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

Database: dm6 Primary Table: chainDserGB1 Row Count: 17,830 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	35471	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7580	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`qName`	MTTC01000817	`varchar(255)`	values
`qSize`	4525942	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	690883	`int(10) unsigned`	range
`qEnd`	693086	`int(10) unsigned`	range
`id`	3803	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	35471	chr2L	23513712	7580	9275	MTTC01000817	4525942	-	690883	693086	3803
585	21211	chr2L	23513712	8729	9281	MTTC01001254	5769022	+	4645638	4646190	6233
585	18119	chr2L	23513712	8730	9275	MTTC01000012	6880660	+	4996992	4997543	7333
585	24621	chr2L	23513712	8733	9275	MTTC01000817	4525942	+	2343371	2343875	5426
585	12845	chr2L	23513712	8733	9296	MTTC01000817	4525942	+	3747180	3747746	10567
73	13475284	chr2L	23513712	11210	828189	MTTC01000175	1789090	+	10448	1501475	49
585	19959	chr2L	23513712	22276	22705	MTTC01000175	1789090	+	122530	122885	6614
585	27905	chr2L	23513712	22705	23259	MTTC01000175	1789090	+	122888	123441	4859
585	8747	chr2L	23513712	23711	23903	MTTC01000175	1789090	+	123444	123636	15455
585	17271	chr2L	23513712	23903	24213	MTTC01000175	1789090	+	123638	123948	7725

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