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

Database: DereCAF1 Primary Table: chainDm6 Row Count: 26,096 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	21208	`double`	range
`tName`	scaffold_1009	`varchar(255)`	values
`tSize`	1528	`int(10) unsigned`	range
`tStart`	2	`int(10) unsigned`	range
`tEnd`	261	`int(10) unsigned`	range
`qName`	chrX	`varchar(255)`	values
`qSize`	23542271	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	11122606	`int(10) unsigned`	range
`qEnd`	11122871	`int(10) unsigned`	range
`id`	9483	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	21208	scaffold_1009	1528	2	261	chrX	23542271	+	11122606	11122871	9483
585	24033	scaffold_103	1756	1418	1756	chr3R	32079331	-	21658739	21659081	8456
585	50161	scaffold_104	3283	2623	3283	chr3L	28110227	-	21267139	21267758	3627
585	17115	scaffold_1074	869	25	261	chr2R	25286936	-	10457169	10457404	11772
585	52879	scaffold_1087	1591	853	1582	chr3L	28110227	-	11251646	11252415	3397
585	11734	scaffold_1120	3858	304	562	chr2R	25286936	+	5262319	5262578	17292
585	21929	scaffold_1131	1340	0	320	chr2L	23513712	-	18644836	18645184	9172
585	136417	scaffold_1144	4503	1	1986	chrX	23542271	-	22132156	22134110	855
585	14581	scaffold_1153	1042	16	212	chr3R	32079331	-	7522514	7522710	13934
585	60560	scaffold_1153	1042	24	1034	chr3R	32079331	-	7521999	7523054	2935

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. erecta genome assembly (DereCAF1) 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