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

Database: dm6 Primary Table: chainDereCAF1 Row Count: 26,096 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	131478	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7482	`int(10) unsigned`	range
`tEnd`	9642	`int(10) unsigned`	range
`qName`	scaffold_4690	`varchar(255)`	values
`qSize`	18748788	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	9388462	`int(10) unsigned`	range
`qEnd`	9390978	`int(10) unsigned`	range
`id`	900	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	131478	chr2L	23513712	7482	9642	scaffold_4690	18748788	-	9388462	9390978	900
585	20546	chr2L	23513712	8733	9282	scaffold_4784	25762168	+	12814765	12815314	9778
1	538379236	chr2L	23513712	10364	8445802	scaffold_4929	26641161	+	39108	17355048	4
585	9515	chr2L	23513712	11065	11216	scaffold_4929	26641161	+	39886	40037	20849
585	12631	chr2L	23513712	18601	21436	scaffold_4929	26641161	+	47777	48136	16119
585	11324	chr2L	23513712	19133	19324	scaffold_4929	26641161	+	45453	45644	17852
585	14140	chr2L	23513712	20169	20408	scaffold_4929	26641161	+	46486	46745	14299
585	46412	chr2L	23513712	20620	21461	scaffold_4929	26641161	+	46964	47781	4059
585	27591	chr2L	23513712	72642	73037	scaffold_4929	26641161	+	100660	101043	7454
585	11021	chr2L	23513712	73037	73191	scaffold_4929	26641161	+	101047	101201	18291

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. melanogaster genome assembly (dm6) 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