The base deficiency is common in PCR products, especially PCR fragments amplified from the genome. In order to solve this issue we can:
(1) Continue sequencing to correct the missing sites by using reverse primer and cover the entire sequence . Alternatively, the PCR product could be cloned into a plasmid and the single clone could be selected and sequenced.
(2) If there should not be any missing sites in the PCR fragment, the PCR conditions can be changed and amplified.
