Table 2. Conflicts between Greengenes and SILVA annotations of identical sequences.

Rank	Conflicts	Blank vs. name	Hierarchy
Phylum	7,804 (1.1%)	92	0
Class	23,082 (3.2%)	489	0
Order	110,308 (15.1%)	2,777	4
Family	45,712 (6.2%)	20,093	0
Genus	62,584 (8.5%)	36,186	203
Total	249,490 (34.1%)	59,637	207

Notes:

Columns are: Rank, the highest rank where there was a disagreement between names in the common nomenclature; Conflicts, the number of disagreements (and as a percentage of annotations in the common nomenclature); Blank, the number of conflicts where the rank was not named in one of the databases; Hierarchy, conflicts where the databases disagreed on the parent name in cases where both the rank and its parent are in the common nomenclature in both databases. The number of conflicts is seen to be largest at Order rank. The reason for this is not clear; possibly, the impact of branching order errors is most severe at intermediate levels of the tree.