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

Database: dm6 Primary Table: netDrhoGB2 Row Count: 216,380

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	7557	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	KB451369	`varchar(255)`	values
`qStart`	315623	`int(10) unsigned`	range
`qEnd`	317858	`int(10) unsigned`	range
`chainId`	5687	`int(10) unsigned`	range
`ali`	1374	`int(10) unsigned`	range
`score`	63332	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	1369	`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`	42	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	7557	9282	-	KB451369	315623	317858	5687	1374	63332	-1	-1	1369	top	0	0	0	-1	-1	-1	-1	0	42
585	2	chr2L	8063	8238	-	KB451369	316763	317295	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	42
585	2	chr2L	8357	8379	-	KB451369	316585	316644	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	8499	8649	-	KB451369	316256	316465	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
73	1	chr2L	11206	256056	+	KB451737	1073	290365	147	117448	6742880	-1	-1	444	top	100	11874	24133	-1	-1	-1	-1	1090	7819
585	2	chr2L	11549	11770	+	KB451737	1414	2169	0	0	0	-1	-1	-1	gap	0	0	543	-1	-1	-1	-1	0	0
585	2	chr2L	12936	13517	+	KB451737	3335	4908	0	0	0	-1	-1	-1	gap	0	57	1006	-1	-1	-1	-1	0	0
585	2	chr2L	15715	16317	+	KB451737	7125	7810	0	0	0	-1	-1	-1	gap	0	93	0	-1	-1	-1	-1	0	0
585	2	chr2L	16439	17049	+	KB451737	7932	8868	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	17165	102381	+	KB451737	8983	110950	0	0	0	-1	-1	-1	gap	20	7782	10899	-1	-1	-1	-1	466	3843

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