TB-Profiler result

Run: bb228a9b-6a02-4ce5-a43c-732416326575
Summary

Run ID: bb228a9b-6a02-4ce5-a43c-732416326575

Sample name:

Date: 26-04-2023 02:32:14

Number of reads: 2263044

Percentage reads mapped: 99.47

Median coverage: 83

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: Sensitive

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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
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.3 Euro-American (LAM) RD115 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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
para-aminosalicylic_acid
cycloserine
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 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 8040 p.Gly247Ser missense_variant 0.97 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
ccsA 619817 c.-74C>A upstream_gene_variant 1.0 capreomycin
amikacin
rpoC 764995 c.1626C>G synonymous_variant 0.99 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rpsA 1834836 p.Met432Thr missense_variant 1.0 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
PPE35 2169081 p.Leu511* stop_gained 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
kasA 2518919 p.Gly269Ser missense_variant 0.98 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339687 c.570C>T synonymous_variant 1.0 delamanid
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fbiA 3640407 c.-136G>C upstream_gene_variant 1.0 delamanid
rpoA 3878627 c.-120T>G upstream_gene_variant 0.17 rifampicin
rpoA 3878630 c.-124delC upstream_gene_variant 0.12 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
ethR 4327405 c.-144C>T upstream_gene_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338646 c.-125A>G upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407720 c.483C>G synonymous_variant 1.0 streptomycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Uncertain significance