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

Database: DbiaGB2 Primary Table: netDm6 Row Count: 189,138 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	AFFD02000002	`varchar(255)`	values
`tStart`	292	`int(10) unsigned`	range
`tEnd`	526	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	chr2R	`varchar(255)`	values
`qStart`	18473848	`int(10) unsigned`	range
`qEnd`	18474091	`int(10) unsigned`	range
`chainId`	13102	`int(10) unsigned`	range
`ali`	233	`int(10) unsigned`	range
`score`	10940	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	243	`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	tNewR	qNewR	tOldR	qOldR	tTrf
585	1	AFFD02000002	292	526	+	chr2R	18473848	18474091	13102	233	10940	-1	-1	243	top	0	-1	-1	-1	-1	0
585	1	AFFD02000003	0	383	-	chr2R	18409877	18410264	5282	381	23197	-1	-1	387	top	0	-1	-1	-1	-1	0
585	1	AFFD02000005	0	478	-	chr3L	19339689	19340185	4059	471	28366	-1	-1	496	top	0	-1	-1	-1	-1	0
585	1	AFFD02000007	1252	1908	-	chrY	356331	356992	2607	656	39152	-1	-1	0	top	36	-1	-1	-1	-1	0
585	1	AFFD02000008	2	1105	+	chr3L	18788914	18789823	2300	619	42652	-1	-1	658	top	0	-1	-1	-1	-1	0
585	2	AFFD02000008	294	306	+	chr3L	18789234	18789234	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0
585	2	AFFD02000008	357	822	+	chr3L	18789285	18789534	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0
585	1	AFFD02000010	0	1271	-	chr3L	18770101	18771348	2639	661	38778	-1	-1	674	top	0	-1	-1	-1	-1	0
585	2	AFFD02000010	340	943	-	chr3L	18770434	18770943	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0
585	1	AFFD02000011	0	1205	-	chr3L	15265279	15266605	2484	719	40368	-1	-1	606	top	0	-1	-1	-1	-1	36

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. biarmipes genome assembly (DbiaGB2) 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