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Table 2 Pearson ρ and mean squared error (MSE) for methods on SetCommona

From: Variant effect predictions capture some aspects of deep mutational scanning experiments

  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]
  1. 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