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

Database: dm6 Primary Table: chainDmojImproved Row Count: 16,232 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`	4463	`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	4463
1	16002130	chr2L	23513712	11215	20757341	scaffold_6500	32352404	+	129814	29485029	3
585	89720	chr2L	23513712	22123	24965	scaffold_6482	2735782	+	2011655	2019038	1259
585	670320	chr2L	23513712	26519	101651	scaffold_6500	32352404	-	32130032	32211289	229
585	8222	chr2L	23513712	75114	75367	scaffold_6540	34148556	-	22314690	22314943	15079
585	58382	chr2L	23513712	95128	96304	scaffold_5990	1339	+	158	1333	1968
585	42368	chr2L	23513712	102541	103767	scaffold_6500	32352404	-	19702597	19703776	2677
585	9452	chr2L	23513712	118635	124932	scaffold_6500	32352404	+	14717759	14718220	12760
585	10051	chr2L	23513712	118718	126234	scaffold_6500	32352404	-	9733442	9734198	11899
585	9478	chr2L	23513712	124543	126230	scaffold_6500	32352404	-	25126243	25130429	12720

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