Schema for SNAP - SNAP Gene Predictions

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Schema for SNAP - SNAP Gene Predictions

Database: DmirGB2 Primary Table: snap Row Count: 18,103 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CM001516-snap.1	`varchar(255)`	values
`chrom`	CM001516	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	1943	`int(10) unsigned`	range
`txEnd`	2232	`int(10) unsigned`	range
`cdsStart`	1943	`int(10) unsigned`	range
`cdsEnd`	2232	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	1943,2181,	`longblob`
`exonEnds`	2138,2232,	`longblob`
`score`	0	`int(11)`	range
`name2`	gene.CM001516-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	CM001516-snap.1	CM001516	-	1943	2232	1943	2232	2	1943,2181,	2138,2232,	0	gene.CM001516-snap.1	unk	unk	0,0,
585	CM001516-snap.2	CM001516	-	4412	4772	4412	4772	1	4412,	4772,	0	gene.CM001516-snap.2	unk	unk	0,
585	CM001516-snap.3	CM001516	+	15164	16790	15164	16790	5	15164,15342,15943,16218,16356,	15315,15759,16158,16324,16790,	0	gene.CM001516-snap.3	unk	unk	0,1,1,0,1,
585	CM001516-snap.4	CM001516	+	16973	18026	16973	18026	1	16973,	18026,	0	gene.CM001516-snap.4	unk	unk	0,
585	CM001516-snap.5	CM001516	+	18571	19054	18571	19054	2	18571,18878,	18644,19054,	0	gene.CM001516-snap.5	unk	unk	0,1,
585	CM001516-snap.6	CM001516	+	19173	23331	19173	23331	4	19173,19731,20817,23254,	19690,20737,20987,23331,	0	gene.CM001516-snap.6	unk	unk	0,1,2,1,
585	CM001516-snap.7	CM001516	+	23489	24251	23489	24251	1	23489,	24251,	0	gene.CM001516-snap.7	unk	unk	0,
585	CM001516-snap.8	CM001516	+	24332	29360	24332	29360	7	24332,24698,25430,25969,26350,26512,29252,	24596,25178,25922,26296,26439,28247,29360,	0	gene.CM001516-snap.8	unk	unk	0,0,0,0,0,2,0,
585	CM001516-snap.9	CM001516	-	29895	40770	29895	40770	6	29895,30534,31094,31826,32581,40702,	29992,31017,31757,32365,32663,40770,	0	gene.CM001516-snap.9	unk	unk	2,2,2,0,2,0,
585	CM001516-snap.10	CM001516	+	41323	44350	41323	44350	5	41323,41432,41776,42274,42504,	41337,41676,41886,42415,44350,	0	gene.CM001516-snap.10	unk	unk	0,2,0,2,2,

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