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

Database: dm6 Primary Table: chainDyakCAF1 Row Count: 26,578 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`score`	130311	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	7432	`int(10) unsigned`	range
`tEnd`	9533	`int(10) unsigned`	range
`qName`	chrX	`varchar(255)`	values
`qSize`	21770863	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	4082417	`int(10) unsigned`	range
`qEnd`	4084900	`int(10) unsigned`	range
`id`	1029	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
585	130311	chr2L	23513712	7432	9533	chrX	21770863	-	4082417	4084900	1029
585	21169	chr2L	23513712	8733	9282	chr3L	24197627	+	12877220	12877769	10458
1	603324149	chr2L	23513712	10115	15034989	chr2L	22324452	+	7509	15143681	3
585	9902	chr2L	23513712	11065	11216	chr2L	22324452	+	8669	8820	21017
585	10459	chr2L	23513712	16650	16811	v2_chr2h_random_004	1180022	+	1167893	1168054	20019
585	9702	chr2L	23513712	16650	16814	v2_chrUn_2157	46777	+	36178	36337	21391
585	9018	chr2L	23513712	16676	16814	v2_chrUn_5475	13051	-	10839	10972	22831
585	9079	chr2L	23513712	19134	19271	chr2L	22324452	+	13613	13750	22688
585	10673	chr2L	23513712	19482	19643	v2_chr2h_random_004	1180022	+	1167893	1168054	19676
585	9916	chr2L	23513712	19482	19646	v2_chrUn_2157	46777	+	36178	36337	20988

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