Exploring sequence variant annotation in Atlantic salmon
(a) Find the ox2g gene for Atlantic salmon and go to the Variation table page. What is the variation name for D374H variant from EVA study PRJEB34225?
(b) Is this variant a missense variant (a Sequence Ontology term) for all transcripts that have been annotated for the ox2g gene?
(c) Why does Ensembl put the G allele first (G/C)?
(d) How many sample genotypes are available for this variant? Do all samples have the same genotype?
(a) Go to the Ensembl species page for Atlantic salmon and search for ox2g.
In the Variation Table, type e.g. 374 and/or D/H in the Filter text box.
The variation name for D374H is 21:28064636:G_C:PRJEB34225.
(b) Click on 21:28064636:G_C:PRJEB34225.
No, 21:28064636:G_C:PRJEB34225 is missense for three ox2g transcripts (ENSSSAT00000055888.2, ENSSSAT00000055982.2, ENSSSAT00000214738.1). It has the intron variant consequence for two ox2g transcripts (ENSSSAT00000195834.1 and ENSSSAT00000055943.2). Note: ox2g has five transcripts (https://feb2023.archive.ensembl.org/Salmo_salar/Gene/Variation_Gene/Table?db=core;g=ENSSSAG00000039791;r=21:27997093-28104998;source=PRJEB34225;v=21:28064636:G_C:PRJEB34225;vdb=variation;vf=21:28064636:G_C:PRJEB34225).
(c) In Ensembl, the allele that is present in the reference genome assembly is put first, i.e. G. In the literature normally the major allele (in the population of interest) is put first. In the case of 21:28064636:G_C:PRJEB34225 the allele in the reference genome is the major allele in all populations studied (Gaspe of New Brunswick, Penobscot River, St. John River).
(d) Click on Sample genotypes on the left menu.
This variant has 80 sample genotypes. It has 16 homozygous G/G genotypes in Gaspe of New Brunswick, 11 homozygous G/G in Penobscot River and in St. John River population, two of the 53 samples have heterozygous G/C genotype and the rest have homozygous G/G genotype. This information comes from EVA study PRJEB34225.
