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

Database: dm6 Primary Table: chainDficRefSeq2 Row Count: 26,523 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	52424	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7553	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	NW_025064092	`varchar(255)`	values
`qSize`	14960694	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	4660754	`int(10) unsigned`	range
`qEnd`	4662868	`int(10) unsigned`	range
`id`	53638	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	52424	chr2L	23513712	7553	9282	NW_025064092	14960694	+	4660754	4662868	53638
585	23926	chr2L	23513712	8724	9275	NW_025064189	9958166	-	7541880	7542431	132478
585	221593	chr2L	23513712	11210	18195	NW_025064326	6727433	+	39064	45609	4689
585	1715000	chr2L	23513712	21965	93305	NW_025064326	6727433	-	6608043	6679507	255
585	8111	chr2L	23513712	28008	28217	NW_025064326	6727433	-	6613756	6613968	335500
585	215070	chr2L	23513712	47652	52309	NW_025064328	24970528	+	24350411	24354961	4997
585	228952	chr2L	23513712	47652	52308	NW_025064389	4937933	-	1266080	1271272	4446
585	205272	chr2L	23513712	47792	52308	NW_025064389	4937933	-	3082793	3086916	5476
585	441264	chr2L	23513712	94682	102000	NW_025064807	1997042	-	624798	631990	1729
73	1803288	chr2L	23513712	102400	153406	NW_025064326	6727433	-	6554266	6604021	235

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