a common reason for base changes is that taq and other polymerases are not perfect and can incorporate wrong bases in the pcr process. If one of these molecules is cloned than sequenced the change will show at 100% of the sequence because it is a clone. Often errors occur near the ends of the sequence because the taq is processing at all temperatures and is its most accurate at high temperature so errors are more common while the primer is just annealing and the enzyme extends at the annealing temperature