Ensembl Variation Schema Documentation

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

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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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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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A table consisting simply of sample_ids representing populations; all data relating to the populations are stored in separate tables (see below).

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

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

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

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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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This table relates a variation_feature to a transcript (see Core documentation). It contains the consequence of the variation e.g. intronic, non-synonymous coding, stop etc, along with the change in amino acid in the resulting protein if applicable.

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

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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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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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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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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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This table holds uncompressed genotypes for given variations.

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

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

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

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

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