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.

Guo et al.

Guo et al. BMC Genomics 2012 13:666   doi:10.1186/1471-2164-13-666

Open Data