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

Database: DhydGB1 Primary Table: chainDm6 Row Count: 13,685 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	203249	`double`	range
`tName`	NWQH01000001	`varchar(255)`	values
`tSize`	3368585	`int(10) unsigned`	range
`tStart`	22741	`int(10) unsigned`	range
`tEnd`	72170	`int(10) unsigned`	range
`qName`	chrX	`varchar(255)`	values
`qSize`	23542271	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	1775700	`int(10) unsigned`	range
`qEnd`	1817646	`int(10) unsigned`	range
`id`	1102	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	203249	NWQH01000001	3368585	22741	72170	chrX	23542271	+	1775700	1817646	1102
585	111855	NWQH01000001	3368585	38663	41176	chr2L	23513712	+	3275955	3278476	1466
585	23452	NWQH01000001	3368585	38677	40144	chrX	23542271	+	5653901	5655189	4548
585	43039	NWQH01000001	3368585	73243	74502	chr3R	32079331	-	23308309	23309590	2666
73	2137727	NWQH01000001	3368585	76075	425547	chrX	23542271	-	21770570	22064414	112
586	7587	NWQH01000001	3368585	226105	231340	chr2R	25286936	+	10533341	10533757	13898
588	197438	NWQH01000001	3368585	430973	441856	chrX	23542271	+	1467869	1475214	1120
588	8248	NWQH01000001	3368585	432224	432504	chr3R	32079331	+	9330981	9331258	12758
588	7960	NWQH01000001	3368585	440547	440927	chr3L	28110227	+	19869186	19870493	13230
588	7641	NWQH01000001	3368585	440581	440954	chr2R	25286936	+	10724281	10725006	13796

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. hydei genome assembly (DhydGB1) 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