Minor allele frequency

The number and proportion of SNP in minor allele frequency (MAF) bins is given for three sets of markers. Set 1 includes all SNP identified during the re-sequencing experiment, with MAF being calculated from sequencing data. Set 2 is the subset of markers selected for inclusion in the SNP array, for which MAF was calculated from sequencing data. Set 3 includes SNP which passed all of the quality control filters, for which MAF was calculated from genotypic data.