TB-Profiler result

Run: ERR323082
Summary

Run ID: ERR323082

Sample name:

Date: 2024-04-15T04:21:50.980193

Number of reads: 3770176

Percentage reads mapped: 99.6

Median coverage: 81.0

Strain: lineage4.1.2;lineage4.3.4.2.1

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 0.69
lineage4.1 Euro-American None 0.3
lineage4.1.2 Euro-American None 0.29
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.76
lineage4.3.4 Euro-American (LAM) RD174 0.72
lineage4.3.4.2 Euro-American (LAM) RD174 0.7
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
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 0.18 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
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 5611 c.372C>T synonymous_variant 0.72 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6140 p.Val301Leu missense_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.36 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.74 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1417140 p.Ala70Ser missense_variant 0.29 ethambutol Not assoc w R
embR 1418018 c.-671C>T upstream_gene_variant 0.35 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673249 c.-191C>T upstream_gene_variant 0.29 ethionamide
isoniazid
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
folC 2747022 p.Val193Ile missense_variant 0.29 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.68 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448894 p.Tyr131Asp missense_variant 0.33 ethionamide Uncertain significance
Rv3083 3449642 p.Asn380Ser missense_variant 0.3 ethionamide Uncertain significance
whiB7 3568921 c.-242G>C upstream_gene_variant 0.28 streptomycin Not assoc w R
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.6 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641164 p.Ile208Val missense_variant 0.38 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.7 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.62 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.23 ethambutol Not assoc w R
aftB 4268861 c.-25T>C upstream_gene_variant 0.25 ethambutol Uncertain significance
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 4408156 p.Leu16Arg missense_variant 0.77 streptomycin Not assoc w R