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Ensembl Variation - Detailed species data count

List of data counts by category and species - Ensembl 92

Structural variant data

There are currently 9 species with structural variant data in the Ensembl Variation databases:

Species Structural variant (e!91 → e!92) Supporting evidence (e!91 → e!92)
Cow
Bos taurus
10,000+ - 104,000+ -
Dog
Canis familiaris
104,000+ - 107,000+ -
Horse
Equus caballus
193,000+ - 193,000+ -
Human
Homo sapiens
4.9 million+ (+57,000) 24 million+ (+153,000)
Macaque
Macaca mulatta
110 - 189 -
Mouse
Mus musculus
791,000+ - 1.2 million+ -
Pig
Sus scrofa
224,000+ - 310,000+ -
Sheep
Ovis aries
2 - 2 -
Zebrafish
Danio rerio
5,000+ - 29,000+ -

Genotype data

This doesn't include the genotypes from projects such as:

  • 1000 Genomes Project
  • ExAC Project
  • gnomAD Project
  • TOPMed Project
  • UK10K Project
  • Mouse Genomes Project
  • NextGen Project
because they are fetched directly from VCF files.

There are currently 19 species with genotype data in the Ensembl Variation databases:

Species Variants with sample genotype (e!91 → e!92) Variants with population genotype (e!91 → e!92)
Chicken
Gallus gallus
3.2 million+ - 3.2 million+ -
Chimpanzee
Pan troglodytes
1,000+ - 1.4 million+ -
Cow
Bos taurus
10,000+ - 10,000+ -
Dog
Canis familiaris
727,000+ - 727,000+ -
Fruitfly
Drosophila melanogaster
6.7 million+ - 6.7 million+ -
Gibbon
Nomascus leucogenys
1.1 million+ - 0 -
Horse
Equus caballus
1.1 million+ - 1.1 million+ -
Human
Homo sapiens
15 million+ - 16 million+ -
Macaque
Macaca mulatta
29 - 29 -
Mouse
Mus musculus
16 million+ - 10 million+ -
Orangutan
Pongo abelii
10 million+ - 0 -
Pig
Sus scrofa
15 - 175 -
Platypus
Ornithorhynchus anatinus
1.1 million+ - 1.1 million+ -
Rat
Rattus norvegicus
5 million+ - 5 million+ -
S. cerevisiae
Saccharomyces cerevisiae
263,000+ - 263,000+ -
Sheep
Ovis aries
64 - 147 -
Turkey
Meleagris gallopavo
0 - 48 -
Zebra Finch
Taeniopygia guttata
1.7 million+ - 1.7 million+ -
Zebrafish
Danio rerio
152,000+ - 151,000+ -

Phenotype data

The list of phenotype/disease/trait association sources by species is available in the page Phenotype sources.

There are currently 14 species with phenotype data in the Ensembl Variation databases:

Species Phenotype (e!91 → e!92) Phenotype association (e!91 → e!92)
Cat
Felis catus
45 (+3) 46 (+4)
Chicken
Gallus gallus
216 (-153) 4,000+ (-745)
Cow
Bos taurus
527 (-149) 100,000+ (+905)
Dog
Canis familiaris
215 (-10) 217 (-12)
Goat
Capra hircus
2 - 2 -
Horse
Equus caballus
80 (-3) 843 (-467)
Human
Homo sapiens
20,000+ (+1,000) 5.1 million+ (+299,000)
Macaque
Macaca mulatta
3 - 3 -
Mouse
Mus musculus
8,000+ (+552) 154,000+ (+12,000)
Pig
Sus scrofa
333 (-294) 17,000+ (-5,000)
Rat
Rattus norvegicus
8,000+ (+252) 66,000+ (+708)
Sheep
Ovis aries
125 (-142) 1,000+ (-590)
Turkey
Meleagris gallopavo
28 - 41 -
Zebrafish
Danio rerio
15,000+ (+576) 50,000+ (+5,000)

Citation data

There are currently 11 species with citation data in the Ensembl Variation databases:

Species Cited sequence variant (e!91 → e!92) Publication (e!91 → e!92)
Chicken
Gallus gallus
750 (+172) 108 (+19)
Cow
Bos taurus
2,000+ (+568) 229 (+29)
Dog
Canis familiaris
329 (+136) 77 (+41)
Goat
Capra hircus
15 - 2 -
Horse
Equus caballus
61 (+3) 8 (+2)
Human
Homo sapiens
280,000+ (+3,000) 99,000+ (+2,000)
Mouse
Mus musculus
8,000+ - 808 -
Pig
Sus scrofa
373 (+36) 47 (+9)
Rat
Rattus norvegicus
105 (+15) 20 (+3)
Sheep
Ovis aries
77 (+10) 17 (+3)
Zebrafish
Danio rerio
37 - 6 -

Prediction data

There are currently 11 species with prediction data in the Ensembl Variation databases:

Species Variants with SIFT data (e!91 → e!92) Variants with PolyPhen data (e!91 → e!92)
Chicken
Gallus gallus
216,000+ - 0 -
Cow
Bos taurus
2 million+ - 0 -
Dog
Canis familiaris
43,000+ (+14) 0 -
Goat
Capra hircus
92,000+ - 0 -
Horse
Equus caballus
91,000+ (+62,000) 0 -
Human
Homo sapiens
4.5 million+ (-10,000) 4.6 million+ (-10,000)
Mouse
Mus musculus
186,000+ (+114) 0 -
Pig
Sus scrofa
210,000+ - 0 -
Rat
Rattus norvegicus
15,000+ - 0 -
Sheep
Ovis aries
222,000+ - 0 -
Zebrafish
Danio rerio
83,000+ (-2,000) 0 -

The full list of species with their assembly versions in Ensembl is available here.