Identification of functional genetic variation in exome sequence analysis

BMC Proceedings

Table 2 Comparison of deleterious SNPs across programs

Program	Number of variants classified	Deleterious		Conditional probability of pairwise prediction
		Number	%	MAPP (%)	SIFT (%)	VarioWatch (%)	PolyPhen-2 (%)
MAPP	3,199	1,472	46.0	100	58	65	78
SIFT	3,562	1,603	45.0	62	100	71	69
VarioWatch	3,429	1,882	54.9	55	58	100	64
PolyPhen-2	3,333	1,757	52.7	65	58	67	100

Each program characterizes a different number of deleterious alleles. The pairwise prediction is calculated by conditioning on the probability of a program predicting a variant as deleterious, given that the comparison program already has predicted it as deleterious. For example, in the first row, among those 1,472 variants that MAPP classifies as deleterious, only 58% are also classified as deleterious by SIFT.

ISSN: 1753-6561