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

Database: DwilCAF1 Primary Table: netDm6 Row Count: 166,731 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	scf2_1100000000004	`varchar(255)`	values
`tStart`	3816	`int(10) unsigned`	range
`tEnd`	5081	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	chr2R	`varchar(255)`	values
`qStart`	19488635	`int(10) unsigned`	range
`qEnd`	19490477	`int(10) unsigned`	range
`chainId`	2633	`int(10) unsigned`	range
`ali`	1127	`int(10) unsigned`	range
`score`	48593	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1657	`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	tNewR	qNewR	tOldR	qOldR
585	1	scf2_1100000000004	3816	5081	+	chr2R	19488635	19490477	2633	1127	48593	-1	-1	1657	top	-1	-1	-1	-1
585	2	scf2_1100000000004	4261	4302	+	chr2R	19489080	19489118	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	2	scf2_1100000000004	4605	4694	+	chr2R	19489421	19490090	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	1	scf2_1100000000016	3869	4538	+	chr2L	14488490	14489083	11260	192	10710	-1	-1	193	top	-1	-1	-1	-1
585	2	scf2_1100000000016	3930	4355	+	chr2L	14488551	14488929	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	2	scf2_1100000000016	4398	4449	+	chr2L	14488972	14488995	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	1	scf2_1100000000048	4395	5851	-	chr3R	28993296	28995393	2896	856	43879	-1	-1	843	top	-1	-1	-1	-1
585	2	scf2_1100000000048	4534	5128	-	chr3R	28994017	28995254	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	1	scf2_1100000000111	1680	1794	-	chr3R	6233467	6233581	12230	114	9845	-1	-1	114	top	-1	-1	-1	-1
585	1	scf2_1100000000158	23	8930	+	chr2L	1743631	1751272	1170	2086	107703	-1	-1	2095	top	-1	-1	-1	-1

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. willistoni genome assembly (DwilCAF1) 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