Table 4.

Imputation accuracy from BEAGLE, fastPHASE and findhap at Illumina 3k (Bovine3K) and 7k (BovineLD) chip

SNP chip	Chromosome	BEAGLE 3.3 (20 iterations)	fastPHASE 1.4 (20 haplotype clusters)	findhap 2.0 (20 iterations)
3k	BTA1	0.943	0.775	0.910
	BTA16	0.930	0.745	0.883
	BTA28	0.914	0.731	0.876
7k	BTA1	0.968	0.906	0.946
	BTA16	0.967	0.891	0.938
	BTA28	0.961	0.879	0.932

SNP = single-nucleotide polymorphism.