TB-Profiler result

Run: SRR13837890
Summary

Run ID: SRR13837890

Sample name:

Date: 2025-03-04T22:23:43.841093

Number of reads: 1468386

Percentage reads mapped: 100.0

Median coverage: 50.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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
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
dnaA 335 p.Thr112Ser missense_variant 1.0 isoniazid Uncertain significance
gyrB 6406 p.Asn389Lys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 575880 p.His178Pro missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 576356 p.Ala337Ser missense_variant 0.98 ethionamide Uncertain significance
isoniazid Uncertain significance
mmaA3 738203 c.-54T>C upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1129c 1254144 p.Thr131Ala missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiC 1303517 p.Met196Arg missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrl 1473558 n.-100T>G upstream_gene_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673792 c.-410G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1833709 c.168C>T synonymous_variant 1.0 pyrazinamide Uncertain significance
rpsA 1834448 p.Lys303* stop_gained 1.0 pyrazinamide Uncertain significance
tlyA 1917605 c.-335G>T upstream_gene_variant 1.0 capreomycin Uncertain significance
tlyA 1918103 p.Val55Ala missense_variant 1.0 capreomycin Uncertain significance
tlyA 1918250 p.Gly104Ala missense_variant 1.0 capreomycin Uncertain significance
bacA 2064591 c.138C>A synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
katG 2156538 c.-427A>T upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2222544 c.621G>A synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
eis 2715078 c.255C>G synonymous_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
folC 2747750 c.-152G>C upstream_gene_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2680 2995806 c.-299_-298insC upstream_gene_variant 1.0 capreomycin Uncertain significance
ald 3086982 p.Ala55Pro missense_variant 1.0 cycloserine Uncertain significance
Rv3083 3449935 p.Ile478Val missense_variant 1.0 ethionamide Uncertain significance
whiB7 3569257 c.-578A>G upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
lpqB 3623916 p.Arg332Gln missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3627581 c.-968G>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiB 3642147 p.Val205Phe missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiB 3642189 p.Gly219Trp missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
clpC1 4039120 p.Ser529Ala missense_variant 1.0 pyrazinamide Uncertain significance
clpC1 4039306 p.Gln467Lys missense_variant 1.0 pyrazinamide Uncertain significance
clpC1 4039400 c.1304delA frameshift_variant 1.0 pyrazinamide Uncertain significance
embC 4239311 c.-552G>C upstream_gene_variant 1.0 ethambutol Uncertain significance
ethA 4327034 p.Tyr147Phe missense_variant 1.0 ethionamide Uncertain significance
gid 4408038 p.Ile55Met missense_variant 1.0 streptomycin Uncertain significance