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

Database: dm6 Primary Table: chainDtakRefSeq2 Row Count: 22,607 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	62857	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7559	`int(10) unsigned`	range
`tEnd`	9472	`int(10) unsigned`	range
`qName`	NW_025323455	`varchar(255)`	values
`qSize`	26170623	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	14639611	`int(10) unsigned`	range
`qEnd`	14642326	`int(10) unsigned`	range
`id`	13910	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	62857	chr2L	23513712	7559	9472	NW_025323455	26170623	-	14639611	14642326	13910
585	46881	chr2L	23513712	7572	9492	NW_025323480	11427507	+	4084934	4087050	21684
1	252136939	chr2L	23513712	11214	21393384	NW_025323500	21766836	+	158442	18304003	2
585	11414	chr2L	23513712	15865	16812	NW_025323474	12075919	-	6740272	6743116	336090
585	7902	chr2L	23513712	16676	16812	NW_025323474	12075919	-	2431456	2431592	917559
585	8044	chr2L	23513712	19508	19644	NW_025323474	12075919	-	6742979	6743116	885638
585	11351	chr2L	23513712	19508	24335	NW_025323474	12075919	-	2431456	2433158	342032
585	7946	chr2L	23513712	28008	28218	NW_025323500	21766836	+	174313	174526	907743
585	8908	chr2L	23513712	73409	73649	NW_025323500	21766836	+	222530	222823	704065
585	8002	chr2L	23513712	73655	73897	NW_025323500	21766836	+	222823	223106	895116

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