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

Database: dm6 Primary Table: chainDgriImproved Row Count: 19,570 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	25288	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8664	`int(10) unsigned`	range
`tEnd`	9283	`int(10) unsigned`	range
`qName`	scaffold_15203	`varchar(255)`	values
`qSize`	11997470	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	2038632	`int(10) unsigned`	range
`qEnd`	2039245	`int(10) unsigned`	range
`id`	5819	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	25288	chr2L	23513712	8664	9283	scaffold_15203	11997470	+	2038632	2039245	5819
585	12837	chr2L	23513712	8816	9257	scaffold_14973	72184	+	50805	51246	11590
585	11714	chr2L	23513712	8816	9225	scaffold_9034	13762	-	13339	13748	12533
585	13378	chr2L	23513712	8816	9257	scaffold_277	1513	-	719	1160	11128
585	13042	chr2L	23513712	8816	9257	scaffold_6935	3535	-	2346	2787	11414
585	12920	chr2L	23513712	8816	9257	scaffold_9137	7527	-	815	1256	11511
585	12837	chr2L	23513712	8816	9257	scaffold_3018	10593	+	6857	7298	11589
585	13173	chr2L	23513712	8816	9257	scaffold_12564	1341	-	749	1190	11293
585	12966	chr2L	23513712	8816	9257	scaffold_14973	72184	+	1435	1876	11471
585	13051	chr2L	23513712	8816	9257	scaffold_6999	5057	-	3861	4302	11404

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