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

Database: dm6 Primary Table: netDyakCAF1 Row Count: 153,710 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7432	`int(10) unsigned`	range
`tEnd`	9533	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	chrX	`varchar(255)`	values
`qStart`	17685963	`int(10) unsigned`	range
`qEnd`	17688446	`int(10) unsigned`	range
`chainId`	1029	`int(10) unsigned`	range
`ali`	2055	`int(10) unsigned`	range
`score`	130311	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	2008	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	0	`int(11)`	range
`qR`	0	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	0	`int(11)`	range
`qTrf`	0	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7432	9533	-	chrX	17685963	17688446	1029	2055	130311	-1	-1	2008	top	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8615	8643	-	chrX	17686892	17686915	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
1	1	chr2L	10115	15034989	+	chr2L	7509	15143681	3	8265181	603324149	-1	-1	76942	top	52154	574074	373709	-1	-1	-1	-1	153779	272087
585	2	chr2L	10262	11214	+	chr2L	7657	8643	0	0	0	-1	-1	-1	gap	0	0	94	-1	-1	-1	-1	0	0
585	3	chr2L	11065	11214	+	chr2L	8669	8818	21017	149	9771	0	26	149	syn	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11670	11706	+	chr2L	9111	9208	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	89
585	2	chr2L	12967	13471	+	chr2L	10466	10645	0	0	0	-1	-1	-1	gap	0	57	70	-1	-1	-1	-1	0	0
585	2	chr2L	15789	16200	+	chr2L	12962	13498	0	0	0	-1	-1	-1	gap	0	93	417	-1	-1	-1	-1	0	0
585	2	chr2L	16579	16822	+	chr2L	13909	14379	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	3	chr2L	16650	16811	+	v2_chr2h_random_004	1167893	1168054	20019	160	10459	-1	-1	161	nonSyn	0	0	27	-1	-1	-1	-1	0	0

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