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

BMC Genomics

Table 4 MNEc2M and MNEc670k Inter-SNP distance at various minor allele frequency cutoffs

Chip	MAF	Mean InterSNP Distance	Median InterSNP distance	Number of SNPs at MAF
MNEc2M	All SNPs	1250	785	1,986,984
	MAF > 0	1255	787	1,978,913
	MAF > 0.01	1334	835	1,862,844
	MAF > 0.03	1590	991	1,562,205
	MAF > 0.05	1876	1162	1,324,205
	MAF > 0.10	2676	1623	928,235
MNEc670k	All SNPs	3756	2172	661,349
	MAF > 0	3768	2178	659,278
	MAF > 0.01	3837	2226	647,481
	MAF > 0.03	4534	2606	547,858
	MAF > 0.05	5199	2980	477,719
	MAF > 0.10	6240	3651	398,055

Inter-SNP distance was calculated between SNPs informative at minor allele cutoffs greater than 0, 0.01, 0.03, 0.05 and 0.10. The number of SNPs included at this MAF cutoff is included. Distance and informativeness was re-calculated on both MNEc2M and MNEc670k arrays which were further broken down by tagging breed group (See Additional file 5: Table S5)

ISSN: 1471-2164