All sites were characterized as either called or N. All Sites designated N were partitioned into one of seven categories. (1) Primer: Primer failure indicating that <50% of the sites between a pair of PCR primers were called; (2) Low Signal: Mean florescence intensity extremely low; (3) High Saturation: Mean florescence intensity near detector limits; (4) Threshold: No model obtained quality score greater than the total threshold; (5) Two Models: Different models fit best on the forward and reverse strands so that no model obtained strand thresholds on both strands; (6) Neighborhood: <50% of the 20 surrounding sites could be called; and (7) Sample: <50% of the samples could be called at a particular site.