The analysis SNP set had 435,291 SNPs including 427,049 autosomal SNPs, 7.988 SNPs on the non-PAR portions of chrX, 239 SNPs on chrXY/PAR1, 15 SNPs on chrY, and 0 SNPs on PAR2. The median SNP missingness was 0.00339 (inter-quartile range 0.00113-0.0105) and the median minor allele frequency was 0.2422 (inter-quartile range 0.1375-0.3646) with similar estimates in cases and controls. The average marker density over the genome was 1 SNP every 7,069 bases (=3,077,088,087 bases / 435,291 SNPs). The median inter-marker distance was 2,911 bases with interquartile range 966-7,374 bases and a 99th percentile of 50.1 kb.
