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

Database: DsuzGB1 Primary Table: netDm6 Row Count: 220,128 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	KI419149	`varchar(255)`	values
`tStart`	4	`int(10) unsigned`	range
`tEnd`	182	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	chr3R	`varchar(255)`	values
`qStart`	7407498	`int(10) unsigned`	range
`qEnd`	7407676	`int(10) unsigned`	range
`chainId`	29720	`int(10) unsigned`	range
`ali`	178	`int(10) unsigned`	range
`score`	9650	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	178	`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	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	KI419149	4	182	-	chr3R	7407498	7407676	29720	178	9650	-1	-1	178	top	0	0	0	0	-1	-1	-1	-1	0	0
585	1	KI419149	500	629	-	chr3R	7407253	7407382	32413	129	8807	-1	-1	129	top	0	0	0	0	-1	-1	-1	-1	0	0
585	1	KI419149	861	5182	-	chr3R	7403515	7407933	961	3244	226520	-1	-1	564	top	0	0	0	125	-1	-1	-1	-1	0	0
585	2	KI419149	1300	1629	-	chr3R	7407382	7407498	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	KI419149	2408	2648	-	chr3R	7406109	7406603	0	0	0	-1	-1	-1	gap	0	0	0	63	-1	-1	-1	-1	0	0
585	2	KI419149	3776	4016	-	chr3R	7404654	7404924	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	KI419149	4428	4653	-	chr3R	7404015	7404231	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	KI419149	4962	4983	-	chr3R	7403713	7403713	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
1	1	KI419149	6224	16035588	+	chr2L	102325	22107244	1	4551782	282075627	-1	-1	235098	top	208589	100	444252	1194925	-1	-1	-1	-1	271669	218076
585	2	KI419149	6839	7131	+	chr2L	102925	102999	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. suzukii genome assembly (DsuzGB1) 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