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

Database: dm6 Primary Table: netDbipGB2 Row Count: 206,738

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	8727	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	AFFE02006513	`varchar(255)`	values
`qStart`	84010	`int(10) unsigned`	range
`qEnd`	84558	`int(10) unsigned`	range
`chainId`	4615	`int(10) unsigned`	range
`ali`	548	`int(10) unsigned`	range
`score`	26650	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	548	`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	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	8727	9275	-	AFFE02006513	84010	84558	4615	548	26650	-1	-1	548	top	0	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11407	76079	+	KB464388	435170	713685	341	18453	674345	-1	-1	969	top	116	7856	1649	-1	-1	-1	-1	152	5043
585	2	chr2L	11523	11772	+	KB464388	435286	436189	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	29
585	2	chr2L	12016	12047	+	KB464388	436433	436461	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12228	12281	+	KB464388	436642	436683	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12934	13517	+	KB464388	437333	437380	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	13653	13677	+	KB464388	437518	437548	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	14884	14931	+	KB464388	438761	438801	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15723	17049	+	KB464388	439593	441189	0	0	0	-1	-1	-1	gap	0	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17136	22114	+	KB464388	441276	660762	0	0	0	-1	-1	-1	gap	116	0	1060	-1	-1	-1	-1	0	4483

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