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

Database: DobsGB1 Primary Table: netDm6 Row Count: 284,618 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	9	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	BDQP01000001	`varchar(255)`	values
`tStart`	481	`int(10) unsigned`	range
`tEnd`	2050267	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	chr3R	`varchar(255)`	values
`qStart`	23034224	`int(10) unsigned`	range
`qEnd`	27202740	`int(10) unsigned`	range
`chainId`	18	`int(10) unsigned`	range
`ali`	228503	`int(10) unsigned`	range
`score`	10963718	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	80857	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	102905	`int(11)`	range
`qR`	156950	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	46272	`int(11)`	range
`qTrf`	35674	`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
9	1	BDQP01000001	481	2050267	-	chr3R	23034224	27202740	18	228503	10963718	-1	-1	80857	top	102905	156950	-1	-1	-1	-1	46272	35674
585	2	BDQP01000001	593	608	-	chr3R	27202643	27202643	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	BDQP01000001	691	829	-	chr3R	27202454	27202563	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	41	0
585	2	BDQP01000001	936	966	-	chr3R	27202346	27202347	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	BDQP01000001	1002	1017	-	chr3R	27202310	27202310	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	BDQP01000001	1179	1197	-	chr3R	27202151	27202151	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	BDQP01000001	1260	1326	-	chr3R	27202046	27202088	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	BDQP01000001	1406	1514	-	chr3R	27201887	27201966	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	BDQP01000001	1559	1780	-	chr3R	27201594	27201842	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	BDQP01000001	1900	1913	-	chr3R	27201474	27201474	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. obscura genome assembly (DobsGB1) 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