TB-Profiler result

Run: SRR29356832
Summary

Run ID: SRR29356832

Sample name:

Date: 2025-07-28T06:19:04.349587

Number of reads: 1569109

Percentage reads mapped: 99.72

Median coverage: 74.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 100.0
lineage4.8 Euro-American (mainly T) RD219 100.0
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
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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918237 c.298C>T synonymous_variant 1.0 capreomycin Uncertain significance
katG 2154158 p.Ser652Ala missense_variant 1.0 isoniazid Uncertain significance
PPE35 2169071 c.1464_1541delGGCGGTGACGACGCCGGCCAACGTTACCGTGGGTGCGTTTGATTTGCCGGGGTTGACGGTGCCGTCGTTGACGATTCC disruptive_inframe_deletion 1.0 pyrazinamide Uncertain significance
PPE35 2169071 p.ValThrThrProAlaAsnVal490AlaMetThrProAlaAsnIle missense_variant 0.44 pyrazinamide Uncertain significance
PPE35 2169071 c.1464_1541delGGCGGTGACGACGCCGGCCAACGTTACCGTGGGTGCGTTTGATTTGCCGGGGTTGACGGTGCCGTCGTTGACGATTCC disruptive_inframe_deletion 0.56 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3087095 c.276C>T synonymous_variant 1.0 cycloserine Uncertain significance
Rv3083 3448507 c.5_*1407del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
mtrA 3627470 c.-121T>C upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242857 p.His999Tyr missense_variant 1.0 ethambutol Uncertain significance
embC 4242879 p.Thr1006Ile missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338497 p.Ala9Ser missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R