ethnic group and MAF criterion, the percent of SNPs lost from the Affymetrix 6.0 and Illumina Human1M arrays after both quality and MAF criteria are applied is about 20%, while that for the Illumina HumanHap550 array is 6%. The table also shows that genome coverage (estimated for HapMap II CEU subjects) is decreased by only 1–2% due to the recommended filters. Supporting information provides data about overlap of SNP filters within and among studies and the physical distribution of SNPs that fail to pass these filters.
