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

Database: dm6 Primary Table: netDtakGB2 Row Count: 218,570

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7559	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	KB461184	`varchar(255)`	values
`qStart`	99098	`int(10) unsigned`	range
`qEnd`	101482	`int(10) unsigned`	range
`chainId`	2241	`int(10) unsigned`	range
`ali`	1239	`int(10) unsigned`	range
`score`	61051	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1263	`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`	192	`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	7559	9275	-	KB461184	99098	101482	2241	1239	61051	-1	-1	1263	top	0	0	0	-1	-1	-1	-1	0	192
585	2	chr2L	8069	8220	-	KB461184	100182	100939	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	192
585	2	chr2L	8357	8671	-	KB461184	99702	100045	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	3	chr2L	8357	8671	+	KB461295	180516	180725	3257	193	8168	-1	-1	0	nonSyn	0	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	8367	8388	+	KB461295	180526	180526	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	8564	8658	+	KB461295	180696	180712	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11214	494946	-	KB460599	5580	557986	43	350532	21171372	-1	-1	833	top	20	26481	13635	-1	-1	-1	-1	9040	7490
585	2	chr2L	11537	11770	-	KB460599	557421	557667	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12943	13505	-	KB460599	556189	556254	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	13628	13667	-	KB460599	555976	556066	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0

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