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

Database: dm6 Primary Table: chainDsecCAF1 Row Count: 29,433 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	122953	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7502	`int(10) unsigned`	range
`tEnd`	9643	`int(10) unsigned`	range
`qName`	super_8	`varchar(255)`	values
`qSize`	3762037	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	2368375	`int(10) unsigned`	range
`qEnd`	2370884	`int(10) unsigned`	range
`id`	1066	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	122953	chr2L	23513712	7502	9643	super_8	3762037	-	2368375	2370884	1066
585	19533	chr2L	23513712	8733	9282	super_0	21120651	+	4987208	4987757	12333
9	161271509	chr2L	23513712	10011	2138629	super_14	2068291	+	18102	2068291	18
585	10212	chr2L	23513712	11065	11216	super_14	2068291	+	19303	19453	22508
585	12240	chr2L	23513712	11214	11393	super_14	2068291	+	19102	19279	18959
585	9371	chr2L	23513712	16650	16791	super_1211	6494	-	1429	1573	24361
585	8426	chr2L	23513712	16676	16803	super_26	826190	-	660951	661078	26757
585	14103	chr2L	23513712	19085	19308	super_14	2068291	+	24200	24425	16597
585	9509	chr2L	23513712	19441	19635	super_26	826190	-	656370	661078	24038
585	9585	chr2L	23513712	19482	19623	super_1211	6494	-	1429	1573	23899

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