Methods for function prediction for non-synonymous mutations*.

* Extensively comparisons of these methods genome-widely have been studied by Thusberg et al. [1], [2] and Dong et al. [3]. Deleterious thresholds for PhyloP, GERP++ RS and SiPhy are defined according to the study by Dong et al. [3]. Deleterious thresholds for SIFT, LRT, MutationTaster, Mutation Assessor, FATHMM and RAdialSVM are based on converted scores used in dbNSFP version 2.3 [45], [46] (converted score is designated as Sc and original score is designated as So): SIFT: Sc = 1-So; LRT: Sc = 1- So *0.5 if Ωc = So *0.5 if Ω> = 1; MutationTaster: Sc = So if the prediction is “A” or “D” or Sc = 1- So if the prediction is “N” or “P”; Mutation Assessor: Sc = (So -(−5.545))/(5.975-(−5.545)); FATHMM: Sc = 1-(So -(−16.13))/(10.64-(−16.13)); RadialSVM: Sc = (1+ So/3.03993691875303)*0.5 if predicted “D” and Sc = (1- So/-2.00575697514507)*0.5 otherwise. More details of the conversion can be found at http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.3.readme.txt.