I evaluated the genome-wide LD decay by using snps separated by at least 10Kb using 'popLDdecay'.
In the figure, each dot represents the mean r^2 of all pairs of snps that are separated at a given distance. The maximum distance corresponds to the length of the longest chromosome.
The trend (general additive model) shows a decay in LD as expected, however, there are many sites with full LD (r^2 = 1) even if they are very far apart in the chromosome.
Since this is a mouse model, with an expected degree of inbreeding, could this explain the pattern described above?
Thanks in advance!