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

Database: dm6 Primary Table: netDeugGB2 Row Count: 189,378

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7557	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	KB464958	`varchar(255)`	values
`qStart`	17595	`int(10) unsigned`	range
`qEnd`	19680	`int(10) unsigned`	range
`chainId`	1399	`int(10) unsigned`	range
`ali`	1492	`int(10) unsigned`	range
`score`	62448	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1470	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	0	`int(11)`	range
`qR`	0	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	0	`int(11)`	range
`qTrf`	0	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7557	9282	+	KB464958	17595	19680	1399	1492	62448	-1	-1	1470	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	7660	7674	+	KB464958	17698	17698	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8040	8232	+	KB464958	18081	18607	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8367	8379	+	KB464958	18742	18791	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11214	203444	+	AFPQ02005124	10301	191265	158	111578	6095794	-1	-1	717	top	10225	2592	-1	-1	-1	-1	913	370
585	2	chr2L	11540	11770	+	AFPQ02005124	10627	10884	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12954	13517	+	AFPQ02005124	12056	12461	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15719	16317	+	AFPQ02005124	14665	15066	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	16426	17049	+	AFPQ02005124	15176	15602	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	17232	20915	+	AFPQ02005124	15783	16446	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0

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