Table 2. Phytophthora species assigned to OTUs in each of two control mixes and the number of reads assigned per OTU by each tool.

Phytophthora species assigned per OTU using Swarm	Number of reads/OTU using Swarm	Phytophthora species assigned per OTU using Bowtie	Number of reads/OTU using Bowtie
Control mix 1 (15 Phytophthora species)
P. pseudosyringae/P. ilicis/P. pluvialis/P. nemorosa	1,595	P. pseudosyringae	135
P. austrocedri	1,373	P. austrocedri	231
P. kernoviae	1,311	P. kernoviae	216
P. cactorum/P. idaei	923	P. cactorum	258
		P. idaei	1
P. gonapodyides	403
P. obscura	383	P. obscura	67
P. ramorum	173	P. ramorum	19
P. chlamydospora	116	P. chlamydospora	15
P. lateralis	100	P. lateralis	18
P. cinnamomi	80	P. cinnamomi	10
P. cambivora	48	P. cambivora	2
P. syringae	5
P. mississippiae	4
P. plurivora	2	P. plurivora	2
Control mix 2 (10 Phytophthora species)
P. capsici/P. glovera/P. Mexicana/P. amaranthi	1,075	P. capsici/P. glovera	147
P. obscura	960	P. obscura	192
P. castanae/P. agathacidica/P. cocois/P. sp. novaeguineae	563	P. castanae/P. agathacidica/P. sp. novaeguineae	116
P. siskiyouensis	369
P. plurivora/P. citricola/P. pachypleura	342	P. plurivora	48
		P. citricola	1
P. foliorum	320	P. foliorum	63
P. rubi/P. fragariae	243	P. rubi	58
		P. fragariae	2
P. fallax	216	P. fallax	22
P. cactorum/P. idaei	33	P. idaei	10