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

Database: dm6 Primary Table: chainDsuzRefSeq2 Row Count: 45,305 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	64482	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7557	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	NW_023496845	`varchar(255)`	values
`qSize`	13739618	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	1685784	`int(10) unsigned`	range
`qEnd`	1687856	`int(10) unsigned`	range
`id`	115680	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	64482	chr2L	23513712	7557	9275	NW_023496845	13739618	+	1685784	1687856	115680
585	23015	chr2L	23513712	8727	9282	NW_023496812	24550668	+	20428467	20429022	452226
1	317357133	chr2L	23513712	11206	13191980	NW_023496800	25589241	-	34742	24116658	2
585	9483	chr2L	23513712	13796	14084	NW_023496845	13739618	-	7158714	7158966	2222836
585	8215	chr2L	23513712	17995	18175	NW_023496800	25589241	-	41749	41929	2778277
585	245278	chr2L	23513712	47631	52312	NW_023496812	24550668	+	21605700	21610343	13331
585	246252	chr2L	23513712	47631	52312	NW_023496812	24550668	+	13936687	13941331	13239
585	245960	chr2L	23513712	47631	52312	NW_023496909	183359	-	169982	174625	13265
585	245879	chr2L	23513712	47631	52312	NW_023496836	6194228	-	696871	701513	13277
585	204543	chr2L	23513712	48542	52312	NW_023496807	14656957	+	11493540	11497292	18683

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