Examples of poor quality allele call AFLP electropherograms. In most cases, the only solution is to run PCR again. A. Some alleles identified as peaks can be called in this example. However, many alleles will go undetected because of the structure of the electropherogram. B. The ABI 3100 was saturated in the beginning of the run and the remaining portion of the run is not complete. C. The reaction stopped working and many alleles will not be automatically called by the allele-calling software. D. The peak intensity is too low for many alleles to be called as present.