TABLE 2 .
Comparison of new gene set and original onea
| New versus old gene prediction | Gene count in complete genome | Gene count in secretome only |
|||
|---|---|---|---|---|---|
| With GPI |
Without GPI |
||||
| Auto | Manual | Auto | Manual | ||
| Matched | 2,662 | 47 (13) | 2 (2) | 155 (55) | 0 |
| Alternative | 1,246 | 19 (6) | 0 | 49 (19) | 1 |
| Different | 2,752 | 31 (6) | 1 | 83 (19) | 10 (4) |
| Merged | 286 | 5 (2) | 0 | 7 (2) | 1 |
| Split | 76 | 1 (1) | 0 | 5 (2) | 0 |
| New | 383 | 6 | 0 | 34 (8) | 0 |
| Total | 7,405 | 109 (28) | 3 (2) | 333 (105) | 12 (4) |
a
Matched, identical old and new gene annotations; alternative, conserved start and stop codons but different splicing; different, different start or stop codons, possibly different splicing; merged, more than one old gene merged into a single new one; split, old gene split into several new ones; new, genes found only in the new predictions (708 original genes were lost); auto, gene annotations as produced by Augustus; manual, manual correction of the start codon. The number of genes whose products were confirmed by mass spectrometry in culture supernatants is given in parentheses. GPI, glycosylphosphatidylinositol.