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

Database: DyakCAF1 Primary Table: netDm6 Row Count: 195,684 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	1	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chrX	`varchar(255)`	values
`tStart`	14834	`int(10) unsigned`	range
`tEnd`	21758878	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	chrX	`varchar(255)`	values
`qStart`	126762	`int(10) unsigned`	range
`qEnd`	23034582	`int(10) unsigned`	range
`chainId`	4	`int(10) unsigned`	range
`ali`	8601244	`int(10) unsigned`	range
`score`	595489114	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	79476	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	232310	`int(11)`	range
`qN`	64420	`int(11)`	range
`tR`	1436436	`int(11)`	range
`qR`	2349696	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	892441	`int(11)`	range
`qTrf`	635088	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	tN	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
1	1	chrX	14834	21758878	+	chrX	126762	23034582	4	8601244	595489114	-1	-1	79476	top	232310	64420	1436436	2349696	-1	-1	-1	-1	892441	635088
585	2	chrX	14989	15260	+	chrX	126922	127366	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	231
585	2	chrX	16060	16329	+	chrX	128168	128563	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	chrX	17265	18078	+	chrX	129520	130690	0	0	0	-1	-1	-1	gap	0	0	526	683	-1	-1	-1	-1	0	0
585	2	chrX	18730	18760	+	chrX	131357	131365	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	chrX	19362	19690	+	chrX	131992	132319	0	0	0	-1	-1	-1	gap	0	0	201	125	-1	-1	-1	-1	0	0
585	2	chrX	20660	20686	+	chrX	133426	133469	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	chrX	21366	21453	+	chrX	134142	134210	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	chrX	22234	22248	+	chrX	134985	134985	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	chrX	22404	22422	+	chrX	135888	135888	0	0	0	-1	-1	-1	gap	0	0	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. yakuba genome assembly (DyakCAF1) 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