Table 2.

SNP quality by MAF and subset¹

	MAF 0–0.1	MAF 0.1-0.2	MAF 0.2-0.3	MAF 0.3-0.4	MAF0.4-0.5	Overall
All Seq SNPs	70825/2.35	8454/1.93	26074/1.94	19092/1.96	30532/1.85	174977/2.08
Overlapped SNPs	4123/2.99	2781/2.8	2799/2.73	2160/2.53	2504/2.69	14367/2.78
Seq SNPs - Chip SNPs	66702/2.31	25673/1.86	23275/1.87	16932/1.9	28028/1.79	160610/2.03
dbSNP SNPs in Seq	53520/2.43	23458/2.21	21798/2.23	16359/2.2	26152/2.05	141287/2.26
dbSNP SNPs not on Chip	49397/2.39	20677/2.15	18999/2.17	14199/2.16	23638/2.00	126920/2.21

¹. Each cell is represented in the format of number of SNPs/TiTv ratio.