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

Database: DmojCAF1 Primary Table: netDariGB1 Row Count: 130,295 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_6618	`varchar(255)`	values
`tStart`	0	`int(10) unsigned`	range
`tEnd`	393	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	LSRM01000002	`varchar(255)`	values
`qStart`	8507726	`int(10) unsigned`	range
`qEnd`	8508122	`int(10) unsigned`	range
`chainId`	6332	`int(10) unsigned`	range
`ali`	393	`int(10) unsigned`	range
`score`	33191	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	0	`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`	33	`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	qN	tR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	scaffold_6618	0	393	+	LSRM01000002	8507726	8508122	6332	393	33191	-1	-1	0	top	0	0	-1	-1	-1	-1	33	0
585	1	scaffold_1447	0	673	-	LSRM01000005	16280260	16280933	3495	673	60621	-1	-1	673	top	0	0	-1	-1	-1	-1	0	0
585	1	scaffold_439	0	688	-	LSRM01000005	16682754	16683430	3599	670	58706	-1	-1	676	top	0	0	-1	-1	-1	-1	0	0
585	2	scaffold_439	349	365	-	LSRM01000005	16683077	16683077	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	1	scaffold_956	130	706	+	LSRM01000005	20895025	20895618	4770	566	43286	-1	-1	593	top	0	0	-1	-1	-1	-1	0	0
585	1	scaffold_1557	0	355	-	LSRM01000001	563230	563585	6825	355	31037	-1	-1	355	top	0	6	-1	-1	-1	-1	0	0
585	1	scaffold_1212	64	753	+	LSRM01000002	25213193	25213889	4010	658	52309	-1	-1	665	top	0	0	-1	-1	-1	-1	35	0
585	2	scaffold_1212	382	394	+	LSRM01000002	25213502	25213502	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	1	scaffold_5269	0	220	-	LSRM01000004	242179	242400	12596	220	18138	-1	-1	221	top	1	31	-1	-1	-1	-1	0	0
585	1	scaffold_5269	243	573	+	LSRM01000002	18792211	18792542	7971	330	26926	-1	-1	331	top	0	0	-1	-1	-1	-1	330	331

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. mojavensis genome assembly (DmojCAF1) 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