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

Database: dm6 Primary Table: chainDanaRefSeq2 Row Count: 33,893 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	28227	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8706	`int(10) unsigned`	range
`tEnd`	9281	`int(10) unsigned`	range
`qName`	NC_057932	`varchar(255)`	values
`qSize`	22161957	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	20120448	`int(10) unsigned`	range
`qEnd`	20121023	`int(10) unsigned`	range
`id`	282186	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	28227	chr2L	23513712	8706	9281	NC_057932	22161957	+	20120448	20121023	282186
585	17671	chr2L	23513712	8733	9273	NC_057929	26427416	-	8210405	8210951	472976
585	1081662	chr2L	23513712	11263	94386	NC_057930	28809199	-	1807439	2121520	891
585	9659	chr2L	23513712	27230	28219	NC_057930	28809199	+	21468557	21469093	811910
585	7857	chr2L	23513712	28008	28217	NC_057930	28809199	-	2049525	2049737	955221
585	216154	chr2L	23513712	47840	52311	NC_057932	22161957	-	8841316	8845757	13297
585	213405	chr2L	23513712	47840	52311	NC_057930	28809199	-	21490032	21494421	13675
585	214208	chr2L	23513712	47840	52311	NC_057931	20566725	-	8518245	8522661	13576
585	216523	chr2L	23513712	47840	52311	NC_057928	27161637	+	25464773	25469214	13257
585	215110	chr2L	23513712	47840	52311	NC_057928	27161637	-	11986597	11991038	13449

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