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

Database: DhydGB1 Primary Table: augustusBUSCO Row Count: 13,929 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	NWQH01000001.g1.t1	`varchar(255)`	values
`chrom`	NWQH01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	22743	`int(10) unsigned`	range
`txEnd`	27129	`int(10) unsigned`	range
`cdsStart`	22743	`int(10) unsigned`	range
`cdsEnd`	27129	`int(10) unsigned`	range
`exonCount`	4	`int(10) unsigned`	range
`exonStarts`	22743,25271,25485,26820,	`longblob`
`exonEnds`	22779,25365,25634,27129,	`longblob`
`score`	0	`int(11)`	range
`name2`	NWQH01000001.g1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	NWQH01000001.g1.t1	NWQH01000001	+	22743	27129	22743	27129	4	22743,25271,25485,26820,	22779,25365,25634,27129,	NWQH01000001.g1	unk	unk	0,0,1,0,
585	NWQH01000001.g2.t1	NWQH01000001	+	27867	32312	27867	32312	4	27867,28045,31673,32213,	27988,28326,32153,32312,	NWQH01000001.g2	unk	unk	0,1,0,0,
585	NWQH01000001.g3.t1	NWQH01000001	-	38662	41104	38662	41104	5	38662,39239,40325,40605,40893,	39180,40217,40543,40741,41104,	NWQH01000001.g3	unk	unk	1,1,2,1,0,
585	NWQH01000001.g4.t1	NWQH01000001	+	47111	51790	47111	51790	4	47111,47178,51164,51548,	47119,47533,51273,51790,	NWQH01000001.g4	unk	unk	0,2,0,1,
585	NWQH01000001.g5.t1	NWQH01000001	-	73243	74676	73243	74676	4	73243,73664,73907,74238,	73600,73850,74177,74676,	NWQH01000001.g5	unk	unk	0,0,0,0,
585	NWQH01000001.g6.t1	NWQH01000001	+	98015	102410	98015	102410	5	98015,98511,99458,101979,102158,	98438,98632,99720,102103,102410,	NWQH01000001.g6	unk	unk	0,0,1,2,0,
585	NWQH01000001.g7.t1	NWQH01000001	-	124207	125005	124207	125005	2	124207,124989,	124443,125005,	NWQH01000001.g7	unk	unk	1,0,
586	NWQH01000001.g8.t1	NWQH01000001	+	142001	142907	142001	142907	2	142001,142724,	142118,142907,	NWQH01000001.g8	unk	unk	0,0,
586	NWQH01000001.g9.t1	NWQH01000001	+	151250	152567	151250	152567	1	151250,	152567,	NWQH01000001.g9	unk	unk	0,
586	NWQH01000001.g10.t1	NWQH01000001	+	155217	155962	155217	155962	3	155217,155655,155777,	155323,155709,155962,	NWQH01000001.g10	unk	unk	0,1,1,

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