TB-Profiler result

Run: ERR13266806
Summary

Run ID: ERR13266806

Sample name:

Date: 2024-10-03T17:18:51.306007

Number of reads: 6493158

Percentage reads mapped: 99.65

Median coverage: 175.0

Strain: lineage3;lineage4.5

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 0.24
lineage4.5 Euro-American RD122 0.75
lineage4 Euro-American None 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 0.28 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
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 7892 c.591G>A synonymous_variant 0.75 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 0.25 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.71 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.22 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.26 rifampicin Not assoc w R
rpoB 761465 c.1659G>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.3 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.28 rifampicin Not assoc w R
rpoC 764293 c.924G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776051 p.Leu810Phe missense_variant 0.22 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 0.27 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 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406101 p.Pro414Ser missense_variant 0.78 streptomycin Uncertain significance
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853597 c.-9G>C upstream_gene_variant 0.71 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.99 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918636 p.Pro233Ser missense_variant 0.75 capreomycin Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.26 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.24 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.72 pyrazinamide Not assoc w R
PPE35 2170872 c.-260C>G upstream_gene_variant 0.12 pyrazinamide
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 0.26 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.26 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.32 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.28 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 3074402 p.Thr24Ala missense_variant 0.3 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.25 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626662 c.-49T>A upstream_gene_variant 0.8 rifampicin
bedaquiline
fbiA 3641088 c.546G>T synonymous_variant 0.18 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpoA 3878575 c.-68C>T upstream_gene_variant 0.64 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.75 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.23 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.19 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 4242075 p.Arg738Gln missense_variant 0.24 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243440 c.208C>T synonymous_variant 0.22 ethambutol Not assoc w R - Interim
whiB6 4338365 p.Cys53Gly missense_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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 0.27 streptomycin Not assoc w R
gid 4408057 p.Leu49Arg missense_variant 0.27 streptomycin Uncertain significance