Table 2.

Summary of training set sizes derived from the data sets outlined in Table 1

Training set name	Positive set (Iter. 1, Iter. 2, Iter. 3)	Negative set (Iter. 1, Iter. 2, Iter 3.)
Disease negative set	DM-SAVs (1,189, 1,189, 2,601)	DM-SNVs (7,729, 7,363, 31,967)
SNP negative set	DM-SAVs (1,189, 1,189, 2,090)	SNP-SNVs (7,339, 7,253, 70,847)
Mixed negative set (disease and SNP)	DM-SAVs (1,189, 1,189, 6,335)	DM-SNVs and SNP-SNVs (15,068, 14,616, 111,630)
Random SNP set (control)	SNP-SNVs (50%) (3,669, 3,669, 9,901)	SNP-SNVs (50%) (3,670, 3,613, 7,349)

Number of training examples for each different iteration (iter. 1, iter. 2 and iter. 3.) are shown in parentheses.