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

Database: dm6 Primary Table: chainDperCAF1 Row Count: 15,232 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	19991	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8733	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	super_13	`varchar(255)`	values
`qSize`	2293547	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	273204	`int(10) unsigned`	range
`qEnd`	273753	`int(10) unsigned`	range
`id`	5799	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	19991	chr2L	23513712	8733	9282	super_13	2293547	+	273204	273753	5799
585	15940	chr2L	23513712	8733	9282	super_40	810552	+	727300	727850	7306
585	19991	chr2L	23513712	8733	9282	super_13	2293547	+	269439	269988	5798
585	9886	chr2L	23513712	8733	9258	super_6	6141320	+	5974263	5974788	11796
585	16088	chr2L	23513712	8734	9282	super_23	1662726	-	234801	235349	7226
585	2064598	chr2L	23513712	11214	117968	super_8	3966273	+	3760998	3886433	197
585	48797	chr2L	23513712	22113	23156	super_8	3966273	+	3757888	3758976	2110
585	27037	chr2L	23513712	23403	24217	super_11692	873	-	4	827	4233
585	8938	chr2L	23513712	27244	28217	super_1	10282868	+	4529128	4529654	13033
585	11397	chr2L	23513712	68355	68773	super_3924	2356	-	38	462	10230

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