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

Database: dm6 Primary Table: chainDbipRefSeq2 Row Count: 26,939 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	26584	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8727	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	NW_025063931	`varchar(255)`	values
`qSize`	15788854	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	9630511	`int(10) unsigned`	range
`qEnd`	9631059	`int(10) unsigned`	range
`id`	195499	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	26584	chr2L	23513712	8727	9275	NW_025063931	15788854	-	9630511	9631059	195499
585	18800	chr2L	23513712	8733	9273	NW_025063897	25839890	-	7661710	7662256	286553
585	795662	chr2L	23513712	11263	76079	NW_025063924	1617217	-	499435	797141	1192
585	10884	chr2L	23513712	27230	28219	NW_025063917	2666325	+	1495771	1496308	480223
585	207710	chr2L	23513712	47613	51975	NW_025063860	28593753	+	23737963	23742276	8300
585	219498	chr2L	23513712	47615	52309	NW_025063913	3454367	-	2923736	2928358	7449
585	224644	chr2L	23513712	47615	52309	NW_025063954	10975651	+	1997768	2002409	7108
585	223980	chr2L	23513712	47615	52309	NW_025063897	25839890	+	21683131	21687777	7160
585	219939	chr2L	23513712	47615	55665	NW_025063971	9440424	+	1164050	1172293	7420
585	212251	chr2L	23513712	47809	52309	NW_025063897	25839890	+	23731864	23736275	7925

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