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

Database: DeugGB2 Primary Table: chainDm6 Row Count: 20,478 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	19569	`double`	range
`tName`	AFPQ02000001	`varchar(255)`	values
`tSize`	1356	`int(10) unsigned`	range
`tStart`	2	`int(10) unsigned`	range
`tEnd`	334	`int(10) unsigned`	range
`qName`	chr3R	`varchar(255)`	values
`qSize`	32079331	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	25394835	`int(10) unsigned`	range
`qEnd`	25395162	`int(10) unsigned`	range
`id`	7059	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	19569	AFPQ02000001	1356	2	334	chr3R	32079331	-	25394835	25395162	7059
585	51155	AFPQ02000004	1047	0	1047	chr3R	32079331	-	25406256	25407444	1980
585	15057	AFPQ02000005	1025	350	945	chr3L	28110227	-	6176790	6177291	9630
585	33898	AFPQ02000006	1030	120	886	chr3L	28110227	-	6240024	6240687	3610
585	27832	AFPQ02000007	1132	3	1131	chr3R	32079331	-	8627379	8628077	4634
585	13004	AFPQ02000008	704	120	696	chr3R	32079331	-	14180013	14180642	11275
585	50466	AFPQ02000009	1056	0	1056	chr3R	32079331	-	14209466	14210358	2034
585	39447	AFPQ02000010	1226	161	1193	chr3R	32079331	+	8917976	8918788	2944
585	60233	AFPQ02000014	1132	6	1123	chr3R	32079331	+	24986428	24987531	1509
585	28639	AFPQ02000015	1022	18	1016	chr3R	32079331	+	24985769	24986666	4477

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. eugracilis genome assembly (DeugGB2) 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