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

Database: dm6 Primary Table: chainDeugGB2 Row Count: 20,478 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	62448	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7557	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	KB464958	`varchar(255)`	values
`qSize`	339757	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	17595	`int(10) unsigned`	range
`qEnd`	19680	`int(10) unsigned`	range
`id`	1399	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	62448	chr2L	23513712	7557	9282	KB464958	339757	+	17595	19680	1399
585	19434	chr2L	23513712	8722	9282	KB465069	5362458	+	4901017	4901577	7113
73	6095794	chr2L	23513712	11214	203444	AFPQ02005124	195501	+	10301	191265	158
585	7977	chr2L	23513712	28008	28220	AFPQ02005124	195501	+	25000	25215	19209
585	9389	chr2L	23513712	73508	73719	AFPQ02005124	195501	+	64926	65137	15806
585	8585	chr2L	23513712	112944	113193	AFPQ02001923	1784	+	1485	1734	17545
585	8746	chr2L	23513712	113008	113280	AFPQ02001246	21089	+	8291	8563	17176
585	30259	chr2L	23513712	115694	116357	AFPQ02005835	352801	+	335316	335980	4212
585	7987	chr2L	23513712	118605	118887	AFPQ02005124	195501	+	115422	115704	19177
585	7614	chr2L	23513712	118632	118998	KB465133	5383265	-	411866	412237	20429

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