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

Database: dm6 Primary Table: chainDnavGB1 Row Count: 12,800 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	9	`smallint(5) unsigned`	range
`score`	1519900	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	11215	`int(10) unsigned`	range
`tEnd`	2044373	`int(10) unsigned`	range
`qName`	LSRL01000002	`varchar(255)`	values
`qSize`	4222574	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	2110	`int(10) unsigned`	range
`qEnd`	4034732	`int(10) unsigned`	range
`id`	69	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
9	1519900	chr2L	23513712	11215	2044373	LSRL01000002	4222574	+	2110	4034732	69
585	91838	chr2L	23513712	22123	24965	LSRL01000006	1309517	+	495788	500640	742
585	703329	chr2L	23513712	26291	101632	LSRL01000002	4222574	-	4130955	4209616	141
585	7831	chr2L	23513712	77159	77560	LSRL01000002	4222574	-	4178364	4178765	12419
585	8630	chr2L	23513712	118712	119034	LSRL01000004	21835025	-	5815028	5815294	11210
585	19631	chr2L	23513712	124468	126223	LSRL01000002	4222574	-	3938707	3939530	4622
585	9573	chr2L	23513712	124550	126212	LSRL01000004	21835025	-	5814966	5817109	10114
586	35358	chr2L	23513712	132594	133682	LSRL01000001	21059900	+	15423792	15428112	2370
586	8398	chr2L	23513712	141887	142394	LSRL01000002	4222574	+	132479	132983	11551
586	12325	chr2L	23513712	166683	167356	LSRL01001117	8426	-	47	3487	7742

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