Table 5

Number of SNPs meeting different criteria for optimizing validation with the sequenom genotyping array
No CS60_MAF1 Whole collection No IS60 Variable in all groups
MAF 1 55,000 28,996 9
(10.21%)
MAF 0.99 108,731 65,500 158
(23.07%)
MAF 0.98 136,694 86,103 211
(30.32%)
MAF 0.97 150,590 96,657 231
(34,04%)
MAF 0.96 160,231 103,976 260
(36,61%)
MAF 0.95 167,718 109,734 277
(38,64%)
MAF 0.7 178,107 168,726 431
(59,42%)

1 Those SNPs having the filter CS60_MAF in Additional file 4 are flanked in a window of 60 bp by other SNPs with values of MAF over the threshold indicated. Columns indicate the number of these SNPs in the whole collection, in the subset free from introns in a flanking window of 60 bp (no IS60), and in the subset variable in all groups. These filters for each SNP of the whole collection are included in Additional file 4.

Blanca et al.

Blanca et al. BMC Genomics 2012 13:280   doi:10.1186/1471-2164-13-280

Open Data