Schema for SNAP - SNAP Gene Predictions

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Schema for SNAP - SNAP Gene Predictions

Database: DanaCAF1 Primary Table: snap Row Count: 16,247 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_10217-snap.1	`varchar(255)`	values
`chrom`	scaffold_10217	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	7019	`int(10) unsigned`	range
`txEnd`	7405	`int(10) unsigned`	range
`cdsStart`	7019	`int(10) unsigned`	range
`cdsEnd`	7405	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	7019,7396,	`longblob`
`exonEnds`	7304,7405,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.scaffold_10217-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	scaffold_10217-snap.1	scaffold_10217	-	7019	7405	7019	7405	2	7019,7396,	7304,7405,	0	gene.scaffold_10217-snap.1	unk	unk	0,0,
585	scaffold_10296-snap.1	scaffold_10296	+	265	1246	265	1246	2	265,970,	590,1246,	0	gene.scaffold_10296-snap.1	unk	unk	0,1,
585	scaffold_10492-snap.1	scaffold_10492	+	58	518	58	518	2	58,341,	191,518,	0	gene.scaffold_10492-snap.1	unk	unk	2,0,
585	scaffold_10550-snap.1	scaffold_10550	+	181	946	181	946	1	181,	946,	0	gene.scaffold_10550-snap.1	unk	unk	0,
585	scaffold_10575-snap.1	scaffold_10575	-	206	4991	206	4991	7	206,401,726,1205,2723,3182,4766,	345,664,946,1792,2751,3190,4991,	0	gene.scaffold_10575-snap.1	unk	unk	2,0,2,0,2,0,0,
585	scaffold_11114-snap.1	scaffold_11114	+	37	966	37	966	1	37,	966,	0	gene.scaffold_11114-snap.1	unk	unk	1,
585	scaffold_11176-snap.1	scaffold_11176	+	883	4792	883	4792	4	883,1402,2137,3502,	1162,1681,2716,4792,	0	gene.scaffold_11176-snap.1	unk	unk	0,0,0,0,
585	scaffold_11239-snap.1	scaffold_11239	-	712	1172	712	1172	2	712,930,	856,1172,	0	gene.scaffold_11239-snap.1	unk	unk	0,1,
585	scaffold_11430-snap.1	scaffold_11430	+	72	686	72	686	1	72,	686,	0	gene.scaffold_11430-snap.1	unk	unk	1,
585	scaffold_11666-snap.1	scaffold_11666	+	28	769	28	769	1	28,	769,	0	gene.scaffold_11666-snap.1	unk	unk	0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

SNAP (snap) Track Description


	Description This track shows predictions from the SNAP program written by Ian Korf. The predictions are based on transcriptional, translational, and donor/acceptor splicing signals, as well as the length and compositional distributions of exons, introns and intergenic regions. References Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59