TB-Profiler result

Run: SRR6650235
Summary

Run ID: SRR6650235

Sample name:

Date: 2024-10-03T23:37:19.603801

Number of reads: 492014

Percentage reads mapped: 99.45

Median coverage: 10.0

Strain: lineage1.1.3.1;lineage3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.77
lineage1.1 Indo-Oceanic RD239 0.19
lineage1 Indo-Oceanic RD239 0.07
lineage1.1.3.1 Indo-Oceanic RD239 0.1
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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
embR 1416816 p.Ala178Thr missense_variant 0.73 ethambutol Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223361 c.-197C>T upstream_gene_variant 0.83 bedaquiline
clofazimine
pncA 2289047 c.195C>T synonymous_variant 0.83 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.77 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.83 isoniazid Not assoc w R
folC 2746655 p.Ala315Gly missense_variant 0.9 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.86 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
alr 3841473 c.-53G>A upstream_gene_variant 0.71 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.83 pyrazinamide
embC 4242075 p.Arg738Gln missense_variant 0.7 ethambutol Not assoc w R