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

Database: DsuzGB1 Primary Table: chainDm6 Row Count: 37,861 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	32416	`double`	range
`tName`	AWUT01012676	`varchar(255)`	values
`tSize`	94595	`int(10) unsigned`	range
`tStart`	21757	`int(10) unsigned`	range
`tEnd`	44754	`int(10) unsigned`	range
`qName`	chr3R	`varchar(255)`	values
`qSize`	32079331	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	3584973	`int(10) unsigned`	range
`qEnd`	3586980	`int(10) unsigned`	range
`id`	8731	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	32416	AWUT01012676	94595	21757	44754	chr3R	32079331	+	3584973	3586980	8731
585	22001	AWUT01012676	94595	54370	55937	chr2L	23513712	+	19605020	19605499	13163
585	8263	AWUT01013263	76167	47555	47793	chr3R	32079331	+	7915947	7916186	34443
585	203792	AWUT01013449	71473	8278	60606	chr2R	25286936	-	21044089	21051112	1026
585	64914	AWUT01013449	71473	62497	65091	chr2R	25286936	-	21049558	21051112	3838
585	18291	AWUT01013449	71473	66301	66608	chr2R	25286936	-	21049303	21049609	15900
585	31348	AWUT01014658	40771	27873	39402	chr2R	25286936	-	19682178	19683049	9061
585	1589680	AWUT01014734	39057	654	32031	chr2L	23513712	+	13482513	13518102	408
585	48480	AWUT01014734	39057	32826	33665	chr2L	23513712	+	13517262	13518102	5453
585	48480	AWUT01014734	39057	34460	35299	chr2L	23513712	+	13517262	13518102	5452

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. suzukii genome assembly (DsuzGB1) 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