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

Database: dm6 Primary Table: netDsuzGB1 Row Count: 206,353

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	5565	`int(10) unsigned`	range
`tEnd`	5883	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	AWUT01022642	`varchar(255)`	values
`qStart`	0	`int(10) unsigned`	range
`qEnd`	287	`int(10) unsigned`	range
`chainId`	17784	`int(10) unsigned`	range
`ali`	287	`int(10) unsigned`	range
`score`	16388	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	287	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	172	`int(11)`	range
`qR`	156	`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	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	5565	5883	-	AWUT01022642	0	287	17784	287	16388	-1	-1	287	top	172	156	-1	-1	-1	-1	0	0
585	2	chr2L	5765	5793	-	AWUT01022642	90	90	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	7557	9275	+	KI420362	1683948	1686020	3866	1316	64482	-1	-1	1340	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8072	8223	+	KI420362	1684484	1684945	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8347	8403	+	KI420362	1685069	1685164	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8547	8733	+	KI420362	1685308	1685484	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11206	101637	+	KI419189	24326	128088	291	54983	3086695	-1	-1	180	top	7932	1716	-1	-1	-1	-1	466	3357
585	2	chr2L	11375	11385	+	KI419189	24498	24498	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12943	13517	+	KI419189	26055	26392	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15726	16203	+	KI419189	28603	28749	0	0	0	-1	-1	-1	gap	93	0	-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