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. Author manuscript; available in PMC: 2007 May 30.
Published in final edited form as: Nature. 2005 Oct 27;437(7063):1299–1320. doi: 10.1038/nature04226

Table 6.

Coverage of simulated Phase I and Phase II HapMap to capture all common SNPs in the ten ENCODE regions

Analysis panel Per cent maximum r2≥ 0.8 Mean maximum r2
Phase I HapMap
 YRI 45 0.67
 CEU 74 0.85
 CHB+JPT 72 0.83
Phase II HapMap
 YRI 81 0.90
 CEU 94 0.97
 CHB+JPT 94 0.97

Simulated Phase I HapMaps were generated from the phased ENCODE data (release 16c1) by randomly picking SNPs that appear in dbSNP build 121 (excluding ‘non-rs’ SNPs in release 16a) for every 5-kb bin until a common SNP was picked (allowing up to three attempts per bin). The Phase II HapMap was simulated by picking SNPs at random to achieve an overall density of 1 SNP per 1 kb. These numbers are averages over 20 independent iterations for all ENCODE regions in all three analysis panels.