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

Database: dm6 Primary Table: chainDsuzGB1 Row Count: 37,861 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	16388	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	5565	`int(10) unsigned`	range
`tEnd`	5883	`int(10) unsigned`	range
`qName`	AWUT01022642	`varchar(255)`	values
`qSize`	290	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	3	`int(10) unsigned`	range
`qEnd`	290	`int(10) unsigned`	range
`id`	17784	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	16388	chr2L	23513712	5565	5883	AWUT01022642	290	-	3	290	17784
585	64482	chr2L	23513712	7557	9275	KI420362	5541558	+	1683948	1686020	3866
585	22901	chr2L	23513712	8727	9275	KI419499	325753	+	324436	324984	12620
585	3086695	chr2L	23513712	11206	101637	KI419189	259405	+	24326	128088	291
585	8215	chr2L	23513712	17995	18175	KI419189	259405	+	31333	31513	34641
585	8945	chr2L	23513712	40374	40542	KI419189	259405	+	57992	58233	31938
585	14883	chr2L	23513712	41259	41516	KI419189	259405	+	59078	59355	19621
585	20667	chr2L	23513712	41741	42390	KI419189	259405	+	54706	55826	14045
585	9124	chr2L	23513712	101872	102056	KI420496	2530	-	257	438	31356
1	282075627	chr2L	23513712	102325	22107244	KI419149	22559587	+	6224	16035588	1

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. 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 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