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

Database: dm6 Primary Table: chainDvirRefSeq1 Row Count: 25,946 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	27031	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8664	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	NW_022587575	`varchar(255)`	values
`qSize`	18091221	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	10208348	`int(10) unsigned`	range
`qEnd`	10208959	`int(10) unsigned`	range
`id`	195280	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	27031	chr2L	23513712	8664	9275	NW_022587575	18091221	-	10208348	10208959	195280
73	780282	chr2L	23513712	11215	152876	NW_022587573	2284986	-	6272	225334	908
585	93924	chr2L	23513712	22122	24968	NW_022587575	18091221	-	11912960	11916208	42714
585	732134	chr2L	23513712	26515	101626	NW_022587573	2284986	+	2163107	2266045	1004
585	9121	chr2L	23513712	75075	75365	NW_022587552	7943991	-	6467269	6467559	502517
585	45885	chr2L	23513712	102541	103770	NW_022587571	9883579	-	3547575	3548758	107401
585	7566	chr2L	23513712	118712	119016	NW_022587571	9883579	-	7867446	7867751	616926
585	8596	chr2L	23513712	118712	119010	NW_022587555	3487065	+	2130324	2130566	528870
585	15079	chr2L	23513712	123223	126239	NW_022587572	14919977	-	3122159	3125145	332636
585	14255	chr2L	23513712	123338	126171	NW_022587571	9883579	-	7866218	7868184	348171

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