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

Database: dm6 Primary Table: chainDrhoGB2 Row Count: 44,349 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	63332	`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`	KB451369	`varchar(255)`	values
`qSize`	500412	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	182554	`int(10) unsigned`	range
`qEnd`	184789	`int(10) unsigned`	range
`id`	5687	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	63332	chr2L	23513712	7557	9282	KB451369	500412	-	182554	184789	5687
585	24125	chr2L	23513712	8679	9282	KB451077	34273	+	14431	15034	16798
73	6742880	chr2L	23513712	11206	256056	KB451737	291548	+	1073	290365	147
585	2398138	chr2L	23513712	21964	102038	KB451737	291548	-	182454	280096	432
585	7774	chr2L	23513712	28008	28218	KB451737	291548	-	188891	189104	43124
585	9272	chr2L	23513712	73503	73720	KB451737	291548	-	242319	242536	37629
585	73297	chr2L	23513712	112758	114198	AFPP02026411	18475	+	11368	14049	4926
585	76184	chr2L	23513712	112853	114157	KB449272	60465	-	45015	46229	4737
585	29056	chr2L	23513712	115697	116352	AFPP02024855	315074	+	253631	254285	14424
585	8979	chr2L	23513712	118635	119016	KB451721	298381	-	45539	45926	38649

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