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

Database: dm6 Primary Table: chainDsimGB2 Row Count: 30,401 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	23164	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	5358	`int(10) unsigned`	range
`tEnd`	5741	`int(10) unsigned`	range
`qName`	CM002913	`varchar(255)`	values
`qSize`	27160941	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	1367	`int(10) unsigned`	range
`qEnd`	1833	`int(10) unsigned`	range
`id`	7916	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	23164	chr2L	23513712	5358	5741	CM002913	27160941	-	1367	1833	7916
585	9922	chr2L	23513712	5692	5856	CM002913	27160941	-	1367	1531	23026
585	125671	chr2L	23513712	7429	9643	CM002914	20829647	-	2841779	2844564	385
585	9760	chr2L	23513712	8733	8927	JPYS01000842	204	+	9	203	23456
585	19144	chr2L	23513712	8733	9282	CM002912	24153973	+	12504301	12504850	10590
1	1677437910	chr2L	23513712	10011	23075708	CM002910	23539531	+	4199	23436784	2
585	9873	chr2L	23513712	11065	11216	CM002910	23539531	+	5320	5471	23139
585	12454	chr2L	23513712	11214	11393	CM002910	23539531	+	5119	5296	18145
585	9371	chr2L	23513712	16650	16791	JPYS01003584	28417	-	471	615	24537
585	17294	chr2L	23513712	19085	19322	CM002910	23539531	+	10287	10543	12295

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