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

Database: DrhoGB2 Primary Table: netDm6 Row Count: 211,353 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	AFPP02000002	`varchar(255)`	values
`tStart`	12	`int(10) unsigned`	range
`tEnd`	1212	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`qName`	chr3R	`varchar(255)`	values
`qStart`	24177676	`int(10) unsigned`	range
`qEnd`	24178546	`int(10) unsigned`	range
`chainId`	13889	`int(10) unsigned`	range
`ali`	665	`int(10) unsigned`	range
`score`	30336	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	665	`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	AFPP02000002	12	1212	+	chr3R	24177676	24178546	13889	665	30336	-1	-1	665	top	-1	-1	-1	-1
585	2	AFPP02000002	140	154	+	chr3R	24177799	24177799	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	2	AFPP02000002	214	232	+	chr3R	24177859	24177859	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	2	AFPP02000002	398	427	+	chr3R	24178017	24178017	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	2	AFPP02000002	566	1011	+	chr3R	24178163	24178357	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	2	AFPP02000002	1142	1153	+	chr3R	24178484	24178484	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	1	AFPP02000003	9079	9386	+	chr3R	22373841	22374148	43011	307	7799	-1	-1	307	top	-1	-1	-1	-1
585	1	KB448225	0	1161	+	chr3R	21071550	21072405	12180	619	34702	-1	-1	634	top	-1	-1	-1	-1
585	2	KB448225	312	818	+	chr3R	21071861	21072082	0	0	0	-1	-1	-1	gap	-1	-1	-1	-1
585	2	KB448225	916	926	+	chr3R	21072175	21072175	0	0	0	-1	-1	-1	gap	-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. rhopaloa genome assembly (DrhoGB2) 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