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

Database: dm6 Primary Table: chainDobsGB1 Row Count: 15,982 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	19155	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8733	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	BDQP01000021	`varchar(255)`	values
`qSize`	1175991	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	15453	`int(10) unsigned`	range
`qEnd`	15995	`int(10) unsigned`	range
`id`	6810	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	19155	chr2L	23513712	8733	9275	BDQP01000021	1175991	+	15453	15995	6810
73	2591410	chr2L	23513712	11214	143142	BDQP01000091	434398	-	146487	295081	228
585	583467	chr2L	23513712	13770	44352	BDQP01000594	37034	+	0	32697	780
585	7725	chr2L	23513712	28008	28217	BDQP01000091	434398	-	161046	161258	15606
585	7725	chr2L	23513712	28008	28217	BDQP01000594	37034	+	12379	12591	15604
585	7688	chr2L	23513712	66743	66877	BDQP01000091	434398	+	229511	229643	15675
585	32634	chr2L	23513712	85169	86069	BDQP01000275	185105	+	33686	34560	4289
585	437234	chr2L	23513712	90962	101301	BDQP01000837	14699	-	82	11804	881
585	8126	chr2L	23513712	113029	113280	BDQP01000224	190040	-	136961	137212	14921
585	8361	chr2L	23513712	113029	113280	BDQP01000008	1553183	-	794598	794849	14540

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