Skip to main content

Table 4 Median difference (\( \overset{\sim }{\Delta } \)) in metagenome quality measures for labeled genomes between simulations of metagenomic-SIP and conventional metagenomics. For all measures, except bin contamination, a difference greater than zero indicates that metagenomic-SIP improved metagenome quality relative to conventional metagenomics. For bin contamination, a difference less than zero indicates improved metagenome quality with metagenomic-SIP. All statistical analyses were single sided, Wilcoxon signed rank tests with an alternate hypothesis of greater than zero, except for bin contamination which used an alternate hypothesis of less than zero. All p-values are adjusted for multiple comparisons (Bonferroni, n = 6)

From: Simulating metagenomic stable isotope probing datasets with MetaSIPSim

Comm. G + C

# Labeled genomes per sample

Buoyant Density window g/ml

\( \overset{\sim }{\Delta } \) Read coverage X (p-value)

\( \overset{\sim }{\Delta } \) Proportion of genome recovered in reads (p-value)

\( \overset{\sim }{\Delta } \) Proportion of genome recovered in contigs (p-value)

\( \overset{\sim }{\Delta } \) NGA50 bp (p-value)

\( \overset{\sim }{\Delta } \) Proportion of genome recovered in best bin (p-value)

\( \overset{\sim }{\Delta } \) Proportion bin contaminated (p-value)

Low

25

1.72–1.77

2.202 (<  0.001)

0.445 (<  0.001)

0.058 (0.027)

18,409 (<  0.001)

0.675 (<  0.001)

−0.007 (NS)

50

1.769 (<  0.001)

0.391 (<  0.001)

0.052 (< 0.001)

19,672 (<  0.001)

0.567 (<  0.001)

−0.038 (<  0.001)

100

1.188 (<  0.001)

0.324 (<  0.001)

0.006 (NS)

7779 (<  0.001)

0.337 (<  0.001)

−0.010 (<  0.001)

High

50

1.70–1.75

0.018 (NS)

0.013 (NS)

−0.032 (NS)

− 212 (NS)

0.019 (NS)

−0.001 (NS)

1.72–1.77

0.589 (<  0.001)

0.241 (<  0.001)

0.026 (NS)

3824 (<  0.001)

0.330 (<  0.001)

−0.017 (0.006)

1.75–1.79

3.935 (<  0.001)

0.388 (<  0.001)

0.102 (0.013)

47,027 (<  0.001)

0.825 (<  0.001)

−0.012 (NS)