TB-Profiler result

Run: SAMEA104362087
Summary

Run ID: SAMEA104362087

Sample name:

Date: 2024-04-15T23:31:36.461749

Number of reads: 7983902

Percentage reads mapped: 99.61

Median coverage: 246.0

Strain: lineage4.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.68
lineage4.1 Euro-American None 0.34
lineage4.1.2 Euro-American None 0.32
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.31
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.69
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide pncA p.His51Arg Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
inhA 1673425 c.-777C>T upstream_gene_variant 0.67 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
pncA 2289090 p.His51Arg missense_variant 0.69 pyrazinamide Assoc w R
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 71 p.Pro24Leu missense_variant 0.66 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.7 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
fgd1 491591 p.Lys270Met missense_variant 0.33 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.39 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.3 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.67 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.29 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 775854 p.Gly876Asp missense_variant 0.32 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781276 c.-284A>C upstream_gene_variant 0.35 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834683 p.Ala381Val missense_variant 0.66 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.31 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.64 isoniazid
Rv2477c 2784248 c.-206C>G upstream_gene_variant 0.64 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.67 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.66 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.27 ethambutol Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.72 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.33 ethambutol Not assoc w R
ethA 4328212 c.-740delC upstream_gene_variant 0.32 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407591 c.612C>T synonymous_variant 0.31 streptomycin Not assoc w R - Interim
gid 4408006 p.Val66Ala missense_variant 0.35 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.72 streptomycin Not assoc w R