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

Database: dm6 Primary Table: netDalbRefSeq1 Row Count: 143,056 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`	8679	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NC_047627	`varchar(255)`	values
`qStart`	32527761	`int(10) unsigned`	range
`qEnd`	32528357	`int(10) unsigned`	range
`chainId`	46708	`int(10) unsigned`	range
`ali`	596	`int(10) unsigned`	range
`score`	26961	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	596	`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	8679	9275	+	NC_047627	32527761	32528357	46708	596	26961	-1	-1	596	top	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11255	152903	-	NC_047628	30580539	30718611	373	18072	767182	-1	-1	0	top	8727	2917	-1	-1	-1	-1	532	381
585	2	chr2L	11371	11402	-	NC_047628	30718474	30718495	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11520	11770	-	NC_047628	30717995	30718356	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	31
585	2	chr2L	11954	12074	-	NC_047628	30717679	30717811	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12227	12280	-	NC_047628	30717468	30717526	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12935	13515	-	NC_047628	30716753	30716813	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14880	14928	-	NC_047628	30715357	30715401	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15722	17050	-	NC_047628	30713274	30714563	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17141	104473	-	NC_047628	30630550	30713183	0	0	0	-1	-1	-1	gap	7782	2275	-1	-1	-1	-1	466	292

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