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

Database: dm6 Primary Table: chainDtakGB2 Row Count: 23,052 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	61051	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7559	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	KB461184	`varchar(255)`	values
`qSize`	430758	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	329276	`int(10) unsigned`	range
`qEnd`	331660	`int(10) unsigned`	range
`id`	2241	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	61051	chr2L	23513712	7559	9275	KB461184	430758	-	329276	331660	2241
585	42871	chr2L	23513712	7572	9275	KB461295	498719	+	178486	181329	3257
73	21171372	chr2L	23513712	11214	494946	KB460599	561866	-	3880	556286	43
585	7568	chr2L	23513712	16676	16812	KB460825	32012	-	12359	12496	22874
585	8044	chr2L	23513712	16676	16812	AFFI02009527	15554	-	12868	13005	21102
585	7902	chr2L	23513712	16676	16812	KB460215	43649	+	34834	34970	21617
585	7568	chr2L	23513712	19508	19644	KB460825	32012	-	12359	12496	22873
585	7902	chr2L	23513712	19508	19644	KB460215	43649	+	34834	34970	21616
585	8044	chr2L	23513712	19508	19644	AFFI02009527	15554	-	12868	13005	21101
585	49172	chr2L	23513712	23756	25206	AFFI02002556	1126	-	0	1126	2816

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