TB-Profiler result

Run: ERR2515863
Summary

Run ID: ERR2515863

Sample name:

Date: 2025-05-17T04:29:03.619780

Number of reads: 714824

Percentage reads mapped: 99.79

Median coverage: 38.0

Strain: lineage4.1.2;lineage4.3.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.65
lineage4.1 Euro-American None 0.29
lineage4.1.2 Euro-American None 0.33
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.68
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 8040 p.Gly247Ser missense_variant 0.84 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
mshA 575909 p.Leu188Val missense_variant 0.53 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.31 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.28 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 778346 c.135C>T synonymous_variant 0.88 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1302955 p.Ser9Ala missense_variant 0.21 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embR 1417140 p.Ala70Ser missense_variant 0.33 ethambutol Not assoc w R
embR 1418018 c.-671C>T upstream_gene_variant 0.23 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
inhA 1673249 c.-953C>T upstream_gene_variant 0.3 ethionamide Uncertain significance
isoniazid 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.65 isoniazid Uncertain significance
folC 2747022 p.Val193Ile missense_variant 0.36 para-aminosalicylic_acid Uncertain significance
folC 2747225 p.Arg125Gln missense_variant 0.59 para-aminosalicylic_acid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.63 para-aminosalicylic_acid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3449642 p.Asn380Ser missense_variant 0.44 ethionamide Uncertain significance
whiB7 3568921 c.-242G>C upstream_gene_variant 0.19 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.66 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.32 ethambutol Not assoc w R
whiB6 4338367 p.Leu52Gln missense_variant 0.97 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 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.91 streptomycin Not assoc w R