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

Database: DmojCAF1 Primary Table: netDhydGB1 Row Count: 297,826 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`	375	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	NWQH01000040	`varchar(255)`	values
`qStart`	250513	`int(10) unsigned`	range
`qEnd`	250841	`int(10) unsigned`	range
`chainId`	5429	`int(10) unsigned`	range
`ali`	326	`int(10) unsigned`	range
`score`	22103	`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	tNewR	qNewR	tOldR	qOldR	tTrf
585	1	scaffold_6618	0	375	-	NWQH01000040	250513	250841	5429	326	22103	-1	-1	0	top	-1	-1	-1	-1	33
585	2	scaffold_6618	95	114	-	NWQH01000040	250746	250746	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0
585	2	scaffold_6618	284	295	-	NWQH01000040	250580	250580	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0
585	2	scaffold_6618	315	328	-	NWQH01000040	250560	250560	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0
585	1	scaffold_1447	3	667	+	NWQH01000007	1104367	1104987	4027	486	28228	-1	-1	486	top	-1	-1	-1	-1	0
585	2	scaffold_1447	301	478	+	NWQH01000007	1104664	1104798	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0
585	1	scaffold_439	0	683	+	NWQH01000007	735654	736547	4963	352	23911	-1	-1	352	top	-1	-1	-1	-1	0
585	2	scaffold_439	234	557	+	NWQH01000007	735931	736421	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1	0
585	1	scaffold_956	270	519	+	NWQH01000145	252087	252336	10066	248	13304	-1	-1	249	top	-1	-1	-1	-1	0
585	1	scaffold_1557	0	348	-	NWQH01000175	106108	106456	4893	348	24171	-1	-1	348	top	-1	-1	-1	-1	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. 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