.Ala70Ser missense_variant 0.12 ethambutol Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
inhA 1673249 c.-953C>T upstream_gene_variant 0.13 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674465 c.264C>T synonymous_variant 0.85 ethionamide Not assoc w R - Interim
isoniazid 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 0.13 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
folC 2747022 p.Val193Ile missense_variant 0.11 para-aminosalicylic_acid Uncertain significance
Rv2681 2996876 c.138A>C synonymous_variant 0.77 capreomycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.3 cycloserine Uncertain significance
whiB7 3568921 c.-242G>C upstream_gene_variant 0.13 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Not assoc w R
whiB7 3569029 c.-350A>G upstream_gene_variant 0.78 amikacin Uncertain significance
kanamycin Not assoc w R
streptomycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.2 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4139670 p.Cys29Tyr missense_variant 0.77 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Not assoc w R
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.11 ethambutol Not assoc w R
embA 4245055 p.Thr608Asn missense_variant 0.83 ethambutol Uncertain significance
aftB 4268861 c.-25T>C upstream_gene_variant 0.15 ethambutol Uncertain significance
ethR 4328183 p.Tyr212Cys missense_variant 0.84 ethionamide 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 4338635 c.-114A>C upstream_gene_variant 0.79 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
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 0.1 streptomycin Not assoc w R