TB-Profiler result

Run: ERR12916919
Summary

Run ID: ERR12916919

Sample name:

Date: 2024-05-22T10:27:56.572822

Number of reads: 9110853

Percentage reads mapped: 99.54

Median coverage: 251.0

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
lineage2.2.1 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
rpoC p.Asp485Asn Uncertain significance Mutation from literature
isoniazid katG p.Ile335Val Uncertain significance Mutation from literature
p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Ile6Ser Uncertain significance Mutation from literature
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine alr p.Leu113Arg Mutation from literature
ethionamide
clofazimine mmpR5 c.291delC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.291delC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin Assoc w R
rpoC 764822 p.Asp485Asn missense_variant 1.0 rifampicin Uncertain significance Mutation from literature
mmpR5 779277 c.291delC frameshift_variant 0.87 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 1.0 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin Assoc w R
capreomycin Assoc w R
amikacin Assoc w R
katG 2155109 p.Ile335Val missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2289225 p.Ile6Ser missense_variant 1.0 pyrazinamide Uncertain significance Mutation from literature
alr 3841083 p.Leu113Arg missense_variant 1.0 cycloserine Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.99 ethambutol 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
Rv0010c 13632 c.-74A>G upstream_gene_variant 0.15 isoniazid
Rv0010c 13635 c.-77C>T upstream_gene_variant 0.16 isoniazid
Rv0010c 13824 c.-266A>T upstream_gene_variant 0.16 isoniazid
Rv0010c 13829 c.-271T>A upstream_gene_variant 0.18 isoniazid
Rv0010c 13834 c.-276A>T upstream_gene_variant 0.17 isoniazid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 655086 c.139_*923del stop_lost&conservative_inframe_deletion&splice_region_variant 1.0 ethionamide
rpoB 761710 p.Val635Asp missense_variant 0.15 rifampicin
rpoB 761713 p.Val636Asp missense_variant 0.16 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
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 0.98 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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
fbiC 1302917 c.-14_-13insA upstream_gene_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
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
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834776 p.Ala412Val missense_variant 1.0 pyrazinamide Uncertain significance
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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.19 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.21 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289370 c.-129C>A upstream_gene_variant 0.18 pyrazinamide
pncA 2289374 c.-133T>G upstream_gene_variant 0.17 pyrazinamide
pncA 2289375 c.-134C>A upstream_gene_variant 0.18 pyrazinamide
pncA 2289379 c.-138T>G upstream_gene_variant 0.17 pyrazinamide
kasA 2518348 c.234A>T synonymous_variant 0.15 isoniazid
Rv2681 2997962 c.1224A>C synonymous_variant 0.12 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339744 c.627A>C synonymous_variant 0.13 clofazimine
pretomanid
delamanid
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 3640879 c.337C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiA 3641280 p.Ile246Met missense_variant 0.14 clofazimine
pretomanid
delamanid
rpoA 3878567 c.-60C>G upstream_gene_variant 0.33 rifampicin
embC 4239281 c.-582C>G upstream_gene_variant 0.12 ethambutol
embC 4239284 c.-579C>G upstream_gene_variant 0.12 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243598 c.366G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4246544 p.Thr11Pro missense_variant 0.42 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.45 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.43 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.43 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.44 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.41 ethambutol Not assoc w R - Interim
embB 4247872 c.1359C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.99 ethambutol Not assoc w R
ethA 4326474 p.Pro334Ala missense_variant 1.0 ethionamide Uncertain significance
ethA 4327418 p.Ala19Glu missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338326 p.Ala66Thr missense_variant 1.0 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 1.0 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