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

Database: DkikGB2 Primary Table: chainDm6 Row Count: 19,480 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	57144	`double`	range
`tName`	AFFH02000026	`varchar(255)`	values
`tSize`	1698	`int(10) unsigned`	range
`tStart`	568	`int(10) unsigned`	range
`tEnd`	1698	`int(10) unsigned`	range
`qName`	chrY	`varchar(255)`	values
`qSize`	3667352	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	3028363	`int(10) unsigned`	range
`qEnd`	3029488	`int(10) unsigned`	range
`id`	2042	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	57144	AFFH02000026	1698	568	1698	chrY	3667352	-	3028363	3029488	2042
585	17589	AFFH02000026	1698	1049	1676	chr2R	25286936	-	8999978	9000605	7360
585	11885	AFFH02000037	1190	83	218	chr3L	28110227	+	17120845	17120980	11281
585	21025	AFFH02000039	454	22	366	chr2R	25286936	-	5867278	5867622	5942
585	11806	AFFH02000049	3104	2298	2621	chr3L	28110227	+	15581162	15581628	11343
585	22896	AFFH02000110	5649	758	4608	chrX	23542271	+	3634894	3637618	5406
585	16185	AFFH02000185	1645	1264	1594	chr2R	25286936	+	9284400	9284703	8061
585	14978	AFFH02000202	1593	1	312	chr2R	25286936	+	1451180	1451455	8799
585	17113	AFFH02000202	1593	1	312	chr2R	25286936	+	5038069	5038378	7590
585	12771	AFFH02000202	1593	1	258	chr2R	25286936	-	23241761	23242018	10501

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. kikkawai genome assembly (DkikGB2) 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