Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

BMC Genomics

Table 1 SNP Sets used at various steps in array design

Set Name	Number of unique sites	Set Description	WGS Data	Array Data
23M	22,557,988	Possible/Discovered Variants	x	-
10M	11,435,936	Array Compatible	x	-
5M	5,443,950	Array Candidate	x	-
2M	2,001,826	Test Array	x	x
1.8M	1,846,988	Test Array Converted	x	x
670k	670,805	Commercial Array	x	x

Variants discovered from whole genome sequencing were filtered at various steps for quality control or using array design criteria. Six distinct sets of variants ranging from the initial ~23M high-quality, variants discovered from WGS to the 670k variants available in the commercial genotyping array are described throughout this manuscript

ISSN: 1471-2164