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

Database: DkikGB2 Primary Table: netDm6 Row Count: 243,226 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	KB458683	`varchar(255)`	values
`tStart`	13540	`int(10) unsigned`	range
`tEnd`	13758	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	chr3R	`varchar(255)`	values
`qStart`	3170451	`int(10) unsigned`	range
`qEnd`	3170669	`int(10) unsigned`	range
`chainId`	11382	`int(10) unsigned`	range
`ali`	218	`int(10) unsigned`	range
`score`	11764	`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`	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	tR	tNewR	qNewR	tOldR	qOldR	tTrf
585	1	KB458683	13540	13758	-	chr3R	3170451	3170669	11382	218	11764	-1	-1	0	top	0	-1	-1	-1	-1	0
585	1	KB458687	5719	22466	+	chr2R	4756168	4757813	2017	1408	57880	-1	-1	0	top	13236	-1	-1	-1	-1	1659
585	2	KB458687	6140	6358	+	chr2R	4756591	4756767	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0
585	2	KB458687	6758	21873	+	chr2R	4757167	4757226	0	0	0	-1	-1	-1	gap	13236	-1	-1	-1	-1	1659
585	1	KB458688	6843	7392	+	chr3L	17240061	17240610	8361	549	15679	-1	-1	549	top	0	-1	-1	-1	-1	0
585	1	KB458688	28958	29761	-	chr3L	15111181	15112090	13260	456	10209	-1	-1	456	top	0	-1	-1	-1	-1	0
585	2	KB458688	29142	29489	-	chr3L	15111453	15111906	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0
585	1	KB458688	99412	99864	-	chr2R	24782267	24782716	17696	449	8033	-1	-1	449	top	0	-1	-1	-1	-1	0
586	1	KB458688	136195	136564	-	chr3R	27154823	27155195	16418	369	8509	-1	-1	372	top	0	-1	-1	-1	-1	0
586	1	KB458688	175999	176334	+	chrX	19671115	19671450	17776	335	8010	-1	-1	335	top	0	-1	-1	-1	-1	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. kikkawai genome assembly (DkikGB2) 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