TB-Profiler result

Run: SRR8692805
Summary

Run ID: SRR8692805

Sample name:

Date: 2024-10-04T22:28:17.629678

Number of reads: 2407160

Percentage reads mapped: 89.1

Median coverage: 65.0

Strain: lineage2.2.1;lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.09
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.07
lineage2.2 East-Asian (Beijing) RD105;RD207 0.15
lineage4 Euro-American None 0.85
lineage4.9 Euro-American (H37Rv-like) None 0.86
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 rplC p.Cys154Arg Assoc w R
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
rplC 801268 p.Cys154Arg missense_variant 0.88 linezolid 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
fgd1 491742 c.960T>C synonymous_variant 0.18 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.13 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.13 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.19 rifampicin Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.15 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.2 bedaquiline Not assoc w R
clofazimine Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406686 p.Val219Ile missense_variant 0.89 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 0.17 capreomycin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.11 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.3 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 0.17 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4407588 c.615A>G synonymous_variant 0.24 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.18 streptomycin Not assoc w R