What are the advantages of sequencing the complete genome compared to sequencing just the hypervariable region?
Because of its relatively short length and high mutation rate, mutations in the hypervariable region can occur over and over again in different populations, reducing their “informativeness”. Another problem is back-mutation, where a polymorphism changes back to the “normal” base. These recurring polymorphisms and back-mutations complicate haplogroup assignment. Sequencing the full length genome yields 15X more information, allowing more refined analysis. More on haplogroups.
