Schema for Chicken Net - Chicken (May 2006 (WUGSC 2.1/galGal3)) Alignment Net
Database: hg19    Primary Table: netGalGal3    Row Count: 445,081
Format description: Database representation of a net of alignments.
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
level 1int(10) unsigned range Level of alignment
tName chr1varchar(255) values Target chromosome
tStart 12178int(10) unsigned range Start on target
tEnd 18381int(10) unsigned range End on target
strand +char(1) values Orientation of query. + or -
qName chr1varchar(255) values Query chromosome
qStart 62069088int(10) unsigned range Start on query
qEnd 62081481int(10) unsigned range End on query
chainId 5655int(10) unsigned range Associated chain Id with alignment details
ali 2596int(10) unsigned range Bases in gap-free alignments
score 78445double range Score - a number proportional to 100x matching bases
qOver -1int(11) range Overlap with parent gap on query side. -1 for undefined
qFar -1int(11) range Distance from parent gap on query side. -1 for undefined
qDup 4960int(11) range Bases with two or more copies in query. -1 for undefined
type topvarchar(255) values Syntenic type: gap/top/syn/nonsyn/inv
tN 0int(11) range Unsequenced bases on target. -1 for undefined
qN 0int(11) range Unsequenced bases on query. -1 for undefined
tR 128int(11) range RepeatMasker bases on target. -1 for undefined
qR 0int(11) range RepeatMasker bases on query. -1 for undefined
tNewR -1int(11) range Lineage specific repeats on target. -1 for undefined
qNewR -1int(11) range Lineage specific repeats on query. -1 for undefined
tOldR -1int(11) range Bases of ancient repeats on target. -1 for undefined
qOldR -1int(11) range Bases of ancient repeats on query. -1 for undefined
tTrf 0int(11) range Bases of tandem repeats on target. -1 for undefined
qTrf 0int(11) range Bases of tandem repeats on query. -1 for undefined
Connected Tables and Joining Fields
      hg19.chainGalGal3.id (via netGalGal3.chainId)
      hg19.chainGalGal3Link.chainId (via netGalGal3.chainId)
Sample Rows
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
5851chr11217818381+chr162069088620814815655259678445-1-14960top001280-1-1-1-100
5852chr11223212596+chr16206914262069537000-1-1-1gap0000-1-1-1-100
5852chr11270112964+chr16206964662070232000-1-1-1gap0000-1-1-1-100
5852chr11339214691+chr16207066762072551000-1-1-1gap0000-1-1-1-100
5852chr11493314944+chr16207319862073198000-1-1-1gap0000-1-1-1-100
5852chr11519215782+chr16207346962073493000-1-1-1gap00910-1-1-1-100
5852chr11595615968+chr16207366862073668000-1-1-1gap0000-1-1-1-100
5852chr11600816027+chr16207370262073702000-1-1-1gap0000-1-1-1-100
5852chr11613316851+chr16207380362074624000-1-1-1gap00370-1-1-1-100
5852chr11750217603+chr16207531862076667000-1-1-1gap0000-1-1-1-100

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