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

Database: dm6 Primary Table: netDereCAF1 Row Count: 170,530 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`	7482	`int(10) unsigned`	range
`tEnd`	9642	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	scaffold_4690	`varchar(255)`	values
`qStart`	9357810	`int(10) unsigned`	range
`qEnd`	9360326	`int(10) unsigned`	range
`chainId`	900	`int(10) unsigned`	range
`ali`	2124	`int(10) unsigned`	range
`score`	131478	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	2119	`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	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7482	9642	-	scaffold_4690	9357810	9360326	900	2124	131478	-1	-1	2119	top	0	0	0	-1	-1	-1	-1	0	0
1	1	chr2L	10364	8445802	+	scaffold_4929	39108	17355048	4	7322340	538379236	-1	-1	7398750	top	52438	301466	627468	-1	-1	-1	-1	102002	529659
585	2	chr2L	11063	11214	+	scaffold_4929	39860	39860	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	3	chr2L	11065	11214	+	scaffold_4929	39886	40035	20849	149	9389	0	26	149	syn	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11567	11621	+	scaffold_4929	40211	40238	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12967	13515	+	scaffold_4929	41584	42219	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	304
585	2	chr2L	15778	16200	+	scaffold_4929	44482	45335	0	0	0	-1	-1	-1	gap	0	93	349	-1	-1	-1	-1	0	0
585	2	chr2L	16572	16822	+	scaffold_4929	45727	45970	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	16994	17021	+	scaffold_4929	46134	46134	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	17666	17815	+	scaffold_4929	46804	46964	0	0	0	-1	-1	-1	gap	0	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