Table 3:

Pilot study: average number of Illumina MiSeq reads, the average number of (pseudo-)reads that passed QC, and the percentage of QC (pseudo-)reads that were assigned to DNA barcodes and OTUs generated per sample.

Experimental	Number of raw	Percentage of QC	Percentage DNA barcode	Percentage OTU clustered
mixture	reads	(pseudo-)readsa	assigned (pseudo-)readsa	(pseudo-)readsa
EM1	466 108	88.07	95.68	83.86
EM2	448 428	86.04	97.24	84.04
EM3	496 328	87.46	96.61	84.34
EM4	273 104	77.38	95.74	80.54
EM5	582 254	96.26	97.84	90.63
EM6	442 574	92.81	97.54	81.48
EM7	394 354	93.04	97.14	80.70
EM8	455 172	79.62	95.66	82.35
EM9	434 326	86.23	97.30	83.60
EM10	387 816	87.73	97.00	75.11
EM10R	723 130	95.59	98.02	87.39
EM11	363 374	84.44	96.74	78.63
EM11R	635 304	91.11	98.21	87.01
EM12	355 634	92.55	97.54	76.54
EM13	405 742	89.46	96.49	77.31
EM14	480 772	85.74	95.98	81.91
EM15	554 602	87.05	88.78	82.98
Averageb	464 648	88.27	96.44	82.26

^a(Pseudo-)reads are the combined QC pseudo-reads and the QC processed unmerged forward and reverse reads.

^bAveraged across the 17 Illumina MiSeq datasets.