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

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

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
  1. 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)