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

Database: DvirCAF1 Primary Table: netDm6 Row Count: 150,979 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	scaffold_10022	`varchar(255)`	values
`tStart`	323	`int(10) unsigned`	range
`tEnd`	1199	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	chrY	`varchar(255)`	values
`qStart`	126440	`int(10) unsigned`	range
`qEnd`	127311	`int(10) unsigned`	range
`chainId`	5249	`int(10) unsigned`	range
`ali`	866	`int(10) unsigned`	range
`score`	19996	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	313	`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	tN	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	scaffold_10022	323	1199	+	chrY	126440	127311	5249	866	19996	-1	-1	313	top	0	-1	-1	-1	-1	0	0
585	1	scaffold_10024	427	4291	-	chr3L	7672416	7678084	5996	674	17669	-1	-1	1055	top	1310	-1	-1	-1	-1	2551	5668
585	2	scaffold_10024	569	735	-	chr3L	7677788	7677942	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	166	154
585	2	scaffold_10024	813	1345	-	chr3L	7677400	7677710	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	532	310
585	2	scaffold_10024	1456	2886	-	chr3L	7677289	7677289	0	0	0	-1	-1	-1	gap	1310	-1	-1	-1	-1	117	0
585	3	scaffold_10024	2776	2886	-	chr3L	7677973	7678084	9453	110	2750	0	684	111	syn	0	-1	-1	-1	-1	110	111
585	2	scaffold_10024	2946	3693	-	chr3L	7676032	7677229	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	747	1197
585	2	scaffold_10024	3834	4149	-	chr3L	7672558	7675891	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	315	3333
585	1	scaffold_10024	4457	4535	-	chr3L	7677710	7677788	13229	78	2899	-1	-1	78	top	0	-1	-1	-1	-1	78	78
585	1	scaffold_10051	0	790	-	chr2L	6152212	6153134	3844	784	26839	-1	-1	730	top	0	-1	-1	-1	-1	437	620

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. virilis genome assembly (DvirCAF1) 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