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Table 2 Correlations

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

Category Name Pearson’s r p-value
B SIFT − 0.493 7.87E-19
B LRT −0.486 2.76E-18
B MutationAssessor −0.573 5.22E-26
B FATHMM −0.054 1.85E-01
B PROVEAN −0.546 1.86E-23
Meta VEST3 −0.699 1.08E-42
Meta MetaSVM 0.285 1.00E + 00
Meta MetaLR −0.482 5.77E-18
Meta M-CAP −0.255 8.09E-06
ML POLYPHEN2 HDIV −0.672 1.67E-38
ML POLYPHEN2 HVAR −0.648 4.53E-35
ML MutationTaster −0.499 2.42E-19
ML CADD −0.595 1.78E-28
ML DANN −0.388 8.51E-12
ML FATHMM-MKL −0.434 1.35E-14
ML GenoCanyon −0.282 7.95E-07
n GERP++ −0.405 9.34E-13
Cons phyloP7way vertebrate −0.441 4.79E-15
Cons phyloP20way mammalian −0.214 1.54E-04
Cons phastCons7way vertebrate −0.486 2.55E-18
Cons phastCons 20 way mammalian −0.256 7.35E-06
Cons SiPhy 29way logOdds −0.389 7.65E-12
  1. Pearson’s r correlation coefficient between rank scores and residual activities, together with the associated p-value for significance scoring, for all the predictors used by wANNOVAR. Bold text is used for the highest correlations. Categories are B for “biologically based prediction method”, ML for “Machine Learning based prediction method”, Meta for “Meta prediction method” and Cons for “Conservation scoring tool”