Table 3.

Median difference ($\widetilde{∆}$) in metagenome quality for labeled genomes between simulations of metagenomic-SIP and conventional shotgun metagenomic data. For all measures, except bin contamination, a difference greater than zero indicates that metagenomic-SIP improved metagenome quality relative to the conventional metagenomics approach. 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)

Community G + C	Seq. depth	$\widetilde{∆}$ Read coverage X (p-value)	$\widetilde{∆}$ Proportion of genome recovered in reads (p-value)	$\widetilde{∆}$ Proportion of genome recovered in contigs (p-value)	$\widetilde{∆}$ NGA50 bp (p-value)	$\widetilde{∆}$ Proportion of genome recovered in best bin (p-value)	$\widetilde{∆}$ Proportion bin contaminated (p-value)
Low	5 M	1.769 (<  0.001)	0.391 (<  0.001)	0.052 (< 0.001)	19,672 (<  0.001)	0.567 (<  0.001)	− 0.038 (<  0.001)
Medium		1.002 (<  0.001)	0.315 (<  0.001)	0.053 (< 0.001)	9251 (<  0.001)	0.353 (<  0.001)	−0.022 (<  0.001)
High		0.596 (<  0.001)	0.240 (<  0.001)	0.026 (NS)	3511 (<  0.001)	0.366 (<  0.001)	− 0.010 (0.001)
Low	10 M	3.561 (<  0.001)	0.237 (<  0.001)	0.004 (0.007)	11,636 (<  0.001)	0.144 (<  0.001)	−0.017 (<  0.001)
Medium		1.992 (<  0.001)	0.306 (<  0.001)	0.007 (< 0.001)	7554 (<  0.001)	0.092 (<  0.001)	−0.011 (<  0.001)
High		1.174 (<  0.001)	0.222 (<  0.001)	0.001 (NS)	7718 (<  0.001)	0.134 (<  0.001)	−0.009 (<  0.001)