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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