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

Database: dm6 Primary Table: chainDanaCAF1 Row Count: 15,346 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	28227	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8706	`int(10) unsigned`	range
`tEnd`	9281	`int(10) unsigned`	range
`qName`	scaffold_12903	`varchar(255)`	values
`qSize`	802071	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	632684	`int(10) unsigned`	range
`qEnd`	633259	`int(10) unsigned`	range
`id`	3511	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	28227	chr2L	23513712	8706	9281	scaffold_12903	802071	+	632684	633259	3511
585	17671	chr2L	23513712	8733	9273	scaffold_13266	19884421	-	1854635	1855181	5950
585	1119348	chr2L	23513712	11263	94386	scaffold_12916	16180835	+	1772617	2083924	223
585	9659	chr2L	23513712	27230	28219	scaffold_12916	16180835	-	8881622	8882158	11655
585	7857	chr2L	23513712	28008	28217	scaffold_12916	16180835	+	2012034	2012246	14709
585	345538	chr2L	23513712	94848	102000	scaffold_12916	16180835	-	14393100	14400085	330
73	1063055	chr2L	23513712	102525	153211	scaffold_12916	16180835	-	14174844	14228854	226
585	79191	chr2L	23513712	108687	114211	scaffold_13230	3602488	+	931696	934318	1093
585	9561	chr2L	23513712	118590	119051	scaffold_12916	16180835	-	14646931	14647336	11792
585	7824	chr2L	23513712	118605	118849	scaffold_12916	16180835	-	14195900	14196144	14768

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