Ovis aries Variation. Ovis aries

This was an ISGC (International Sheep Genomics Consortium) project, involving multiple partners and funding agencies (for details see http://www.sheephapmap.org/participants.php). Sixty eight domestic sheep from 44 breeds and 5 wild animals were sequenced with an Illumina HiSeq to around 15x each. Sequences were mapped onto the sheep reference genome OARv3.1 (GenBank Assembly ID: GCA_000298735.1). Variant detection used two methods, and to be included in this set SNP had to be independently called by both. Further, SNPs had to pass a variety of filters (alternative allele frequency >= 0.02, depth filter, neighbouring SNPs filter, etc.). A subset of these SNPs was selected for inclusion on the Illumina Sheep HD BeadChip.