Schema for SNAP - SNAP Gene Predictions

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Schema for SNAP - SNAP Gene Predictions

Database: DpseGB3 Primary Table: snap Row Count: 18,775 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CH379058-snap.1	`varchar(255)`	values
`chrom`	CH379058	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	130	`int(10) unsigned`	range
`txEnd`	557	`int(10) unsigned`	range
`cdsStart`	130	`int(10) unsigned`	range
`cdsEnd`	557	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	130,541,	`longblob`
`exonEnds`	477,557,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.CH379058-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	CH379058-snap.1	CH379058	-	130	557	130	557	2	130,541,	477,557,	0	gene.CH379058-snap.1	unk	unk	1,0,
585	CH379058-snap.2	CH379058	+	2856	14405	2856	14405	7	2856,6228,7636,8127,10191,12776,14351,	3006,6412,7739,8217,10236,12873,14405,	0	gene.CH379058-snap.2	unk	unk	0,0,1,2,2,2,0,
585	CH379058-snap.3	CH379058	-	17120	22628	17120	22628	1	17120,	22628,	0	gene.CH379058-snap.3	unk	unk	0,
585	CH379058-snap.4	CH379058	-	26783	27497	26783	27497	2	26783,27440,	26939,27497,	0	gene.CH379058-snap.4	unk	unk	0,0,
585	CH379058-snap.5	CH379058	+	40573	48580	40573	48580	3	40573,43176,48541,	40714,43272,48580,	0	gene.CH379058-snap.5	unk	unk	0,0,0,
585	CH379058-snap.6	CH379058	-	45890	46115	45890	46115	1	45890,	46115,	0	gene.CH379058-snap.6	unk	unk	0,
585	CH379058-snap.7	CH379058	+	49114	51015	49114	51015	2	49114,50935,	49274,51015,	0	gene.CH379058-snap.7	unk	unk	0,1,
585	CH379058-snap.8	CH379058	+	52434	58473	52434	58473	7	52434,56117,56367,56796,57379,57841,58214,	52481,56243,56395,56860,57776,58099,58473,	0	gene.CH379058-snap.8	unk	unk	0,2,2,0,1,2,2,
585	CH379058-snap.9	CH379058	-	53572	56086	53572	56086	3	53572,55639,55922,	53685,55836,56086,	0	gene.CH379058-snap.9	unk	unk	1,2,0,
585	CH379058-snap.10	CH379058	+	58811	59477	58811	59477	3	58811,58972,59383,	58899,59324,59477,	0	gene.CH379058-snap.10	unk	unk	0,1,2,

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