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

Database: DsimGB2 Primary Table: netDm6 Row Count: 95,425 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	CM002910	`varchar(255)`	values
`tStart`	213	`int(10) unsigned`	range
`tEnd`	1742	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	chr2R	`varchar(255)`	values
`qStart`	25254822	`int(10) unsigned`	range
`qEnd`	25257247	`int(10) unsigned`	range
`chainId`	758	`int(10) unsigned`	range
`ali`	1514	`int(10) unsigned`	range
`score`	90926	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	2302	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	355	`int(11)`	range
`qR`	903	`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`	31	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tN	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	CM002910	213	1742	-	chr2R	25254822	25257247	758	1514	90926	-1	-1	2302	top	0	0	355	903	-1	-1	-1	-1	0	31
585	1	CM002910	1742	1799	-	chr2R	25256340	25256397	1613	57	3394	-1	-1	57	top	0	0	0	16	-1	-1	-1	-1	0	0
1	1	CM002910	4199	23436784	+	chr2L	10011	23075708	2	20181723	1677437910	-1	-1	120704	top	5937	200	2134188	1887017	-1	-1	-1	-1	171113	289051
585	2	CM002910	4498	4530	+	chr2L	10368	10368	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	CM002910	4907	4927	+	chr2L	10759	10888	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	CM002910	4978	4995	+	chr2L	10939	10939	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	CM002910	5117	5144	+	chr2L	11061	11064	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	25	0
585	2	CM002910	7227	7533	+	chr2L	13145	13471	0	0	0	-1	-1	-1	gap	0	0	287	57	-1	-1	-1	-1	0	0
585	2	CM002910	9997	10010	+	chr2L	15983	15983	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	CM002910	10076	10138	+	chr2L	16049	16090	0	0	0	-1	-1	-1	gap	0	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. simulans genome assembly (DsimGB2) 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