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

Database: dm6 Primary Table: netDficGB2 Row Count: 199,849

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7553	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	KB456926	`varchar(255)`	values
`qStart`	117686	`int(10) unsigned`	range
`qEnd`	119800	`int(10) unsigned`	range
`chainId`	2648	`int(10) unsigned`	range
`ali`	1078	`int(10) unsigned`	range
`score`	48803	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	874	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	0	`int(11)`	range
`qR`	0	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	0	`int(11)`	range
`qTrf`	0	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7553	9282	-	KB456926	117686	119800	2648	1078	48803	-1	-1	874	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	7811	7862	-	KB456926	119450	119531	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8058	8658	-	KB456926	118310	119254	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11210	18195	-	KB457373	1528317	1534860	380	3839	220871	-1	-1	0	top	150	0	-1	-1	-1	-1	0	0
585	2	chr2L	11358	11404	-	KB457373	1534437	1534709	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11540	11770	-	KB457373	1534026	1534301	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12947	13517	-	KB457373	1532731	1532845	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15722	17049	-	KB457373	1529441	1530523	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17140	18109	-	KB457373	1528403	1529350	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	21965	93305	+	KB457373	1454649	1526001	236	35033	1698025	-1	-1	0	top	7782	630	-1	-1	-1	-1	152	570

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