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

Database: dm6 Primary Table: netDwilRefSeq2 Row Count: 159,796 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`	NW_025814052	`varchar(255)`	values
`qStart`	8041229	`int(10) unsigned`	range
`qEnd`	8041825	`int(10) unsigned`	range
`chainId`	300509	`int(10) unsigned`	range
`ali`	596	`int(10) unsigned`	range
`score`	25291	`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	qTrf
585	1	chr2L	8679	9275	+	NW_025814052	8041229	8041825	300509	596	25291	-1	-1	596	top	0	0	-1	-1	-1	-1	0
585	1	chr2L	11214	17139	-	NW_025814050	3079926	3087895	19562	3471	151400	-1	-1	0	top	150	53	-1	-1	-1	-1	44
585	2	chr2L	11526	11764	-	NW_025814050	3087228	3087574	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0
585	2	chr2L	11905	12086	-	NW_025814050	3086897	3087087	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0
585	2	chr2L	12934	13512	-	NW_025814050	3085998	3086050	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0
585	2	chr2L	13628	13676	-	NW_025814050	3085828	3085879	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0
585	2	chr2L	14875	14935	-	NW_025814050	3084633	3084635	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0
585	2	chr2L	15725	17049	-	NW_025814050	3080016	3083843	0	0	0	-1	-1	-1	gap	93	53	-1	-1	-1	-1	44
585	1	chr2L	22118	24974	+	NW_025814053	5557089	5559495	43004	2327	101449	-1	-1	0	top	249	0	-1	-1	-1	-1	0
585	2	chr2L	24216	24744	+	NW_025814053	5559209	5559265	0	0	0	-1	-1	-1	gap	249	0	-1	-1	-1	-1	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