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

Database: dm6 Primary Table: chainDrhoRefSeq2 Row Count: 83,380 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	69342	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7557	`int(10) unsigned`	range
`tEnd`	9519	`int(10) unsigned`	range
`qName`	NW_025335123	`varchar(255)`	values
`qSize`	26507916	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	20479120	`int(10) unsigned`	range
`qEnd`	20481799	`int(10) unsigned`	range
`id`	89387	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	69342	chr2L	23513712	7557	9519	NW_025335123	26507916	-	20479120	20481799	89387
585	24125	chr2L	23513712	8679	9282	NW_025335043	15806012	-	11354614	11355217	327628
585	15592	chr2L	23513712	11206	11549	NW_025335083	27004956	-	93559	93900	535060
1	410099815	chr2L	23513712	11206	22851708	NW_025335083	27004956	-	95817	26914209	1
585	2383908	chr2L	23513712	21964	102038	NW_025335083	27004956	+	26785375	26898754	346
585	7774	chr2L	23513712	28008	28218	NW_025335083	27004956	+	26791813	26792026	1421990
585	238118	chr2L	23513712	47588	55665	NW_025335043	15806012	-	14037810	14049335	11990
585	224502	chr2L	23513712	47600	52303	NW_025335059	11808632	+	5370662	5375185	13329
585	212659	chr2L	23513712	47615	52312	NW_025335033	1001701	+	411223	415603	14531
585	231420	chr2L	23513712	47644	52312	NW_025335043	15806012	-	254888	259457	12690

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