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

Database: dm6 Primary Table: netDereRefSeq1 Row Count: 219,877 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	1	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	5508	`int(10) unsigned`	range
`tEnd`	8445802	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	NW_020825200	`varchar(255)`	values
`qStart`	39318	`int(10) unsigned`	range
`qEnd`	17665413	`int(10) unsigned`	range
`chainId`	4	`int(10) unsigned`	range
`ali`	7337965	`int(10) unsigned`	range
`score`	539417899	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	7621846	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	302045	`int(11)`	range
`qR`	336014	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	102002	`int(11)`	range
`qTrf`	827554	`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
1	1	chr2L	5508	8445802	+	NW_020825200	39318	17665413	4	7337965	539417899	-1	-1	7621846	top	302045	336014	-1	-1	-1	-1	102002	827554
585	2	chr2L	5741	9887	+	NW_020825200	39567	42755	0	0	0	-1	-1	-1	gap	318	1123	-1	-1	-1	-1	0	161
585	3	chr2L	7482	9642	-	NW_020825209	6880216	6882732	44654	2124	131478	-1	-1	2119	nonSyn	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9955	10364	+	NW_020825200	42823	43400	0	0	0	-1	-1	-1	gap	38	28	-1	-1	-1	-1	0	0
585	2	chr2L	11063	11214	+	NW_020825200	44152	44152	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	3	chr2L	11065	11214	+	NW_020825200	44178	44327	1299528	149	9389	0	26	149	syn	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11567	11621	+	NW_020825200	44503	44530	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12967	13515	+	NW_020825200	45876	46511	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	304
585	2	chr2L	15778	15796	+	NW_020825200	48774	48908	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15967	16200	+	NW_020825200	49083	49627	0	0	0	-1	-1	-1	gap	0	349	-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