TB-Profiler result

Run: SRR15369010
Summary

Run ID: SRR15369010

Sample name:

Date: 2024-10-05T14:23:44.778712

Number of reads: 6543033

Percentage reads mapped: 84.63

Median coverage: 183.0

Strain: lineage2.2.1.1;lineage4.5

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.21
lineage2 East-Asian RD105 0.8
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.79
lineage2.2 East-Asian (Beijing) RD105;RD207 0.82
lineage4 Euro-American None 0.21
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.81
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
inhA 1673425 c.-777C>T upstream_gene_variant 0.24 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer 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 7892 c.591G>A synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 0.83 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.8 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.23 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.79 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.8 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.81 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.8 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 0.79 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.78 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776964 p.Thr506Ile missense_variant 0.73 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.81 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 0.77 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303026 c.96G>A synonymous_variant 0.21 pretomanid
delamanid
clofazimine
Rv1258c 1406760 c.580_581insC frameshift_variant 0.8 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833734 p.Ala65Thr missense_variant 0.21 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.75 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 0.8 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.79 pyrazinamide Not assoc w R
PPE35 2168605 p.Pro670Ser missense_variant 0.23 pyrazinamide
PPE35 2170568 p.Ile15Met missense_variant 0.26 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
kasA 2518871 p.His253Tyr missense_variant 0.8 isoniazid
eis 2714211 c.1122G>A synonymous_variant 0.23 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.86 kanamycin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.81 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8 pyrazinamide Not assoc w R - Interim
lpqB 3623269 p.Ala548Thr missense_variant 0.78 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.74 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038318 p.Pro796Leu missense_variant 0.2 pyrazinamide Not assoc w R
clpC1 4040654 c.51G>A synonymous_variant 0.17 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.77 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.81 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.81 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 4338646 c.-125A>G upstream_gene_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.75 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.76 streptomycin Not assoc w R