VEP analysis of variants in Verticillium dahliae
Verticillium wilt caused by Verticillium dahliae is a notorious soil-borne fungal disease that threatens the yield of economic crops worldwide. We have identified four variants in Verticillium dahliae JR2 chromosome 5:
- C->G at 698711
- G->T at 698935
- G->A at 700313
- C->A at 701484
Use VEP in Ensembl Fungi to answer the following questions:
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Have these variants already been annotated in Ensembl?
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What genes are affected by the variants? What are their gene IDs?
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Are any of the variants predicted to be missense variants?
Go to any Ensembl Fungi page and click on Tools in the navigation bar at the top of the page. Click on Variant Effect Predictor and change your species to Verticillium dahliae JR2 by clicking on Change species.
Enter a descriptive name for your VEP job. You will need to convert your variants into one of VEP’s supported input formats. We have converted the variants into the Ensembl default format below. Paste the variants into Input data:.
5 698711 698711 C/G
5 698935 698935 G/T
5 700313 700313 G/A
5 701484 701484 C/A
Click Run at the bottom of the page. When your job is done, click View reesults.
- You can find the number of existing and novel variants in the Summary statistics of the results.
4 variants were analysed, of which 3 are novel.
- You can also find the number of overlapped genes in the Summary statistics.
4 genes are affected.
Sort the table by Gene by clicking on the column name. Count the number of unique gene IDs.
The gene IDs are: VDAG_JR2_Chr5g02150a, VDAG_JR2_Chr5g02160a, VDAG_JR2_Chr5g02170a and VDAG_JR2_Chr5g02171a.
- Filter the table as follows: Consequence
is missense_variant.Yes, the third variant (5_700313_G/A) is predicted to have a missense effect on gene VDAG_JR2_Chr5g02170a.
