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

Database: dm6 Primary Table: netDsimRefSeq3 Row Count: 169,728 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	1	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	4992	`int(10) unsigned`	range
`tEnd`	23512345	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NC_052520	`varchar(255)`	values
`qStart`	60468	`int(10) unsigned`	range
`qEnd`	23749786	`int(10) unsigned`	range
`chainId`	2	`int(10) unsigned`	range
`ali`	20432154	`int(10) unsigned`	range
`score`	1696072952	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	2940870	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	200	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	2270178	`int(11)`	range
`qR`	2477267	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	328752	`int(11)`	range
`qTrf`	283548	`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
1	1	chr2L	4992	23512345	+	NC_052520	60468	23749786	2	20432154	1696072952	-1	-1	2940870	top	200	2270178	2477267	-1	-1	-1	-1	328752	283548
585	2	chr2L	5204	5216	+	NC_052520	60675	61725	0	0	0	-1	-1	-1	gap	0	0	891	-1	-1	-1	-1	12	1050
585	2	chr2L	5393	5489	+	NC_052520	61897	62883	0	0	0	-1	-1	-1	gap	0	0	887	-1	-1	-1	-1	0	986
585	3	chr2L	5393	5478	-	NC_052523	28132221	28132306	188364	85	5133	-1	-1	85	nonSyn	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	6005	6553	+	NC_052520	64317	65256	0	0	0	-1	-1	-1	gap	0	10	897	-1	-1	-1	-1	0	939
585	3	chr2L	6005	6072	-	NC_052523	28131831	28131898	142691	67	3840	-1	-1	45	nonSyn	0	10	7	-1	-1	-1	-1	0	0
585	2	chr2L	6680	9673	+	NC_052520	65378	78303	0	0	0	-1	-1	-1	gap	0	0	8841	-1	-1	-1	-1	0	1903
585	3	chr2L	6776	6858	-	NC_052523	28131853	28131935	130586	82	4494	-1	-1	82	nonSyn	0	0	44	-1	-1	-1	-1	0	0
585	3	chr2L	7429	9643	-	NC_052525	18665881	18668458	52153	2136	126069	-1	-1	2120	nonSyn	0	0	0	-1	-1	-1	-1	0	81
585	4	chr2L	7790	7802	-	NC_052525	18668102	18668102	0	0	0	-1	-1	-1	gap	0	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