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

Database: dm6 Primary Table: netDficRefSeq2 Row Count: 232,518 Data last updated: 2022-08-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7553	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NW_025064092	`varchar(255)`	values
`qStart`	4660754	`int(10) unsigned`	range
`qEnd`	4662868	`int(10) unsigned`	range
`chainId`	53638	`int(10) unsigned`	range
`ali`	1177	`int(10) unsigned`	range
`score`	52424	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	799	`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	tNewR	qNewR	tOldR	qOldR
585	1	chr2L	7553	9282	+	NW_025064092	4660754	4662868	53638	1177	52424	-1	-1	799	top	0	-1	-1	-1	-1
585	2	chr2L	7811	7862	+	NW_025064092	4661023	4661104	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1
585	2	chr2L	8058	8220	+	NW_025064092	4661300	4661774	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1
585	2	chr2L	8319	8658	+	NW_025064092	4661873	4662244	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1
585	1	chr2L	11210	18195	+	NW_025064326	39064	45609	4689	3841	221593	-1	-1	0	top	150	-1	-1	-1	-1
585	2	chr2L	11358	11404	+	NW_025064326	39215	39487	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1
585	2	chr2L	11540	11770	+	NW_025064326	39623	39898	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1
585	2	chr2L	12947	13517	+	NW_025064326	41080	41194	0	0	0	-1	-1	-1	gap	57	-1	-1	-1	-1
585	2	chr2L	15722	17049	+	NW_025064326	43403	44485	0	0	0	-1	-1	-1	gap	93	-1	-1	-1	-1
585	2	chr2L	17140	18109	+	NW_025064326	44576	45523	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1

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