Table 3.
Annotation statistics for ESTIMA:Songbird Build 3
| Build 3 | Percent total | 20 K array subset | Percent of array | Percent of Build 3 category | |
| Unique sequences after assembly | 31658 | 100% | 17214 | 100% | 54% |
| A) ALL HITS BY DATABASE | |||||
| Gga Genome | 21601 | 68% | 12396 | 72% | 57% |
| Chicken_TC | 20208 | 64% | 11715 | 68% | 58% |
| Gga Unigene | 17980 | 57% | 10490 | 61% | 58% |
| NCBI_Chicken_RNA | 15904 | 50% | 9110 | 53% | 57% |
| Ensembl_Chicken_cdna_all | 14609 | 46% | 8348 | 48% | 57% |
| Ensembl_Chicken_cdna_abinitio | 13223 | 42% | 7588 | 44% | 57% |
| Chicken IPI | 13219 | 42% | 7898 | 46% | 60% |
| Hs Unigene | 12373 | 39% | 7224 | 42% | 58% |
| NCBI_Chicken_protein | 7776 | 25% | 4517 | 26% | 58% |
| Hits against any database | 24466 | 77% | 13803 | 80% | 56% |
| B) Hierarchy of CUSTOM ANNOTATION | |||||
| 1 Use IPI-annotation* | 13219 | 42% | 7553 | 44% | 57% |
| 2 in GGA_Unigene but not IPI | 5614 | 18% | 3364 | 20% | 60% |
| 3 in HS but not IPI or GGA_unigene | 265 | 1% | 104 | 1% | 39% |
| Total number of "custom annotations" | 19098 | 60% | 11021 | 64% | 58% |
| 4 additional "conserved in chicken" | 5368 | 17% | 2784 | 16% | 52% |
| Hits against any database | 24466 | 77% | 13805 | 80% | 56% |
| 5 remainder = "TGU-specific" (no hits) | 7192 | 23% | 3409 | 20% | 47% |
| 31658 | 100% | 17214 | 100% | 54% | |
| *C) IPI Annotations | |||||
| Number of sequences with IPI identifiers | 13219 | 7898 | (Unigene used for 345) | ||
| Number of unique IPI identifiers | 8127 | 6035 | |||
| All identifiers in IPI release 3.26 | 25500 | 25500 | |||
| Fraction of total IPI identifiers | 32% | 24% | |||