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

Database: DhydGB1 Primary Table: geneidCEGMA Row Count: 19,165 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid_cegma-NWQH01000...	`varchar(255)`	values
`chrom`	NWQH01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	25271	`int(10) unsigned`	range
`txEnd`	32312	`int(10) unsigned`	range
`cdsStart`	25271	`int(10) unsigned`	range
`cdsEnd`	32312	`int(10) unsigned`	range
`exonCount`	7	`int(10) unsigned`	range
`exonStarts`	25271,25485,26820,27805,280...	`longblob`
`exonEnds`	25365,25634,26989,27988,283...	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-NWQH01000001_1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,1,0,1,1,0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	mRNA_geneid_cegma-NWQH01000001_1	NWQH01000001	+	25271	32312	25271	32312	7	25271,25485,26820,27805,28045,31673,32213,	25365,25634,26989,27988,28326,32153,32312,	geneid_cegma-NWQH01000001_1	unk	unk	0,1,0,1,1,0,0,
585	mRNA_geneid_cegma-NWQH01000001_2	NWQH01000001	-	38662	43116	38662	43116	5	38662,39239,40325,40605,43006,	39180,40217,40543,40758,43116,	geneid_cegma-NWQH01000001_2	unk	unk	1,1,2,2,0,
585	mRNA_geneid_cegma-NWQH01000001_3	NWQH01000001	+	45749	64771	45749	64771	5	45749,47184,51164,59849,64651,	45826,47533,51273,59902,64771,	geneid_cegma-NWQH01000001_3	unk	unk	0,2,0,1,0,
585	mRNA_geneid_cegma-NWQH01000001_4	NWQH01000001	+	68939	68999	68939	68999	1	68939,	68999,	geneid_cegma-NWQH01000001_4	unk	unk	0,
585	mRNA_geneid_cegma-NWQH01000001_5	NWQH01000001	-	71498	71648	71498	71648	1	71498,	71648,	geneid_cegma-NWQH01000001_5	unk	unk	0,
585	mRNA_geneid_cegma-NWQH01000001_6	NWQH01000001	-	73243	74676	73243	74676	4	73243,73664,73907,74238,	73600,73850,74177,74676,	geneid_cegma-NWQH01000001_6	unk	unk	0,0,0,0,
585	mRNA_geneid_cegma-NWQH01000001_7	NWQH01000001	-	78027	90569	78027	90569	5	78027,85714,88147,89061,90544,	78102,85733,88235,89088,90569,	geneid_cegma-NWQH01000001_7	unk	unk	0,2,1,1,0,
585	mRNA_geneid_cegma-NWQH01000001_8	NWQH01000001	+	91168	91255	91168	91255	1	91168,	91255,	geneid_cegma-NWQH01000001_8	unk	unk	0,
585	mRNA_geneid_cegma-NWQH01000001_9	NWQH01000001	+	97964	106082	97964	106082	6	97964,98511,99554,101481,101979,105926,	98438,98632,99720,101532,102103,106082,	geneid_cegma-NWQH01000001_9	unk	unk	0,0,1,2,2,0,
585	mRNA_geneid_cegma-NWQH01000001_10	NWQH01000001	+	107109	124469	107109	124469	5	107109,107913,110807,124032,124299,	107210,107977,110926,124058,124469,	geneid_cegma-NWQH01000001_10	unk	unk	0,2,0,2,1,

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