TB-Profiler result

Run: SRR29273771
Summary

Run ID: SRR29273771

Sample name:

Date: 2025-02-11T12:25:07.251110

Number of reads: 3039630

Percentage reads mapped: 99.64

Median coverage: 99.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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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
lineage4.8 Euro-American (mainly T) RD219 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Arg Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Gln141Pro Assoc w R
streptomycin rpsL p.Lys88Gln Assoc w R - Interim
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
rpoB 761140 p.His445Arg missense_variant 1.0 rifampicin Assoc w R
rpsL 781821 p.Lys88Gln missense_variant 1.0 streptomycin Assoc w R - Interim
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2288820 p.Gln141Pro missense_variant 1.0 pyrazinamide Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol Uncertain significance 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 1478 p.His493Arg missense_variant 1.0 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575891 p.Ala182Thr missense_variant 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 656761 p.Thr237Ile missense_variant 1.0 ethionamide Uncertain significance
rpoB 760081 p.Asp92Gly missense_variant 1.0 rifampicin Uncertain significance
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 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472319 n.474C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin
streptomycin
amikacin Uncertain significance
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
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
mtrB 3626251 c.363T>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
clpC1 4040941 c.-237G>T upstream_gene_variant 1.0 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242928 c.3066A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247595 p.Cys361Ser missense_variant 0.99 ethambutol Uncertain significance
aftB 4268040 p.Leu266Pro missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338593 c.-73delT upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin