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

Database: dm6 Primary Table: netDyakRefSeq3 Row Count: 210,144 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`	5244	`int(10) unsigned`	range
`tEnd`	23511915	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NC_052527	`varchar(255)`	values
`qStart`	59703	`int(10) unsigned`	range
`qEnd`	29806101	`int(10) unsigned`	range
`chainId`	4	`int(10) unsigned`	range
`ali`	7524625	`int(10) unsigned`	range
`score`	542699237	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	6936584	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	200	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	2269571	`int(11)`	range
`qR`	7845030	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	328500	`int(11)`	range
`qTrf`	854336	`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	5244	23511915	+	NC_052527	59703	29806101	4	7524625	542699237	-1	-1	6936584	top	200	2269571	7845030	-1	-1	-1	-1	328500	854336
585	2	chr2L	5395	10115	+	NC_052527	59856	61495	0	0	0	-1	-1	-1	gap	0	579	222	-1	-1	-1	-1	0	0
585	3	chr2L	7432	9533	-	NC_052526	18240862	18243345	48279	2055	130311	-1	-1	2008	nonSyn	0	0	0	-1	-1	-1	-1	0	0
585	4	chr2L	8615	8643	-	NC_052526	18241791	18241814	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	10262	11214	+	NC_052527	61643	62629	0	0	0	-1	-1	-1	gap	0	0	94	-1	-1	-1	-1	0	0
585	3	chr2L	11065	11214	+	NC_052527	62655	62804	2023597	149	9771	0	26	149	syn	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11670	11706	+	NC_052527	63097	63194	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	89
585	2	chr2L	12967	13471	+	NC_052527	64452	64631	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15789	15851	+	NC_052527	66948	67037	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15970	16200	+	NC_052527	67157	67484	0	0	0	-1	-1	-1	gap	0	0	293	-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