Ensembl Variation Tables Description

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

Introduction

This document gives a high-level description of the tables that make up the Ensembl variation schema. Tables are listed by alphabetical order, and the purpose of each table is explained. It is intended to allow people to familiarise themselves with the schema when encountering it for the first time, or when they need to use some tables that they've not used before.

This document refers to version 63 of the Ensembl variation schema.

A PDF document of the schema is available here.
A colour legend is available at the bottom of the page.



List of the tables:



allele Show columns

This table stores information about each of a variation's alleles, along with population frequencies.

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allele_group Show columns

This table, along with allele_group_allele, represents a particular multi-marker allele of a given multi-marker variation, or haplotype. It stores an associated population frequency.

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allele_group_allele Show columns

This table represents an allele of one variation in a multi-marker variation, or haplotype. It stores a string of the allele.

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associate_study Show columns

This table contains identifiers of associated studies (e.g. NHGRI and EGA studies with the same pubmed identifier).

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attrib Show columns

Defines various attributes used elsewhere in the database

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attrib_set Show columns

Groups related attributes together

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attrib_type Show columns

Defines the set of possible attribute types used in the attrib table

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compressed_genotype_single_bp Show columns

This table holds genotypes compressed using the pack() method in Perl. These genotypes are mapped to particular genomic locations rather than variation objects. The data have been compressed to reduce table size and increase the speed of the web code.

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failed_allele Show columns

Contains alleles that did not pass the Ensembl filters

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failed_description Show columns

This table contains descriptions of reasons for a variation being flagged as failed.

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failed_variation Show columns

For various reasons it may be necessary to store information about a variation that has failed quality checks in the Variation pipeline. This table acts as a flag for such failures.

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flanking_sequence Show columns

This table contains the upstream and downstream sequence surrounding a variation. Since each variation is defined by its flanking sequence, this table has a one-to-one relationship with the variation table.

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httag Show columns

This table represents the equivalent of a tagged_variation_feature for multi-marker variations, representing an instance where a haplotype is tagged by or tags another marker.

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individual Show columns

Stores information about an identifiable individual, including gender and the identifiers of the individual's parents (if known).

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individual_genotype_multiple_bp Show columns

This table holds uncompressed genotypes for given variations.

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individual_population Show columns

This table resolves the many-to-many relationship between the individual and population tables; i.e. samples may belong to more than one population. Hence it is composed of rows of individual and population identifiers.

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individual_type Show columns

This table resolves the many-to-many relationship between the individual and population tables; i.e. samples may belong to more than one population. Hence it is composed of rows of individual and population identifiers.

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meta Show columns

This table stores various metadata relating to the database, generally used by the Ensembl web code.


meta_coord Show columns

This table gives the coordinate system used by various tables in the database.


phenotype Show columns

This table stores details of the phenotypes associated with variation annotations.

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polyphen_prediction Show columns

Stores the PolyPhen 2 prediction for every possible amino acid substitution in the ensembl proteome

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population Show columns

A table consisting simply of sample_ids representing populations; all data relating to the populations are stored in separate tables (see below).
A population may be an ethnic group (e.g. caucasian, hispanic), assay group (e.g. 24 europeans), strain, phenotypic group (e.g. blue eyed, diabetes) etc. Populations may be composed of other populations by defining relationships in the population_structure table.

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population_genotype Show columns

This table stores alleles and frequencies for variations in given populations.

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population_structure Show columns

This table stores hierarchical relationships between populations by relating them as populations and sub-populations.

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protein_info Show columns

Contains information about each translation in the ensembl proteome, used by the nsSNP prediction tables

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protein_position Show columns

Table with a row for each position in every ensembl translation, used by the nsSNP prediction tables

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read_coverage Show columns

This table stores the read coverage in the resequencing of individuals. Each row contains an individual ID, chromosomal coordinates and a read coverage level.

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sample Show columns

Sample is used as a generic catch-all term to cover individuals, populations and strains; it contains a name and description, as well as a size if applicable to the population.

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sample_synonym Show columns

Used to store alternative names for populations when data comes from multiple sources.

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seq_region Show columns

This table stores the relationship between Ensembl's internal coordinate system identifiers and traditional chromosome names.

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sift_prediction Show columns

Stores the SIFT prediction for every possible amino acid substitution in the ensembl proteome

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source Show columns

This table contains details of the source from which a variation is derived. Most commonly this is NCBI's dbSNP; other sources include SNPs called by Ensembl.

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structural_variation Show columns

This table stores information about structural variation features.

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study Show columns

This table contains details of the studies. The studies information can come from internal studies (DGVa, EGA) or from external studies (Uniprot, NHGRI, ...).

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subsnp_handle Show columns

This table contains the SubSNP(ss) ID and the name of the submitter handle of dbSNP.

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supporting_structural_variation Show columns

This table stores the name of the supporting evidence for the structural variants (e.g. DGVa structural variants).

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tagged_variation_feature Show columns

This table lists variation features that are tagged by another variation feature. Tag pairs are defined as having an r2 > 0.99.

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tmp_individual_genotype_single_bp Show columns

his table is only needed for create master schema when run healthcheck system. Needed for other species, but human, so keep it.

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transcript_variation Show columns

This table relates a single allele of a variation_feature to a transcript (see Core documentation). It contains the consequence of the allele e.g. intron_variant, non_synonymous_codon, stop_lost etc, along with the change in amino acid in the resulting protein if applicable.

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variation Show columns

This is the schema's generic representation of a variation, defined as a genetic feature that varies between individuals of the same species.The most common type is the single nucleotide variation (SNP) though the schema also accommodates copy number variations (CNVs) and structural variations (SVs).A variation is defined by its flanking sequence rather than its mapped location on a chromosome; a variation may in fact have multiple mappings across a genome.This table stores a variation's name (commonly an ID of the form e.g. rs123456, assigned by dbSNP), along with a validation status and ancestral (or reference) allele.

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variation_annotation Show columns

This table stores information linking genotypes and phenotypes. It stores various fields pertaining to the study conducted, along with the associated gene, risk allele frequency and a p-value.

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variation_feature Show columns

This table represents mappings of variations to genomic locations. It stores an allele string representing the different possible alleles that are found at that locus e.g. "A/T" for a SNP, as well as a "worst case" consequence of the mutation. It also acts as part of the relationship between variations and transcripts.

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variation_group Show columns

This table represents the equivalent of a variation for a multi-marker variation.

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variation_group_feature Show columns

This table represents the equivalent of a variation_feature for multi-marker variations, mapping a haplotype to a chromosomal coordinate system.

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variation_group_variation Show columns

This table represents an individual variation that makes up a multi-marker variation, and resolves the many-to-many relationship between variation and variation_group.

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variation_set Show columns

This table containts the name of sets and subsets of variations stored in the database. It usually represents the name of the project or subproject where a group of variations has been identified.

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variation_set_structure Show columns

This table stores hierarchical relationships between variation sets by relating them as variation sets and variation subsets.

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variation_set_variation Show columns

A table for mapping variations to variation_sets.

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variation_synonym Show columns

This table allows for a variation to have multiple IDs, generally given by multiple sources.

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Colour legend

Other tables
Tables containing individual data
Tables containing sets of variations
Tables containing source and study data
Tables containing metadata
Tables containing "failed" data
Tables containing attribute data
Tables concerning protein data