Schema for Drosophila Chain/Net - Drosophila Genomes, Chain and Net Alignments

Database: dm6 Primary Table: chainDpseGB3 Row Count: 15,465 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	9663	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8733	`int(10) unsigned`	range
`tEnd`	9258	`int(10) unsigned`	range
`qName`	CM000070	`varchar(255)`	values
`qSize`	30819483	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	30597513	`int(10) unsigned`	range
`qEnd`	30598038	`int(10) unsigned`	range
`id`	12127	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	9663	chr2L	23513712	8733	9258	CM000070	30819483	+	30597513	30598038	12127
585	19605	chr2L	23513712	8733	9282	CH379064	12541198	-	4237248	4237797	5871
585	16091	chr2L	23513712	8734	9282	CH379067	1469181	-	71037	71585	7261
585	12679	chr2L	23513712	8899	9282	CH379070	9197557	+	8506578	8506961	9187
585	2082198	chr2L	23513712	11214	117968	CH379059	1235759	-	1100467	1226334	166
585	30004	chr2L	23513712	22324	23056	CH379059	1235759	-	1097740	1098527	3799
585	8823	chr2L	23513712	27244	28219	CH379060	11685562	+	3037107	3037635	13265
73	817779	chr2L	23513712	117330	153215	CH379059	1235759	+	140714	180827	263
585	11344	chr2L	23513712	118607	119543	CH379059	1235759	-	896388	897174	10228
585	8712	chr2L	23513712	118717	119513	CH379061	6594820	+	2712082	2712795	13428

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

Drosophila Chain/Net (drosophilaChainNet) Track Description


	Description Genomic scaffolds from each Drosophila species are aligned against the D. melanogaster genome assembly (dm6) using LAST with default parameters. The alignments are then processed using the UCSC whole genome alignment protocol (i.e. chaining and netting). References Chain/Net Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003 100(20): 11484-11489. LAST Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93.

Description