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

Database: dm6 Primary Table: netDobsGB1 Row Count: 237,591 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`	8733	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	BDQP01000021	`varchar(255)`	values
`qStart`	15453	`int(10) unsigned`	range
`qEnd`	15995	`int(10) unsigned`	range
`chainId`	6810	`int(10) unsigned`	range
`ali`	542	`int(10) unsigned`	range
`score`	19155	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	542	`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	8733	9275	+	BDQP01000021	15453	15995	6810	542	19155	-1	-1	542	top	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11214	143142	-	BDQP01000091	139317	287911	228	53224	2591410	-1	-1	0	top	8727	5408	-1	-1	-1	-1	532	797
585	2	chr2L	11526	11770	-	BDQP01000091	287225	287592	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12935	13517	-	BDQP01000091	285997	286049	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15716	17048	-	BDQP01000091	281726	283784	0	0	0	-1	-1	-1	gap	93	207	-1	-1	-1	-1	0	0
585	2	chr2L	17141	22113	-	BDQP01000091	279203	281633	0	0	0	-1	-1	-1	gap	0	628	-1	-1	-1	-1	0	0
585	2	chr2L	24217	24719	-	BDQP01000091	277035	277079	0	0	0	-1	-1	-1	gap	249	0	-1	-1	-1	-1	0	14
585	2	chr2L	25065	25988	-	BDQP01000091	275525	276689	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	26079	26282	-	BDQP01000091	275174	275435	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	26467	26523	-	BDQP01000091	274935	274980	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Drosophila Chain/Net (drosophilaChainNet) 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 Chain/Net Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003 100(20): 11484-11489. LAST Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93.

Description