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

Database: dm6 Primary Table: netDmojRefSeq2 Row Count: 137,299 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`	8656	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NW_025318667	`varchar(255)`	values
`qStart`	5803074	`int(10) unsigned`	range
`qEnd`	5803700	`int(10) unsigned`	range
`chainId`	35708	`int(10) unsigned`	range
`ali`	626	`int(10) unsigned`	range
`score`	25759	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	617	`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	8656	9282	+	NW_025318667	5803074	5803700	35708	626	25759	-1	-1	617	top	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11215	302660	+	NW_025318858	66929	2505887	3	69773	2233466	-1	-1	5966	top	11912	126128	-1	-1	-1	-1	1130	105263
585	2	chr2L	11521	11770	+	NW_025318858	67227	67548	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11959	12077	+	NW_025318858	67737	67873	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12943	13516	+	NW_025318858	68739	68774	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	14890	14930	+	NW_025318858	70139	70218	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15733	17049	+	NW_025318858	71021	72869	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	17140	93472	+	NW_025318858	72960	85978	0	0	0	-1	-1	-1	gap	7782	0	-1	-1	-1	-1	152	0
585	3	chr2L	22123	24965	+	NW_025318667	31246404	31253782	8757	2220	89722	-1	-1	0	nonSyn	249	3666	-1	-1	-1	-1	0	0
585	4	chr2L	22689	22737	+	NW_025318667	31246973	31249362	0	0	0	-1	-1	-1	gap	0	1638	-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