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

Database: dm6 Primary Table: chainDficGB2 Row Count: 21,574 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	48803	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7553	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	KB456926	`varchar(255)`	values
`qSize`	490760	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	370960	`int(10) unsigned`	range
`qEnd`	373074	`int(10) unsigned`	range
`id`	2648	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	48803	chr2L	23513712	7553	9282	KB456926	490760	-	370960	373074	2648
585	23926	chr2L	23513712	8724	9275	KB457322	2307182	-	2099955	2100506	6467
585	220871	chr2L	23513712	11210	18195	KB457373	1541693	-	6833	13376	380
585	1698025	chr2L	23513712	21965	93305	KB457373	1541693	+	1454649	1526001	236
585	8111	chr2L	23513712	28008	28217	KB457373	1541693	+	1460361	1460573	19705
585	442142	chr2L	23513712	94682	102000	KB457561	912194	+	799460	806653	294
73	1812073	chr2L	23513712	102400	153406	KB457373	1541693	+	1402168	1451917	231
585	8464	chr2L	23513712	113008	113280	AFFG02004019	1105	-	385	657	18731
585	28343	chr2L	23513712	115708	116352	KB457522	3457230	-	2709531	2710187	5384
585	8339	chr2L	23513712	118562	118849	KB457373	1541693	+	1423699	1423983	19061

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