Ensembl TrainingEnsembl Home

<- Back to exercise page

VEP for turkey data

My GWAS and sequencing experiments of two groups of turkeys (wild versus domesticated) have identified a few variants associated with body size:

chr 3, genomic coordinate 71541903, alleles C/A, forward strand
chr 18, genomic coordinate 24867, alleles G/A, forward strand
chr 23, genomic coordinate 153938, alleles C/T, forward strand
chr 22, genomic coordinate 10699690, alleles C/G, forward strand
chr 1, genomic coordinate 48884151, alleles A/G, forward strand

(a) Which genes and transcripts do these variants map to?

(b) What are the consequence terms for these variants?

(c) What is the most frequent coding consequence observed in this list?

Go to the Variant Effect Predictor (VEP) under Tools on the top banner of any Ensembl page.

Copy the following into the Paste data text box:

3 71541903 71541903 C/A
18 24867 24867 G/A
23 153938 153938 C/T
22 10699690 10699690 C/G
1 48884151 48884151 A/G

Note that this is the Ensembl default format (chr start end reference/alternate alleles). For additional formats accepted by VEP, have a look here: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html

Click Run.

(a) In the Results table, you’ll see that the variants fall into nine genes (one is intergenic).

(b) The consequence terms are listed in the Consequence column and Consequences (all) chart and include intron_variant, upstream_gene_variant, missense_variant, and downstream_gene_variant.

(c) The most frequent coding consequence is missense_variant. This is shown in one of the pie charts above the table.