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VEP in Ensembl Bacteria

In Ensembl Bacteria the genome for Bacteroides fragilis 638R and launch the VEP tool. Use VEP to predict the effects of a 7 bp deletion of TCTACAA on the supercontig FQ312004 at the position 258140-258146. Use the results to answer the following questions:

  1. How many genes does the indel overlap? What are their gene symbols?

  2. What is the most common consequence of the variant?

  3. What is the most severe consequence? What gene does it affect and what does it do?

Type Bacteroides fragilis 638R into the species search box, then select the genome. You are now in the species information page. Click on Variant Effect Predictor at the bottom left. Next, you want to make sure your variant is in one of VEP’s supported variant formats. We have converted the variant into the Ensembl default VEP format. You can enter the following into the input box: FQ312004 258140 258146 TCTACAA/- +

Make sure you name your VEP job something descriptive, so it’s easier for you to find later on. Click Run to get the results.

  1. Find the number of overlapped genes in the Summary statistics. You can find their gene symbols under the Symbol column in the table below.

    The indel overlaps 14 different genes. 12 have the following symbols assigned to them: traA, traD, traE, traF, traG, traI, traJ, traK, traL, traM, traN and traO. 2 genes do not have a gene symbol.

  2. Sort the table by Consequence by clicking on the column name.

    The most common consequences are downstream_gene_variant (n=6) and upstream_gene_variant (n=6).

  3. You can find a list of calculated consequences sorted by severity in the [Ensembl Variation documentation](https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html#consequences).

    According to the calculated variant consequence list, the most severe consequence is frameshift_variant on the traI gene. The gene is a putative conjugative transposon protein traI.