Table 2.

Effect of missing marker data and minor allele frequency on prediction accuracy.

Method	0% missing	0% missing	0% missing	≤10% missing	≤10% missing	≤10% missing	≤30% missing	≤30% missing	≤30% missing
	- 0% MAF	- ≥5% MAF	- ≥10% MAF	- 0% MAF	- ≥5% MAF	- ≥10% MAF	- 0% MAF	- ≥5% MAF	- ≥10% MAF
Ridge Regression	0.681	0.679	0.669	0.669	0.676	0.671	0.660	0.674	0.670
Kinship Gauss	0.697	0.710	0.702	0.692	0.701	0.695	0.688	0.698	0.702
Bayes Cπ	-	0.678	0.662	-	0.688	0.674	-	0.668	0.683
Bayes B	-	0.674	0.655	-	0.680	0.660	-	0.663	0.663
Bayes LASSO	0.660	0.681	0.666	0.684	0.671	0.665	0.672	0.657	0.680
Random Forest	0.694	0.713	0.705	0.709	0.694	0.693	0.698	0.689	0.697

Miss, Missing marker data; MAF, Minor Allele Frequency.