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

Database: dm6 Primary Table: chainDmojCAF1 Row Count: 14,247 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	25759	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8656	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	scaffold_6308	`varchar(255)`	values
`qSize`	3356042	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	1385917	`int(10) unsigned`	range
`qEnd`	1386543	`int(10) unsigned`	range
`id`	3711	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	25759	chr2L	23513712	8656	9282	scaffold_6308	3356042	+	1385917	1386543	3711
1	18939021	chr2L	23513712	11215	20757341	scaffold_6500	32352404	+	129814	29485029	3
585	89720	chr2L	23513712	22123	24965	scaffold_6482	2735782	+	2011655	2019038	913
585	697261	chr2L	23513712	26291	101651	scaffold_6500	32352404	-	32129761	32211289	202
585	8222	chr2L	23513712	75114	75367	scaffold_6540	34148556	-	22314690	22314943	12991
585	58382	chr2L	23513712	95128	96304	scaffold_5990	1339	+	158	1333	1453
585	43959	chr2L	23513712	102541	103767	scaffold_6500	32352404	-	19702597	19703776	1988
585	9471	chr2L	23513712	118712	126212	scaffold_6680	24764193	-	6295183	6297641	11021
585	10413	chr2L	23513712	118718	119513	scaffold_6500	32352404	-	9733442	9734156	9973
585	12490	chr2L	23513712	123338	124932	scaffold_6500	32352404	+	14716744	14718220	8217

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