Fig. 2

Precision quantification of microbial contamination in sequencing experiments. For each of n = 32 HeLa input masses (measured in triplicate), microbial contaminants were identified if the inverse linear relationship associating log₁₀-transformed rpm of any given microbe with the log₁₀-transformed sample mass demonstrated an adjusted R² ≥ 0.7. By solving the equation contaminant mass/ERCC mass = contaminant reads/ERCC reads, the estimated mass of each contaminant in each sample was calculated. The top contaminating taxa were E. coli (2.59 ± 0.67 ag), S. cerevisiae (1.02 ± 0.30 ag), S. maltophilia (0.61 ± 0.49 ag), unspecified cloning vector (0.43 ± 0.17 ag), and A. xylosoxidans (0.40 ± 0.27 ag), respectively. The estimated mass of all contaminants (excluding human and low-quality reads) in each sample was 9.1 ± 2.0 ag