TB-Profiler result

Run: 9b9a54ce-96e9-400e-8272-095e2af9d718
Summary

Run ID: 9b9a54ce-96e9-400e-8272-095e2af9d718

Sample name:

Date: 27-02-2023 12:56:38

Number of reads: 1504295

Percentage reads mapped: 98.91

Median coverage: 49

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Pre-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.Met306Val Assoc w R
pyrazinamide pncA p.Ile133Thr Assoc w R
moxifloxacin gyrA p.Ser91Pro Assoc w R
levofloxacin gyrA p.Ser91Pro Assoc w R
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rpsL p.Lys43Arg Assoc w R
amikacin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
clofazimine
ethionamide
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 7572 p.Ser91Pro 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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin Assoc w R
capreomycin Assoc w R
aminoglycosides Uncertain significance
amikacin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R
pncA 2288844 p.Ile133Thr missense_variant 1.0 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 1.0 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 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 0.98 capreomycin Uncertain significance
amikacin Uncertain significance
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 764817 p.Val483Gly missense_variant 1.0 rifampicin
rpoC 766645 p.Glu1092Asp missense_variant 1.0 rifampicin Uncertain significance
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
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 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1473927 n.270C>T non_coding_transcript_exon_variant 0.18 linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.17 linezolid Uncertain significance
rrl 1474948 n.1291C>T non_coding_transcript_exon_variant 0.13 linezolid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol
aftB 4267635 p.Arg401Gln missense_variant 0.11 capreomycin
amikacin
aftB 4267647 p.Asp397Gly missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
aftB 4267889 c.948C>T synonymous_variant 0.13 capreomycin
amikacin
aftB 4268862 c.-26G>A upstream_gene_variant 0.12 capreomycin
amikacin
ethA 4326450 p.Thr342Ala missense_variant 1.0 ethionamide 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 0.98 streptomycin Uncertain significance