TB-Profiler result

Run: SRR13837739
Summary

Run ID: SRR13837739

Sample name:

Date: 2025-03-05T06:04:38.953162

Number of reads: 2936406

Percentage reads mapped: 100.0

Median coverage: 100.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid ddn c.4_5insA Assoc w R - Interim Confers DLM-PMD cross-resistance
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
ddn 3986847 c.4_5insA frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-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
fgd1 490804 p.Tyr8Asn missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 490893 c.111C>T synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mshA 575498 p.Ala51Pro missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 656747 p.Val242Ile missense_variant 1.0 ethionamide Uncertain significance
Rv0565c 656828 p.Tyr215His missense_variant 1.0 ethionamide Uncertain significance
rpoC 763663 c.294C>A synonymous_variant 1.0 rifampicin Uncertain significance
rpoC 763955 p.Lys196Gln missense_variant 1.0 rifampicin Uncertain significance
rpoC 765682 p.Asn771Lys missense_variant 1.0 rifampicin Uncertain significance
rpoC 766342 c.2973C>A synonymous_variant 1.0 rifampicin Uncertain significance
rpsL 781579 p.Leu7Arg missense_variant 1.0 streptomycin Uncertain significance
Rv1129c 1254119 p.Ser139Phe missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
embR 1416509 p.Arg280Pro missense_variant 1.0 ethambutol Uncertain significance
rrl 1474164 n.507C>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674315 c.114C>G synonymous_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2154959 c.1153C>A synonymous_variant 1.0 isoniazid Uncertain significance
PPE35 2170236 c.376_377insG frameshift_variant 1.0 pyrazinamide Uncertain significance
pncA 2290061 c.-820C>T upstream_gene_variant 0.99 pyrazinamide Uncertain significance
folC 2747798 c.-200A>T upstream_gene_variant 0.99 para-aminosalicylic_acid Uncertain significance
pepQ 2860252 p.Thr56Ser missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2680 2996652 p.Val183Ala missense_variant 1.0 capreomycin Uncertain significance
Rv2752c 3065651 p.Arg181Gly missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv3083 3448855 p.Val118Ile missense_variant 1.0 ethionamide Uncertain significance
whiB7 3569074 c.-395A>G upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
mtrB 3626557 p.Met19Ile missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3626629 c.-17_-16insT upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
rpoA 3877765 p.Ala248Gly missense_variant 1.0 rifampicin Uncertain significance
panD 4044948 c.-667A>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
embB 4247059 c.546C>G synonymous_variant 1.0 ethambutol Uncertain significance
embB 4247144 p.Ser211Pro missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269553 p.Ala94Gly missense_variant 1.0 ethambutol Uncertain significance
gid 4408259 c.-57G>C upstream_gene_variant 1.0 streptomycin Uncertain significance