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

Database: dm6 Primary Table: netDbusRefSeq1 Row Count: 117,413 Data last updated: 2022-08-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	8674	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NC_046608	`varchar(255)`	values
`qStart`	12258598	`int(10) unsigned`	range
`qEnd`	12259199	`int(10) unsigned`	range
`chainId`	21111	`int(10) unsigned`	range
`ali`	601	`int(10) unsigned`	range
`score`	24683	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	601	`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	8674	9275	+	NC_046608	12258598	12259199	21111	601	24683	-1	-1	601	top	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11214	17136	+	NC_046604	18611973	18616821	1040	3359	138414	-1	-1	0	top	150	0	-1	-1	-1	-1	0	0
585	2	chr2L	11347	11776	+	NC_046604	18612109	18612343	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11905	12077	+	NC_046604	18612472	18612650	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12934	13506	+	NC_046604	18613501	18613542	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	13627	13672	+	NC_046604	18613663	18613716	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15719	17049	+	NC_046604	18615777	18616734	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	1	chr2L	22122	24974	+	NC_046608	18632670	18635039	4055	2333	89274	-1	-1	0	top	249	0	-1	-1	-1	-1	0	0
585	2	chr2L	24227	24734	+	NC_046608	18634772	18634802	0	0	0	-1	-1	-1	gap	249	0	-1	-1	-1	-1	0	0
585	1	chr2L	26520	102011	-	NC_046604	18618178	18679128	231	15121	621065	-1	-1	0	top	7533	1573	-1	-1	-1	-1	466	548

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