TB-Profiler result

Run: SRR13837620
Summary

Run ID: SRR13837620

Sample name:

Date: 2024-04-15T22:29:14.820686

Number of reads: 293837

Percentage reads mapped: 97.01

Median coverage: 10.0

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
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 capreomycin
amikacin
kanamycin
rpoB 761961 p.Pro719Thr missense_variant 1.0 rifampicin
rpoC 764895 p.Ile509Thr missense_variant 1.0 rifampicin
mmpL5 777574 p.Phe303Leu missense_variant 1.0 clofazimine
bedaquiline
mmpL5 777578 c.903C>G synonymous_variant 1.0 clofazimine
bedaquiline
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
folC 2746862 p.Leu246Arg missense_variant 1.0 para-aminosalicylic_acid
folC 2747268 p.Asp111His missense_variant 1.0 para-aminosalicylic_acid
whiB7 3569222 c.-543G>A upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
mtrB 3625247 p.Arg456Pro missense_variant 1.0 bedaquiline
rifampicin
clpC1 4038468 p.Asp746Gly missense_variant 1.0 pyrazinamide
clpC1 4040148 p.Lys186Ile missense_variant 1.0 pyrazinamide
embC 4240125 p.Cys88Tyr missense_variant 1.0 ethambutol