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

Database: dm6 Primary Table: netDsuzRefSeq2 Row Count: 240,866 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`	9275	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NW_023496845	`varchar(255)`	values
`qStart`	1685784	`int(10) unsigned`	range
`qEnd`	1687856	`int(10) unsigned`	range
`chainId`	115680	`int(10) unsigned`	range
`ali`	1316	`int(10) unsigned`	range
`score`	64482	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1340	`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	9275	+	NW_023496845	1685784	1687856	115680	1316	64482	-1	-1	1340	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8072	8223	+	NW_023496845	1686320	1686781	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8347	8403	+	NW_023496845	1686905	1687000	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8547	8733	+	NW_023496845	1687144	1687320	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
1	1	chr2L	11206	13191980	-	NW_023496800	1472583	25554499	2	5059777	317357133	-1	-1	1193744	top	499041	767888	-1	-1	-1	-1	142203	480053
585	2	chr2L	11375	11385	-	NW_023496800	25554327	25554327	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12943	13517	-	NW_023496800	25552433	25552770	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15726	16203	-	NW_023496800	25550076	25550222	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	16410	17049	-	NW_023496800	25548334	25549845	0	0	0	-1	-1	-1	gap	0	439	-1	-1	-1	-1	0	39
585	2	chr2L	17229	20800	-	NW_023496800	25547492	25548155	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