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Table 2 Bulk sequencing and filtering stats for all three communities

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

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
  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
  2. 2Three conditions: polymerase (GoTaq vs. AccuPrime) × PCR cycles (35 vs. 22) × excess DNA (no human DNA vs. 10-fold excess)
  3. 3Four independent libraries
  4. 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
  5. 5EE is cumulative expected error across the full read