The common map of both linkage and GWAS data is designed in the following way. With the genetic position of the linkage markers (microsatellite as in here) and physical position of both linkage and GWAS markers (microsatellite and SNPs), the genetic positions of all the GWAS markers (SNPs) are calculated based on equation (2):(2)where gm denotes the genetic position of a marker, in centi-Morgan (cM) unit; pm denotes the physical position of a marker, in base pair units; MSlast is the last microsatellite marker on a chromosome, . Because at both ends of a chromosome when the physical position of a SNP is either smaller than the 1st microsatellite marker or larger than the last microsatellite marker, there is only one microsatellite marker that can be referred to compute the genetic position for the SNP. We simply use the convention that 1cM ≈ 106 base pairs to convert a SNP’s physical map to its genetic map. While a SNP is in between two microsatellite markers, we use the ratio and multiply this ratio with the genetic distance between these two
