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

Database: dm6 Primary Table: chainDeleGB2 Row Count: 19,989 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	57506	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7555	`int(10) unsigned`	range
`tEnd`	9283	`int(10) unsigned`	range
`qName`	KB458310	`varchar(255)`	values
`qSize`	1232523	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	533963	`int(10) unsigned`	range
`qEnd`	536124	`int(10) unsigned`	range
`id`	1596	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	57506	chr2L	23513712	7555	9283	KB458310	1232523	-	533963	536124	1596
585	23577	chr2L	23513712	8732	9282	KB458613	3589426	+	1195792	1196342	5435
585	242403	chr2L	23513712	11206	17248	AFFF02006222	37888	-	10171	18853	382
585	758226	chr2L	23513712	21970	39875	AFFF02005312	133111	-	115583	133072	265
585	7821	chr2L	23513712	28008	28218	AFFF02005312	133111	-	121536	121749	18953
585	8069	chr2L	23513712	28404	28642	AFFF02005312	133111	-	121147	121382	18189
585	249539	chr2L	23513712	34179	39875	AFFF02001439	7782	-	2201	7743	375
585	406300	chr2L	23513712	34258	57509	AFFF02005865	24132	+	25	23951	318
585	247518	chr2L	23513712	34258	39875	AFFF02006222	37888	-	25	5487	377
585	370393	chr2L	23513712	57296	74144	AFFF02005857	17872	+	0	17714	328

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