Ensembl Variation Database Description

About Variation Data | Database Description | Variation Sources | Variation Tables Description | Perl API

Database Description

The Ensembl Variation database stores two types of variation data, depending it comes from an external source or data it is calculated on site.


Database Schema

The tables of the database are described in the Variation Tables Description page.
The database schema is described in the following pdf.


Database Load

The variations databases can be loaded using dumped files from the Ensembl FTP.
For Ensembl 61, it takes a couple of minutes to load the largest tables for Human on our servers, e.g:

TableLoading time
variation24 minutes
variation_feature13 minutes
flanking_sequence3 minutes
compressed_genotype_single_bp13 minutes
population_genotype30 minutes

The load of the largest table in the Human variation database (allele table) takes almost 3 hours.

See below some settings of our server:

VariableValue
myisam_data_pointer_size6
myisam_max_sort_file_size9223372036853727232
myisam_recover_optionsOFF
myisam_repair_threads1
myisam_sort_buffer_size67108864
myisam_stats_methodnulls_unequal
myisam_use_mmapOFF

Ensembl Software Support

Ensembl is an open project and we would like to encourage correspondence and discussions on any subject on any aspect of Ensembl. Please see the Ensembl Contacts page for suitable options getting in touch with us.