Comparison # 3, Annotation Version: 1, date: 2007-05-12 01:02:07

some FL-assemblies may have been deprecated to EST status

Annotation Classification for Alignment Assemblies
	FL-assemblies		EST-assemblies
	PASS	fail	PASS	fail
Incorporated	558		2656
UTR addition	1652		2253
Gene extension	153	15	180	0
Internal gene structure rearrangement		0		1605
-passes homology tests	925		774
-fails homology, passes ORF span	0		0
Gene Merging	41	289	43	230
Gene Splitting	57	26
Alt Splicing Isoform		169
-passes homology test	639		273 169
-fails homology, passes ORF span	0		0
New Gene	662	103		2924
Alt splice of new gene	31	3	9	26
FL-assembly fails gene requirements		0
Antisense		853		0
Single-exon EST-assembly incompatible				1099
delayed incorporation due to gene merging		0		19
delayed incorporation due to gene splitting		8
Total	18444

Gene Comparison Overview

A total of 10720 genes mapped to PASA assemblies
8652 FL-assemblies mapped to 6946 genes
Successful Incorporations by Genes
Genes supported by PASA assemblies	8820
Genes supported by 7030 FL assemblies	6229
Genes supported by 4045 EST assemblies only (no FL assemblies)	2591
Failed Incorporations by Genes
Genes failing PASA assembly incorporation	3577
of these, 1677 genes successfully incorporate other PASA assemblies
Genes failing FL assembly incorporation	1318
but 601 of these genes incorporate other FL assemblies successfully.
Genes failing EST assemblies only	2259

The same gene may be counted in multiple categories.

Human Review is needed for PASA-FAILED models

status_id	Description	Num Gene Model Updates	Num Alt Splice isoforms to Add	Num Novel Genes to Add
19	EST assembly aligns to intergenic region.	0	0	2924
22	fl-cdna assembly provides novel gene which overlaps existing annotations	103	0	0
30	FL-cDNA overlaps multiple genes, but found incapable of merging them.	289	0	0
35	EST-assembly overlaps multiple genes, but found incapable of merging them.	230	0	0
41	FL-cDNAs suggest split single gene into multiple genes, failed automation	26	0	0
42	FL-cDNA aligns as antisense to existing annotated gene	267	0	586
7	gene-compatible fl-cdna assembly alters protein, fails validation.	15	0	0
18	EST assembly stitched into gene model fails validation.	1605	0	0
38	Delayed incorporation of EST-assembly due to successful merging operation.	19	0	0
39	Delayed incorporation of FL-assembly due to successful splitting operation	6	0	0
45	fl-cdna assembly provides isoform for novel gene which overlaps existing annotations	0	3	0
28	EST-assembly stitched into a FL-alignment but fails validation tests.	0	26	0
21	fl-cdna assembly provides alternate splicing isoform, fails validation	0	169	0
34	single-exon EST-assembly fails gene compatibility test	1099	0	0
	Totals (some models in multiple classes)	3659	198	3510

Proposed PASA-valid Annotation Updates [counts as unique models, not genes]

status_id	Description	Num Gene Model Updates	Num Alt Splice isoforms to Add	Num Novel Genes to Add
4	gene-compatible fl-cdna assembly alters UTRs.	1652	0	0
6	gene-compatible fl-cdna assembly alters protein, passed validation.	153	0	0
8	incompatible fl-cdna assembly alignment updates gene structure.	925	0	0
9	incompatible fl-cdna assembly provides alternative splicing isoform, passes validation.	0	639	0
10	fl-cdna assembly provides a novel gene.	0	0	662
24	FL-cDNA assembly stitched by EST assembly to provide alt splicing isoform.	0	169	0
26	FL-cDNA spans single gene and allowed to STOMP it.	0	0	0
29	FL-cDNA found capable of merging multiple genes	41	0	0
33	FL-assembly STOMPS new splice isoform	0	0	0
40	FL-cDNAs split single gene into multiple genes	57	0	0
44	FL-cDNA provides alt splicing isoform of a novel gene	0	31	0
13	EST assembly extends UTRs.	2179	0	0
14	EST assembly alters protein sequence, passes validation.	180	0	0
16	EST assembly properly stitched into gene structure.	754	0	0
17	EST assembly stitched into Gene model requires alternative splicing isoform. (deprecated, see status_ids: 24,25)	0	0	0
25	EST assembly stitched into Gene model requires alternative splicing isoform.	0	273	0
27	EST-assembly stitched into a FL-alignment providing new alt splice isoform.	0	9	0
31	EST-stitched assembly STOMPS model lacking transcript support.	0	0	0
32	EST-stitched gene w/preexisting transcript support STOMPS a new alt splicing variation.	0	0	0
36	EST-assembly found capable of merging multiple genes.	43	0	0
	Totals (some models in multiple classes)	5851	1121	662

Retrieve Lists of Genes Corresponding to Pass and Fail Categories.

Summarize Gene Structure Updates to be Performed.