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

Database: dm6 Primary Table: chainDhydRefSeq1 Row Count: 18,922 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	24341	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8664	`int(10) unsigned`	range
`tEnd`	9257	`int(10) unsigned`	range
`qName`	NW_022045714	`varchar(255)`	values
`qSize`	1081237	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	724815	`int(10) unsigned`	range
`qEnd`	725408	`int(10) unsigned`	range
`id`	73931	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	24341	chr2L	23513712	8664	9257	NW_022045714	1081237	+	724815	725408	73931
73	2585969	chr2L	23513712	11215	302504	NW_022045682	5146216	+	25648	2512782	83
585	91541	chr2L	23513712	22122	24968	NW_022045721	820879	-	248744	252986	17922
585	690376	chr2L	23513712	26515	102031	NW_022045682	5146216	-	5034598	5109671	470
585	8177	chr2L	23513712	27127	28221	NW_022045656	10619989	-	3880021	3880603	192702
585	40095	chr2L	23513712	102610	103770	NW_022045678	7178267	-	6864717	6865823	46454
585	8322	chr2L	23513712	118635	119016	NW_022045678	7178267	+	2292856	2293249	190026
585	11031	chr2L	23513712	118712	119543	NW_022045682	5146216	-	4841173	4841846	148920
585	34357	chr2L	23513712	123339	126223	NW_022045682	5146216	-	4839879	4841847	53012
585	10630	chr2L	23513712	123721	126171	NW_022045678	7178267	+	2292211	2293687	153331

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