Table 2.
Number of tags and coverage using variants with call rate ≥ 0.4 by various r2 thresholds by category
| MAF ≥ 0.05 | r2 ≥ 0.8 | r2 ≥ 0.9 | r2 ≥ 1.0 | |||
|---|---|---|---|---|---|---|
| category* | number of tags | coverage (%) | number of tags | coverage (%) | number of tags | coverage (%) |
| HapMap (n=90) | 29 | 81.4 | 36 | 76.3 | 72 | 56.1 |
| 1000 Genome (n=233) | 60 | 98.0 | 78 | 97.6 | 165 | 96.0 |
| resequence (n=253) | 65 | 100 | 84 | 100 | 175 | 100 |
| MAF ≥ 0.01 | r2 ≥ 0.8 | r2 ≥ 0.9 | r2 ≥ 1.0 | |||
|---|---|---|---|---|---|---|
| category* | number of tags | coverage (%) | number of tags | coverage (%) | number of tags | coverage (%) |
| HapMap (n=94) | 31 | 65.1 | 37 | 61.2 | 75 | 41.3 |
| 1000 Genome (n=282) | 76 | 85.5 | 93 | 84.9 | 196 | 82.1 |
| resequence (n=358) | 117 | 100 | 136 | 100 | 259 | 100 |
*
HapMap CEU (release 28) and 1000 Genome CEU (pilot 1 low-coverage data, 10-2010 release) were compared with variants discovered by resequencing Number of matched variants available in each dataset is in parenthesis. 1000 Genome is inclusive of all HapMap reported SNPs