TB-Profiler result

Run: 40bc83ad-4d4b-426c-ab05-9d63da5cfb99
Summary

Run ID: 40bc83ad-4d4b-426c-ab05-9d63da5cfb99

Sample name:

Date: 15-03-2023 12:51:56

Number of reads: 1036918

Percentage reads mapped: 98.88

Median coverage: 28

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: XDR-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 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 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
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
moxifloxacin gyrA p.Ala90Val Assoc w R
levofloxacin gyrA p.Ala90Val Assoc w R
bedaquiline
delamanid
pretomanid
linezolid rplC p.Cys154Arg Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
amikacin
kanamycin eis c.-12C>T Assoc w R
capreomycin
clofazimine
ethionamide ethA c.110delA Assoc w R
c.110delA Uncertain significance
para-aminosalicylic_acid
cycloserine
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin Uncertain significance
moxifloxacin Assoc w R
levofloxacin Assoc w R
fluoroquinolones Uncertain significance
ciprofloxacin Uncertain significance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 1.0 linezolid Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin Assoc w R
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol Assoc w R
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide Assoc w R
ethionamide Uncertain significance
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 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
ccsA 620748 c.858T>G synonymous_variant 0.4 capreomycin
amikacin
rpoB 760504 p.Lys233Met missense_variant 0.11 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 764703 p.Lys445Arg missense_variant 1.0 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpR5 779242 p.Val85Phe missense_variant 1.0 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471656 n.-190G>C upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12 ethionamide
isoniazid
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12 ethionamide
isoniazid
fabG1 1673357 c.-83G>A upstream_gene_variant 0.13 ethionamide
isoniazid
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14 ethionamide
isoniazid
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14 ethionamide
isoniazid
fabG1 1673380 c.-60C>G upstream_gene_variant 0.34 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.31 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.29 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
eis 2715477 c.-145G>C upstream_gene_variant 0.18 kanamycin
amikacin
ald 3086731 c.-89A>G upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Uncertain significance
fbiA 3640390 c.-153A>G upstream_gene_variant 1.0 delamanid
alr 3840812 c.609T>G synonymous_variant 1.0 cycloserine
rpoA 3878599 c.-92C>G upstream_gene_variant 0.18 rifampicin
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embB 4246544 p.Thr11Pro missense_variant 0.5 ethambutol Uncertain significance
embB 4246567 c.54_55insT frameshift_variant 0.26 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
ethA 4328372 c.-899C>T upstream_gene_variant 0.12 ethionamide
whiB6 4338371 p.Thr51Pro missense_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Uncertain significance
gid 4408021 p.Arg61His missense_variant 0.11 streptomycin