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VEP analysis of rice variants

You’ll find a VCF file here. This is a small subset of the outcome of Oryza sativa Japonica Group whole genome sequencing and variant calling experiment.

Analyse the variants in this file with the VEP and determine:

(a) How many genes and transcripts are affected by variants in this file?

(b) Do these variants result in a change in the proteins encoded by any of the Ensembl genes? What genes? What is the amino acid change?

Go to plants.ensembl.org and click on the link Tools at the top of the page. Click on Variant Effect Predictor and select Species: Oryza sativa Japonica Group.

Either click on Choose file and select the file to upload it, or paste the URL for the file into the Or provide file URL: box.

Click Run at the bottom of the page.

When your job is listed as Done, click View Results.

(a) The number of affected genes and transcripts is shown in the summary table at the top.

Eight genes and eight transcripts are affected by these variants.

(b) Use the filters to view only missense variants. The filters are found above the detailed results table in the middle.

Select Consequence and is from the drop-down menus. Then type missense_variant into the box; this will autocomplete. Click Add.

One variant is a missense variant. It causes an L/R change in the gene OS09G0103500.