Table 3 

Values of π (prior) used in the Bayesian analysis in the sires 

S.S. in Sires 
Total 
SSR 
SSR/2 
SSRx2 



Milk Yield 
370 
40,668 
0.0091 
0.0045 
0.0182 


Fat Yield 
370 
40,668 
0.0091 
0.0045 
0.0182 


Protein Yield 
385 
40,668 
0.0095 
0.0047 
0.0189 


Fat % 
216 
40,668 
0.0053 
0.0027 
0.0106 


Protein % 
229 
40,668 
0.0056 
0.0028 
0.0113 


SCS 
9 
40,668 
0.0002 
0.0001 
0.0004 


Fat % = fat percentage; Protein % = protein percentage; SCS = somatic cell score; S.S. in Sires = number of significant SNPs from the single SNP regression model in the sires for a particular trait; Total = total number of SNPs in the analysis; SSR = value of π based on the number of significant SNPs from the single SNP regression model in the sires (i.e. for milk yield, 370/40668 = 0.0091); SSR/2 = half the value of π than that of the SSR prior; SSRx2 = twice the value of π than that of the SSR prior For the Bayesian analysis three different priors were used for each trait; these priors represent the proportion of SNPs believed to affect the particular trait. The SSR prior for a trait is calculated by dividing the total number of significant SNPs from the single SNP regression analysis in the sires by the total number of SNPs in the analysis (i.e. 40,668). The other two priors, SSR/2 and SSRx2 are simply the half and double the SSR prior respectively 

Meredith et al. BMC Genetics 2012 13:21 doi:10.1186/147121561321 