Table 1. Number of SNPs by minor allele frequency split by pairwise r2 to any of the genotyped SNPs on the Affymetrix platform
| Minor allele frequency (MAF) | |||
| Low frequency (MAF < 5%) |
Intermediate frequency (MAF 5%-20%) |
High frequency (MAF 20%-50%) |
|
|---|---|---|---|
| r2 | [MAF < 5%] | [MAF 5%-20%] | [MAF 20%-50%] |
| r2 = 1 | 112,153 (33%) | 291,171 (40%) | 379,247 (34%) |
| r2 > 0.5 | 33,724 (10%) | 249,031 (34%) | 530,915 (48%) |
| r2 < 0.5 | 198,368 (58%) | 194,498 (26%) | 195,753 (18%) |
| Total | 344,245 (100%) | 734,700 (100%) | 1,105,915 (100%) |
