Table 1.

Parameter values for simulating phenotypes, dependent on PolyPhen-2 scores.

PolyPhen-2 score	Probability that variant is causal	Mean of Normally distributed effect on phenotype	Standard deviation normally distributed effect on phenotype
Benign	0.05	1.00	0.5
Possibly damaging	0.35	1.65	0.5
Probably damaging	0.45	2.00	0.5
Missing	0.001	1.20	0.5

Background random variability in phsenotype was normally generated with mean 0 and standard deviation between 0.5 and 1.5.