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

Database: dm6 Primary Table: netDrhoRefSeq2 Row Count: 249,679 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`	7557	`int(10) unsigned`	range
`tEnd`	9519	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NW_025335123	`varchar(255)`	values
`qStart`	6026117	`int(10) unsigned`	range
`qEnd`	6028796	`int(10) unsigned`	range
`chainId`	89387	`int(10) unsigned`	range
`ali`	1509	`int(10) unsigned`	range
`score`	69342	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1382	`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`	53	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7557	9519	-	NW_025335123	6026117	6028796	89387	1509	69342	-1	-1	1382	top	0	0	0	-1	-1	-1	-1	0	53
585	2	chr2L	8063	8238	-	NW_025335123	6027700	6028233	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	42
585	2	chr2L	8357	8379	-	NW_025335123	6027522	6027581	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8499	8649	-	NW_025335123	6027193	6027402	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9282	9328	-	NW_025335123	6026465	6026560	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9383	9436	-	NW_025335123	6026197	6026410	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
1	1	chr2L	11206	22851708	-	NW_025335083	90747	26909139	1	6598043	410099815	-1	-1	3668585	top	200	1712545	2001772	-1	-1	-1	-1	286889	921050
585	2	chr2L	11549	11770	-	NW_025335083	26908041	26908798	0	0	0	-1	-1	-1	gap	0	0	496	-1	-1	-1	-1	0	0
585	2	chr2L	12936	13517	-	NW_025335083	26905302	26906875	0	0	0	-1	-1	-1	gap	0	57	1006	-1	-1	-1	-1	0	0
585	2	chr2L	15715	16317	-	NW_025335083	26902399	26903085	0	0	0	-1	-1	-1	gap	0	93	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