TB-Profiler result

Run: SRR13837917
Summary

Run ID: SRR13837917

Sample name:

Date: 2024-10-04T18:09:50.754236

Number of reads: 1469038

Percentage reads mapped: 98.0

Median coverage: 49.0

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 154 p.Gln52* stop_gained 1.0 isoniazid Uncertain significance
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
gyrA 9494 p.Tyr731* stop_gained 1.0 levofloxacin
moxifloxacin
fgd1 491771 p.Pro330Leu missense_variant 1.0 pretomanid
delamanid
clofazimine
Rv0565c 657479 c.-9A>G upstream_gene_variant 1.0 ethionamide
rpoB 762948 p.Gln1048Glu missense_variant 0.97 rifampicin
rpoC 767026 c.3657G>C synonymous_variant 1.0 rifampicin
fbiC 1303155 c.225G>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1304225 p.Gly432Asp missense_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1305046 p.Ser706Pro missense_variant 0.98 pretomanid
delamanid
clofazimine
Rv1258c 1406433 c.907delA frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416546 p.Thr268Ser missense_variant 1.0 ethambutol
rrs 1471511 n.-335C>A upstream_gene_variant 0.98 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474652 n.995T>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
tsnR 1854352 p.Cys249Trp missense_variant 1.0 linezolid
bacA 2063152 p.Arg526Leu missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
bacA 2064648 p.Trp27Cys missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
ndh 2102315 p.Ile243Thr missense_variant 1.0 isoniazid
delamanid
ethionamide
katG 2156722 c.-611G>A upstream_gene_variant 1.0 isoniazid
kasA 2518563 p.Ala150Gly missense_variant 1.0 isoniazid
kasA 2519015 p.Ser301Ala missense_variant 1.0 isoniazid
Rv2477c 2783171 c.871delT frameshift_variant 1.0 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2680 2995958 c.-147G>A upstream_gene_variant 1.0 capreomycin
Rv3236c 3612913 p.Leu68Phe missense_variant 1.0 pyrazinamide
lpqB 3624794 c.117G>C synonymous_variant 1.0 rifampicin
bedaquiline
glpK 4138701 p.Gln352Pro missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138728 p.Ala343Gly missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
ethA 4326245 p.Asp410Ala missense_variant 1.0 ethionamide
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
gid 4408070 p.Trp45Arg missense_variant 1.0 streptomycin Uncertain significance