TB-Profiler result

Run: SRR13861250
Summary

Run ID: SRR13861250

Sample name:

Date: 2025-09-15T16:22:45.457264

Number of reads: 1119550

Percentage reads mapped: 56.03

Median coverage: 38.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 100.0
lineage4.9 Euro-American (H37Rv-like) None 100.0
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 fbiC c.1301delC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1304229 c.1301delC frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 8880 p.Lys527Gln missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mmaA3 737817 c.333A>G synonymous_variant 0.97 isoniazid Uncertain significance
rpoB 760972 p.Arg389Leu missense_variant 1.0 rifampicin Uncertain significance
rpoC 765111 p.Met581Lys missense_variant 1.0 rifampicin Uncertain significance
rpoC 765161 p.Glu598Lys missense_variant 1.0 rifampicin Uncertain significance
rpoC 765540 p.Ala724Val missense_variant 1.0 rifampicin Uncertain significance
rpoC 767068 c.3699G>T synonymous_variant 1.0 rifampicin Uncertain significance
mmpR5 778439 c.-551C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 801357 p.His183Gln missense_variant 1.0 linezolid Uncertain significance
rrs 1472288 n.444delT non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tsnR 1853872 c.267G>T synonymous_variant 1.0 linezolid Uncertain significance
tlyA 1917989 p.Ala17Gly missense_variant 1.0 capreomycin Uncertain significance
bacA 2063805 c.924G>A synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
bacA 2064585 c.144C>A synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
ndh 2102525 p.Phe173Tyr missense_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
ndh 2102538 c.504_505insT frameshift_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
Rv1979c 2222978 p.Ile63Phe missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223052 p.Glu38Val missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
pncA 2289415 c.-174C>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
kasA 2518057 c.-58A>C upstream_gene_variant 1.0 isoniazid Uncertain significance
kasA 2518799 p.Pro229Ser missense_variant 0.97 isoniazid Uncertain significance
eis 2714983 p.Ala117Glu missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2784409 c.-367T>A upstream_gene_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2784611 c.-569A>T upstream_gene_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
fbiA 3640404 c.-139C>A upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiB 3642056 c.522C>G synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3877967 p.Thr181Ser missense_variant 1.0 rifampicin Uncertain significance
rpoA 3877972 c.535delG frameshift_variant 1.0 rifampicin Uncertain significance
clpC1 4039777 c.927_928insG frameshift_variant 1.0 pyrazinamide Uncertain significance
glpK 4138934 c.822A>C synonymous_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embB 4247545 p.Ser344Arg missense_variant 1.0 ethambutol Uncertain significance
aftB 4268812 p.Ser9Pro missense_variant 1.0 ethambutol Uncertain significance