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

Database: dm6 Primary Table: chainDvirCAF1 Row Count: 14,478 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	27031	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8664	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	scaffold_12970	`varchar(255)`	values
`qSize`	11907090	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	2559725	`int(10) unsigned`	range
`qEnd`	2560336	`int(10) unsigned`	range
`id`	3813	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	27031	chr2L	23513712	8664	9275	scaffold_12970	11907090	-	2559725	2560336	3813
9	793969	chr2L	23513712	11215	1093020	scaffold_13246	2672878	+	72851	2669417	230
585	93924	chr2L	23513712	22122	24968	scaffold_12970	11907090	-	4243164	4246412	1136
585	744725	chr2L	23513712	26515	101626	scaffold_13246	2672878	-	2490390	2587358	250
585	9121	chr2L	23513712	75075	75365	scaffold_12855	10161210	-	7527380	7527670	11787
585	7507	chr2L	23513712	101042	101190	scaffold_988	1356	-	106	254	14539
585	45885	chr2L	23513712	102541	103770	scaffold_12963	20206255	-	17722105	17723288	2229
585	8596	chr2L	23513712	118712	119010	scaffold_13049	25233164	-	1387946	1388188	12606
585	7566	chr2L	23513712	118712	119016	scaffold_12723	5802038	-	1794769	1795074	14436
585	15079	chr2L	23513712	123223	126239	scaffold_12963	20206255	-	2626472	2629458	7125

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