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

Database: DobsGB1 Primary Table: chainDm6 Row Count: 15,982 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	9	`smallint(5) unsigned`	range
`score`	10963718	`double`	range
`tName`	BDQP01000001	`varchar(255)`	values
`tSize`	2050314	`int(10) unsigned`	range
`tStart`	481	`int(10) unsigned`	range
`tEnd`	2050267	`int(10) unsigned`	range
`qName`	chr3R	`varchar(255)`	values
`qSize`	32079331	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	4876591	`int(10) unsigned`	range
`qEnd`	9045107	`int(10) unsigned`	range
`id`	18	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
9	10963718	BDQP01000001	2050314	481	2050267	chr3R	32079331	-	4876591	9045107	18
585	10828	BDQP01000001	2050314	28337	30661	chrX	23542271	+	3164683	3165666	11432
585	32383	BDQP01000001	2050314	49967	51612	chr2R	25286936	+	16415324	16418960	4327
585	44362	BDQP01000001	2050314	50094	51622	chr3R	32079331	+	12713702	12715138	3257
585	24439	BDQP01000001	2050314	50325	51471	chr2R	25286936	+	16415679	16416741	5523
585	9255	BDQP01000001	2050314	50765	51247	chr2R	25286936	+	16434697	16435179	13232
585	18333	BDQP01000001	2050314	88673	89998	chr3L	28110227	+	14988068	14990539	7091
585	17490	BDQP01000001	2050314	88697	89999	chr2L	23513712	-	11458551	11460748	7428
585	12321	BDQP01000001	2050314	96980	97317	chr3R	32079331	-	4983581	4983918	10212
585	22934	BDQP01000001	2050314	100746	101373	chr3R	32079331	-	4979916	4980878	5812

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. obscura genome assembly (DobsGB1) 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