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

Database: DperCAF1 Primary Table: chainDm6 Row Count: 15,232 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	9	`smallint(5) unsigned`	range
`score`	16425280	`double`	range
`tName`	super_0	`varchar(255)`	values
`tSize`	11822988	`int(10) unsigned`	range
`tStart`	20	`int(10) unsigned`	range
`tEnd`	6374034	`int(10) unsigned`	range
`qName`	chr3R	`varchar(255)`	values
`qSize`	32079331	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	9265251	`int(10) unsigned`	range
`qEnd`	23835119	`int(10) unsigned`	range
`id`	17	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
9	16425280	super_0	11822988	20	6374034	chr3R	32079331	-	9265251	23835119	17
585	11387	super_0	11822988	10514	10747	chr3R	32079331	-	9272535	9272762	10236
585	21159	super_0	11822988	80069	80759	chr3R	32079331	-	9330863	9331532	5488
585	7537	super_0	11822988	81301	81706	chr3R	32079331	-	9329229	9329637	15282
585	13672	super_0	11822988	81718	82093	chr3R	32079331	-	9329676	9330051	8553
585	8599	super_0	11822988	99359	99649	chrX	23542271	-	3018925	3019215	13515
585	9483	super_0	11822988	109365	109539	chr3R	32079331	-	21667531	21667705	12311
585	13695	super_0	11822988	109592	109810	chr3R	32079331	-	21667762	21667980	8540
585	36074	super_0	11822988	109808	110486	chr3R	32079331	-	21668040	21668718	3069
585	42337	super_0	11822988	110672	111333	chr3R	32079331	-	21668960	21669621	2536

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Drosophila Chain/Net (drosophilaChainNet) Track Description


	Description Genomic scaffolds from each Drosophila species are aligned against the D. persimilis genome assembly (DperCAF1) using LAST with default parameters. The alignments are then processed using the UCSC whole genome alignment protocol (i.e. chaining and netting). References Chain/Net Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003 100(20): 11484-11489. LAST Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93.

Description