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

Database: DanaCAF1 Primary Table: augustusBUSCO Row Count: 12,826 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	scaffold_0.g26.t1	`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`	scaffold_0.g26	`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	scaffold_0.g26.t1	scaffold_0	+	0	334	0	334	2	0,157,	96,334,	scaffold_0.g26	unk	unk	0,0,
585	scaffold_10296.g87.t1	scaffold_10296	+	265	1246	265	1246	2	265,970,	590,1246,	scaffold_10296.g87	unk	unk	0,1,
585	scaffold_10492.g86.t1	scaffold_10492	+	341	518	341	518	1	341,	518,	scaffold_10492.g86	unk	unk	0,
585	scaffold_10550.g17.t1	scaffold_10550	+	181	1002	181	1002	1	181,	1002,	scaffold_10550.g17	unk	unk	0,
585	scaffold_10575.g6.t1	scaffold_10575	-	128	4991	128	4991	5	128,401,726,1205,4766,	345,589,946,1726,4991,	scaffold_10575.g6	unk	unk	2,0,2,0,0,
585	scaffold_11022.g23.t1	scaffold_11022	+	441	910	441	910	1	441,	910,	scaffold_11022.g23	unk	unk	0,
585	scaffold_11114.g29.t1	scaffold_11114	+	0	966	0	966	1	0,	966,	scaffold_11114.g29	unk	unk	0,
585	scaffold_11176.g126.t1	scaffold_11176	+	317	4792	317	4792	1	317,	4792,	scaffold_11176.g126	unk	unk	1,
585	scaffold_11239.g48.t1	scaffold_11239	-	712	1152	712	1152	2	712,930,	856,1152,	scaffold_11239.g48	unk	unk	0,0,
585	scaffold_11338.g41.t1	scaffold_11338	-	1030	1206	1030	1206	1	1030,	1206,	scaffold_11338.g41	unk	unk	1,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Augustus Genes (BUSCO) (augustusBUSCO) Track Description


	Description This track shows the gene models from the Augustus gene predictor using the species-specific parameters estimated from a training set produced by BUSCO. Methods The training set used to estimate the species-specific parameters for the Augustus analysis was produced by BUSCO using the arthropoda_odb9 dataset. Transposons remnants identified by RepeatMasker were provided as hints to the Augustus gene predictor. The following additional parameters were used with the Augustus gene predictor: --strand=both --noInFrameStop=true --gff3=on --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --cds=on --singlestrand=false --UTR=off --genemodel=partial References Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015 Oct 1;31(19):3210-2.

Description