Table 3. Verification of assay on amplified libraries with shotgun sequencing data.

	qPCR assay results		Shotgun sequencing results
Sample	Primer set	Relative to maximum1	Endogenous DNA	Mapping and BLASTfindings	Relative to maximum2
AR 6	Plant genome	2.26%	5.04%	Vitis v. nuDNA	13.85%
	Chloroplast	0.58%		Vitis v. cpDNA	0.66%
	Bacteria	Maximum		Bacteria	Maximum
	Fungi	0.75%		Fungi	3.06%
Fe 2599	Plant genome	N/A 3	0.14%	Vitis v. nuDNA	0.56%
	Chloroplast	11.34%		Vitis v. cpDNA	0.01%
	Bacteria	Maximum		Bacteria	Maximum
	Fungi	11.42%		Fungi	2.66%
AZ 935	Plant genome	Maximum	92.38%	Zea m. nuDNA	Maximum
	Chloroplast	25.53%		Zea m. cpDNA.	0.30%
	Bacteria	20.73%		Bacteria	0.32%
	Fungi	0.91%		Fungi	0.06%
PLM 4	Plant genome	Maximum	90.59%	Zea m. nuDNA	Maximum
	Chloroplast	7.75%		Zea m. cpDNA.	0.19%
	Bacteria	32.99%		Bacteria	0.55%
	Fungi	7.75%		Fungi	0.41%
MEX 1	Plant genome	N/A	80.86%	Zea m. nuDNA	Maximum
	Chloroplast	Maximum		Zea m. cpDNA.	0.15%
	Bacteria	11.10%		Bacteria	3.89%
	Fungi	0.31%		Fungi	0.46%
CMAG 10189	Plant genome	N/A	11.00%	Zea m. nuDNA	51.73%
	Chloroplast	N/A		Zea m. cpDNA.	0.08%
	Bacteria	Maximum		Bacteria	Maximum
	Fungi	41.18%		Fungi	18.49%
CMAG 10237	Plant genome	N/A	24.69%	Zea m. nuDNA	99.39%
	Chloroplast	2.52%		Zea m. cpDNA.	0.05%
	Bacteria	Maximum		Bacteria	Maximum
	Fungi	1.63%		Fungi	6.98%

¹As discussed in the methods section, the assay percentages are meant as a guide to compare samples and are not expected to match the absolute values yielded via shotgun sequencing.

²The scaled shotgun sequencing results do not include reads without BLAST matches or reads which matched higher taxonomic levels (e.g., eukaryotes or metazoa).

³ N/A indicates the primer set did not fluoresce before the negative control for the sample.