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

Database: DmirGB2 Primary Table: augustusBUSCO Row Count: 13,658 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	CM001516.g1.t1	`varchar(255)`	values
`chrom`	CM001516	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	1943	`int(10) unsigned`	range
`txEnd`	4772	`int(10) unsigned`	range
`cdsStart`	1943	`int(10) unsigned`	range
`cdsEnd`	4772	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	1943,4478,	`longblob`
`exonEnds`	2138,4772,	`longblob`
`score`	0	`int(11)`	range
`name2`	CM001516.g1	`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	CM001516.g1.t1	CM001516	-	1943	4772	1943	4772	2	1943,4478,	2138,4772,	CM001516.g1	unk	unk	0,0,
585	CM001516.g2.t1	CM001516	+	15164	16790	15164	16790	7	15164,15381,15810,16042,16218,16314,16382,	15315,15759,15954,16158,16256,16324,16790,	CM001516.g2	unk	unk	0,1,1,1,0,2,0,
585	CM001516.g3.t1	CM001516	+	16973	18026	16973	18026	1	16973,	18026,	CM001516.g3	unk	unk	0,
585	CM001516.g4.t1	CM001516	+	18571	21013	18571	21013	5	18571,18878,19130,19789,20817,	18644,19050,19736,20737,21013,	CM001516.g4	unk	unk	0,1,2,2,2,
585	CM001516.g5.t1	CM001516	+	23489	29360	23489	29360	8	23489,24179,24309,24698,25969,26350,26512,29252,	24113,24243,24596,25922,26296,26439,28247,29360,	CM001516.g5	unk	unk	0,0,1,0,0,0,2,0,
585	CM001516.g6.t1	CM001516	-	30530	32317	30530	32317	3	30530,31094,31826,	31017,31757,32317,	CM001516.g6	unk	unk	2,2,0,
585	CM001516.g7.t1	CM001516	+	41785	44350	41785	44350	4	41785,42274,42504,43577,	41886,42415,43505,44350,	CM001516.g7	unk	unk	0,2,2,1,
585	CM001516.g8.t1	CM001516	+	46343	46843	46343	46843	2	46343,46539,	46465,46843,	CM001516.g8	unk	unk	0,2,
585	CM001516.g9.t1	CM001516	+	48663	50124	48663	50124	1	48663,	50124,	CM001516.g9	unk	unk	0,
585	CM001516.g10.t1	CM001516	+	55450	66501	55450	66501	9	55450,60574,61099,61417,64040,64220,64628,65129,66342,	55564,60991,61253,61569,64133,64571,64807,66264,66501,	CM001516.g10	unk	unk	0,0,0,1,0,0,0,2,0,

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