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

Database: dm6 Primary Table: netDserGB1 Row Count: 257,663 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`	7580	`int(10) unsigned`	range
`tEnd`	9275	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	MTTC01000817	`varchar(255)`	values
`qStart`	3832856	`int(10) unsigned`	range
`qEnd`	3835059	`int(10) unsigned`	range
`chainId`	3803	`int(10) unsigned`	range
`ali`	725	`int(10) unsigned`	range
`score`	35471	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	697	`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	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7580	9275	-	MTTC01000817	3832856	3835059	3803	725	35471	-1	-1	697	top	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	7693	8663	-	MTTC01000817	3833468	3834946	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11210	828189	+	MTTC01000175	10448	1501475	49	251736	13475284	-1	-1	120	top	40185	226039	-1	-1	-1	-1	14582	127451
585	2	chr2L	11368	11406	+	MTTC01000175	10609	10787	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	11536	11770	+	MTTC01000175	10917	11211	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	12951	13515	+	MTTC01000175	12398	12650	0	0	0	-1	-1	-1	gap	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	13628	13675	+	MTTC01000175	12763	12875	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	14882	14920	+	MTTC01000175	14100	14140	0	0	0	-1	-1	-1	gap	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	15723	17049	+	MTTC01000175	14943	16596	0	0	0	-1	-1	-1	gap	93	262	-1	-1	-1	-1	0	0
585	2	chr2L	17136	21963	+	MTTC01000175	16683	19585	0	0	0	-1	-1	-1	gap	0	349	-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