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

Database: dm6 Primary Table: chainDbusGB1 Row Count: 12,742 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	24683	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8674	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	CP012528	`varchar(255)`	values
`qSize`	23724088	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	616523	`int(10) unsigned`	range
`qEnd`	617124	`int(10) unsigned`	range
`id`	4083	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	24683	chr2L	23513712	8674	9275	CP012528	23724088	-	616523	617124	4083
585	9292	chr2L	23513712	8706	8924	CP012524	22510139	+	13182335	13182554	10488
585	207451	chr2L	23513712	11214	106393	CP012523	33300182	-	32196482	32266593	646
585	89274	chr2L	23513712	22122	24974	CP012528	23724088	+	6305828	6308197	1322
585	637810	chr2L	23513712	26520	102011	CP012523	33300182	+	1037032	1097495	207
585	9373	chr2L	23513712	28001	28217	CP012523	33300182	+	1038530	1038749	10397
585	44868	chr2L	23513712	102541	103769	CP012523	33300182	+	33151408	33152566	2424
73	555454	chr2L	23513712	108678	152872	CP012523	33300182	+	23915027	23960201	245
585	11489	chr2L	23513712	118712	119500	CP012525	28180402	-	2363207	2364312	8501
585	18690	chr2L	23513712	118933	126247	CP012523	33300182	+	8124894	8129477	5364

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. melanogaster genome assembly (dm6) 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