Finding genetic variation in Ensembl, demo

Demo: The gene tab

View all variants within a gene sequence

In any of the sequence views shown in the Gene and Transcript tabs, you can view variants on the sequence. You can do this by clicking on Configure this page from any of these views.

Let’s take a look at the Gene sequence view for TraesCS4A02G446800 in wheat. Search for TraesCS4A02G446800 and go to the Sequence view.

If you can’t see variants marked on this view, click on Configure this page and select Show variants: Yes and show links.

Find out more about a variant by clicking on it.

You can add variants to all other sequence views in the same way.

You can go to the Variation tab by clicking on the variant ID. For now, we’ll explore more ways of finding variants.

View all variants within a gene in tabular format

To view all the sequence variations in table form, click the Variant table link at the left of the gene tab

You can filter the table to only show the variants you’re interested in. For example, click on Consequences: All, then select the variant consequences you’re interested in.

You can also filter by other columns such as, Evidence or Class.

Demo: The location tab

Visualise variants within a region

Let’s have a look at variants in the Location tab. Click on the Location tab in the top bar.

Configure this page and open Variation from the left-hand menu.

There are various options for turning on variants. You can turn on variants by source, by frequency, presence of a phenotype or by individual genome they were isolated from. Turn on the following all sequence variants in Normal.

Click on a variant to find out more information. It may be easier to see the individual variants if you zoom in.

Demo: The variant tab

Variant summary

Let’s have a look at a specific variant. The easiest way to find a specific variant is to search for it. Search for BA00249348 and click through to the Variant tab.

Variant consequences specific features

The icons show you what information is available for this variant. Click on Genes and regulation, or follow the link at the left.

This variant is found in TraesCS4A02G446800 only.

Genotype frequency

Let’s look at population genetics. Either click on Explore this variant in the left hand menu then click on the Genotype frequency icon, or click on Genotype frequency in the left-hand menu.

Genotype frequency

We can see which strains these genotypes were observed in by going to Sample Genotypes.