Simulation of Base (Historical) Population and Determining Accuracy of Linkage Disequilibrium in Genomic Simulated Studies

To investigate accuracy of linkage disequilibrium (LD) in genomic simulation studies a base population was simulated in two statuses LD with values of zero and one in first generation. Effective population size، LD and variance of markers frequency were used for determination of simulation accuracy. The results showed a high correlation between actual and expected effective population sizes. Also observed and expected LD’s were nearly similar and the given trend was improved with increasing effective population size. In addition، the variances of the observed and expected free recombination markers frequency were adapted with each other. According to the evaluated criteria the base population was accurately simulated which it could be used to generate the reference population. Based on the results، we suggest that proposed criteria should be used to verify the simulation after creating of historical population in genomic simulated studies.