Table 3 Genomic coverage, mean r2between tagged SNPs and their tagSNPs (calculated as in the study by Barrett et al. 2006 [4]) and mean r2of all SNPs and their tagSNPs. Common SNPs with MAF ≥ 0.05 were evaluated using Phase II HapMap (v. 21) data
CEU | JPT + CHB | YRI | |||||||
|---|---|---|---|---|---|---|---|---|---|
coverage (%) | mean r2 tagged SNPs | all SNPs | coverage (%) | mean r2 tagged SNPs | all SNPs | coverage (%) | SNPs | all SNPs | |
Illumina HumanHap 300 | 76 | 0.96 | 0.87 | 64 | 0.96 | 0.81 | 28 | 0.96 | 0.57 |
Illumina HumanHap 550 | 86 | 0.97 | 0.93 | 83 | 0.97 | 0.91 | 48 | 0.96 | 0.73 |
Affymetrix GeneChip 100 k | 32 | 0.96 | 0.54 | 33 | 0.96 | 0.53 | 15 | 0.96 | 0.37 |
Affymetrix GeneChip 500 k | 64 | 0.98 | 0.82 | 66 | 0.97 | 0.83 | 40 | 0.97 | 0.68 |