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

Database: dm6 Primary Table: chainDariGB1 Row Count: 13,402 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	25995	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8656	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	LSRM01000001	`varchar(255)`	values
`qSize`	26536676	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	5528044	`int(10) unsigned`	range
`qEnd`	5528670	`int(10) unsigned`	range
`id`	3404	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	25995	chr2L	23513712	8656	9282	LSRM01000001	26536676	+	5528044	5528670	3404
9	5583124	chr2L	23513712	11215	8133955	LSRM01000002	27840087	+	2103	20044919	24
585	75337	chr2L	23513712	22123	23876	LSRM01000006	2233968	+	779821	783664	1050
585	18309	chr2L	23513712	23920	24965	LSRM01000704	2706	+	126	697	5041
585	696199	chr2L	23513712	26291	101651	LSRM01000002	27840087	-	27744098	27826691	175
585	8098	chr2L	23513712	75114	75367	LSRM01000005	29979347	-	19654568	19654821	12416
585	44071	chr2L	23513712	102541	103767	LSRM01000002	27840087	-	16146573	16147748	1860
585	9736	chr2L	23513712	118712	126212	LSRM01000004	22052390	-	6662983	6664621	10038
585	11729	chr2L	23513712	123685	126230	LSRM01000002	27840087	-	20889356	20896502	8248
585	8895	chr2L	23513712	123727	124932	LSRM01000002	27840087	+	13628366	13629452	11147

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