TB-Profiler result

Run: SRR25206857
Summary

Run ID: SRR25206857

Sample name:

Date: 2024-10-03T23:14:14.425725

Number of reads: 10610070

Percentage reads mapped: 99.54

Median coverage: 373.0

Strain: lineage2.2.1;lineage4.2

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 0.83
lineage4.2 Euro-American None 0.17
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.83
lineage2.2 East-Asian (Beijing) RD105;RD207 0.83
lineage4 Euro-American None 0.17
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 rpsL p.Lys43Arg 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
rpsL 781687 p.Lys43Arg missense_variant 0.82 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.84 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.82 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.82 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.85 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.84 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.8 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.85 rifampicin Not assoc w R
rpoC 765148 c.1779C>T synonymous_variant 0.17 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 776100 p.Thr794Ile missense_variant 0.78 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.82 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 778453 p.Thr10Ala missense_variant 0.16 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781512 c.-48A>G upstream_gene_variant 0.15 streptomycin
rplC 800204 c.-605T>C upstream_gene_variant 0.17 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.84 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 0.81 pyrazinamide Not assoc w R - Interim
tsnR 1853631 p.Val9Glu missense_variant 0.18 linezolid
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 2063685 c.1044G>A synonymous_variant 0.17 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.16 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.84 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.84 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 2715707 c.-375C>T upstream_gene_variant 0.81 kanamycin
amikacin
Rv2477c 2783242 c.801C>T synonymous_variant 0.18 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
ald 3086742 c.-78A>C upstream_gene_variant 0.13 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339343 p.Gly76Ser missense_variant 0.14 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fbiD 3339349 p.Asp78Asn missense_variant 0.14 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv3083 3449771 p.Pro423Leu missense_variant 0.15 ethionamide Uncertain significance
Rv3236c 3612320 p.Leu266Pro missense_variant 0.16 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.87 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 0.86 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.83 ethambutol Not assoc w R
embA 4244079 p.Val283Ile missense_variant 0.16 ethambutol
embB 4246433 c.-81T>C upstream_gene_variant 0.17 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.87 ethambutol Not assoc w R
ethA 4328322 c.-849G>A upstream_gene_variant 0.19 ethionamide
whiB6 4338309 c.213T>C synonymous_variant 0.17 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
whiB6 4338505 p.Ala6Glu missense_variant 0.18 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 0.86 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.82 streptomycin Not assoc w R