TB-Profiler result

Run: SRR13861289
Summary

Run ID: SRR13861289

Sample name:

Date: 2024-10-05T13:01:50.856718

Number of reads: 2800887

Percentage reads mapped: 46.73

Median coverage: 95.0

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
moxifloxacin
gyrA 7018 c.-284G>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
mshA 576668 c.1322dupA frameshift_variant&stop_gained 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 656976 c.495G>A synonymous_variant 1.0 ethionamide
Rv0565c 657336 c.135G>C synonymous_variant 1.0 ethionamide
rpoC 765100 c.1731G>C synonymous_variant 1.0 rifampicin
mmpL5 776059 p.Val808Met missense_variant 1.0 bedaquiline
clofazimine
fbiC 1304599 p.Ile557Phe missense_variant 1.0 pretomanid
delamanid
clofazimine
embR 1417348 c.-1A>T upstream_gene_variant 1.0 ethambutol
rrl 1473631 n.-27T>C upstream_gene_variant 1.0 capreomycin
linezolid
rpsA 1833855 p.Lys105Thr missense_variant 1.0 pyrazinamide
tlyA 1917702 c.-238G>C upstream_gene_variant 1.0 capreomycin
bacA 2064233 c.495dupG frameshift_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
katG 2156789 c.-678G>T upstream_gene_variant 1.0 isoniazid
PPE35 2170030 p.Met195Leu missense_variant 1.0 pyrazinamide
kasA 2518276 p.Trp54* stop_gained 1.0 isoniazid
kasA 2518352 p.Met80Val missense_variant 1.0 isoniazid
eis 2714478 c.855C>A synonymous_variant 1.0 kanamycin
amikacin
Rv2681 2997465 p.Val243Leu missense_variant 1.0 capreomycin
Rv2752c 3065335 p.Leu286Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
mtrB 3626280 p.Thr112Pro missense_variant 1.0 rifampicin
bedaquiline
fbiA 3640236 c.-307T>A upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiA 3640307 c.-236C>G upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiB 3641019 c.-516G>A upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiB 3641941 p.Leu136Gln missense_variant 1.0 pretomanid
delamanid
clofazimine
glpK 4139862 c.-107C>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4241292 p.Leu477Gln missense_variant 1.0 ethambutol Uncertain significance
embC 4242011 p.Leu717Val missense_variant 1.0 ethambutol
embB 4248720 p.Gly736Ala missense_variant 1.0 ethambutol
embB 4249676 p.Arg1055Cys missense_variant 1.0 ethambutol
aftB 4267927 p.Ala304Ser missense_variant 1.0 ethambutol Uncertain significance