	Exons included in Negatives					Exons excluded from Negatives and Positives			
Method	PhastCons	GERP++	SiPhy-omega	SiPhy-pi		PhastCons	GERP++	SiPhy-omega	SiPhy-pi
CNEP	0.79	0.86	0.86	0.84		0.79	0.86	0.87	0.84
CNEP - matched	0.79	0.86	0.86	0.84		0.79	0.86	0.86	0.84
CNEP - five classifiers per element set	0.79	0.86	0.86	0.84		0.79	0.86	0.86	0.84
CNEP - single classifier per element set	0.76	0.83	0.83	0.80		0.76	0.83	0.83	0.80
CNEP - 2015 features only	0.75	0.82	0.82	0.81		0.75	0.82	0.83	0.81
CNEP - excluding ChromHMM features	0.78	0.86	0.86	0.83		0.78	0.86	0.86	0.83
CNEP - ChromHMM features only	0.70	0.76	0.77	0.76		0.70	0.76	0.77	0.76
All Features Count	0.62	0.64	0.68	0.69		0.62	0.64	0.68	0.69
All DNase-seq Count	0.67	0.71	0.74	0.74		0.67	0.71	0.75	0.75
Roadmap Epigenomics DNase-seq Count	0.67	0.71	0.74	0.73		0.67	0.72	0.74	0.74
Segway Encyclopedia - 'conservation-associated activity score	0.57	0.60	0.64	0.66		0.58	0.61	0.66	0.67
FitCons2 - 'cell-type integrated score	0.57	0.58	0.62	0.62		0.58	0.59	0.63	0.63
									
"CNEP - on sample of 50,000 data points genomewide"	0.81	0.84	0.87	0.84		0.81	0.84	0.87	0.85
"DeepSea max data set - on sample of 50,000 data points genomewide"	0.64	0.65	0.66	0.66		0.65	0.66	0.67	0.67
"DeepSea average data set - on sample of 50,000 data points genomewide"	0.52	0.53	0.53	0.54		0.53	0.53	0.55	0.54
									
CNEP - on sample of 1 million data points on chr10	0.81	0.84	0.86	0.84		0.81	0.84	0.86	0.84
Random Forest - on sample of 1 million data points on chr10	0.77	0.80	0.82	0.81		0.77	0.80	0.83	0.82
