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

Database: dm6 Primary Table: netDbusGB1 Row Count: 119,304 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`	8674	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	CP012528	`varchar(255)`	values
`qStart`	23106964	`int(10) unsigned`	range
`qEnd`	23107565	`int(10) unsigned`	range
`chainId`	4083	`int(10) unsigned`	range
`ali`	601	`int(10) unsigned`	range
`score`	24683	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	601	`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	8674	9275	-	CP012528	23106964	23107565	4083	601	24683	-1	-1	601	top	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11214	17136	-	CP012523	1098852	1103700	646	3359	138479	-1	-1	0	top	150	0	-1	-1	-1	-1	0	0
585	2	chr2L	11347	11776	-	CP012523	1103330	1103564	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11905	12077	-	CP012523	1103023	1103201	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12934	13506	-	CP012523	1102131	1102172	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	13627	13672	-	CP012523	1101957	1102010	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15719	17049	-	CP012523	1098939	1099896	0	0	0	-1	-1	-1	gap	93	0	-1	-1	-1	-1	0	0
585	1	chr2L	22122	24974	+	CP012528	6305828	6308197	1322	2333	89274	-1	-1	0	top	249	0	-1	-1	-1	-1	0	0
585	2	chr2L	24227	24734	+	CP012528	6307930	6307960	0	0	0	-1	-1	-1	gap	249	0	-1	-1	-1	-1	0	0
585	1	chr2L	26520	102011	+	CP012523	1037032	1097495	207	15548	637810	-1	-1	0	top	7533	3746	-1	-1	-1	-1	466	527

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