Table 2.

Summary of assignments of reads that were not assigned to the same taxa by phymm and NBC

	A sample			B sample
	Assigned by Phymm as	Assigned by NBC as	%	Assigned by Phymm as	Assigned by NBC as	%
Domain	Virus	Bacteria	89.92	Virus	Bacteria	87.5
	Archaea	Bacteria	3.57	Virus	Archaea	4.6
	Virus	Archaea	2.69	Bacteria	Virus	3.72
	Bacteria	Archaea	2.08	Archaea	Bacteria	2.46
	Bacteria	Virus	1.74	Bacteria	Archaea	1.65
				Archaea	Virus	0.06
Phylum	Cyanobacteria	Firmicutes	15.36	Proteobacteria	Firmicutes	15.75
	Firmicutes	Proteobacteria	15.34	Firmicutes	Proteobacteria	14.62
	Proteobacteria	Firmicutes	13.55	Cyanobacteria	Proteobacteria	9.51
	Cyanobacteria	Proteobacteria	8.47	Proteobacteria	Bacteroidetes	5.26
	Firmicutes	Super Bacteroidetes/Chlorobi group	3.91	Proteobacteria	Cyanobacteria	4.85
	Proteobacteria	Super Bacteroidetes/Chlorobi group	3.56	Firmicutes	Cyanobacteria	4.76
	Proteobacteria	Cyanobacteria	3.05	Cyanobacteria	Firmicutes	4.26
	Firmicutes	Cyanobacteria	2.74	Proteobacteria	Super Bacteroidetes/Chlorobi group	3.14
	Firmicutes	Fusobacteria	2.56	Firmicutes	Super Bacteroidetes/Chlorobi group	2.93
	Proteobacteria	Bacteroidetes	2.16	Proteobacteria	Actinobacteria	2.27
Class	Bacilli	Gammaproteobacteria	10.75	Alphaproteobacteria	Gammaproteobacteria	6.43
	Bacilli	Clostridia	6.54	Gammaproteobacteria	Bacilli	5.59
	Gammaproteobacteria	Bacilli	6.36	Bacilli	Gammaproteobacteria	5.46
	Bacilli	Eproteobacteria	5.94	Gammaproteobacteria	Betaproteobacteria	4.97
	Gammaproteobacteria	Betaproteobacteria	4.73	Gammaproteobacteria	Alphaproteobacteria	4.38
	Gammaproteobacteria	Clostridia	4.33	Gammaproteobacteria	Actinobacteria (class)	4.37
	Negativicutes	Bacilli	2.73	Alphaproteobacteria	Betaproteobacteria	4.2
	Bacilli	Flavobacteria	2.65	Bacilli	Eproteobacteria	3.71
	Alphaproteobacteria	Clostridia	2.5	Gammaproteobacteria	Eproteobacteria	2.56
	Bacilli	Fusobacteria (class)	2.35	Gammaproteobacteria	Clostridia	2.51

Percent of reads differently assigned at this taxonomic level.