Schema for Fugu Net - Fugu (Oct. 2004 (JGI 4.0/fr2)) Alignment Net
Database: hg19    Primary Table: netFr2    Row Count: 247,738
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 24867int(10) unsigned range End on target
strand +char(1) values Orientation of query. + or -
qName chrUnvarchar(255) values Query chromosome
qStart 81157031int(10) unsigned range Start on query
qEnd 81162051int(10) unsigned range End on query
chainId 8888int(10) unsigned range Associated chain Id with alignment details
ali 2294int(10) unsigned range Bases in gap-free alignments
score 67978double 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 2397int(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 1848int(11) range RepeatMasker bases on target. -1 for undefined
qR 639int(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 173int(11) range Bases of tandem repeats on target. -1 for undefined
qTrf 33int(11) range Bases of tandem repeats on query. -1 for undefined
Connected Tables and Joining Fields
      hg19.chainFr2.id (via netFr2.chainId)
      hg19.chainFr2Link.chainId (via netFr2.chainId)
Sample Rows
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
5851chr11217824867+chrUn81157031811620518888229467978-1-12397top001848639-1-1-1-117333
5852chr11224312877+chrUn8115709681157137000-1-1-1gap00013-1-1-1-100
5852chr11305613073+chrUn8115733481157334000-1-1-1gap0000-1-1-1-100
5852chr11308713110+chrUn8115734881157348000-1-1-1gap0000-1-1-1-100
5852chr11315513168+chrUn8115738781157387000-1-1-1gap0000-1-1-1-100
5852chr11337914697+chrUn8115758481158259000-1-1-1gap00084-1-1-1-100
5852chr11490114916+chrUn8115845981158459000-1-1-1gap0000-1-1-1-100
5852chr11493014963+chrUn8115847381158473000-1-1-1gap0000-1-1-1-100
5852chr11506215751+chrUn8115856881158826000-1-1-1gap009119-1-1-1-100
5852chr11595116640+chrUn8115902581159145000-1-1-1gap00020-1-1-1-100

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