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

Database: dm6 Primary Table: chainDereRefSeq1 Row Count: 113,399 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	1	`smallint(5) unsigned`	range
`score`	539417899	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	5508	`int(10) unsigned`	range
`tEnd`	8445802	`int(10) unsigned`	range
`qName`	NW_020825200	`varchar(255)`	values
`qSize`	22146549	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	39318	`int(10) unsigned`	range
`qEnd`	17665413	`int(10) unsigned`	range
`id`	4	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
1	539417899	chr2L	23513712	5508	8445802	NW_020825200	22146549	+	39318	17665413	4
585	131478	chr2L	23513712	7482	9642	NW_020825209	16326836	-	9444104	9446620	44654
585	20546	chr2L	23513712	8733	9282	NW_020825198	26197553	+	13075639	13076188	543386
585	9515	chr2L	23513712	11065	11216	NW_020825200	22146549	+	44178	44329	1299528
585	11324	chr2L	23513712	19133	19324	NW_020825200	22146549	+	49745	49936	1058600
585	14140	chr2L	23513712	20169	20408	NW_020825200	22146549	+	50778	51037	830563
585	46412	chr2L	23513712	20620	21461	NW_020825200	22146549	+	51256	52073	206036
585	27591	chr2L	23513712	72642	73037	NW_020825200	22146549	+	113156	113539	389804
585	11021	chr2L	23513712	73037	73191	NW_020825200	22146549	+	113543	113697	1091846
585	19918	chr2L	23513712	73409	73747	NW_020825200	22146549	+	112166	112559	564840

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