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

Database: DgriCAF1 Primary Table: chainDm6 Row Count: 15,776 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	21606	`double`	range
`tName`	scaffold_10016	`varchar(255)`	values
`tSize`	1893	`int(10) unsigned`	range
`tStart`	2	`int(10) unsigned`	range
`tEnd`	388	`int(10) unsigned`	range
`qName`	chr2L	`varchar(255)`	values
`qSize`	23513712	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	14517733	`int(10) unsigned`	range
`qEnd`	14518114	`int(10) unsigned`	range
`id`	5516	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	21606	scaffold_10016	1893	2	388	chr2L	23513712	-	14517733	14518114	5516
585	14872	scaffold_10018	1736	585	1443	chr2L	23513712	-	6639812	6640981	8154
585	16451	scaffold_10021	1177	57	1079	chr3R	32079331	+	29569445	29569895	7364
585	8537	scaffold_10023	2296	69	2177	chr3R	32079331	+	16940826	16941409	13898
585	24582	scaffold_10024	1328	847	1327	chr3L	28110227	-	11169405	11169885	4849
585	9730	scaffold_10025	1055	34	909	chr3L	28110227	+	6462480	6463348	12224
585	22991	scaffold_10026	3822	93	3602	chr3L	28110227	-	24714348	24716836	5191
585	22034	scaffold_10027	1206	235	902	chr3L	28110227	+	8229571	8230211	5426
585	9165	scaffold_10027	1206	305	732	chr3L	28110227	-	18709454	18709816	12967
585	60336	scaffold_10030	26756	6747	22488	chr3L	28110227	+	21569517	21573423	1959

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. grimshawi genome assembly (DgriCAF1) 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