23 April 2020 0 8K Report

The recombination frequency of 2 unlinked genes is 50% (independent assortment, which is maximal achievable recombination frequency. For linked genes, their θ should be 0 < θ < 0.5 (not inclusive 0 and 0.5). To me, θ = 0 is just doesn't make sense as the absence of recombination only exists in the context of a single gene (but now we are investigating 2 genes). θ = 0.5 is also doesn't make sense as it is the value for unlinked genes, hence a contradiction will occur when we are referring it to linked genes (even with them at the 2 most farthest ends of chromosome. With some alterations of the LOD formula (I designate "n" (total sample) for R+NR, and the θ itself), I got LOD = 0 when θ = 0.5 and LOD = undefined when θ = 0. So, it somehow correlates with my intuition. As for LOD = negative, it just doesn't make sense to me. First, there are only either linkage present or absent, hence "negative linkage" should not exist. Second, with my alteration on the LOD formula, I got LOD = negative when "n" = negative (which is illogical). So, I think LOD has no negative value in linkage genetics (but not for other aspects of statistics). Is my intuition correct?

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