Schema for SNAP - SNAP Gene Predictions

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Schema for SNAP - SNAP Gene Predictions

Database: DereCAF1 Primary Table: snap Row Count: 16,219 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_1230-snap.1	`varchar(255)`	values
`chrom`	scaffold_1230	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	250	`int(10) unsigned`	range
`txEnd`	964	`int(10) unsigned`	range
`cdsStart`	250	`int(10) unsigned`	range
`cdsEnd`	964	`int(10) unsigned`	range
`exonCount`	4	`int(10) unsigned`	range
`exonStarts`	250,423,741,886,	`longblob`
`exonEnds`	367,667,832,964,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.scaffold_1230-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	2,1,0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	scaffold_1230-snap.1	scaffold_1230	-	250	964	250	964	4	250,423,741,886,	367,667,832,964,	0	gene.scaffold_1230-snap.1	unk	unk	2,1,0,0,
585	scaffold_1240-snap.1	scaffold_1240	-	388	1364	388	1364	1	388,	1364,	0	gene.scaffold_1240-snap.1	unk	unk	2,
585	scaffold_1245-snap.1	scaffold_1245	-	424	1156	424	1156	1	424,	1156,	0	gene.scaffold_1245-snap.1	unk	unk	1,
585	scaffold_1246-snap.1	scaffold_1246	+	330	1113	330	1113	1	330,	1113,	0	gene.scaffold_1246-snap.1	unk	unk	0,
585	scaffold_1247-snap.1	scaffold_1247	-	22	1170	22	1170	2	22,298,	275,1170,	0	gene.scaffold_1247-snap.1	unk	unk	0,1,
585	scaffold_1251-snap.1	scaffold_1251	+	758	1475	758	1475	1	758,	1475,	0	gene.scaffold_1251-snap.1	unk	unk	0,
585	scaffold_1252-snap.1	scaffold_1252	-	22	727	22	727	2	22,697,	616,727,	0	gene.scaffold_1252-snap.1	unk	unk	0,0,
585	scaffold_1253-snap.1	scaffold_1253	-	299	1874	299	1874	2	299,1724,	1328,1874,	0	gene.scaffold_1253-snap.1	unk	unk	1,1,
585	scaffold_1255-snap.1	scaffold_1255	+	318	900	318	900	1	318,	900,	0	gene.scaffold_1255-snap.1	unk	unk	0,
585	scaffold_1259-snap.1	scaffold_1259	-	133	1248	133	1248	2	133,993,	220,1248,	0	gene.scaffold_1259-snap.1	unk	unk	2,2,

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