TB-Profiler result

Run: SRR25827778
Summary

Run ID: SRR25827778

Sample name:

Date: 2024-04-16T11:49:40.519001

Number of reads: 2561106

Percentage reads mapped: 96.41

Median coverage: 86.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Met Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin eis c.-14C>T Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
capreomycin
kanamycin eis c.-14C>T Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide ethA p.Trp240* Assoc w R
clofazimine mmpR5 c.211delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.211delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
mmpR5 779199 c.211delG frameshift_variant 0.65 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.38 streptomycin Assoc w R
rpsL 781822 p.Lys88Met missense_variant 0.71 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.61 linezolid Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289162 p.Leu27Pro missense_variant 0.29 pyrazinamide Assoc w R
eis 2715346 c.-14C>T upstream_gene_variant 0.59 amikacin Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embB 4247429 p.Met306Val missense_variant 0.4 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.62 ethambutol Assoc w R
ethA 4326754 p.Trp240* stop_gained 0.65 ethionamide 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 5078 c.-162_-161insG upstream_gene_variant 0.31 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7581 p.Asp94Ser missense_variant 0.3 levofloxacin
moxifloxacin
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 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.65 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
nusG 734757 c.504T>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.38 rifampicin Uncertain significance
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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.72 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 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 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1673784 c.-418G>T upstream_gene_variant 0.17 ethionamide
isoniazid
inhA 1673787 c.-415G>C upstream_gene_variant 0.18 ethionamide
isoniazid
inhA 1673799 c.-403T>C upstream_gene_variant 0.19 ethionamide
isoniazid
inhA 1673802 c.-400A>G upstream_gene_variant 0.18 ethionamide
isoniazid
inhA 1673808 c.-394A>C upstream_gene_variant 0.18 ethionamide
isoniazid
fabG1 1673829 p.Asn130Lys missense_variant 0.18 ethionamide
isoniazid
fabG1 1673830 p.Lys131Arg missense_variant 0.18 ethionamide
isoniazid
inhA 1673838 c.-364T>C upstream_gene_variant 0.19 ethionamide
isoniazid
inhA 1673841 c.-361A>G upstream_gene_variant 0.19 ethionamide
isoniazid
fabG1 1673844 p.Met135Ile missense_variant 0.18 ethionamide
isoniazid
inhA 1673847 c.-355A>C upstream_gene_variant 0.19 ethionamide
isoniazid
inhA 1673853 c.-349A>C upstream_gene_variant 0.19 ethionamide
isoniazid
inhA 1673856 c.-346T>C upstream_gene_variant 0.18 ethionamide
isoniazid
inhA 1673859 c.-343G>C upstream_gene_variant 0.19 ethionamide
isoniazid
inhA 1673865 c.-337C>G upstream_gene_variant 0.19 ethionamide
isoniazid
fabG1 1673870 p.Ser144Met missense_variant 0.2 ethionamide
isoniazid
inhA 1673877 c.-325C>G upstream_gene_variant 0.2 ethionamide
isoniazid
fabG1 1673905 p.Ser156Ala missense_variant 0.19 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 1.0 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 0.99 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170018 p.Ala199Ser missense_variant 0.68 pyrazinamide
Rv1979c 2221889 p.Val426Ile missense_variant 0.73 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
ribD 2986827 c.-12G>A upstream_gene_variant 0.76 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.4 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 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 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640243 c.-300T>C upstream_gene_variant 0.7 clofazimine
pretomanid
delamanid
fbiA 3640301 c.-242G>A upstream_gene_variant 0.7 clofazimine
pretomanid
delamanid
rpoA 3877969 p.Ala180Val missense_variant 0.76 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4246085 p.Glu951Asp missense_variant 0.65 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.43 ethionamide Uncertain significance
whiB6 4338233 p.Ser97Pro missense_variant 0.72 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 0.99 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R