Table 2.

Pearson ρ and mean squared error (MSE) for methods on SetCommon^a

	deleterious SAVs (n = 17,781)		beneficial SAVs (n = 15,200)
	ρ	MSE	ρ	MSE
SNAP2	0.41 [0.40, 0.42]	0.3 [0.30, 0.30]	0.02 [0.01, 0.04]	0.23 [0.23, 0.24]
Envision	0.1 [0.08, 0.11]	0.06 [0.06, 0.07]	−0.14 [−0.16, − 0.13]	0.05 [0.04, 0.05]
Naïve Conservation	0.29 [0.27, 0.30]	0.19 [0.19, 0.19]	−0.08 [− 0.09, − 0.06]	0.19 [0.19, 0.20]

^aSetCommon denotes the set of SAVs with predictions from every method (see Methods). ρ denotes Spearman ρ (higher is better), MSE the mean squared error (lower is better, Methods, SOM_Note3). Values in brackets are 95% confidence intervals