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LOD scores

The LOD (logarithm of odds) score is the statistical test most used in genetic linkage calculations (indicating the likelihood of linkage vs. non-linkage).


If two markers are unlinked, then the odds (Ou) of getting exactly x recombinant progeny and y parental-type progeny is: (0.5x)(0.5y).

If the markers are linked, with a recombination frequency of r, then the odds ratio (OL) is given by (rx)[(1-r)y].
The odds ratio is OL/OU and the LOD score is log10 (OL/OU).