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If the following loci indicated the presence of an SNP in flu strains, is Locus 2 and Locus 3, which are located 10 bp apart in linkage disequilibrium?

"When alleles and molecular markers are associated with each other at a frequency that is significantly higher than expected by random chance, they are said to exhibit linkage disequilibrium" Brooker's Genetics

Both loci seem to be linked, but how do I determine if it is significant enough to be considered in disequilibrium or not.


As per the definition you gave, you check whether there is a statistical association between the two. If knowing when allele is present at a locus does not affect the probability of finding a given allele at the other locus, then they are independent (there is no association). Otherwise, there is an association and hence the two loci are in linkage disequilirium.

See wikipedia > Linakge disequilibrium for more info.


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