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

Database: dm6 Primary Table: netDtakRefSeq2 Row Count: 238,196 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`	7559	`int(10) unsigned`	range
`tEnd`	9472	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NW_025323455	`varchar(255)`	values
`qStart`	11528297	`int(10) unsigned`	range
`qEnd`	11531012	`int(10) unsigned`	range
`chainId`	13910	`int(10) unsigned`	range
`ali`	1274	`int(10) unsigned`	range
`score`	62857	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	2715	`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`	231	`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	7559	9472	-	NW_025323455	11528297	11531012	13910	1274	62857	-1	-1	2715	top	0	0	-1	-1	-1	-1	0	231
585	2	chr2L	8069	8220	-	NW_025323455	11529724	11530469	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	190
585	2	chr2L	8357	8671	-	NW_025323455	11529239	11529587	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	41
585	3	chr2L	8357	8671	+	NW_025323480	4086044	4086268	21684	199	8662	-1	-1	0	nonSyn	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	8367	8388	+	NW_025323480	4086054	4086054	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	8564	8658	+	NW_025323480	4086239	4086255	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9275	9436	-	NW_025323455	11528333	11528635	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
1	1	chr2L	11214	21393384	+	NW_025323500	158442	18304003	2	4080375	252136939	-1	-1	743169	top	1003056	890285	-1	-1	-1	-1	210802	445018
585	2	chr2L	11537	11770	+	NW_025323500	158761	159007	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12943	13505	+	NW_025323500	160174	160239	0	0	0	-1	-1	-1	gap	57	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