EVA SNP release 7 for 40 assemblies

[Gerardo Perez]

Hello Everyone,

We are happy to announce the release of the EVA SNP Release 7 tracks for 40 assemblies, which now include bosTau9, ce11, and rn6. These tracks contain mappings of single nucleotide variants and small insertions and deletions (indels) — collectively Simple Nucleotide Variants (SNVs) — from the European Variation Archive (EVA) Release 7. The full list of assemblies that contain the EVA SNP release 7 track is below:

• A. gambiae (anoGam3)
• C. intestinalis (ci3)
• Bison (bisBis1)
• Cat (felCat8), (felCat9)
• Chicken (galGal4), (galGal5), (galGal6)
• Chimp (panTro4), (panTro5)
• Cow (bosTau7) (bosTau9)
• Crab-eating macaque (macFas5)
• D. melanogaster (dm6)
• Dog (canFam3)
• C. elegans (ce11)
• Gorilla (gorGor3), (gorGor4)
• Green monkey (chlSab2)
• Horse (equCab3)
• Marmoset (calJac3)
• Mouse (mm10), (mm39)
• Nile tilapia (oreNil2)
• Orangutan (ponAbe3)
• Pig (susScr3), (susScr11)
• Rat (rn5), (rn6), (rn7)
• Rhesus (rheMac8), (rheMac10)
• S. cerevisiae (sacCer3)
• Sheep (oviAri3), (oviAri4)
• Turkey (melGal5)
• Zebra finch (taeGut2)
• Zebrafish (danRer7), (danRer10), (danRer11)

These variants are classified by EVA into one of the following sequence ontology terms:

• substitution — A single nucleotide in the reference is replaced by another, alternate allele.
• deletion — One or more nucleotides are deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is a deletion of an A may be represented as Ref = GA and Alt = G.
• insertion — One or more nucleotides are inserted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the Alternate Allele field (Alt). E.g. a variant that is an insertion of a T may be represented as Ref = G and Alt = GT.
• delins — Similar to a tandem repeat, in that the runs of Ref and Alt Alleles are of different length, except that there is more than one type of nucleotide, e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC.
• multipleNucleotideVariant — More than one nucleotide is substituted by an equal number of different nucleotides, e.g., Ref = AA, Alt = GC.
• sequence alteration — A parent term meant to signify a deviation from another sequence. Can be assigned to variants that have not been characterized yet.

The variants have also been annotated with our Variant Annotation Integrator tool with functional classes such as synonymous variant, missense variant, stop gained, etc. For additional details on the track colors, as well as the filters and metadata on each variant, see the track description page.

We would like to thank the European Variation Archive for making these data publicly available. We would also like to thank Gerardo Perez, Luis Nassar, and Angie Hinrichs for the creation and release of these tracks.