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

Database: dm6 Primary Table: netDobsRefSeq2 Row Count: 232,177 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	8733	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NW_024542865	`varchar(255)`	values
`qStart`	5701980	`int(10) unsigned`	range
`qEnd`	5702522	`int(10) unsigned`	range
`chainId`	151737	`int(10) unsigned`	range
`ali`	542	`int(10) unsigned`	range
`score`	19155	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	542	`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	8733	9275	+	NW_024542865	5701980	5702522	151737	542	19155	-1	-1	542	top	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11214	143142	-	NW_024542824	1387618	1537727	156	52557	2564689	-1	-1	0	top	8727	4836	-1	-1	-1	-1	532	1800
585	2	chr2L	11526	11770	-	NW_024542824	1537041	1537408	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12935	13517	-	NW_024542824	1535813	1535865	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15716	17048	-	NW_024542824	1531501	1533600	0	0	0	-1	-1	-1	gap	93	117	-1	-1	-1	-1	0	0
585	2	chr2L	17141	22113	-	NW_024542824	1528592	1531408	0	0	0	-1	-1	-1	gap	0	460	-1	-1	-1	-1	0	0
585	2	chr2L	24217	24720	-	NW_024542824	1526423	1526468	0	0	0	-1	-1	-1	gap	249	0	-1	-1	-1	-1	0	19
585	2	chr2L	25065	25988	-	NW_024542824	1524913	1526077	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	26079	26282	-	NW_024542824	1524562	1524823	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	26467	26523	-	NW_024542824	1524323	1524368	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RefSeq Drosophila Chain/Net (refseqDrosChainNet) 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 Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. doi: 10.1073/pnas.1932072100.

Description