TB-Profiler result

Run: ERR176709
Summary

Run ID: ERR176709

Sample name:

Date: 2024-10-04T12:40:21.089305

Number of reads: 2521838

Percentage reads mapped: 99.61

Median coverage: 54.0

Strain: lineage3.1.1;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
lineage3 East-African-Indian RD750 0.65
lineage4.3 Euro-American (LAM) None 0.39
lineage3.1.1 East-African-Indian RD750 0.66
lineage4 Euro-American None 0.3
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.39
lineage4.3.4 Euro-American (LAM) RD174 0.36
lineage4.3.4.2 Euro-American (LAM) RD174 0.37
lineage3.1 East-African-Indian RD750 0.77
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.42 isoniazid Assoc w R High-level resistance
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 758 p.Asp253Ala missense_variant 0.71 isoniazid Uncertain significance
gyrB 6140 p.Val301Leu missense_variant 0.29 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
fgd1 491742 c.960T>C synonymous_variant 0.79 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.7 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.64 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.6 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.57 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.48 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.52 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254580 c.-46C>G upstream_gene_variant 0.45 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
katG 2154724 p.Arg463Leu missense_variant 0.52 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.7 pyrazinamide Not assoc w R
PPE35 2170461 p.Gly51Glu missense_variant 0.66 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.63 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.56 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.77 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.7 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
thyA 3073868 p.Thr202Ala missense_variant 0.43 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.37 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.3 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.37 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.64 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4241539 c.1677T>C synonymous_variant 0.3 ethambutol Not assoc w R - Interim
embC 4241562 p.Arg567His missense_variant 0.74 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.63 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326113 p.Pro454Leu missense_variant 0.29 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.73 streptomycin Not assoc w R
gid 4408150 p.Leu18His missense_variant 0.37 streptomycin
gid 4408156 p.Leu16Arg missense_variant 0.37 streptomycin Not assoc w R