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

Database: dm6 Primary Table: chainDwilCAF1 Row Count: 15,855 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	12720	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8662	`int(10) unsigned`	range
`tEnd`	9266	`int(10) unsigned`	range
`qName`	scf2_1100000004822	`varchar(255)`	values
`qSize`	3585778	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	100842	`int(10) unsigned`	range
`qEnd`	101446	`int(10) unsigned`	range
`id`	9656	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	12720	chr2L	23513712	8662	9266	scf2_1100000004822	3585778	+	100842	101446	9656
585	25291	chr2L	23513712	8679	9275	scf2_1100000004909	12416693	+	10595781	10596377	4882
585	151398	chr2L	23513712	11214	17139	scf2_1100000004585	8906247	-	7098055	7106033	901
585	101449	chr2L	23513712	22118	24974	scf2_1100000004590	4753960	-	703885	706291	1236
585	747151	chr2L	23513712	26515	102000	scf2_1100000004851	637489	-	494619	577610	264
585	10176	chr2L	23513712	35092	35813	scf2_1100000011884	953	+	21	711	11829
585	8157	chr2L	23513712	77159	77555	scf2_1100000004851	637489	-	542933	543329	14749
9	1767294	chr2L	23513712	102539	1157838	scf2_1100000004585	8906247	+	1813304	3611976	117
585	27563	chr2L	23513712	102830	103764	scf2_1100000004943	16660200	+	3050520	3051365	4502
585	7531	chr2L	23513712	118933	119543	scf2_1100000004585	8906247	-	6831206	6831711	15912

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