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

Database: DereCAF1 Primary Table: geneidCEGMA Row Count: 15,550 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid_cegma-scaffold_...	`varchar(255)`	values
`chrom`	scaffold_1000	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	380	`int(10) unsigned`	range
`txEnd`	419	`int(10) unsigned`	range
`cdsStart`	380	`int(10) unsigned`	range
`cdsEnd`	419	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	380,	`longblob`
`exonEnds`	419,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-scaffold_1000_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-scaffold_1000_1	scaffold_1000	-	380	419	380	419	1	380,	419,	geneid_cegma-scaffold_1000_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_1002_1	scaffold_1002	-	1299	1311	1299	1311	1	1299,	1311,	geneid_cegma-scaffold_1002_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_1007_1	scaffold_1007	-	810	816	810	816	1	810,	816,	geneid_cegma-scaffold_1007_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_1009_1	scaffold_1009	+	0	18	0	18	1	0,	18,	geneid_cegma-scaffold_1009_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_1010_1	scaffold_1010	+	1975	1987	1975	1987	1	1975,	1987,	geneid_cegma-scaffold_1010_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_1012_1	scaffold_1012	-	1355	1367	1355	1367	1	1355,	1367,	geneid_cegma-scaffold_1012_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_102_1	scaffold_102	-	2377	2383	2377	2383	1	2377,	2383,	geneid_cegma-scaffold_102_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_1023_1	scaffold_1023	+	1265	1268	1265	1268	1	1265,	1268,	geneid_cegma-scaffold_1023_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_1029_1	scaffold_1029	+	0	33	0	33	1	0,	33,	geneid_cegma-scaffold_1029_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_103_1	scaffold_103	-	1733	1745	1733	1745	1	1733,	1745,	geneid_cegma-scaffold_103_1	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