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Table 1 Accuracy Indexes

From: Challenging popular tools for the annotation of genetic variations with a real case, pathogenic mutations of lysosomal alpha-galactosidase

Category Predictor Raw Accuracy Balanced accuracy F1-score Matthew’s correlation coefficient
B SIFT 0.749 0.549 0.241 0.092
B LRT 0.794 0.576 0.280 0.162
B MutationAssessor 0.191 0.460 0.247 −0.106
B FATHMM 0.846 0.500 0.000 0.000
B PROVEAN 0.737 0.557 0.258 0.103
Meta MetaSVM 0.846 0.500 0.000 0.000
Meta MetaLR 0.846 0.500 0.000 0.000
Meta M-CAP 0.846 0.500 0.000 0.000
ML Polyphen2_HDIV 0.771 0.592 0.310 0.175
ML Polyphen2_HVAR 0.691 0.621 0.341 0.188
ML MutationTaster 0.194 0.433 0.230 −0.156
ML FATHMM-MKL 0.829 0.505 0.063 0.022
  1. Accuracy indexes measuring the ability to differentiate severe from mild GLA mutations for all the predictors used by wANNOVAR. Categories are B for “biologically based prediction method”, ML for “Machine Learning based prediction method”, and Meta for “Meta prediction method”