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

Database: DariGB1 Primary Table: geneidCEGMA Row Count: 19,272 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid_cegma-LSRM01000...	`varchar(255)`	values
`chrom`	LSRM01000001	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	6123	`int(10) unsigned`	range
`txEnd`	6213	`int(10) unsigned`	range
`cdsStart`	6123	`int(10) unsigned`	range
`cdsEnd`	6213	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	6123,	`longblob`
`exonEnds`	6213,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-LSRM01000001_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-LSRM01000001_1	LSRM01000001	-	6123	6213	6123	6213	1	6123,	6213,	geneid_cegma-LSRM01000001_1	unk	unk	0,
585	mRNA_geneid_cegma-LSRM01000001_2	LSRM01000001	+	11137	11651	11137	11651	2	11137,11607,	11174,11651,	geneid_cegma-LSRM01000001_2	unk	unk	0,1,
585	mRNA_geneid_cegma-LSRM01000001_3	LSRM01000001	-	14550	15744	14550	15744	1	14550,	15744,	geneid_cegma-LSRM01000001_3	unk	unk	0,
585	mRNA_geneid_cegma-LSRM01000001_4	LSRM01000001	+	21525	21864	21525	21864	1	21525,	21864,	geneid_cegma-LSRM01000001_4	unk	unk	0,
585	mRNA_geneid_cegma-LSRM01000001_5	LSRM01000001	+	30904	32784	30904	32784	2	30904,32740,	30944,32784,	geneid_cegma-LSRM01000001_5	unk	unk	0,1,
585	mRNA_geneid_cegma-LSRM01000001_6	LSRM01000001	-	33867	41913	33867	41913	3	33867,37414,41855,	33888,37440,41913,	geneid_cegma-LSRM01000001_6	unk	unk	0,1,0,
585	mRNA_geneid_cegma-LSRM01000001_7	LSRM01000001	+	43308	44536	43308	44536	2	43308,44412,	43322,44536,	geneid_cegma-LSRM01000001_7	unk	unk	0,2,
585	mRNA_geneid_cegma-LSRM01000001_8	LSRM01000001	+	56903	58395	56903	58395	2	56903,58365,	56930,58395,	geneid_cegma-LSRM01000001_8	unk	unk	0,0,
585	mRNA_geneid_cegma-LSRM01000001_9	LSRM01000001	-	62856	66754	62856	66754	3	62856,64406,66048,	63409,65226,66754,	geneid_cegma-LSRM01000001_9	unk	unk	2,1,0,
585	mRNA_geneid_cegma-LSRM01000001_10	LSRM01000001	+	67641	69510	67641	69510	3	67641,67781,68153,	67703,68093,69510,	geneid_cegma-LSRM01000001_10	unk	unk	0,2,2,

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