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

Database: dm6 Primary Table: chainDbiaRefSeq2 Row Count: 25,804 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	63353	`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_025319364	`varchar(255)`	values
`qSize`	26062673	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	1580869	`int(10) unsigned`	range
`qEnd`	1582924	`int(10) unsigned`	range
`id`	40424	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	63353	chr2L	23513712	7557	9275	NW_025319364	26062673	+	1580869	1582924	40424
585	18023	chr2L	23513712	7862	8528	NW_025319364	26062673	+	1576106	1577068	217055
585	23843	chr2L	23513712	8721	9282	NW_025319430	24655300	-	21623294	21623855	152142
1	230270304	chr2L	23513712	11214	22107244	NW_025319395	23381765	+	48388	18888934	3
585	8530	chr2L	23513712	17999	18196	NW_025319395	23381765	+	56495	56699	576175
585	10567	chr2L	23513712	27230	28241	NW_025319395	23381765	-	18019504	18020083	425765
585	25878	chr2L	23513712	115664	116352	NW_025319364	26062673	+	6336382	6337098	136345
585	8342	chr2L	23513712	118635	119079	NW_025319395	23381765	+	4495382	4495830	595477
585	8977	chr2L	23513712	118712	126216	NW_025319430	24655300	+	4630013	4631142	534431
585	8302	chr2L	23513712	123339	123613	NW_025319395	23381765	+	1130469	1130743	599698

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