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

Database: dm6 Primary Table: netDvirRefSeq1 Row Count: 153,191 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`	8664	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NW_022587575	`varchar(255)`	values
`qStart`	7882262	`int(10) unsigned`	range
`qEnd`	7882873	`int(10) unsigned`	range
`chainId`	195280	`int(10) unsigned`	range
`ali`	611	`int(10) unsigned`	range
`score`	27031	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	610	`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	8664	9275	-	NW_022587575	7882262	7882873	195280	611	27031	-1	-1	610	top	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11215	152876	-	NW_022587573	2059652	2278714	908	19638	780282	-1	-1	1151	top	8727	27149	-1	-1	-1	-1	532	45616
585	2	chr2L	11521	11771	-	NW_022587573	2278055	2278414	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11902	12078	-	NW_022587573	2277757	2277924	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12941	13517	-	NW_022587573	2276854	2276896	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15756	17049	-	NW_022587573	2271945	2274624	0	0	0	-1	-1	-1	gap	93	117	-1	-1	-1	-1	0	0
585	2	chr2L	17141	93472	-	NW_022587573	2243655	2271853	0	0	0	-1	-1	-1	gap	7782	12678	-1	-1	-1	-1	152	347
585	3	chr2L	22122	24968	-	NW_022587575	6175013	6178261	42714	2153	93924	-1	-1	0	nonSyn	249	0	-1	-1	-1	-1	0	0
585	4	chr2L	22689	22737	-	NW_022587575	6177307	6177691	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	22937	22972	-	NW_022587575	6177059	6177107	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