Table 1.
Expected relative abundances of each 16S rRNA gene-containing plasmid (E and T) or amplicon (P) in the in vitro-simulated communities (iv-SCs).
Figure 1.
The relative abundances of recovered reads in V3V4P and V3V4T iv-SCs (Figure 1A) and V6P and V6T iv-SCs (Figure 1B) are plotted against their respective theoretical relative abundances.
The solid lines represent the ideal 1∶1 scenario (i.e., observed matching expected perfectly).
Table 2.
Spearman rank (ρ) and log-log transformed Pearson (r) correlation coefficients of error-free sequences with their respective theoretical frequencies.
Figure 2.
The observed relative abundances of all error-free sequence in the equal-abundance iv-SCs (V3V4E: red; V6E: blue).
The pool of error-free sequences for V6E (14,761 reads) was resampled 10,000 times with replacement to match the number of V3V4E error-free sequences (4,609 reads) and used to calculate 95% confidence intervals for V6E.
Table 3.
Spearman rank (ρ) and log-log transformed Pearson (r) correlation coefficients of relative abundances of corresponding sequences in P and T iv-SCs.
Table 4.
Unidirectional hybrid PCR primers; 454 adapter sequence in italic, MID sequence in brackets.
Table 5.
Summary statistics for the community analysis using several de-noising algorithms on the iv-SCs containing 20 known sequences.
Figure 3.
Rank-frequency plots of V6P OTUs generated by SLP, AmpliconNoise, and PyroTagger.
Abundances are shown in log scale. True OTUs (green): OTUs with a reference sequence as its representative; Miscalled OTUs (blue): OTUs containing a reference sequence, but not as its representative; False-Derived OTUs (red): OTUs composed entirely of erroneous reads that are not chimeric, contamination, or closely matching a reference sequence not found in any True or Miscalled OTUs; Near-Match OTUs (orange): OTUs containing sequence(s) that closely match a reference sequence not found in any True or Miscalled OTUs; Contamination/E. coli (dark gray): OTUs composed of sequences affiliated with E. coli (cloning host); Contamination/Other (light gray): OTUs composed of sequences affiliated with potential contaminants; Chimeric OTUs (yellow): OTUs composed of manually identified chimeric sequences; Theoretical (white): expected OTUs.
Table 6.
Spearman rank (ρ) and log-log transformed Pearson (r) correlation coefficients of true and miscalled OTUs identified by de-noising algorithms with their respective expected frequencies.
Table 7.
Summary statistics for chimera-check of iv-SCs.