TB-Profiler result

Run: ERR181686
Summary

Run ID: ERR181686

Sample name:

Date: 2024-04-15T11:09:55.727900

Number of reads: 3651586

Percentage reads mapped: 99.79

Median coverage: 82.0

Strain: lineage3.1.1;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.07
lineage4.3 Euro-American (LAM) None 0.88
lineage3.1.1 East-African-Indian RD750 0.08
lineage4 Euro-American None 0.9
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.9
lineage4.3.4 Euro-American (LAM) RD174 0.9
lineage4.3.4.2 Euro-American (LAM) RD174 0.9
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
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
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 6140 p.Val301Leu missense_variant 0.92 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
rpoB 762434 c.2628T>G synonymous_variant 0.18 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.1 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.87 rifampicin Not assoc w R
rpoC 767083 c.3714C>T synonymous_variant 0.86 rifampicin Not assoc w R - Interim
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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.11 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
PPE35 2170461 p.Gly51Glu missense_variant 0.19 pyrazinamide 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
pncA 2289047 c.195C>T synonymous_variant 0.11 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.14 pyrazinamide
thyA 3073868 p.Thr202Ala missense_variant 0.94 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.93 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.93 cycloserine
alr 3840869 c.552C>G synonymous_variant 0.86 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.88 pyrazinamide Not assoc w R
embC 4240172 p.Val104Met missense_variant 0.12 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.11 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245286 p.Leu685Ser missense_variant 0.12 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 0.92 streptomycin Not assoc w R