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

Database: dm6 Primary Table: netDmojImproved Row Count: 101,113

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	8656	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	scaffold_6308	`varchar(255)`	values
`qStart`	1385917	`int(10) unsigned`	range
`qEnd`	1386543	`int(10) unsigned`	range
`chainId`	4463	`int(10) unsigned`	range
`ali`	626	`int(10) unsigned`	range
`score`	25759	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	617	`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	8656	9282	+	scaffold_6308	1385917	1386543	4463	626	25759	-1	-1	617	top	0	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11215	302504	+	scaffold_6500	129814	2550953	3	70492	1999717	-1	-1	8710	top	40002	11912	110273	-1	-1	-1	-1	1130	88427
585	2	chr2L	11521	11770	+	scaffold_6500	130112	130433	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12943	13516	+	scaffold_6500	131624	131660	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14890	14930	+	scaffold_6500	133025	133104	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15734	17049	+	scaffold_6500	133908	135756	0	0	0	-1	-1	-1	gap	0	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17140	104473	+	scaffold_6500	135847	224337	0	0	0	-1	-1	-1	gap	25	7782	2424	-1	-1	-1	-1	466	1165
585	3	chr2L	22123	24965	+	scaffold_6482	2011655	2019038	1259	2220	89720	-1	-1	0	nonSyn	0	249	4155	-1	-1	-1	-1	0	27
585	4	chr2L	22689	22737	+	scaffold_6482	2012224	2014614	0	0	0	-1	-1	-1	gap	0	0	1760	-1	-1	-1	-1	0	0
585	4	chr2L	23876	23920	+	scaffold_6482	2015760	2018463	0	0	0	-1	-1	-1	gap	0	0	2395	-1	-1	-1	-1	0	27

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