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

Database: DvirCAF1 Primary Table: chainDm6 Row Count: 14,478 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	19996	`double`	range
`tName`	scaffold_10022	`varchar(255)`	values
`tSize`	4321	`int(10) unsigned`	range
`tStart`	323	`int(10) unsigned`	range
`tEnd`	1199	`int(10) unsigned`	range
`qName`	chrY	`varchar(255)`	values
`qSize`	3667352	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	126440	`int(10) unsigned`	range
`qEnd`	127311	`int(10) unsigned`	range
`id`	5249	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	19996	scaffold_10022	4321	323	1199	chrY	3667352	+	126440	127311	5249
585	8100	scaffold_10024	4653	427	2945	chr3L	28110227	-	20433967	20434365	13373
585	17669	scaffold_10024	4653	427	4291	chr3L	28110227	-	20432143	20437811	5996
585	7936	scaffold_10024	4653	427	1454	chr3L	28110227	-	20432827	20434076	13697
585	11323	scaffold_10024	4653	2776	4291	chr3L	28110227	-	20432143	20434337	9453
585	8546	scaffold_10024	4653	3693	4291	chr3L	28110227	-	20432143	20432969	12674
585	8178	scaffold_10024	4653	4149	4535	chr3L	28110227	-	20432143	20432517	13229
585	26839	scaffold_10051	4919	0	790	chr2L	23513712	-	17360578	17361500	3844
585	16727	scaffold_10051	4919	0	539	chr2L	23513712	-	17360725	17361258	6393
585	8929	scaffold_10051	4919	5	473	chr2L	23513712	-	18574867	18575335	12073

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. virilis genome assembly (DvirCAF1) 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