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

Database: dm6 Primary Table: chainDobsRefSeq2 Row Count: 21,140 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	19155	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8733	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	NW_024542865	`varchar(255)`	values
`qSize`	10007629	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	5701980	`int(10) unsigned`	range
`qEnd`	5702522	`int(10) unsigned`	range
`id`	151737	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	19155	chr2L	23513712	8733	9275	NW_024542865	10007629	+	5701980	5702522	151737
73	2564689	chr2L	23513712	11214	143142	NW_024542824	3001326	-	1463599	1613708	156
585	7725	chr2L	23513712	28008	28217	NW_024542824	3001326	-	1478587	1478799	391430
585	7584	chr2L	23513712	115722	115912	NW_024542891	1779466	-	360520	360704	401842
585	8655	chr2L	23513712	118712	119050	NW_024542769	2385783	+	937410	937692	329597
585	9751	chr2L	23513712	118717	119513	NW_024542883	5438638	-	1526106	1526840	288828
585	16597	chr2L	23513712	123338	124926	NW_024542766	8243687	+	756521	757996	175562
585	32862	chr2L	23513712	123339	126223	NW_024542824	3001326	+	1735450	1737455	82105
585	8098	chr2L	23513712	124464	124749	NW_024542824	3001326	-	1584755	1585043	364620
585	13541	chr2L	23513712	124536	126187	NW_024542883	5438638	-	1526025	1526835	213516

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RefSeq Drosophila Chain/Net (refseqDrosChainNet) Track Description


	Description Genomic scaffolds from each Drosophila species are aligned against the D. melanogaster genome assembly (dm6) using LAST with default parameters. The alignments are then processed using the UCSC whole genome alignment protocol (i.e. chaining and netting). References Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. doi: 10.1073/pnas.1932072100.

Description