Table 2.

Bulk sequencing and filtering stats for all three communities

Source1	BEI-EC2	CAMI3	HSMC-MS4
Type	Mock	Mock	Human
Total samples	8	1	122
Total # SMRTcells	4	1	85
Total pol reads	396,625	53,164	2,997,060
N50 pol read length in kb	23,523	21,220	18,837
Avg read length in pol reads	12,997	11,232	11,940
Avg Phred-quality in pol reads	9.89	9.5	9.35
Avg EE of pol reads5	1868.82	1727.44	1653.9
EE per kb of pol reads	143.79	153.8	138.52
Avg CCS passes	14.04	13.06	11.48
Avg Phred-quality in CCS reads	40.46	40.84	39.26
Avg CCS length	1454	1481	1417
Avg EE for all CCS reads5	5.36	3.15	7.16
EE per kb of CCS reads	3.69	2.13	5.05
Total CCS yield (> 4 passes)	163,689	19,576	787,302
Size filtered (0.5–2 kb)	131,413	16,061	498,007
Host filtered	163,670	19,574	704,935
Primer matched	131,856	16,156	498,820
Percent passed primary filters	80.4	81.8	63.1

¹In addition to mixed species communities, seven independent negative reagent controls and four positive controls (2 x DNA from pure cultures of Escherichia coli and Agrobacterium tumefaciens) were run

²Three conditions: polymerase (GoTaq vs. AccuPrime) × PCR cycles (35 vs. 22) × excess DNA (no human DNA vs. 10-fold excess)

³Four independent libraries

⁴Twelve subjects with healthy sinuses sampled at six sinonasal anatomic locations, both swab and biopsy. Twenty samples (mostly sites E and F) were not collected or not run

⁵EE is cumulative expected error across the full read