TB-Profiler result

Run: SRR13837727
Summary

Run ID: SRR13837727

Sample name:

Date: 2025-03-06T01:08:18.762503

Number of reads: 2936409

Percentage reads mapped: 100.0

Median coverage: 98.0

Strain: lineage4.9

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 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 katG p.Gly234Glu Uncertain significance Mutation from literature
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 2155411 p.Gly234Glu missense_variant 1.0 isoniazid 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
Rv0010c 13524 p.Gly12Ala missense_variant 1.0 isoniazid Uncertain significance
mshA 576259 c.912C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ccsA 620690 p.Val267Glu missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
Rv0565c 657622 c.-152G>A upstream_gene_variant 1.0 ethionamide Uncertain significance
mmaA3 738209 c.-60A>T upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoB 759805 c.-2T>C upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoB 761961 p.Pro719Thr missense_variant 0.99 rifampicin Uncertain significance
rpoC 764895 p.Ile509Thr missense_variant 1.0 rifampicin Uncertain significance
mmpL5 777574 p.Phe303Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 777578 c.903C>G synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 778982 c.-502A>C upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 801169 p.Lys121* stop_gained 0.99 linezolid Uncertain significance
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476479 n.2822T>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1918432 p.Pro165Thr missense_variant 1.0 capreomycin Uncertain significance
ndh 2101769 p.Arg425His missense_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2155508 p.Ala202Ser missense_variant 1.0 isoniazid Uncertain significance
pncA 2289474 c.-233C>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
folC 2746862 p.Leu246Arg missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
folC 2747268 p.Asp111His missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2752c 3065109 c.1083A>G synonymous_variant 0.99 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
whiB7 3568816 c.-137C>T upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
whiB7 3569222 c.-543G>A upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
lpqB 3624508 p.Ile135Val missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625247 p.Arg456Pro missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
clpC1 4038468 p.Asp746Gly missense_variant 1.0 pyrazinamide Uncertain significance
clpC1 4040148 p.Lys186Ile missense_variant 1.0 pyrazinamide Uncertain significance
embC 4240125 p.Cys88Tyr missense_variant 1.0 ethambutol Uncertain significance
ethR 4327643 p.Thr32Ile missense_variant 1.0 ethionamide Uncertain significance