TB-Profiler result

Run: SRR28351185
Summary

Run ID: SRR28351185

Sample name:

Date: 2024-05-22T10:21:08.371650

Number of reads: 5474971

Percentage reads mapped: 99.68

Median coverage: 161.0

Strain: lineage2.2.1.1;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: RR-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 0.25
lineage2 East-Asian RD105 0.65
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.67
lineage2.2 East-Asian (Beijing) RD105;RD207 0.63
lineage4 Euro-American None 0.38
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.3
lineage4.3.4 Euro-American (LAM) RD174 0.22
lineage4.3.4.2 Euro-American (LAM) RD174 0.27
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.61
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
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
rpoB 761095 p.Leu430Pro missense_variant 0.76 rifampicin 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
gyrB 6140 p.Val301Leu missense_variant 0.3 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 0.56 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.57 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.77 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.55 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.56 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.57 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.27 rifampicin Not assoc w R
rpoC 767083 c.3714C>T synonymous_variant 0.2 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
mmpL5 776100 p.Thr794Ile missense_variant 0.66 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.69 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.62 clofazimine
bedaquiline
rpsL 781301 c.-259C>T upstream_gene_variant 0.67 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.59 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.57 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.56 pyrazinamide Not assoc w R - Interim
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 0.75 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.63 pyrazinamide Not assoc w R
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.6 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.69 amikacin Not assoc w R
kanamycin Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.19 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.65 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.62 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.3 cycloserine
alr 3840869 c.552C>G synonymous_variant 0.32 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.23 pyrazinamide Not assoc w R
embC 4239274 c.-589C>G upstream_gene_variant 0.14 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.64 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.61 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.65 ethambutol Not assoc w R
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 4407588 c.615A>G synonymous_variant 0.53 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.63 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.21 streptomycin Not assoc w R