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

Database: DtakGB2 Primary Table: chainDm6 Row Count: 23,052 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	98102	`double`	range
`tName`	AFFI02000003	`varchar(255)`	values
`tSize`	44791	`int(10) unsigned`	range
`tStart`	10544	`int(10) unsigned`	range
`tEnd`	32421	`int(10) unsigned`	range
`qName`	chr2R	`varchar(255)`	values
`qSize`	25286936	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	19991041	`int(10) unsigned`	range
`qEnd`	19992676	`int(10) unsigned`	range
`id`	1346	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	98102	AFFI02000003	44791	10544	32421	chr2R	25286936	-	19991041	19992676	1346
585	8552	AFFI02000003	44791	32114	32321	chrX	23542271	+	13615689	13615896	19510
585	175681	AFFI02000003	44791	39460	42504	chr2R	25286936	+	5092040	5095084	907
585	48815	AFFI02000005	1039	0	1039	chr3L	28110227	-	24310411	24311371	2830
585	37430	AFFI02000006	1072	9	1066	chr3L	28110227	-	24308897	24309668	3752
585	36482	AFFI02000007	1157	242	1157	chr3L	28110227	-	24308295	24309022	3852
585	1149784	AFFI02000009	32834	947	30710	chr3R	32079331	-	18659507	18685524	558
585	23443	AFFI02000009	32834	16088	17098	chr2R	25286936	+	23381531	23382529	6420
585	42259	AFFI02000009	32834	26007	27476	chr3R	32079331	+	13396781	13398193	3302
585	22675	AFFI02000009	32834	26021	26409	chr2R	25286936	-	871692	872235	6696

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. takahashii genome assembly (DtakGB2) 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