Table 1.

MAF distribution of resequencing discovered SNPs and indels with regard to dbSNP, 1000 Genome, and HapMap inclusion

	SNP			Indel			Total
Content	count	MAF		count	MAF		count	MAF
		average	(min-max), median		average	(min-max), median		average	(min-max), median
dbSNPa	47	0.040	(0.006-0.449), 0.013	5	0.167	(0.029-0.272), 0.217	52	0.052	(0.006-0.449), 0.014
1000 Genomeb	179	0.167	(0.007-0.481), 0.103	18	0.222	(0.019-0.482), 0.130	197	0.172	(0.007-0.482), 0.103
HapMapc	97	0.258	(0.007-0.473), 0.280	0	-	-	97	0.258	(0.007-0.473), 0.280
Noveld	103	0.011	(0.006-0.051), 0.008	20	0.076	(0.017-0.278), 0.031	123	0.021	(0.006-0.278), 0.008
Totale	426			43			469	0.137	(0.006-0.482), 0.054

^adbSNP (b132) reported, exclusive of 1000 Genome or HapMap reported ones

^b1000 Genome CEU (pilot 1 low-coverage data, 10-2010 release) reported, exclusive of HapMap CEU (release 28) reported ones

^cHapMap CEU reported SNPs

^dNovel polymorphisms previously not reported by dbSNP or 1000 Genome CEU data

^ePolymorphism counts and MAF estimation was performed after exclusion of 90 variants with call rate ≤ 40% in 80 (78 PLCO + 2 CEU founders) unrelated Europeans