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

Database: DmojCAF1 Primary Table: chainDariGB1 Row Count: 34,067 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	30504	`double`	range
`tName`	scaffold_100	`varchar(255)`	values
`tSize`	1892	`int(10) unsigned`	range
`tStart`	0	`int(10) unsigned`	range
`tEnd`	423	`int(10) unsigned`	range
`qName`	LSRM01001280	`varchar(255)`	values
`qSize`	1729	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	1299	`int(10) unsigned`	range
`qEnd`	1729	`int(10) unsigned`	range
`id`	6942	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	30504	scaffold_100	1892	0	423	LSRM01001280	1729	-	1299	1729	6942
585	77144	scaffold_1005	1225	151	1027	LSRM01000006	2233968	-	1232272	1233166	2704
585	22094	scaffold_1008	949	0	276	LSRM01000002	27840087	+	20877873	20878132	9918
585	100579	scaffold_1020	1249	44	1249	LSRM01000004	22052390	+	1487865	1489131	1764
585	192043	scaffold_1029	2544	0	2380	LSRM01000003	23952536	-	3411380	3413782	795
585	24009	scaffold_103	1823	1466	1819	LSRM01000460	3653	-	0	352	9052
585	11550	scaffold_1030	1277	0	126	LSRM01000003	23952536	+	8049933	8050059	21130
585	35158	scaffold_1030	1277	122	505	LSRM01000005	29979347	+	18763882	18764265	5939
585	45199	scaffold_1031	977	11	977	LSRM01000002	27840087	+	7235340	7236516	4572
585	74327	scaffold_1033	1165	0	947	LSRM01000002	27840087	+	24523575	24524530	2836

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