Comparison # 1, Annotation Version: 1, date: 2008-11-01 17:20:58

some FL-assemblies may have been deprecated to EST status

Annotation Classification for Alignment Assemblies
	FL-assemblies		EST-assemblies
	PASS	fail	PASS	fail
Incorporated	0		6351
UTR addition	0		2388
Gene extension	0	0	655	0
Internal gene structure rearrangement		0		1604
-passes homology tests	0		783
-fails homology, passes ORF span	0		0
Gene Merging	0	0	160	677
Gene Splitting	0	0
Alt Splicing Isoform		0
-passes homology test	0		1102 0
-fails homology, passes ORF span	0		0
New Gene	0	0		3094
Alt splice of new gene	0	0	0	0
FL-assembly fails gene requirements		0
Antisense		0		452
Single-exon EST-assembly incompatible				908
delayed incorporation due to gene merging		0		37
delayed incorporation due to gene splitting		0
Total	18211

Gene Comparison Overview

A total of 10595 genes mapped to PASA assemblies
0 FL-assemblies mapped to 0 genes
Successful Incorporations by Genes
Genes supported by PASA assemblies	9151
Genes supported by 0 FL assemblies	0
Genes supported by 11439 EST assemblies only (no FL assemblies)	9151
Failed Incorporations by Genes
Genes failing PASA assembly incorporation	3085
of these, 1641 genes successfully incorporate other PASA assemblies
Genes failing FL assembly incorporation	0
but 0 of these genes incorporate other FL assemblies successfully.
Genes failing EST assemblies only	3085

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	3094
35	EST-assembly overlaps multiple genes, but found incapable of merging them.	677	0	0
18	EST assembly stitched into gene model fails validation.	1604	0	0
38	Delayed incorporation of EST-assembly due to successful merging operation.	32	0	0
34	single-exon EST-assembly fails gene compatibility test	908	0	0
43	EST assembly aligns as antisense to existing annotated gene	0	0	452
	Totals (some models in multiple classes)	3221	0	3546

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.	0	0	0
6	gene-compatible fl-cdna assembly alters protein, passed validation.	0	0	0
8	incompatible fl-cdna assembly alignment updates gene structure.	0	0	0
9	incompatible fl-cdna assembly provides alternative splicing isoform, passes validation.	0	0	0
10	fl-cdna assembly provides a novel gene.	0	0	0
24	FL-cDNA assembly stitched by EST assembly to provide alt splicing isoform.	0	0	0
26	FL-cDNA spans single gene and allowed to STOMP it.	0	0	0
29	FL-cDNA found capable of merging multiple genes	0	0	0
33	FL-assembly STOMPS new splice isoform	0	0	0
40	FL-cDNAs split single gene into multiple genes	0	0	0
44	FL-cDNA provides alt splicing isoform of a novel gene	0	0	0
13	EST assembly extends UTRs.	2332	0	0
14	EST assembly alters protein sequence, passes validation.	650	0	0
16	EST assembly properly stitched into gene structure.	765	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	1102	0
27	EST-assembly stitched into a FL-alignment providing new alt splice isoform.	0	0	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.	160	0	0
	Totals (some models in multiple classes)	3765	1102	0

Retrieve Lists of Genes Corresponding to Pass and Fail Categories.

Summarize Gene Structure Updates to be Performed.