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

Database: dm6 Primary Table: chainDwilRefSeq2 Row Count: 28,467 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	12720	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8662	`int(10) unsigned`	range
`tEnd`	9266	`int(10) unsigned`	range
`qName`	NW_025814049	`varchar(255)`	values
`qSize`	4257295	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	112178	`int(10) unsigned`	range
`qEnd`	112782	`int(10) unsigned`	range
`id`	594415	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	12720	chr2L	23513712	8662	9266	NW_025814049	4257295	-	112178	112782	594415
585	25291	chr2L	23513712	8679	9275	NW_025814052	15674760	+	8041229	8041825	300509
585	151400	chr2L	23513712	11214	17139	NW_025814050	24296367	-	21208472	21216441	19562
585	101449	chr2L	23513712	22118	24974	NW_025814053	9450810	+	5557089	5559495	43004
585	729311	chr2L	23513712	26515	102000	NW_025814050	24296367	+	24142506	24223800	730
585	8157	chr2L	23513712	77159	77555	NW_025814050	24296367	+	24189100	24189496	961413
9	1728043	chr2L	23513712	102539	1157838	NW_025814050	24296367	+	3093007	4895456	189
585	27563	chr2L	23513712	102830	103764	NC_061086	33854152	+	3142875	3143720	271895
585	7530	chr2L	23513712	118933	119543	NW_025814050	24296367	-	20941613	20942120	1068967
585	34967	chr2L	23513712	123339	126222	NW_025814050	24296367	-	20940119	20942120	206509

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