What is the meaning of 100% concordance?
One special case of RI strain results deserves particular attention when complete concordance is observed between the SDP patterns obtained for two different loci. In this special case, the Haldane-Waddington formulation (Equations 9.8 and 9.9) leads to a linkage distance estimate of 0 cM. However, if the two loci under analysis were independently-derived and known not to be identical, an estimate of zero distance clearly makes no sense. Based on intuitive grounds alone, one would expect there to be a strong likelihood that the two loci are actually separated from each other by a significant distance, especially when the total number of RI strains typed is small. An accurate estimate of the median expected recombination fraction r-bar (leading directly to an estimate of the median expected linkage distance d-bar) that separates two completely concordant loci can be obtained by determining the midline of the area under the associated probability density function as discussed in Appendix
