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

Database: DgriCAF1 Primary Table: netDm6 Row Count: 154,975 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	scaffold_15217	`varchar(255)`	values
`tStart`	2	`int(10) unsigned`	range
`tEnd`	340	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	chr2L	`varchar(255)`	values
`qStart`	7700008	`int(10) unsigned`	range
`qEnd`	7700346	`int(10) unsigned`	range
`chainId`	9278	`int(10) unsigned`	range
`ali`	338	`int(10) unsigned`	range
`score`	13053	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	338	`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	qTrf
585	1	scaffold_15217	2	340	+	chr2L	7700008	7700346	9278	338	13053	-1	-1	338	top	0	-1	-1	-1	-1	0	0
585	1	scaffold_15706	75	505	+	chr3L	7675889	7676304	13828	258	8583	-1	-1	258	top	0	-1	-1	-1	-1	0	415
585	2	scaffold_15706	143	312	+	chr3L	7675957	7676114	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0	157
585	1	scaffold_15209	89	628	+	chrX	21370297	21370728	10523	182	11400	-1	-1	0	top	363	-1	-1	-1	-1	83	0
585	2	scaffold_15209	164	521	+	chrX	21370372	21370621	0	0	0	-1	-1	-1	gap	355	-1	-1	-1	-1	83	0
585	1	scaffold_2793	0	712	-	chr2L	9653907	9654471	6097	487	19736	-1	-1	487	top	0	-1	-1	-1	-1	0	0
585	2	scaffold_2793	400	625	-	chr2L	9653994	9654071	0	0	0	-1	-1	-1	gap	0	-1	-1	-1	-1	0	0
585	1	scaffold_1175	0	638	-	chr2L	2480357	2480964	8429	245	14422	-1	-1	245	top	110	-1	-1	-1	-1	73	49
585	2	scaffold_1175	46	57	-	chr2L	2480918	2480918	0	0	0	-1	-1	-1	gap	4	-1	-1	-1	-1	0	0
585	2	scaffold_1175	142	264	-	chr2L	2480715	2480834	0	0	0	-1	-1	-1	gap	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. grimshawi genome assembly (DgriCAF1) 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