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

Database: dm6 Primary Table: chainDmirGB2 Row Count: 13,915 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	17603	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	8694	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`qName`	CM001517	`varchar(255)`	values
`qSize`	30136903	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	7280711	`int(10) unsigned`	range
`qEnd`	7281299	`int(10) unsigned`	range
`id`	5513	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	17603	chr2L	23513712	8694	9282	CM001517	30136903	-	7280711	7281299	5513
585	17075	chr2L	23513712	8694	9282	CM001517	30136903	+	27947830	27948418	5722
585	19926	chr2L	23513712	8733	9282	CM001516	22123056	-	10097616	10098165	4728
585	2092689	chr2L	23513712	11214	117977	CM001520	28826359	+	28540902	28669921	151
585	8034	chr2L	23513712	23099	23219	CM001520	28826359	+	28538899	28539019	13078
585	9129	chr2L	23513712	27244	28219	CM001520	28826359	+	18891113	18891641	11468
73	823662	chr2L	23513712	114096	153215	CM001520	28826359	-	289723	330440	236
585	10599	chr2L	23513712	118712	119543	CM001520	28826359	+	28338376	28339057	9769
585	8976	chr2L	23513712	118717	119513	CM001520	28826359	-	24816432	24817145	11676
585	14788	chr2L	23513712	123726	124926	CM001520	28826359	-	12840171	12841243	6746

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