TB-Profiler result

Run: SRR13837997
Summary

Run ID: SRR13837997

Sample name:

Date: 2025-03-05T16:13:12.057475

Number of reads: 2936608

Percentage reads mapped: 100.0

Median coverage: 98.0

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 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
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 pepQ c.248_249insA Assoc w R - Interim
para-aminosalicylic_acid
delamanid
bedaquiline pepQ c.248_249insA Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
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
pepQ 2860170 c.248_249insA frameshift_variant 1.0 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
clofazimine Assoc w R - Interim
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 4992 c.-248_-247insT upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7018 c.-284G>T upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 576668 c.1322dupA frameshift_variant&stop_gained 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 656976 c.495G>A synonymous_variant 1.0 ethionamide Uncertain significance
Rv0565c 657336 c.135G>C synonymous_variant 1.0 ethionamide Uncertain significance
rpoC 765100 c.1731G>C synonymous_variant 0.99 rifampicin Uncertain significance
mmpL5 776059 p.Val808Met missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
fbiC 1304599 p.Ile557Phe missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embR 1417348 c.-1A>T upstream_gene_variant 1.0 ethambutol Uncertain significance
rrl 1473631 n.-27T>C upstream_gene_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833855 p.Lys105Thr missense_variant 1.0 pyrazinamide Uncertain significance
tlyA 1917702 c.-238G>C upstream_gene_variant 1.0 capreomycin Uncertain significance
bacA 2064233 c.495dupG frameshift_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
katG 2156789 c.-678G>T upstream_gene_variant 1.0 isoniazid Uncertain significance
PPE35 2170030 p.Met195Leu missense_variant 1.0 pyrazinamide Uncertain significance
kasA 2518276 p.Trp54* stop_gained 1.0 isoniazid Uncertain significance
kasA 2518352 p.Met80Val missense_variant 1.0 isoniazid Uncertain significance
eis 2714478 c.855C>A synonymous_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2681 2997465 p.Val243Leu missense_variant 1.0 capreomycin Uncertain significance
Rv2752c 3065335 p.Leu286Arg missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
mtrB 3626280 p.Thr112Pro missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiA 3640236 c.-307T>A upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiA 3640307 c.-236C>G upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiB 3641019 c.-516G>A upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiB 3641941 p.Leu136Gln missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
glpK 4139862 c.-107C>A upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4241292 p.Leu477Gln missense_variant 1.0 ethambutol Uncertain significance
embC 4242011 p.Leu717Val missense_variant 1.0 ethambutol Uncertain significance
embB 4248720 p.Gly736Ala missense_variant 1.0 ethambutol Uncertain significance
embB 4249676 p.Arg1055Cys missense_variant 1.0 ethambutol Uncertain significance
aftB 4267927 p.Ala304Ser missense_variant 1.0 ethambutol Uncertain significance