TB-Profiler result

Run: ERR11082273
Summary

Run ID: ERR11082273

Sample name:

Date: 2024-10-05T05:18:02.392016

Number of reads: 5837317

Percentage reads mapped: 99.63

Median coverage: 169.0

Strain: lineage2.2.1;lineage4.7

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 0.54
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.58
lineage2.2 East-Asian (Beijing) RD105;RD207 0.58
lineage4.7 Euro-American (mainly T) None 0.43
lineage4 Euro-American None 0.44
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.Tyr319Cys Assoc w R
pyrazinamide pncA p.Gln10Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
ethionamide ethA p.Tyr140* Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.61 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.6 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.56 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.53 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Pro missense_variant 0.57 pyrazinamide Assoc w R
embB 4247469 p.Tyr319Cys missense_variant 0.54 ethambutol Assoc w R
ethA 4327054 p.Tyr140* stop_gained 0.57 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 6358 c.1119C>T synonymous_variant 0.48 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.61 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.52 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.57 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.62 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.57 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.49 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.47 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.57 rifampicin Not assoc w R
rpoC 766744 p.Gln1125His missense_variant 0.57 rifampicin Uncertain significance
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 0.49 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.51 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.54 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 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.56 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.36 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.61 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.52 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 0.57 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.6 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
ald 3086731 c.-89A>G upstream_gene_variant 0.55 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.53 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.57 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.48 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.59 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4240768 c.906G>A synonymous_variant 0.51 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.57 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.47 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.5 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.63 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.53 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin 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 4338732 c.-211C>T upstream_gene_variant 0.54 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.62 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.56 streptomycin Not assoc w R