Web VEP analysis of variants in Oryza sativa Japonica (rice)
You’ll find a VCF file here. This is a small subset of the outcome of Oryza sativa Japonica whole-genome sequencing and variant-calling experiment. Analyse the variants in this file with the VEP tool in Ensembl Plants and determine the following:
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How many genes and transcripts are affected by variants in this file?
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Do these variants result in a change in the proteins encoded by any of the Ensembl genes? Which genes are affected? What is the amino acid change? What is the pathogenicity prediction score for this change?
Go to Ensembl Plants and click on Tools at the top of the page. Click on Variant Effect Predictor and select Oryza sativa Japonica Group from the Species menu.
Either click on Choose file and select the file to upload it, or directly paste the URL into the Or provide file URL: box. Click Run at the bottom of the page. When your job is done, click View results.
- The number of affected genes and transcripts is shown in the Summary statistics table at the top.
8 genes and 8 transcripts are affected by these variants.
- 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_variantinto the boxe. Add to apply your filter.1 variant is a missense variant. It causes a leucine to arginine (L/R) at position 16 change in the gene OS09G0103500. The SIFT score is 0.01 (Deleterious low confidence). Refere to this link for more information on SIFT (https://sift.bii.a-star.edu.sg/).
