Genome-wide Association Simulator - Number of Breaks

This page describes the artificial crossover rate

This number defines the average number of crossovers (breaks) per cM. This number multiplied by the genetic length of a chromosome (sex averaged in cM) = average numumber of crossovers for the whole chromosome.

Example: the genetic length (sex averaged in cM) of chromosome 10 is 173. If the average number of crossovers per cM is set to 1.0 (corresponding to one meiosis), we have

               1.0 * 173 = 173

So 173 is the mean of the average number of crossovers for the simulated chromosome 10.

We typically recommend that the crossover rate be set at a value 1.0, which corresponds roughly to assuming 100 meiotic events separating independently generated chromosomes. A value of 0.01 corresponds to a single meiosis. We generating the breaks, we apply a linkage-disequilibrium map, which makes it unlikely that haplotype blocks will be broken.

Note that the introduction of crossovers is intended to increase haplotype novelty and reduce long-range association, not to truly simulate population genetic history. Even with zero crossovers, our resampling of HapMap data ensures that the generated haplotypes are essentially an unbiased reflection of the population.