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

Database: dm6 Primary Table: chainDkikGB2 Row Count: 19,480 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	35455	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7570	`int(10) unsigned`	range
`tEnd`	9281	`int(10) unsigned`	range
`qName`	KB459500	`varchar(255)`	values
`qSize`	195988	`int(10) unsigned`	range
`qStrand`	+	`char(1)`	values
`qStart`	10880	`int(10) unsigned`	range
`qEnd`	13005	`int(10) unsigned`	range
`id`	3367	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	35455	chr2L	23513712	7570	9281	KB459500	195988	+	10880	13005	3367
585	20370	chr2L	23513712	8679	9273	KB459686	1750656	+	1476550	1477150	6177
585	8761	chr2L	23513712	9024	9245	KB459688	1198805	-	101885	102106	15848
585	198657	chr2L	23513712	11205	17136	AFFH02008258	25579	-	5764	11256	730
585	37669	chr2L	23513712	11210	12934	KB459959	890123	-	5385	6179	3144
585	40455	chr2L	23513712	11210	12474	KB459962	150991	-	5440	6766	2916
73	6923774	chr2L	23513712	22113	634192	KB459624	998533	+	435861	994438	148
585	1220055	chr2L	23513712	25993	94386	KB459624	998533	-	482420	559711	404
585	7838	chr2L	23513712	28008	28217	KB459624	998533	-	484545	484757	18333
585	175772	chr2L	23513712	94849	102000	KB458751	149409	+	138312	141991	766

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