Table 5. Assignment of Illumina sequencing reads to bins.

				CCD−			CCD+
Mapping step	Reference	Program	Match criterion	Starting reads (000s)	Mapped reads (000s)	Percent of total reads mapping	Starting reads (000s)	Mapped reads (000s)	Percent of total reads mapping
1	Honey bee reference sequence	Bowtie	V = 2	19,276	16,921	87.8%	41,950	37,692	89.9%
2	Reference sequence for known eukaryotic, prokaryotic, and viral associates of honey bee	Bowtie	V = 2, best	2,355	195	1.0%	4,258	496	1.2%
3	Assembly contigs	Bowtie	V = 2, best	2,160	1,586	8.2%	3,762	2,992	7.1%
4	Silva LSU and SSU ribosomal databases (4/21/2010)	Bowtie	V = 3	574	116	0.6%	770	293	0.7%
5	NCBI Univec database	Mega BLAST	E <0.01	458	41	0.2%	477	11	0.03%
6	Honey bee reference sequence	Mega BLAST	E <0.01	417	63	0.32%	466	69	0.16%

Match criteria are the conditions under which an aligned read is considered a valid mapping. For Bowtie, this column shows the number of mismatches (the parameter ‘V’) and whether the match was required to be the best match in the reference database. For Mega BLAST, the minimum expectation of the match is shown.