TB-Profiler result

Run: SRR28389852
Summary

Run ID: SRR28389852

Sample name:

Date: 2024-05-22T19:15:04.448489

Number of reads: 4313096

Percentage reads mapped: 99.46

Median coverage: 123.5

Strain: lineage2.2.1.1;lineage4.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.53
lineage4.1 Euro-American None 0.47
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.5
lineage2.2 East-Asian (Beijing) RD105;RD207 0.48
lineage4 Euro-American None 0.49
lineage4.1.1 Euro-American (X-type) None 0.48
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.49
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid ddn p.Leu49Pro Assoc w R - Interim
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
ddn 3986989 p.Leu49Pro missense_variant 0.43 delamanid Assoc w R - Interim
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
dnaA 414 c.414G>A synonymous_variant 0.52 isoniazid 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 0.99 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 13526 c.33G>C synonymous_variant 0.5 isoniazid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.51 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.57 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.52 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.5 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.58 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.5 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.5 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.44 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 0.46 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.45 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.53 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.48 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.51 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 0.57 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472687 n.842A>G non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473084 n.1239T>C non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.4 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 0.64 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.54 pyrazinamide Not assoc w R
PPE35 2170894 c.-282C>T upstream_gene_variant 0.49 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.49 amikacin Not assoc w R
kanamycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568431 c.249C>G synonymous_variant 0.17 streptomycin
amikacin
kanamycin
Rv3236c 3612229 c.888C>T synonymous_variant 0.42 pyrazinamide Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.55 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 0.44 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4238992 c.-871C>A upstream_gene_variant 0.48 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.52 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.46 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.39 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.45 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.5 ethambutol Not assoc w R
ethR 4328030 p.Ala161Gly missense_variant 0.15 ethionamide
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 0.51 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.52 streptomycin Not assoc w R
gid 4408406 c.-204A>G upstream_gene_variant 0.42 streptomycin