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

Database: dm6 Primary Table: netDpseGB3 Row Count: 234,180 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	8733	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	CH379064	`varchar(255)`	values
`qStart`	8303401	`int(10) unsigned`	range
`qEnd`	8303950	`int(10) unsigned`	range
`chainId`	5871	`int(10) unsigned`	range
`ali`	549	`int(10) unsigned`	range
`score`	19605	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	549	`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	8733	9282	-	CH379064	8303401	8303950	5871	549	19605	-1	-1	549	top	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11214	117968	-	CH379059	9425	135292	166	42783	2082198	-1	-1	0	top	8407	8328	-1	-1	-1	-1	497	1477
585	2	chr2L	11522	11721	-	CH379059	134605	134968	0	0	0	-1	-1	-1	gap	0	18	-1	-1	-1	-1	0	0
585	2	chr2L	12936	13515	-	CH379059	133323	133379	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15717	17048	-	CH379059	129000	131111	0	0	0	-1	-1	-1	gap	93	77	-1	-1	-1	-1	0	0
585	2	chr2L	17141	22113	-	CH379059	125949	128907	0	0	0	-1	-1	-1	gap	0	556	-1	-1	-1	-1	0	0
585	2	chr2L	22941	22988	-	CH379059	125058	125113	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	24217	24734	-	CH379059	123785	123828	0	0	0	-1	-1	-1	gap	249	0	-1	-1	-1	-1	0	0
585	2	chr2L	25070	26282	-	CH379059	121961	123449	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	26412	26523	-	CH379059	121672	121822	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