Schema for Augustus - Augustus Gene Predictions

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Schema for Augustus - Augustus Gene Predictions

Database: DyakCAF1 Primary Table: augustus Row Count: 13,637 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	chr2L.g1.t1	`varchar(255)`	values
`chrom`	chr2L	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	9279	`int(10) unsigned`	range
`txEnd`	12822	`int(10) unsigned`	range
`cdsStart`	9279	`int(10) unsigned`	range
`cdsEnd`	12822	`int(10) unsigned`	range
`exonCount`	5	`int(10) unsigned`	range
`exonStarts`	9279,9784,10693,10856,12106,	`longblob`
`exonEnds`	9722,10427,10799,12048,12822,	`longblob`
`score`	0	`int(11)`	range
`name2`	chr2L.g1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	2,1,0,2,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	chr2L.g1.t1	chr2L	-	9279	12822	9279	12822	5	9279,9784,10693,10856,12106,	9722,10427,10799,12048,12822,	0	chr2L.g1	unk	unk	2,1,0,2,0,
585	chr2L.g2.t1	chr2L	-	16689	29753	16689	29753	17	16689,17518,17769,18264,18715,19281,21194,21490,22503,22955,23238,23487,24943,27371,28097,28211,29220,	17455,17711,17865,18649,18997,19407,21393,21928,22700,23134,23432,23574,25510,27815,28144,28695,29753,	0	chr2L.g2	unk	unk	2,1,1,0,0,0,2,2,0,1,2,2,2,2,0,2,0,
585	chr2L.g3.t1	chr2L	-	29805	47705	29805	47705	4	29805,32040,32502,47635,	31957,32237,33059,47705,	0	chr2L.g3	unk	unk	2,0,1,0,
585	chr2L.g4.t1	chr2L	+	56139	65401	56139	65401	7	56139,56413,56602,59103,61796,64196,64380,	56277,56545,59046,59300,62173,64312,65401,	0	chr2L.g4	unk	unk	0,0,0,2,1,0,2,
585	chr2L.g5.t1	chr2L	+	65718	67377	65718	67377	2	65718,67150,	66871,67377,	0	chr2L.g5	unk	unk	0,1,
585	chr2L.g6.t1	chr2L	-	72463	80745	72463	80745	2	72463,80732,	73485,80745,	0	chr2L.g6	unk	unk	1,0,
585	chr2L.g7.t1	chr2L	+	84208	93305	84208	93305	12	84208,84698,87227,87873,89130,89917,90107,90361,90594,91893,92369,93246,	84249,87178,87814,89070,89862,90049,90288,90540,90965,92246,92798,93305,	0	chr2L.g7	unk	unk	0,2,1,0,0,0,0,1,0,2,1,1,
585	chr2L.g8.t1	chr2L	-	93839	95179	93839	95179	4	93839,94370,94760,94881,	94314,94702,94825,95179,	0	chr2L.g8	unk	unk	2,0,1,0,
585	chr2L.g9.t1	chr2L	-	95302	95935	95302	95935	1	95302,	95935,	0	chr2L.g9	unk	unk	0,
585	chr2L.g10.t1	chr2L	+	98063	102729	98063	102729	6	98063,99782,99927,100177,101876,102620,	98187,99860,100050,100290,102556,102729,	0	chr2L.g10	unk	unk	0,1,1,1,0,2,

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

Augustus (augustus) Track Description


	Description This track shows the gene predictions from the Augustus program. The predictions are based on hints provided by the SPALN alignments of D. melanogaster proteins against the D. yakuba genome assembly, as well as splice junction predictions and assembled transcripts derived from D. yakuba RNA-Seq data. References Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. doi: 10.1093/bioinformatics/btn013. Iwata H, Gotoh O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Res. 2012 Nov 1;40(20):e161. doi: 10.1093/nar/gks708. Haas BJ et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512. Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 2019 Dec 16;20(1):278.