Ensembl Variation - Available species
Species with databases
We currently have 19 vertebrate species with variation databases. A range of different information is available:
| Short variant | Long variant | Genotype | Association | Prediction | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Species | Sequence variant | (e!113 → e!114) | Source(s) | Structural variant | Sample | Population | Phenotype | Citation | SIFT | PolyPhen |
Cat - Abyssinian
Felis catus abyssinian
|
3.2 M | 1 source | - | - | - |  |
- | |
- | |
Cattle
Bos taurus
|
103 M | (+6.8 million) | 1 source | |
|
|
|
|
|
- |
Chicken
Gallus gallus
|
25 M | (-669,000) | 1 source | - | |
|
|
|
|
- |
Chicken (Red Jungle fowl)
Gallus gallus
|
26 M | (-1.1 million) | 1 source | - | - | - | |
|
|
- |
Dog
Canis lupus familiaris
|
46 M | (+8.6 million) | 1 source | |
|
|
|
|
|
- |
Dog - Boxer
Canis lupus familiarisboxer
|
35 M | - | 1 source | |
|
|
|
|
|
- |
Domestic cat
Felis catus
|
3.2 M | (-3,000) | 1 source | - | - | - | |
- | |
- |
Goat
Capra hircus
|
34 M | (-4.2 million) | 1 source | - | |
|
|
|
|
- |
Horse
Equus caballus
|
40 M | (-2,000) | 1 source | |
|
|
|
|
|
- |
Human
Homo sapiens
|
1.1 B | (+246,000) | 4 sources | |
|
|
|
|
|
|
Mouse
Mus musculus
|
125 M | (+3 million) | 1 source | |
|
|
|
|
|
- |
Norway rat - BN/NHsdMcwi
Rattus norvegicus
|
9.5 M | (+179) | 1 source | - | - | - | |
|
|
- |
Opossum
Monodelphis domestica
|
1.1 M | - | 1 source | - | - | - | - | - | - | - |
Pig
Sus scrofa
|
70 M | (-438,000) | 1 source | |
- | - | |
|
|
- |
Platypus
Ornithorhynchus anatinus
|
1.3 M | - | 1 source | - | |
|
- | - | - | - |
Sheep
Ovis aries rambouillet
|
89 M | (+2,000) | 1 source | |
|
|
|
|
|
- |
Sheep (texel)
Ovis aries
|
61 M | - | 1 source | |
|
|
|
|
|
- |
Tetraodon
Tetraodon nigroviridis
|
902 K | - | 1 source | - | - | - | - | - | - | - |
Zebrafish
Danio rerio
|
18 M | (-19,000) | 1 source | |
- | - | |
|
|
- |
Dynamically loaded species
We have extended our API to provide Ensembl views of variant data held at the European Variant Archive ( EVA).- Species supported this way have:
- variant pages showing any available genotypes and allele frequencies
- dynamically predicted gene consequences
- variant tracks by location in the Region in Detail view
- variant tables by location
- They do not have:
- BioMart support
- the option to search by variant name
- variant data in Ensembl VEP caches ( use the custom option for this)
Species supported this way:
We currently have 28 species supported this way:
| Genotype | ||||
|---|---|---|---|---|
| Species | Variant | (e!113 → e!114) | Sample | Population |
American bison
Bison bison bison
|
19 K | - | - | - |
American mink
Neovison vison
|
34 K | - | - | |
Atlantic salmon
Salmo salar
|
15 M | - | |
|
Chimpanzee
Pan troglodytes
|
22 M | - | - | - |
Collared flycatcher
Ficedula albicollis
|
37 K | - | - | - |
Crab-eating macaque
Macaca fascicularis
|
1.6 M | - | - | - |
Domestic yak
Bos grunniens
|
30 M | (+30 million) | - | - |
European seabass
Dicentrarchus labrax
|
37 K | - | - | - |
Gibbon
Nomascus leucogenys
|
1.1 M | - | - | - |
Golden-collared manakin
Manacus vitellinus
|
124 K | (+124,000) | - | - |
Great Tit
Parus major
|
497 K | (-1,000) | |
|
Greater amberjack
Seriola dumerili
|
9 M | (-2,000) | - | - |
Guinea Pig
Cavia porcellus
|
844 K | - | - | - |
Japanese quail
Coturnix japonica
|
8 K | - | - | - |
Macaque
Macaca mulatta
|
50 M | - | - | - |
Mallard
Anas platyrhynchos
|
337 K | - | - | - |
Mouse Lemur
Microcebus murinus
|
129 K | (+129,000) | - | - |
Nile tilapia
Oreochromis niloticus
|
63 K | - | - | |
Northern American deer mouse
Peromyscus maniculatus bairdii
|
81 M | (+81 million) | - | - |
Pike-perch
Sander lucioperca
|
975 K | - | - | - |
Prairie vole
Microtus ochrogaster
|
8 K | - | - | - |
Rabbit
Oryctolagus cuniculus
|
83 K | - | |
|
Rainbow trout
Oncorhynchus mykiss
|
33 K | - | - | - |
Sumatran orangutan
Pongo abelii
|
9.5 M | - | - | - |
Turkey
Meleagris gallopavo
|
5 K | (-2) | - | - |
Vervet-AGM
Chlorocebus sabaeus
|
67 M | - | |
|
White-tufted-ear marmoset
Callithrix jacchus
|
14 M | (-1) | - | - |
Zebra finch
Taeniopygia guttata
|
1.5 M | - | - | - |
Other species
The full list of species in Ensembl, with their assembly versions, is available here.
Note: We only provide variant caches for species with Ensembl databases, but the
Ensembl Variant Effect Predictor can be used to annotate variant data for any species with gene annotation. VCF files can be used directly in Ensembl VEP in place of a variant cache where available.
Restricted access data
Ensembl displays some human variant datasets with restricted access. We make these data visible as tracks on the genome browser, which can be turned on using the 'Configure this page' menu.
LOVD
We display only the high-quality curated data from the LOVD databases.
DECIPHER
We display both structural variants and short variants from DECIPHER. Data provided are only available for display in the browser, and not for bulk download.
Access to bulk data may be obtained directly from DECIPHER (https://www.deciphergenomics.org/about/data-sharing) and is subject to a Data Access Agreement, in which the user certifies that no attempt to identify individual patients will be undertaken. The same restrictions apply to the public data displayed in this browser no one is authorized to attempt to identify patients by any means.
Other data
Mastermind
We display short variants from the Genomenon Mastermind Cited Variants Reference (https://www.genomenon.com/cvr/).
If a variant has multiple alternative alleles, please note that HGVS and Mastermind output will only be displayed for one allele.