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

Database: dm6 Primary Table: netDsimGB2 Row Count: 109,596 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`	5358	`int(10) unsigned`	range
`tEnd`	5741	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	CM002913	`varchar(255)`	values
`qStart`	27159108	`int(10) unsigned`	range
`qEnd`	27159574	`int(10) unsigned`	range
`chainId`	7916	`int(10) unsigned`	range
`ali`	372	`int(10) unsigned`	range
`score`	23164	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	466	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	172	`int(11)`	range
`qR`	155	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	29	`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	tN	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	5358	5741	-	CM002913	27159108	27159574	7916	372	23164	-1	-1	466	top	0	0	172	155	-1	-1	-1	-1	29	0
585	2	chr2L	5478	5489	-	CM002913	27159360	27159454	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	5741	5856	-	CM002913	27159410	27159525	23026	115	6958	-1	-1	115	top	0	0	1	0	-1	-1	-1	-1	0	0
585	1	chr2L	7429	9643	-	CM002914	17985083	17987868	385	2136	125671	-1	-1	2254	top	0	5	0	0	-1	-1	-1	-1	0	477
585	2	chr2L	7793	7805	-	CM002914	17987375	17987375	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8074	8089	-	CM002914	17986672	17987106	0	0	0	-1	-1	-1	gap	0	5	0	0	-1	-1	-1	-1	0	166
585	2	chr2L	8630	8640	-	CM002914	17986083	17986083	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9304	9316	-	CM002914	17985413	17985413	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	9582	9593	-	CM002914	17985133	17985133	0	0	0	-1	-1	-1	gap	0	0	0	0	-1	-1	-1	-1	0	0
1	1	chr2L	10011	23075708	+	CM002910	4199	23436784	2	20181723	1677437910	-1	-1	162290	top	200	5937	1881971	2143006	-1	-1	-1	-1	289006	171137

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