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

Database: dm6 Primary Table: chainDsimRefSeq3 Row Count: 82,749 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	58665	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	4992	`int(10) unsigned`	range
`tEnd`	6680	`int(10) unsigned`	range
`qName`	NC_052525	`varchar(255)`	values
`qSize`	22032822	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	20314	`int(10) unsigned`	range
`qEnd`	22424	`int(10) unsigned`	range
`id`	132125	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	58665	chr2L	23513712	4992	6680	NC_052525	22032822	+	20314	22424	132125
585	58665	chr2L	23513712	4992	6680	NC_052525	22032822	+	20830	22940	132126
585	14361	chr2L	23513712	4992	5204	NC_052520	23857595	+	65332	65539	602686
585	58665	chr2L	23513712	4992	6680	NC_052525	22032822	+	21862	23972	132128
585	54121	chr2L	23513712	4992	6005	NC_052525	22032822	+	23410	25159	144306
585	59302	chr2L	23513712	4992	6858	NC_052523	28149585	-	6116	17732	130586
585	23983	chr2L	23513712	4992	5393	NC_052520	23857595	+	64116	65545	361733
585	58665	chr2L	23513712	4992	6680	NC_052525	22032822	+	18250	20360	132121
585	58534	chr2L	23513712	4992	6680	NC_052525	22032822	+	22894	25004	132471
585	58665	chr2L	23513712	4992	6680	NC_052525	22032822	+	21346	23456	132127

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