Schema for SNAP - SNAP Gene Predictions

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Schema for SNAP - SNAP Gene Predictions

Database: DperCAF1 Primary Table: snap Row Count: 19,870 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	super_0-snap.1	`varchar(255)`	values
`chrom`	super_0	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	31784	`int(10) unsigned`	range
`txEnd`	32191	`int(10) unsigned`	range
`cdsStart`	31784	`int(10) unsigned`	range
`cdsEnd`	32191	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	31784,32065,	`longblob`
`exonEnds`	32006,32191,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.super_0-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	super_0-snap.1	super_0	+	31784	32191	31784	32191	2	31784,32065,	32006,32191,	0	gene.super_0-snap.1	unk	unk	0,0,
585	super_0-snap.2	super_0	-	34257	53673	34257	53673	12	34257,34853,35301,37526,38231,38485,38912,39697,43764,44611,45558,53615,	34270,35204,37325,37836,38427,38570,39178,40021,44015,44686,45727,53673,	0	gene.super_0-snap.2	unk	unk	2,2,0,2,1,0,1,1,2,2,1,0,
585	super_0-snap.3	super_0	-	53819	63721	53819	63721	4	53819,54680,61214,63649,	54646,55194,61223,63721,	0	gene.super_0-snap.3	unk	unk	1,0,0,0,
585	super_0-snap.4	super_0	+	63655	65714	63655	65714	2	63655,64016,	64003,65714,	0	gene.super_0-snap.4	unk	unk	0,0,
585	super_0-snap.5	super_0	+	65961	68040	65961	68040	1	65961,	68040,	0	gene.super_0-snap.5	unk	unk	0,
585	super_0-snap.6	super_0	+	69461	72022	69461	72022	2	69461,71855,	71748,72022,	0	gene.super_0-snap.6	unk	unk	0,1,
585	super_0-snap.7	super_0	+	78158	80801	78158	80801	3	78158,79541,79701,	78201,79637,80801,	0	gene.super_0-snap.7	unk	unk	0,1,1,
585	super_0-snap.8	super_0	+	80903	83293	80903	83293	4	80903,81065,82321,82668,	81009,82108,82446,83293,	0	gene.super_0-snap.8	unk	unk	0,1,0,2,
585	super_0-snap.9	super_0	-	83360	84050	83360	84050	1	83360,	84050,	0	gene.super_0-snap.9	unk	unk	0,
585	super_0-snap.10	super_0	+	84686	87143	84686	87143	7	84686,85059,85598,85769,86491,86736,86994,	85000,85500,85707,86432,86676,86930,87143,	0	gene.super_0-snap.10	unk	unk	0,2,2,0,0,2,1,

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