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

Database: dm6 Primary Table: netDnavRefSeq1 Row Count: 129,221 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`	8673	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NW_022052058	`varchar(255)`	values
`qStart`	74	`int(10) unsigned`	range
`qEnd`	683	`int(10) unsigned`	range
`chainId`	10546	`int(10) unsigned`	range
`ali`	609	`int(10) unsigned`	range
`score`	25252	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	609	`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	8673	9282	-	NW_022052058	74	683	10546	609	25252	-1	-1	609	top	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11215	152876	+	NW_022045913	2619	145097	338	19100	799253	-1	-1	0	top	8727	1944	-1	-1	-1	-1	532	1361
585	2	chr2L	11521	11770	+	NW_022045913	2927	3255	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11941	12077	+	NW_022045913	3426	3580	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12947	13516	+	NW_022045913	4449	4480	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14877	14930	+	NW_022045913	5832	5910	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15725	17049	+	NW_022045913	6705	8263	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17139	93472	+	NW_022045913	8353	21298	0	0	0	-1	-1	-1	gap	7782	0	-1	-1	-1	-1	152	0
585	3	chr2L	22123	22693	-	NW_022047217	1042	1615	11976	570	22568	-1	-1	0	nonSyn	0	0	-1	-1	-1	-1	0	0
585	3	chr2L	22731	23876	-	NW_022049059	94	1246	4294	1144	53488	-1	-1	0	nonSyn	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