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

Database: dm6 Primary Table: chainDserRefSeq1 Row Count: 32,347 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	35471	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7580	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	NW_018367028	`varchar(255)`	values
`qSize`	4525942	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	690883	`int(10) unsigned`	range
`qEnd`	693086	`int(10) unsigned`	range
`id`	122055	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	35471	chr2L	23513712	7580	9275	NW_018367028	4525942	-	690883	693086	122055
585	21211	chr2L	23513712	8729	9281	NW_018367465	5769022	+	4645638	4646190	201668
585	18119	chr2L	23513712	8730	9275	NW_018366221	6880660	+	4996992	4997543	228842
585	24621	chr2L	23513712	8733	9275	NW_018367028	4525942	+	2343371	2343875	176237
585	12845	chr2L	23513712	8733	9296	NW_018367028	4525942	+	3747180	3747746	301038
73	13131511	chr2L	23513712	11210	828189	NW_018366386	1789090	+	10448	1501475	50
585	19959	chr2L	23513712	22276	22705	NW_018366386	1789090	+	122530	122885	212234
585	27905	chr2L	23513712	22705	23259	NW_018366386	1789090	+	122888	123441	155982
585	8747	chr2L	23513712	23711	23903	NW_018366386	1789090	+	123444	123636	395587
585	17271	chr2L	23513712	23903	24213	NW_018366386	1789090	+	123638	123948	238190

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