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

Database: dm6 Primary Table: chainDmauRefSeq1 Row Count: 165,739 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	57118	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	4992	`int(10) unsigned`	range
`tEnd`	5978	`int(10) unsigned`	range
`qName`	NC_046667	`varchar(255)`	values
`qSize`	24228064	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	39875	`int(10) unsigned`	range
`qEnd`	46289	`int(10) unsigned`	range
`id`	348295	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	57118	chr2L	23513712	4992	5978	NC_046667	24228064	+	39875	46289	348295
585	70235	chr2L	23513712	4992	60581	NC_046672	23222241	+	169033	197653	278143
585	58568	chr2L	23513712	4992	6028	NC_046667	24228064	+	25392	33384	339022
585	14447	chr2L	23513712	4992	5259	NC_046667	24228064	+	46118	46506	1407047
585	39138	chr2L	23513712	4992	5680	NC_046672	23222241	+	171438	176496	528280
585	22040	chr2L	23513712	4992	5374	NC_046667	24228064	+	44159	46320	961218
585	20418	chr2L	23513712	4992	5346	NC_046672	23222241	+	173843	176496	1036106
585	58377	chr2L	23513712	4992	6028	NC_046667	24228064	+	33449	42207	340265
585	41547	chr2L	23513712	4992	5708	NC_046667	24228064	+	42272	46320	496539
585	58441	chr2L	23513712	4992	6028	NC_046667	24228064	+	22740	31242	339873

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