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

Database: DyakCAF1 Primary Table: chainDm6 Row Count: 26,578 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	1	`smallint(5) unsigned`	range
`score`	603324149	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	22324452	`int(10) unsigned`	range
`tStart`	7509	`int(10) unsigned`	range
`tEnd`	15143681	`int(10) unsigned`	range
`qName`	chr2L	`varchar(255)`	values
`qSize`	23513712	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	10115	`int(10) unsigned`	range
`qEnd`	15034989	`int(10) unsigned`	range
`id`	3	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
1	603324149	chr2L	22324452	7509	15143681	chr2L	23513712	+	10115	15034989	3
585	9902	chr2L	22324452	8669	8820	chr2L	23513712	+	11065	11216	21017
585	9079	chr2L	22324452	13613	13750	chr2L	23513712	+	19134	19271	22688
585	14492	chr2L	22324452	14379	14733	chr2L	23513712	+	19654	19993	14827
585	12681	chr2L	22324452	14958	15203	chr2L	23513712	+	20200	20427	16783
585	47495	chr2L	22324452	15376	16256	chr2L	23513712	+	20583	21480	4377
585	7645	chr2L	22324452	22899	23111	chr2L	23513712	+	28008	28217	26439
585	9623	chr2L	22324452	61840	62078	chr2L	23513712	+	73409	73594	21530
585	8417	chr2L	22324452	62078	62202	chr2L	23513712	+	73597	73721	24256
585	7827	chr2L	22324452	63005	63114	chr2L	23513712	+	72875	72984	25891

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. yakuba genome assembly (DyakCAF1) 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