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

Database: dm6 Primary Table: chainDgriCAF1 Row Count: 15,776 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	73	`smallint(5) unsigned`	range
`score`	794681	`double`	range
`tName`	chr2L	`varchar(255)`	values
`tSize`	23513712	`int(10) unsigned`	range
`tStart`	11215	`int(10) unsigned`	range
`tEnd`	152877	`int(10) unsigned`	range
`qName`	scaffold_15252	`varchar(255)`	values
`qSize`	17193109	`int(10) unsigned`	range
`qStrand`	-	`char(1)`	values
`qStart`	32735	`int(10) unsigned`	range
`qEnd`	191046	`int(10) unsigned`	range
`id`	217	`int(10) unsigned`	range

Sample Rows

bin	score	tName	tSize	tStart	tEnd	qName	qSize	qStrand	qStart	qEnd	id
73	794681	chr2L	23513712	11215	152877	scaffold_15252	17193109	-	32735	191046	217
585	13536	chr2L	23513712	11819	12325	scaffold_15081	4274704	-	4214638	4215156	8971
585	91697	chr2L	23513712	22122	24965	scaffold_15203	11997470	+	11318992	11321751	1234
585	732951	chr2L	23513712	26287	102000	scaffold_15252	17193109	+	17060607	17145283	243
585	8020	chr2L	23513712	27244	28217	scaffold_15252	17193109	-	3975072	3975603	14773
585	10364	chr2L	23513712	75070	75368	scaffold_14624	4233967	+	2311923	2312221	11530
585	8999	chr2L	23513712	76695	77560	scaffold_15252	17193109	+	17109489	17110390	13201
585	32493	chr2L	23513712	101013	101627	scaffold_15252	17193109	+	17148161	17149002	3659
585	47567	chr2L	23513712	102541	103764	scaffold_15126	8399593	+	2522361	2523603	2477
585	10380	chr2L	23513712	118635	119538	scaffold_15252	17193109	+	3652705	3653584	11506

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