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

Database: dm6 Primary Table: netDeugRefSeq2 Row Count: 221,818 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`	7557	`int(10) unsigned`	range
`tEnd`	9516	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NW_024572115	`varchar(255)`	values
`qStart`	595842	`int(10) unsigned`	range
`qEnd`	598539	`int(10) unsigned`	range
`chainId`	52293	`int(10) unsigned`	range
`ali`	1609	`int(10) unsigned`	range
`score`	67611	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1443	`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	7557	9516	-	NW_024572115	595842	598539	52293	1609	67611	-1	-1	1443	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	7649	7692	-	NW_024572115	598419	598447	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8040	8232	-	NW_024572115	597527	598053	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8367	8379	-	NW_024572115	597343	597392	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9282	9308	-	NW_024572115	596397	596453	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9383	9447	-	NW_024572115	595911	596322	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11214	277315	+	NW_024573245	16892	302232	89	165264	9426549	-1	-1	872	top	11912	31812	-1	-1	-1	-1	1130	31434
585	2	chr2L	11540	11770	+	NW_024573245	17218	17475	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12954	13517	+	NW_024573245	18648	19053	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15719	16317	+	NW_024573245	21257	21658	0	0	0	-1	-1	-1	gap	93	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