TB-Profiler result

Run: 1d2f53e0-b84e-4c65-a3e0-7a714eb8c034
Summary

Run ID: 1d2f53e0-b84e-4c65-a3e0-7a714eb8c034

Sample name:

Date: 13-02-2024 08:27:27

Number of reads: 1903624

Percentage reads mapped: 99.24

Median coverage: 64

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 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
gyrB 6998 p.Arg587Cys missense_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
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 8694 c.1393C>T synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491591 p.Lys270Met missense_variant 1.0 delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 576482 p.Val379Leu missense_variant 0.17 ethionamide
isoniazid
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.99 rifampicin Uncertain significance
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
embR 1416821 p.Ala176Gly missense_variant 1.0 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
tlyA 1917972 c.33A>G synonymous_variant 0.98 capreomycin
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
rpoA 3878630 c.-123G>C upstream_gene_variant 0.17 rifampicin
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Uncertain significance
embA 4246458 p.Glu1076Gln missense_variant 1.0 ethambutol
embB 4246584 p.Arg24Pro missense_variant 0.53 ethambutol
embB 4249273 p.Asp920Glu missense_variant 1.0 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance