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

Database: DficGB2 Primary Table: netDm6 Row Count: 218,072 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	AFFG02000001	`varchar(255)`	values
`tStart`	3171	`int(10) unsigned`	range
`tEnd`	8437	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	chr3L	`varchar(255)`	values
`qStart`	5718596	`int(10) unsigned`	range
`qEnd`	5723225	`int(10) unsigned`	range
`chainId`	375	`int(10) unsigned`	range
`ali`	3496	`int(10) unsigned`	range
`score`	224185	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	0	`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`	65	`int(11)`	range
`qTrf`	38	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	AFFG02000001	3171	8437	+	chr3L	5718596	5723225	375	3496	224185	-1	-1	0	top	-1	-1	-1	-1	65	38
585	2	AFFG02000001	4245	4512	+	chr3L	5719681	5719838	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0	0
585	2	AFFG02000001	4689	4722	+	chr3L	5720045	5720085	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0	0
585	2	AFFG02000001	5016	5442	+	chr3L	5720406	5720499	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0	0
585	2	AFFG02000001	5714	5724	+	chr3L	5720784	5720838	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0	0
585	2	AFFG02000001	6018	6067	+	chr3L	5721132	5721199	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0	0
585	2	AFFG02000001	6175	6618	+	chr3L	5721307	5721762	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0	0
585	2	AFFG02000001	7097	7112	+	chr3L	5722248	5722248	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0	0
585	2	AFFG02000001	7175	7582	+	chr3L	5722311	5722378	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0	0
585	2	AFFG02000001	7779	7819	+	chr3L	5722575	5722600	0	0	0	-1	-1	-1	gap	-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. ficusphila genome assembly (DficGB2) 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