Table 2. Features of the metagenomes generated by 454 pyrosequencing of three hydrocarbon-degrading methanogenic enrichment cultures.
| NAPDC | SCADC | TOLDC | |
|---|---|---|---|
| Number of raw reads post-quality control (QC) | 368 209 | 667 134 | 550 247 |
| Unassembled reads post-QC (bp) | 130 215 413 | 230 716 341 | 215 982 194 |
| Mean read length post-QC (bp) | 353.65 | 345.83 | 392.52 |
| Newbler assembly | |||
| Total length of contigs (bp) | 9 473 370 | 17 382 962 | 20 280 655 |
| Number of contigs | 8471 | 15 274 | 10 888 |
| Range of contig lengths (bp) | 200–26 000 | 200–26 000 | 200–28 000 |
| Mean contig length (bp) | 1118 | 1138 | 1863 |
| Largest contig (bp) | 25 813 | 26 073 | 28 253 |
| Number of singletons | 161 851 | 326 382 | 179 067 |
| N50 | 1330 | 1343 | 2813 |
| Number of predicted proteins | 133 107 | 261 378 | 170 842 |
| Number of rRNA genesa | 23/54/155 | 46/135/267 | 29/104/189 |
| Number of tRNA genes | 816 | 1322 | 891 |
| MG-RAST data (assembled) | |||
| MG-RAST ID | 4492772.3 | 4492619.3 | 4492778.3 |
| Metagenome size (bp) | 64 676 632 | 127 644 733 | 89 513 841 |
| Average sequence length (bp) | 379±352 | 373±310 | 471±647 |
| Number of sequences | 170 322 | 341 656 | 189 955 |
| GC content (%) | 49±8% | 50±9% | 53±9% |
| Number of predicted ORFs | 162 642 | 325 794 | 187 741 |
| ORFs with predicted function | 94 562 | 184 014 | 105 547 |
| Alpha diversityb | 662 | 771 | 907 |
Abbreviations: NAPDC, naphtha-degrading culture; SCADC, short chain alkane-degrading culture; TOLDC, toluene-degrading culture.
a
5S, 16S and 23S, respectively.
b
Number of distinct species in a given metagenome sample as calculated by MG-RAST.