Table 5.

Number of random covariates (windows) and computation time for each model

Modela		Number of random effectsb			Computation time (h)d
		Fatc	Lwtc	SCSc	Fatc	Lwtc	SCSc
BayesA	SNP	37,226	37,356	37,229	13.1	6.6	13.0
	Hap125e	37,848	37,775	37,898	15.2	7.8	15.1
	Hap250f	64,724	64,634	64,730	23.5	13.1	24.4
BayesB	SNP	18,589	18,637	18,629	10.0	5.1	9.9
	Hap125e	18,899	18,831	18,954	13.6	6.2	13.9
	Hap250f	32,332	32,273	32,388	18.1	9.2	18.0
BayesN	SNP	17,748 (4701)	17,639 (4671)	18,254 (4805)	26.7	12.5	25.6
	Hap125e	18,451 (8264)	18,303 (8223)	18,711 (8344)	30.2	16.0	30.0
	Hap250f	31,596 (4737)	31,281 (4706)	32,103 (4809)	37.6	18.9	38.1

^aSNP = SNP model with 250 kb windows

^bAverage number of SNPs or haplotype alleles fitted in each chain of the MCMC

^cFat = Milk fat yield; Lwt = liveweight; SCS = somatic cell score

^dComputation time for running the analysis on the training set containing all breeds with a chain length of 41,000

^eHap125 = Haplotypes of length 125 kb, fitting only haplotype alleles >10% frequency in training data set

^fHap250 = Haplotypes of length 250 kb, fitting only haplotype alleles >1% frequency in training data set