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Table 2 Summary of errors and richness estimates when different criteria were used to merge OPFs. OPFs were merged when at least one peptide fragment in each OPF overlapped at least 5 aa and had a BSR value that was above the user specified level by the merge penalty. The type I error rate is the fraction of OPFs from the closed genome that correspond to multiple OPFs from the individual sequence reads. The type II error rate is the fraction of OPFs from the individual sequence reads that corresponded to more than one OPF from the closed genome sequence.

From: A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

Merge Penalty Type I Error Rate Type II Error Rate Observed Richness Richness Estimation (True Richness = 3,730)
     Chao1 ACE Jackknife
Penalty = 0.00 0.063 0.129 2,927 3,038 2,976 3,137
Penalty = 0.05 0.067 0.100 3,223 3,332 3,271 3,413
Penalty = 0.10 0.071 0.074 3,462 3,574 3,510 3,653
Penalty = 0.15 0.080 0.056 3,642 3,757 3,691 3,839
Penalty = 0.20 0.091 0.046 3,810 3,925 3,858 4,004
No merge 0.719 0.003 11,538 11,668 11,616 11,968