Schema for Geneid Genes (BUSCO) - Geneid Gene Predictions with CEGMA Training Set

Database: DperCAF1 Primary Table: geneidCEGMA Row Count: 20,204 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid_cegma-super_0_1	`varchar(255)`	values
`chrom`	super_0	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	25093	`int(10) unsigned`	range
`txEnd`	25135	`int(10) unsigned`	range
`cdsStart`	25093	`int(10) unsigned`	range
`cdsEnd`	25135	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	25093,	`longblob`
`exonEnds`	25135,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-super_0_1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	mRNA_geneid_cegma-super_0_1	super_0	+	25093	25135	25093	25135	1	25093,	25135,	geneid_cegma-super_0_1	unk	unk	0,
585	mRNA_geneid_cegma-super_0_2	super_0	+	31784	33970	31784	33970	3	31784,32065,33964,	32006,32143,33970,	geneid_cegma-super_0_2	unk	unk	0,0,0,
585	mRNA_geneid_cegma-super_0_3	super_0	-	34774	47937	34774	47937	8	34774,34853,35301,38231,38485,38912,39452,47887,	34796,35075,37410,38427,38618,39278,39576,47937,	geneid_cegma-super_0_3	unk	unk	2,2,2,1,0,0,2,0,
585	mRNA_geneid_cegma-super_0_4	super_0	-	53819	55119	53819	55119	2	53819,54870,	54671,55119,	geneid_cegma-super_0_4	unk	unk	0,0,
585	mRNA_geneid_cegma-super_0_5	super_0	+	59524	62149	59524	62149	3	59524,59625,61877,	59536,59659,62149,	geneid_cegma-super_0_5	unk	unk	0,0,1,
585	mRNA_geneid_cegma-super_0_6	super_0	+	63935	68040	63935	68040	2	63935,66008,	65587,68040,	geneid_cegma-super_0_6	unk	unk	0,2,
585	mRNA_geneid_cegma-super_0_7	super_0	+	69461	71762	69461	71762	1	69461,	71762,	geneid_cegma-super_0_7	unk	unk	0,
585	mRNA_geneid_cegma-super_0_8	super_0	+	74568	80801	74568	80801	3	74568,77776,79701,	74579,77796,80801,	geneid_cegma-super_0_8	unk	unk	0,2,1,
585	mRNA_geneid_cegma-super_0_9	super_0	+	81322	82456	81322	82456	2	81322,82279,	82108,82456,	geneid_cegma-super_0_9	unk	unk	0,0,
585	mRNA_geneid_cegma-super_0_10	super_0	-	83360	84050	83360	84050	1	83360,	84050,	geneid_cegma-super_0_10	unk	unk	0,

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

Geneid Genes (BUSCO) (geneidCEGMA) Track Description


	Description This track shows the gene predictions produced by geneid using species-specific parameters. Methods The species-specific geneid parameters were produced by CEGMA. References Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007 May 1;23(9):1061-7. Parra G, Blanco E, Guigó R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5.

Description