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

Database: dm6 Primary Table: chainDbusRefSeq1 Row Count: 13,821 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	24683	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8674	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	NC_046608	`varchar(255)`	values
`qSize`	22692164	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	12258598	`int(10) unsigned`	range
`qEnd`	12259199	`int(10) unsigned`	range
`id`	21111	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	24683	chr2L	23513712	8674	9275	NC_046608	22692164	+	12258598	12259199	21111
585	9292	chr2L	23513712	8706	8924	NC_046605	24078396	-	15800710	15800929	58442
585	207353	chr2L	23513712	11214	106393	NC_046604	19111714	+	18611973	18682571	1040
585	89274	chr2L	23513712	22122	24974	NC_046608	22692164	+	18632670	18635039	4055
585	621065	chr2L	23513712	26520	102011	NC_046604	19111714	-	432586	493536	231
585	9373	chr2L	23513712	28001	28217	NC_046604	19111714	-	434084	434303	57997
585	44685	chr2L	23513712	102541	103769	NC_046604	19111714	+	9627578	9628736	10423
73	553084	chr2L	23513712	108678	152872	NC_046604	19111714	-	18154292	18200167	261
585	10796	chr2L	23513712	118712	126216	NC_046606	20459230	-	19273790	19274932	50748
585	18690	chr2L	23513712	118933	126247	NC_046604	19111714	-	4345454	4350037	28814

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