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

Database: dm6 Primary Table: netDserRefSeq1 Row Count: 263,241 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`	7580	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NW_018367028	`varchar(255)`	values
`qStart`	3832856	`int(10) unsigned`	range
`qEnd`	3835059	`int(10) unsigned`	range
`chainId`	122055	`int(10) unsigned`	range
`ali`	725	`int(10) unsigned`	range
`score`	35471	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	697	`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	7580	9275	-	NW_018367028	3832856	3835059	122055	725	35471	-1	-1	697	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	7693	8663	-	NW_018367028	3833468	3834946	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11210	828189	+	NW_018366386	10448	1501475	50	244588	13131511	-1	-1	0	top	40185	156224	-1	-1	-1	-1	14582	127451
585	2	chr2L	11368	11406	+	NW_018366386	10609	10787	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11536	11770	+	NW_018366386	10917	11211	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12951	13515	+	NW_018366386	12398	12650	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	13628	13675	+	NW_018366386	12763	12875	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	14882	14920	+	NW_018366386	14100	14140	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15723	17049	+	NW_018366386	14943	16596	0	0	0	-1	-1	-1	gap	93	136	-1	-1	-1	-1	0	0
585	2	chr2L	17136	21963	+	NW_018366386	16683	19585	0	0	0	-1	-1	-1	gap	0	151	-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