The extent of linkage disequilibrium and haplotype sharing around a polymorphic site

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Abstract

Various expressions related to the length of a conserved haplotype around a polymorphism of known frequency are derived. We obtain exact expressions for the probability that no recombination has occurred in a sample or subsample. We obtain an approximation for the probability that no recombination that could give rise to a detectable recombination event (through the four-gamete test) has occurred. The probabilities can be used to obtain approximate distributions for the length of variously defined haplotypes around a polymorphic site. The implications of our results for data analysis, and in particular for detecting selection, are discussed.

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Innan, H., & Nordborg, M. (2003). The extent of linkage disequilibrium and haplotype sharing around a polymorphic site. Genetics, 165(1), 437–444. https://doi.org/10.1093/genetics/165.1.437

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