|
Annotation statistics for ESTIMA:Songbird Build 3 |
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| 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% |
|
|
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| A) ALL HITS BY DATABASE |
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| 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% |
|||
Replogle et al. BMC Genomics 2008 9:131 doi:10.1186/1471-2164-9-131 |
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