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

Database: DyakCAF1 Primary Table: geneidCEGMA Row Count: 18,250 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid_cegma-chr2L_1	`varchar(255)`	values
`chrom`	chr2L	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	4432	`int(10) unsigned`	range
`txEnd`	15908	`int(10) unsigned`	range
`cdsStart`	4432	`int(10) unsigned`	range
`cdsEnd`	15908	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	4432,9465,15888,	`longblob`
`exonEnds`	4520,9507,15908,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-chr2L_1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,1,1,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	mRNA_geneid_cegma-chr2L_1	chr2L	+	4432	15908	4432	15908	3	4432,9465,15888,	4520,9507,15908,	geneid_cegma-chr2L_1	unk	unk	0,1,1,
585	mRNA_geneid_cegma-chr2L_2	chr2L	-	16689	47705	16689	47705	13	16689,17769,19442,21194,21490,22503,27559,28097,28211,30184,30752,32502,47635,	17144,17865,19464,21393,21928,22700,27815,28144,28404,30395,31284,33059,47705,	geneid_cegma-chr2L_2	unk	unk	1,1,0,2,2,0,2,0,2,1,0,1,0,
585	mRNA_geneid_cegma-chr2L_3	chr2L	+	55250	56498	55250	56498	2	55250,56413,	55348,56498,	geneid_cegma-chr2L_3	unk	unk	0,2,
585	mRNA_geneid_cegma-chr2L_4	chr2L	+	58564	70512	58564	70512	3	58564,64380,70491,	59046,64669,70512,	geneid_cegma-chr2L_4	unk	unk	0,2,0,
585	mRNA_geneid_cegma-chr2L_5	chr2L	-	72463	80745	72463	80745	3	72463,73236,80732,	72846,73485,80745,	geneid_cegma-chr2L_5	unk	unk	1,1,0,
585	mRNA_geneid_cegma-chr2L_6	chr2L	+	84208	87907	84208	87907	2	84208,87873,	84249,87907,	geneid_cegma-chr2L_6	unk	unk	0,2,
585	mRNA_geneid_cegma-chr2L_7	chr2L	-	88665	88788	88665	88788	1	88665,	88788,	geneid_cegma-chr2L_7	unk	unk	0,
585	mRNA_geneid_cegma-chr2L_8	chr2L	+	90394	93305	90394	93305	6	90394,90594,90940,91893,92369,93246,	90427,90724,90965,92246,92798,93305,	geneid_cegma-chr2L_8	unk	unk	0,0,1,2,1,1,
585	mRNA_geneid_cegma-chr2L_9	chr2L	-	95302	95935	95302	95935	1	95302,	95935,	geneid_cegma-chr2L_9	unk	unk	0,
585	mRNA_geneid_cegma-chr2L_10	chr2L	+	98063	102729	98063	102729	7	98063,99782,99927,100210,101108,101876,102620,	98187,99860,100050,100345,101221,102556,102729,	geneid_cegma-chr2L_10	unk	unk	0,1,1,1,1,0,2,

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

Methods

References