Table 3. Permutational multivariate analysis (PERMANOVA) testing differences in OTU composition between indexed PCRs and Illumina MiSeq runs.

Jaccard considers only the presence-absence of OTUs whereas Bray–Curtis also takes into account differences in abundance of reads between samples.

	Source of variation	Df	SS	F Model	R2	P-value
Jaccard	MiSeq Runs	1	0.059	1.049	0.078	0.414
	Indexed PCRs	6	0.357	1.059	0.474	0.367
	Residuals	6	0.337		0.448
Bray–Curtis	MiSeq Runs	1	0.000	4.888	0.007	<0.001
	Indexed PCRs	6	0.051	106.886	0.983	<0.001
	Residuals	6	0.000		0.009

Notes.

Df

degrees of freedom

SS

sum of squares

F Model

F value by permutation