Figure 6. In the Brooks et al. (2015) experiment, bias is primarily driven by DNA extraction and is not substantially reduced by 16S copy-number (CN) correction.

Panel A shows the bias estimate for each step in the experimental workflow (DNA extraction, PCR amplification, and sequencing + (bio)informatics), as well as the bias imposed by performing 16S CN correction (i.e. dividing by the estimated number of 16S copies per genome). Bias is shown as relative to the average taxon—that is, the efficiency of each taxon is divided by the geometric mean efficiency of all seven taxa—and the estimated efficiencies are shown as the best estimate multiplied and divided by two geometric standard errors. Panel B shows the composition through the workflow, starting from an even mixture of all seven taxa, obtained by sequentially multiplying the best estimates in Panel A.

Figure 6—figure supplement 1. PCR bias and total bias vs. bias predicted by 16S copy number.

In the Brooks et al. (2015) experiment, variation in 16S copy number is moderately predictive of PCR bias (A) but not of total bias (B). The grey line corresponds to $y=x$, or perfect agreement between CN and the estimated bias.