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

Database: dm6 Primary Table: chainDbipGB2 Row Count: 18,980 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	26650	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8727	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	AFFE02006513	`varchar(255)`	values
`qSize`	124171	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	39613	`int(10) unsigned`	range
`qEnd`	40161	`int(10) unsigned`	range
`id`	4615	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	26650	chr2L	23513712	8727	9275	AFFE02006513	124171	-	39613	40161	4615
585	18119	chr2L	23513712	8733	9273	KB464395	1726526	-	420275	420821	7012
73	1143422	chr2L	23513712	11407	277268	KB464388	2431713	+	435170	1677265	341
585	275940	chr2L	23513712	76422	94386	KB464138	596799	+	7771	31063	652
585	27456	chr2L	23513712	91815	94343	AFFE02005830	24825	-	11532	13614	4455
585	349938	chr2L	23513712	94848	102000	KB464388	2431713	-	1981547	1988499	594
73	1038693	chr2L	23513712	102525	153338	KB464388	2431713	-	1771511	1821696	358
585	8888	chr2L	23513712	112944	113297	AFFE02001729	6113	-	2475	2828	15381
585	7642	chr2L	23513712	113008	113280	KB463184	32529	+	17855	18127	18519
585	7816	chr2L	23513712	118605	118849	KB464388	2431713	-	1792940	1793184	17986

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