Schema for SNAP - SNAP Gene Predictions

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Schema for SNAP - SNAP Gene Predictions

Database: DtakGB2 Primary Table: snap Row Count: 20,161 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	AFFI02000001-snap.1	`varchar(255)`	values
`chrom`	AFFI02000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	6773	`int(10) unsigned`	range
`txEnd`	8780	`int(10) unsigned`	range
`cdsStart`	6773	`int(10) unsigned`	range
`cdsEnd`	8780	`int(10) unsigned`	range
`exonCount`	4	`int(10) unsigned`	range
`exonStarts`	6773,6880,7003,8749,	`longblob`
`exonEnds`	6817,6930,7199,8780,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.AFFI02000001-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,2,1,2,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	AFFI02000001-snap.1	AFFI02000001	+	6773	8780	6773	8780	4	6773,6880,7003,8749,	6817,6930,7199,8780,	0	gene.AFFI02000001-snap.1	unk	unk	0,2,1,2,
585	AFFI02000003-snap.1	AFFI02000003	-	29065	32341	29065	32341	3	29065,30912,32328,	29133,31179,32341,	0	gene.AFFI02000003-snap.1	unk	unk	1,1,0,
585	AFFI02000004-snap.1	AFFI02000004	-	4306	6062	4306	6062	2	4306,5836,	4557,6062,	0	gene.AFFI02000004-snap.1	unk	unk	1,0,
585	AFFI02000004-snap.2	AFFI02000004	-	6812	7643	6812	7643	1	6812,	7643,	0	gene.AFFI02000004-snap.2	unk	unk	0,
585	AFFI02000009-snap.1	AFFI02000009	+	7776	17120	7776	17120	5	7776,10222,11516,15454,16065,	7791,11046,12293,15708,17120,	0	gene.AFFI02000009-snap.1	unk	unk	0,0,2,2,1,
585	AFFI02000009-snap.2	AFFI02000009	+	17689	19534	17689	19534	3	17689,18383,19046,	18043,18780,19534,	0	gene.AFFI02000009-snap.2	unk	unk	0,0,1,
585	AFFI02000009-snap.3	AFFI02000009	+	19833	20195	19833	20195	2	19833,20060,	19983,20195,	0	gene.AFFI02000009-snap.3	unk	unk	0,0,
585	AFFI02000009-snap.4	AFFI02000009	+	21249	26014	21249	26014	6	21249,24069,24284,25295,25831,26001,	21321,24204,24644,25424,25845,26014,	0	gene.AFFI02000009-snap.4	unk	unk	0,0,0,0,0,2,
585	AFFI02000009-snap.5	AFFI02000009	-	26034	26334	26034	26334	1	26034,	26334,	0	gene.AFFI02000009-snap.5	unk	unk	0,
585	AFFI02000009-snap.6	AFFI02000009	+	27122	27467	27122	27467	1	27122,	27467,	0	gene.AFFI02000009-snap.6	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