Table 2.

Number of positives and negatives used for training, tuning, and testing each model

Model Number	Genomes Used in Training	Tissue	Negative Set	Positives (Training, Validation, Test)	Negatives (Training, Validation, Test)	Negatives:Positives (Training, Validation, Test)
1	mm10	Brain	Flanking Regions	21,594, 2416, 4576	35,640, 4018, 7440	1.65:1, 1.66:1, 1.63:1
2	mm10	Brain	OCRs in Other Tissues	21,594, 2416, 4576	427,174, 70,504, 82,172	19.78:1, 29.18:1, 17.96:1
3	mm10	Brain	Large G/C- and Repeat-Matched	21,594, 2416, 4576	175,912, 23,880, 32,008	8.15:1, 9.88:1, 6.99:1
4	mm10	Brain	Small G/C- and Repeat-Matched	21,594, 2416, 4576	35,358, 4776, 6654	1.64:1, 1.98:1, 1.45:1
5	mm10	Brain	Dinucleotide-Shuffled OCRs	21,594, 2416, 4576	215,940, 24,160, 45,760	10:1, 10:1, 10:1
6	mm10	Brain	Non-OCR Orths. of OCRs	21,594, 2416, 4576	25,086, 3456, 4694	1.16:1, 1.43:1, 1.03:1
7	mm10	Liver	Non-OCR Orths. of OCRs	32,498, 4032, 7752	22,890, 2994, 4434	1:1.42, 1:1.35, 1:1.75
8	mm10, hg38, rheMac8, rn6	Brain	Non-OCR Orths. of OCRs	74,688, 9036, 15,266	111,206, 14,650, 19,688	1.49:1, 1.62:1, 1.29:1
9	mm10, rheMac8, rn6	Liver	Non-OCR Orths. of OCRs	81,886, 10,428, 17,688	67,278, 8680, 14,544	1:1.22, 1:1.20, 1:1.22