Table 1.

Agreement between prediction programs

Program	MAPP (%)	SIFT (%)	VarioWatch (%)	PolyPhen-2 (%)
MAPP	100
SIFT	64.6	100
VarioWatch	59.4	62.9	100
PolyPhen-2	71.4	64.2	62.9	100

For the off-diagonal values, this table looks at pairwise agreements between the four prediction programs in predicting whether a variant is tolerated or deleterious. For example, 64.6% of the time, MAPP and SIFT agreed on their prediction, whereas VarioWatch and SIFT only agreed 62.9% of the time. The highest agreement is between MAPP and PolyPhen-2, and the lowest agreement is between MAPP and VarioWatch.