TB-Profiler result

Run: SRR26399496
Summary

Run ID: SRR26399496

Sample name:

Date: 2024-10-05T02:42:06.487149

Number of reads: 2997305

Percentage reads mapped: 99.51

Median coverage: 93.0

Strain: lineage2.2.1.1;lineage4.4.1.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.67
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.67
lineage2.2 East-Asian (Beijing) RD105;RD207 0.7
lineage4.4.1 Euro-American (S-type) None 0.33
lineage4 Euro-American None 0.33
lineage4.4.1.1 Euro-American None 0.35
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.71
lineage4.4 Euro-American None 0.29
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin gid c.373delC Assoc w R
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
ahpC 2726145 c.-48G>A upstream_gene_variant 0.35 isoniazid Uncertain significance Mutation from literature
gid 4407829 c.373delC frameshift_variant 0.28 streptomycin 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
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 0.68 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.65 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.69 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.7 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.65 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.62 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 0.73 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.74 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.68 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302716 c.-215G>A upstream_gene_variant 0.59 pretomanid
delamanid
clofazimine
Rv1258c 1406760 c.580_581insC frameshift_variant 0.67 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.73 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
bacA 2064691 p.Ser13Cys missense_variant 0.31 kanamycin
capreomycin
streptomycin
amikacin
ndh 2102990 p.Val18Ala missense_variant 0.25 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.64 isoniazid Not assoc w R
katG 2155612 p.Phe167Cys missense_variant 0.34 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.67 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.37 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
eis 2714846 p.Val163Ile missense_variant 0.65 kanamycin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087657 p.Pro280Ser missense_variant 0.68 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.44 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 0.25 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.65 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.75 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.26 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 0.65 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.64 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.6 ethambutol Not assoc w R
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 0.62 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.69 streptomycin Not assoc w R