Schema for Zebra finch Net - Zebra finch (Jul. 2008 (WUGSC 3.2.4/taeGut1)) Alignment Net

Database: hg19 Primary Table: netTaeGut1 Row Count: 402,078
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`	18492	`int(10) unsigned`	range	End on target
`strand`	-	`char(1)`	values	Orientation of query. + or -
`qName`	chr1A	`varchar(255)`	values	Query chromosome
`qStart`	72291516	`int(10) unsigned`	range	Start on query
`qEnd`	72304954	`int(10) unsigned`	range	End on query
`chainId`	3029	`int(10) unsigned`	range	Associated chain Id with alignment details
`ali`	3502	`int(10) unsigned`	range	Bases in gap-free alignments
`score`	91904	`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`	8977	`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`	200	`int(11)`	range	Unsequenced bases on query. -1 for undefined
`tR`	128	`int(11)`	range	RepeatMasker bases on target. -1 for undefined
`qR`	1541	`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`	0	`int(11)`	range	Bases of tandem repeats on target. -1 for undefined
`qTrf`	0	`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
585	1	chr1	12178	18492	-	chr1A	72291516	72304954	3029	3502	91904	-1	-1	8977	top	200	128	1541	-1	-1	-1	-1
585	2	chr1	12484	12532	-	chr1A	72304574	72304627	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1
585	2	chr1	12541	12560	-	chr1A	72304565	72304565	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1
585	2	chr1	12701	12959	-	chr1A	72303869	72304398	0	0	0	-1	-1	-1	gap	0	0	46	-1	-1	-1	-1
585	2	chr1	13115	13199	-	chr1A	72303642	72303711	0	0	0	-1	-1	-1	gap	0	0	14	-1	-1	-1	-1
585	2	chr1	13414	13424	-	chr1A	72303434	72303434	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1
585	2	chr1	13516	14685	-	chr1A	72302099	72303347	0	0	0	-1	-1	-1	gap	0	0	122	-1	-1	-1	-1
585	2	chr1	15079	15726	-	chr1A	72300774	72301279	0	0	0	-1	-1	-1	gap	0	91	29	-1	-1	-1	-1
585	2	chr1	15770	15792	-	chr1A	72300730	72300730	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1
585	2	chr1	16263	16273	-	chr1A	72300241	72300241	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1

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