Analysis of recovery efficiency after 454/Roche GS FLX sequencing of a cloned DNA mock community. A) Bar graph illustrating proportional recovery of 16S rRNA gene pyrosequence reads from a plasmid DNA mock community. A total of 28,161 sequence reads were used for this analysis (Additional File 4). Each of the 10 templates consisted of a bacterial 16S rRNA gene sequence cloned in a bacterial plasmid. "Even mix" indicates that the same copy number for each of the 10 templates was used in the amplification reaction. "Staggered mix" indicates different amounts. The "Staggered mix 2" sample was amplified with a different polymerase mixture (Promega's GreenTaq Master Mix, Madison, WI) instead of AmpliTaq which was used in all other experiments, revealing that the two mixtures yielded similar results. The taxonomic assignments in this and subsequent figures are color coded as indicated. B) Scatter plot comparing the theoretical proportion of each input sequences (x-axis) to the proportions inferred from 454 GS FLX sequence data (y-axis).