Genotypes were scored by clustering intensity measurements as previously described15. In addition, quality scores similar to Phred scores were computed for each genotype call, based on a combination of experimental metrics correlated to data quality. Assays with overall call rates less than 80% or with poor average quality scores were flagged as failed. About 38% of the tiled assays failed these basic criteria, and the remainder were processed using the more rigorous HapMap Project data quality control filters. For analysis of the whole genome, probes for 4,373,926 distinct SNPs were tiled onto 32 chip designs, with 32 SNPs tiled in replicate onto each chip design for quality control (QC). Perlegen did not type the samples by plates as had been done for the Phase I genotyping, instead typing large numbers of SNPs one sample at a time. Consequently, blank wells on each plate were not included as a component of QC for this genotyping. In the Phase I HapMap a single JPT sample had been excluded because of technical problems. Perlegen typed a replacement sample (from the original JPT collection)
