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

Database: dm6 Primary Table: netDeleRefSeq2 Row Count: 245,467 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`	7555	`int(10) unsigned`	range
`tEnd`	9283	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NW_024545513	`varchar(255)`	values
`qStart`	23731895	`int(10) unsigned`	range
`qEnd`	23734056	`int(10) unsigned`	range
`chainId`	55941	`int(10) unsigned`	range
`ali`	1388	`int(10) unsigned`	range
`score`	56670	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	820	`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	7555	9283	-	NW_024545513	23731895	23734056	55941	1388	56670	-1	-1	820	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	7662	7692	-	NW_024545513	23733892	23733949	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8069	8379	-	NW_024545513	23732802	23733506	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11206	17248	+	NW_024545730	5176	13860	5338	4124	241839	-1	-1	0	top	150	1758	-1	-1	-1	-1	0	481
585	2	chr2L	11639	11770	+	NW_024545730	5606	5727	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12946	13515	+	NW_024545730	6904	7673	0	0	0	-1	-1	-1	gap	57	335	-1	-1	-1	-1	0	0
585	2	chr2L	13645	13675	+	NW_024545730	7803	7856	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15726	16317	+	NW_024545730	9908	11090	0	0	0	-1	-1	-1	gap	93	203	-1	-1	-1	-1	0	0
585	2	chr2L	16439	17027	+	NW_024545730	11212	13642	0	0	0	-1	-1	-1	gap	0	1220	-1	-1	-1	-1	0	481
585	1	chr2L	21970	39875	+	NW_024546167	21915439	21932924	829	14705	757280	-1	-1	0	top	696	181	-1	-1	-1	-1	43	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