Table 3.
Comparison of the top 10 reads from the naive Bayes analysis of the Sargasso Sea set for 9 mers and 15 mers and a side-by-side comparison with MEGAN results. There are 7 common strains between the naive Bayes sets substantiating their presence in the sample. Not all NBC “best matches” are found in MEGAN (indicated by “None”), and this can be due to “no hits” or to not having that strain in the database. An interesting NBC find is that Trichodesmium erythraeum has been found to compose 0.6% of the sample. It has been extensively found in the Sargasso Sea, but no prior methods show this presence in the Sargasso Sea data set.
| 9 mers | 15 mers | ||||
|---|---|---|---|---|---|
| High-strain content in sample (genome size of both sides) | No. of reads | No. of MEGAN reads | High-strain content in sample | No. of reads | No. of MEGAN reads |
| Burkholderia 383 (9.3 M) | 693 | 514 | Burkholderia 383 (9.3 M) | 2044 | 514 |
| Burkholderia Cenocepacia AU 1054 (14.6 M) | 684 | 13 | Clostridium Beijerinckii NCIMB 8052 (12 M) | 1698 | 2 |
| Clostridium beijerinckii NCIMB 8052 (12 M) | 623 | 2 | Shewanella ANA-3 (10.3 M) | 989 | 186 |
| Shewanella ANA-3 (10.3 M) | 562 | 186 | Trichodesmium erythraeum IMS101 (15.6 M) | 584 | 2 |
| Trichodesmium erythraeum IMS101 (15.6 M) | 533 | 2 | Flavobacterium johnsoniae UW101 (12.2 M) | 481 | 10 |
| Burholderia xenovorans LB400 (19.6 M) | 404 | None | Sorangium cellulosum So Ce 56 (26 M) | 309 | None |
| Shewanella MR-4 (9.4 M) | 329 | 14 | Shewanella oneidensis MR-1 (10.4 M) | 297 | 78 |
| Burholderia ambifaria/cepacia AMMD (15 M) | 265 | 91 | Shewanella MR-4 (9.4 M) | 245 | 14 |
| Alkaliphilius metalliredigens QYMF (9.8 M) | 261 | None | Burkholderia cenocepacia HI2424 (15.5 M) | 219 | 102 |
| Shewanella MR-7 (9.6 M) | 250 | 26 | Shewanella MR-7 (9.6 M) | 206 | 26 |
| Acidobacteria bacterium Ellin345 (11.6 M) | 187 | None | Burkholderia xenovorans LB400 (19.6 M) | 198 | None |