Assay comparison for genotyping. The discrimination potential of Assay1 (A, B) and Assay2 (C, D) was evaluated with 10 ng of genomic DNA. Panels A and C represent the number of molecules predicted for known genotypes according to the priming probabilities presented in Table 3. The error bars in panels A and C are 99% confidence intervals associated with each value. Panels B and D are the results obtained from individual trees of unknown genotypes. The (+) and (-) above each bar indicate whether the observed number of molecules is within (+) or outside (-) of the 99% confidence interval from panels A and C, respectively. This criterion was used to discriminate between the presence or absence of an allele. Thus, comparison of panels A and C enables genotyping with Assay1: the numbers of molecules for Trees 14, 17, 20 are within the predicted intervals for a GT/GG heterozygote. Similarly, the numbers of molecules for Trees 2, 4, 6 are within the intervals predicted for a GT/GT homozygote. In contrast, the numbers of molecules predicted for all genotypes with Assay2 are too similar to one another to assign genotypes.