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

Database: DanaCAF1 Primary Table: geneidCEGMA Row Count: 20,427 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid_cegma-scaffold_0_1	`varchar(255)`	values
`chrom`	scaffold_0	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	0	`int(10) unsigned`	range
`txEnd`	334	`int(10) unsigned`	range
`cdsStart`	0	`int(10) unsigned`	range
`cdsEnd`	334	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	0,157,	`longblob`
`exonEnds`	96,334,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-scaffold_0_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	name2	cdsStartStat	cdsEndStat	exonFrames
585	mRNA_geneid_cegma-scaffold_0_1	scaffold_0	+	0	334	0	334	2	0,157,	96,334,	geneid_cegma-scaffold_0_1	unk	unk	0,0,
585	mRNA_geneid_cegma-scaffold_1000_1	scaffold_1000	-	1108	1138	1108	1138	1	1108,	1138,	geneid_cegma-scaffold_1000_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10002_1	scaffold_10002	-	7998	8004	7998	8004	1	7998,	8004,	geneid_cegma-scaffold_10002_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10003_1	scaffold_10003	+	1233	1254	1233	1254	1	1233,	1254,	geneid_cegma-scaffold_10003_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10007_1	scaffold_10007	-	4743	4748	4743	4748	1	4743,	4748,	geneid_cegma-scaffold_10007_1	unk	unk	1,
585	mRNA_geneid_cegma-scaffold_10010_1	scaffold_10010	-	3402	3411	3402	3411	1	3402,	3411,	geneid_cegma-scaffold_10010_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10012_1	scaffold_10012	-	7291	7321	7291	7321	1	7291,	7321,	geneid_cegma-scaffold_10012_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10013_1	scaffold_10013	+	6030	6045	6030	6045	1	6030,	6045,	geneid_cegma-scaffold_10013_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10014_1	scaffold_10014	-	1418	1433	1418	1433	1	1418,	1433,	geneid_cegma-scaffold_10014_1	unk	unk	0,
585	mRNA_geneid_cegma-scaffold_10015_1	scaffold_10015	-	15	21	15	21	1	15,	21,	geneid_cegma-scaffold_10015_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