TB-Profiler result

Run: SRR13837863
Summary

Run ID: SRR13837863

Sample name:

Date: 2025-03-09T17:21:46.691171

Number of reads: 2936573

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 pncA p.Thr153Asn Mutation from literature
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
pncA 2288784 p.Thr153Asn missense_variant 1.0 pyrazinamide Mutation from literature
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 750 c.750C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
dnaA 1200 c.1200C>T synonymous_variant 1.0 isoniazid Uncertain significance
gyrA 9494 p.Tyr731* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491771 p.Pro330Leu missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv0565c 657479 c.-9A>G upstream_gene_variant 1.0 ethionamide Uncertain significance
rpoB 762948 p.Gln1048Glu missense_variant 1.0 rifampicin Uncertain significance
rpoC 767026 c.3657G>C synonymous_variant 1.0 rifampicin Uncertain significance
fbiC 1303155 c.225G>C synonymous_variant 0.99 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304225 p.Gly432Asp missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1305046 p.Ser706Pro missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1406433 c.907delA frameshift_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
embR 1416546 p.Thr268Ser missense_variant 1.0 ethambutol Uncertain significance
rrs 1471511 n.-335C>A upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474652 n.995T>G non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1854352 p.Cys249Trp missense_variant 1.0 linezolid Uncertain significance
bacA 2063152 p.Arg526Leu missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
bacA 2064648 p.Trp27Cys missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
ndh 2102315 p.Ile243Thr missense_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2156722 c.-611G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
kasA 2518563 p.Ala150Gly missense_variant 0.99 isoniazid Uncertain significance
kasA 2519015 p.Ser301Ala missense_variant 1.0 isoniazid Uncertain significance
Rv2477c 2783171 c.871delT frameshift_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2680 2995958 c.-147G>A upstream_gene_variant 1.0 capreomycin Uncertain significance
Rv3236c 3612913 p.Leu68Phe missense_variant 1.0 pyrazinamide Uncertain significance
lpqB 3624794 c.117G>C synonymous_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
glpK 4138701 p.Gln352Pro missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
glpK 4138728 p.Ala343Gly missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
ethA 4326245 p.Asp410Ala missense_variant 1.0 ethionamide Uncertain significance
ethA 4327132 c.342C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethA 4327893 c.-420C>A upstream_gene_variant 1.0 ethionamide Uncertain significance
gid 4408070 p.Trp45Arg missense_variant 1.0 streptomycin Uncertain significance