Schema for SNAP - SNAP Gene Predictions

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Schema for SNAP - SNAP Gene Predictions

Database: DbusGB1 Primary Table: snap Row Count: 12,682 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CP012523-snap.1	`varchar(255)`	values
`chrom`	CP012523	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	34561	`int(10) unsigned`	range
`txEnd`	45516	`int(10) unsigned`	range
`cdsStart`	34561	`int(10) unsigned`	range
`cdsEnd`	45516	`int(10) unsigned`	range
`exonCount`	6	`int(10) unsigned`	range
`exonStarts`	34561,38845,42334,42770,437...	`longblob`
`exonEnds`	37830,40134,42707,43181,448...	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.CP012523-snap.1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,2,1,1,0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	CP012523-snap.1	CP012523	-	34561	45516	34561	45516	6	34561,38845,42334,42770,43722,45498,	37830,40134,42707,43181,44872,45516,	0	gene.CP012523-snap.1	unk	unk	1,2,1,1,0,0,
585	CP012523-snap.2	CP012523	-	90497	90884	90497	90884	1	90497,	90884,	0	gene.CP012523-snap.2	unk	unk	0,
585	CP012523-snap.3	CP012523	+	91620	93601	91620	93601	2	91620,91729,	91665,93601,	0	gene.CP012523-snap.3	unk	unk	0,0,
585	CP012523-snap.4	CP012523	+	94410	99588	94410	99588	11	94410,94667,95078,95540,96284,96977,97181,97784,98112,98413,99028,	94605,94887,95477,95785,96495,97118,97725,97996,98283,98554,99588,	0	gene.CP012523-snap.4	unk	unk	0,0,1,1,0,1,1,2,1,1,1,
585	CP012523-snap.5	CP012523	+	99675	101280	99675	101280	3	99675,100286,101165,	100224,101101,101280,	0	gene.CP012523-snap.5	unk	unk	0,0,2,
585	CP012523-snap.6	CP012523	+	105611	109828	105611	109828	3	105611,105809,106540,	105639,106489,109828,	0	gene.CP012523-snap.6	unk	unk	0,1,0,
585	CP012523-snap.7	CP012523	-	110982	111957	110982	111957	1	110982,	111957,	0	gene.CP012523-snap.7	unk	unk	0,
585	CP012523-snap.8	CP012523	+	112398	112989	112398	112989	3	112398,112530,112896,	112456,112841,112989,	0	gene.CP012523-snap.8	unk	unk	0,1,0,
585	CP012523-snap.9	CP012523	+	115173	116307	115173	116307	4	115173,115264,115582,115954,	115199,115530,115756,116307,	0	gene.CP012523-snap.9	unk	unk	0,2,1,1,
73	CP012523-snap.10	CP012523	-	128700	131725	128700	131725	3	128700,130727,131640,	128727,131068,131725,	0	gene.CP012523-snap.10	unk	unk	0,1,0,

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