Schema for Gene Prediction - Gene Prediction

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Schema for Gene Prediction - Gene Prediction

Database: Radish Primary Table: genePred Row Count: 46,514

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	Rs025080.1	`varchar(255)`	values
`chrom`	R1	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	828	`int(10) unsigned`	range
`txEnd`	2526	`int(10) unsigned`	range
`cdsStart`	978	`int(10) unsigned`	range
`cdsEnd`	2319	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	828,	`longblob`
`exonEnds`	2526,	`longblob`
`score`	0	`int(11)`	range
`name2`	Rs025080	`varchar(255)`	values
`cdsStartStat`	incmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	incmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	Rs025080.1	R1	+	828	2526	978	2319	1	828,	2526,	0	Rs025080	incmpl	incmpl	0,
585	Rs035250.1	R1	+	21058	21755	21058	21755	2	21058,21440,	21364,21755,	0	Rs035250	incmpl	incmpl	0,0,
585	Rs035280.1	R1	-	34617	35130	34617	35130	2	34617,34978,	34873,35130,	0	Rs035280	incmpl	incmpl	1,0,
585	Rs035290.1	R1	+	42452	43198	42452	43198	3	42452,42785,43020,	42546,42831,43198,	0	Rs035290	incmpl	incmpl	0,2,1,
585	Rs035300.1	R1	-	54460	55423	54642	55229	2	54460,54985,	54854,55423,	0	Rs035300	incmpl	incmpl	2,0,
585	Rs035320.1	R1	+	75209	78577	75474	78249	6	75209,77011,77540,77769,77988,78171,	76788,77131,77657,77859,78096,78577,	0	Rs035320	incmpl	incmpl	0,0,0,0,0,0,
585	Rs035330.1	R1	-	78953	80084	78965	80084	1	78953,	80084,	0	Rs035330	incmpl	incmpl	0,
585	Rs035340.1	R1	-	81084	82792	81226	82747	6	81084,81322,81813,81975,82272,82597,	81241,81682,81897,82060,82502,82792,	0	Rs035340	incmpl	incmpl	0,0,0,1,0,0,
585	Rs000040.1	R1	-	98041	99279	98144	99279	4	98041,98436,98620,99205,	98228,98479,98740,99279,	0	Rs000040	incmpl	incmpl	0,1,1,0,
586	Rs000940.1	R1	-	165959	168042	165959	167868	3	165959,166358,167090,	166037,166450,168042,	0	Rs000940	incmpl	incmpl	0,2,0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.