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

Database: dm6 Primary Table: netDgriImproved Row Count: 103,565

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	8664	`int(10) unsigned`	range
`tEnd`	9283	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	scaffold_15203	`varchar(255)`	values
`qStart`	2038632	`int(10) unsigned`	range
`qEnd`	2039245	`int(10) unsigned`	range
`chainId`	5819	`int(10) unsigned`	range
`ali`	613	`int(10) unsigned`	range
`score`	25288	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	597	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	0	`int(11)`	range
`qR`	472	`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	8664	9283	+	scaffold_15203	2038632	2039245	5819	613	25288	-1	-1	597	top	0	472	-1	-1	-1	-1	0	0
73	1	chr2L	11215	152877	-	scaffold_15252	17002063	17160374	237	17947	771471	-1	-1	0	top	8727	7852	-1	-1	-1	-1	532	1544
585	2	chr2L	11521	11770	-	scaffold_15252	17159716	17160066	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12934	13517	-	scaffold_15252	17158492	17158542	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14098	14127	-	scaffold_15252	17157880	17157912	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15718	17050	-	scaffold_15252	17154147	17156300	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17141	104471	-	scaffold_15252	17058926	17154056	0	0	0	-1	-1	-1	gap	7782	3785	-1	-1	-1	-1	466	867
585	3	chr2L	22122	24965	+	scaffold_15203	11318992	11321751	1455	2234	91697	-1	-1	0	nonSyn	249	98	-1	-1	-1	-1	0	0
585	4	chr2L	22689	22737	+	scaffold_15203	11319562	11319628	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	23876	23922	+	scaffold_15203	11320764	11321190	0	0	0	-1	-1	-1	gap	0	98	-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