Table 2.
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