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

Database: DgriCAF1 Primary Table: geneidCEGMA Row Count: 21,293 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_100	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	140	`int(10) unsigned`	range
`txEnd`	152	`int(10) unsigned`	range
`cdsStart`	140	`int(10) unsigned`	range
`cdsEnd`	152	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	140,	`longblob`
`exonEnds`	152,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-scaffold_100_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_100_1	scaffold_100	-	140	152	140	152	1	140,	152,	geneid_cegma-scaffold_100_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10012_1	scaffold_10012	+	801	891	801	891	1	801,	891,	geneid_cegma-scaffold_10012_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10016_1	scaffold_10016	+	2	385	2	385	2	2,240,	178,385,	geneid_cegma-scaffold_10016_1	unk	unk	0,2,
585	mRNA_geneid_cegma-scaffold_10017_1	scaffold_10017	-	1097	1115	1097	1115	1	1097,	1115,	geneid_cegma-scaffold_10017_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10018_1	scaffold_10018	+	1638	1680	1638	1680	1	1638,	1680,	geneid_cegma-scaffold_10018_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10019_1	scaffold_10019	-	172	926	172	926	2	172,904,	213,926,	geneid_cegma-scaffold_10019_1	unk	unk	1,0,
585	mRNA_geneid_cegma-scaffold_10020_1	scaffold_10020	-	56	74	56	74	1	56,	74,	geneid_cegma-scaffold_10020_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10021_1	scaffold_10021	+	664	688	664	688	1	664,	688,	geneid_cegma-scaffold_10021_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10022_1	scaffold_10022	-	742	754	742	754	1	742,	754,	geneid_cegma-scaffold_10022_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10023_1	scaffold_10023	+	1369	1375	1369	1375	1	1369,	1375,	geneid_cegma-scaffold_10023_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