Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

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

ISSN: 2049-2618