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

Database: DmirGB2 Primary Table: chainDm6 Row Count: 13,915 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	18256	`double`	range
`tName`	CM001516	`varchar(255)`	values
`tSize`	22123056	`int(10) unsigned`	range
`tStart`	2035	`int(10) unsigned`	range
`tEnd`	4886	`int(10) unsigned`	range
`qName`	chr2L	`varchar(255)`	values
`qSize`	23513712	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	8439715	`int(10) unsigned`	range
`qEnd`	8440167	`int(10) unsigned`	range
`id`	5298	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	18256	CM001516	22123056	2035	4886	chr2L	23513712	-	8439715	8440167	5298
585	10359	CM001516	22123056	4526	4733	chr2L	23513712	-	8439743	8439950	10019
585	8205	CM001516	22123056	4611	4850	chr3R	32079331	+	8656273	8656512	12810
585	63594	CM001516	22123056	15217	16791	chrX	23542271	-	11510898	11512487	1171
73	2134581	CM001516	22123056	18564	184240	chrX	23542271	-	21477273	21614463	148
585	13764	CM001516	22123056	23906	24815	chr2R	25286936	+	18692772	18699952	7308
585	16147	CM001516	22123056	23932	24596	chr3R	32079331	-	20728991	20729523	6120
585	10891	CM001516	22123056	23932	24596	chr2R	25286936	+	19470682	19471389	9463
585	10779	CM001516	22123056	24308	24596	chrX	23542271	+	1376758	1377046	9571
585	8732	CM001516	22123056	24309	24590	chr3R	32079331	-	20731438	20731719	12005

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. miranda genome assembly (DmirGB2) 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