Schema for Tetraodon Net - Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Alignment Net

Database: hg19 Primary Table: netTetNig2 Row Count: 248,384
Format description: Database representation of a net of alignments.

field	example	SQL type	info	description
`bin`	585	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`level`	1	`int(10) unsigned`	range	Level of alignment
`tName`	chr1	`varchar(255)`	values	Target chromosome
`tStart`	12178	`int(10) unsigned`	range	Start on target
`tEnd`	24888	`int(10) unsigned`	range	End on target
`strand`	-	`char(1)`	values	Orientation of query. + or -
`qName`	chr13	`varchar(255)`	values	Query chromosome
`qStart`	3636336	`int(10) unsigned`	range	Start on query
`qEnd`	3664656	`int(10) unsigned`	range	End on query
`chainId`	11723	`int(10) unsigned`	range	Associated chain Id with alignment details
`ali`	1922	`int(10) unsigned`	range	Bases in gap-free alignments
`score`	55831	`double`	range	Score - a number proportional to 100x matching bases
`qOver`	-1	`int(11)`	range	Overlap with parent gap on query side. -1 for undefined
`qFar`	-1	`int(11)`	range	Distance from parent gap on query side. -1 for undefined
`qDup`	2121	`int(11)`	range	Bases with two or more copies in query. -1 for undefined
`type`	top	`varchar(255)`	values	Syntenic type: gap/top/syn/nonsyn/inv
`tN`	0	`int(11)`	range	Unsequenced bases on target. -1 for undefined
`qN`	100	`int(11)`	range	Unsequenced bases on query. -1 for undefined
`tR`	1848	`int(11)`	range	RepeatMasker bases on target. -1 for undefined
`qR`	4405	`int(11)`	range	RepeatMasker bases on query. -1 for undefined
`tNewR`	-1	`int(11)`	range	Lineage specific repeats on target. -1 for undefined
`qNewR`	-1	`int(11)`	range	Lineage specific repeats on query. -1 for undefined
`tOldR`	-1	`int(11)`	range	Bases of ancient repeats on target. -1 for undefined
`qOldR`	-1	`int(11)`	range	Bases of ancient repeats on query. -1 for undefined
`tTrf`	173	`int(11)`	range	Bases of tandem repeats on target. -1 for undefined
`qTrf`	262	`int(11)`	range	Bases of tandem repeats on query. -1 for undefined

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	chr1	12178	24888	-	chr13	3636336	3664656	11723	1922	55831	-1	-1	2121	top	100	1848	4405	-1	-1	-1	-1	173	262
585	2	chr1	12243	12877	-	chr13	3664550	3664591	0	0	0	-1	-1	-1	gap	0	0	17	-1	-1	-1	-1	0	0
585	2	chr1	13056	13078	-	chr13	3664368	3664368	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr1	13092	13103	-	chr13	3664354	3664354	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr1	13160	13180	-	chr13	3664306	3664306	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr1	13379	14675	-	chr13	3663346	3664114	0	0	0	-1	-1	-1	gap	0	0	162	-1	-1	-1	-1	0	0
585	2	chr1	14720	14730	-	chr13	3663301	3663301	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr1	14843	14860	-	chr13	3663169	3663169	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr1	14869	14892	-	chr13	3663160	3663160	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr1	14908	14931	-	chr13	3663144	3663144	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.