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

Database: DanaCAF1 Primary Table: chainDm6 Row Count: 15,346 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	18763	`double`	range
`tName`	scaffold_0	`varchar(255)`	values
`tSize`	1069	`int(10) unsigned`	range
`tStart`	0	`int(10) unsigned`	range
`tEnd`	342	`int(10) unsigned`	range
`qName`	chr3R	`varchar(255)`	values
`qSize`	32079331	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	9033474	`int(10) unsigned`	range
`qEnd`	9033813	`int(10) unsigned`	range
`id`	5535	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	18763	scaffold_0	1069	0	342	chr3R	32079331	-	9033474	9033813	5535
585	30890	scaffold_1002	814	70	537	chr3L	28110227	-	6338113	6338590	3148
585	38713	scaffold_1002	814	70	705	chr2R	25286936	+	4702479	4703282	2459
585	28653	scaffold_1002	814	70	534	chr3L	28110227	-	762483	762931	3453
585	31904	scaffold_1002	814	97	730	chr2R	25286936	-	19611198	19611833	3039
585	27276	scaffold_1002	814	149	686	chr3L	28110227	+	24009446	24010078	3657
585	22307	scaffold_1002	814	224	710	chr3R	32079331	-	11244863	11245398	4579
585	21038	scaffold_1002	814	264	702	chr2R	25286936	+	6488031	6488604	4862
585	22668	scaffold_1002	814	288	713	chr3L	28110227	+	22803099	22803622	4491
585	18993	scaffold_1002	814	330	679	chr3L	28110227	+	24437043	24437557	5466

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. ananassae genome assembly (DanaCAF1) 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