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

Database: dm6 Primary Table: chainDbiaGB2 Row Count: 20,854 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	63418	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7557	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	KB462640	`varchar(255)`	values
`qSize`	1647654	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	5376	`int(10) unsigned`	range
`qEnd`	7431	`int(10) unsigned`	range
`id`	1354	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	63418	chr2L	23513712	7557	9275	KB462640	1647654	+	5376	7431	1354
585	23988	chr2L	23513712	7862	8921	KB462640	1647654	+	452	1623	5046
585	23760	chr2L	23513712	8721	9282	KB462895	1018708	-	200797	201358	5116
585	2925235	chr2L	23513712	11214	102039	KB462393	113471	+	16253	110590	144
585	8530	chr2L	23513712	17999	18196	KB462393	113471	+	24358	24562	17707
73	7060544	chr2L	23513712	102360	254403	AFFD02005643	173328	-	1096	172128	116
585	25878	chr2L	23513712	115664	116352	KB462463	5756469	-	3024214	3024930	4580
585	8342	chr2L	23513712	118635	119079	KB462394	1294069	+	42555	43003	18222
585	30068	chr2L	23513712	123339	126223	KB462696	3592495	-	789180	791276	3778
585	12345	chr2L	23513712	124543	126232	KB462394	1294069	-	50243	51048	11350

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