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

Database: DbusGB1 Primary Table: chainDm6 Row Count: 12,742 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	14588	`double`	range
`tName`	CP012523	`varchar(255)`	values
`tSize`	33300182	`int(10) unsigned`	range
`tStart`	23	`int(10) unsigned`	range
`tEnd`	1473	`int(10) unsigned`	range
`qName`	chr2L	`varchar(255)`	values
`qSize`	23513712	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	388995	`int(10) unsigned`	range
`qEnd`	389829	`int(10) unsigned`	range
`id`	6879	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	14588	CP012523	33300182	23	1473	chr2L	23513712	+	388995	389829	6879
585	383880	CP012523	33300182	2489	46211	chr2L	23513712	+	606155	651710	367
585	27900	CP012523	33300182	17104	19120	chr2L	23513712	-	22889502	22891329	3691
585	143446	CP012523	33300182	78723	93487	chr2L	23513712	-	19274885	19288730	881
585	17622	CP012523	33300182	90653	90884	chr3L	28110227	+	3899476	3899707	5704
585	17072	CP012523	33300182	90654	90884	chr3L	28110227	+	3900617	3900847	5905
585	18014	CP012523	33300182	90654	90884	chrX	23542271	+	6277378	6277608	5573
585	18014	CP012523	33300182	90654	90884	chrX	23542271	+	6277834	6278064	5572
585	16839	CP012523	33300182	90654	90884	chrX	23542271	+	6282725	6282955	5983
585	16817	CP012523	33300182	90654	90884	chr3L	28110227	+	3900389	3900619	5995

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. busckii genome assembly (DbusGB1) 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