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

Database: dm6 Primary Table: chainDhydGB1 Row Count: 13,685 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	24210	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8664	`int(10) unsigned`	range
`tEnd`	9257	`int(10) unsigned`	range
`qName`	NWQH01000219	`varchar(255)`	values
`qSize`	158466	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	27067	`int(10) unsigned`	range
`qEnd`	27660	`int(10) unsigned`	range
`id`	4424	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	24210	chr2L	23513712	8664	9257	NWQH01000219	158466	-	27067	27660	4424
73	726198	chr2L	23513712	11215	148157	NWQH01000238	139079	-	2988	139043	466
585	91661	chr2L	23513712	22122	24968	NWQH01000183	223671	-	37021	41271	1635
585	703790	chr2L	23513712	26291	102031	NWQH01000238	139079	+	50108	125193	474
585	7869	chr2L	23513712	27127	28221	NWQH01000023	1984663	-	1360514	1361096	13373
585	40095	chr2L	23513712	102610	103770	NWQH01000140	310477	-	239481	240587	2825
585	8322	chr2L	23513712	118635	119016	NWQH01000010	1411534	+	158151	158544	12644
585	10931	chr2L	23513712	118712	119543	NWQH01000249	123278	+	19316	19989	9503
585	34257	chr2L	23513712	123339	126223	NWQH01000249	123278	+	18022	19990	3226
585	8592	chr2L	23513712	123721	124713	NWQH01000010	1411534	+	157501	158329	12220

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