Table 2. Assignment of contigs to species of origin^a.

A	B	C	D	E
Type of Organism	No. by TopSortb	No. With Genomic Evidencec	No. Without Genomic Evidencec	False-Positive Rate (%)d
Cnidarian	28,026	26,219	1807	6.4
Dinoflagellate	23,794	1126	22,668	4.7
Fungi	166	18	148	10.8e
Bacteria	731	185	546	25.3e

^aThe full list of assignments of individual contigs to their species of origin is provided in File S5.

^bSee text.

^cGenomic evidence was defined as ≥10 paired-end reads aligning from Aiptasia genomic DNA libraries prepared from aposymbiotic anemones (see Materials and Methods).

^dClassified as cnidarian by TopSort but lacking genomic evidence or classified as noncnidarian by TopSort but with apparent matches to Aiptasia genomic DNA.

^eMany of these are presumably transcripts from contaminants that were present on the surfaces or in the gastric cavity of the anemones from which the genomic DNA was prepared. However, the high rate of apparent false-positives among the putatively bacterial and fungal sequences probably also reflects Bayes’ rule, whereby the ratio of false-positives to true-positives is high when the a priori probability of a true-positive is low.