TB-Profiler result

Run: ERR13261692
Summary

Run ID: ERR13261692

Sample name:

Date: 2025-02-11T20:36:23.243572

Number of reads: 5906017

Percentage reads mapped: 99.87

Median coverage: 181.0

Strain: lineage4.3.4.2;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.55
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.45
lineage4.3.4 Euro-American (LAM) RD174 0.55
lineage4.3.4.2 Euro-American (LAM) RD174 0.55
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
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
katG 2155168 p.Ser315Thr missense_variant 0.54 isoniazid Assoc w R High-level 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
dnaA 371 p.Pro124Leu missense_variant 0.48 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.6 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
hadA 731803 c.-127A>G upstream_gene_variant 0.63 isoniazid
rpoC 764995 c.1626C>G synonymous_variant 0.57 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254588 c.-54T>G upstream_gene_variant 0.55 levofloxacin
moxifloxacin
isoniazid
rifampicin
atpE 1460992 c.-53A>C upstream_gene_variant 0.36 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.53 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2747453 p.Arg49Gln missense_variant 0.57 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.64 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.5 cycloserine
ald 3087026 p.Asp69Glu missense_variant 0.45 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.57 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.54 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840764 c.657G>C synonymous_variant 0.4 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.54 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248736 c.2223G>T synonymous_variant 0.47 ethambutol Not assoc w R - Interim
whiB6 4338238 p.Leu95Pro missense_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338404 p.Arg40Cys missense_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338600 c.-79T>C upstream_gene_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 0.61 kanamycin
capreomycin
amikacin
gid 4408054 p.Leu50Arg missense_variant 0.62 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.59 streptomycin Not assoc w R