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

Database: dm6 Primary Table: chainDnavRefSeq1 Row Count: 16,027 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	25252	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8673	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	NW_022052058	`varchar(255)`	values
`qSize`	838	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	155	`int(10) unsigned`	range
`qEnd`	764	`int(10) unsigned`	range
`id`	10546	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	25252	chr2L	23513712	8673	9282	NW_022052058	838	-	155	764	10546
73	799253	chr2L	23513712	11215	152876	NW_022045913	588174	+	2619	145097	338
585	22568	chr2L	23513712	22123	22693	NW_022047217	8846	-	7231	7804	11976
585	53488	chr2L	23513712	22731	23876	NW_022049059	1538	-	292	1444	4294
585	18180	chr2L	23513712	23920	24965	NW_022048336	2235	+	1133	1725	15382
585	692420	chr2L	23513712	26291	101632	NW_022045913	588174	-	496358	574707	387
585	7831	chr2L	23513712	77159	77560	NW_022045913	588174	-	543566	543967	39836
585	43665	chr2L	23513712	102541	103767	NW_022045923	481508	+	233516	234703	5348
585	10155	chr2L	23513712	118635	124932	NW_022045912	594250	+	444763	445224	29937
585	10301	chr2L	23513712	118712	119513	NW_022045915	550720	-	466680	467393	29534

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