In the simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: this is referred to as the number of substitutions (other kinds of differences between haplotypes can also occur, for example, the insertion of a section of nucleic acid in one haplotype that is not present in another).
U najjednostavnijem slučaju, razlika između dva haplotipa se procenjuje brojanjem lokusa na kojima imaju različite baze: ovo se naziva broj zamena (druge vrste razlika između haplotipova može doći, na primer je insercije (umetanja) jednog dela nukleinskih kiselina u jedan haplotip koji nije prisutan u drugom).