Schema for Orangutan Net - Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Alignment Net
Database: hg19    Primary Table: netPonAbe2    Row Count: 795,774
Format description: Database representation of a net of alignments.
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
level 1int(10) unsigned Level of alignment
tName chr1varchar(255) Target chromosome
tStart 11462int(10) unsigned Start on target
tEnd 11610int(10) unsigned End on target
strand +char(1) Orientation of query. + or -
qName chr12_randomvarchar(255) Query chromosome
qStart 8391153int(10) unsigned Start on query
qEnd 8391300int(10) unsigned End on query
chainId 71766int(10) unsigned Associated chain Id with alignment details
ali 147int(10) unsigned Bases in gap-free alignments
score 10678double Score - a number proportional to 100x matching bases
qOver -1int(11) Overlap with parent gap on query side. -1 for undefined
qFar -1int(11) Distance from parent gap on query side. -1 for undefined
qDup 147int(11) Bases with two or more copies in query. -1 for undefined
type topvarchar(255) Syntenic type: gap/top/syn/nonsyn/inv
tN 0int(11) Unsequenced bases on target. -1 for undefined
qN 0int(11) Unsequenced bases on query. -1 for undefined
tR 107int(11) RepeatMasker bases on target. -1 for undefined
qR 106int(11) RepeatMasker bases on query. -1 for undefined
tNewR -1int(11) Lineage specific repeats on target. -1 for undefined
qNewR -1int(11) Lineage specific repeats on query. -1 for undefined
tOldR -1int(11) Bases of ancient repeats on target. -1 for undefined
qOldR -1int(11) Bases of ancient repeats on query. -1 for undefined
tTrf 0int(11) Bases of tandem repeats on target. -1 for undefined
qTrf 0int(11) Bases of tandem repeats on query. -1 for undefined
Connected Tables and Joining Fields
      hg19.chainPonAbe2.id (via netPonAbe2.chainId)
      hg19.chainPonAbe2Link.chainId (via netPonAbe2.chainId)
Sample Rows
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
5851chr11146211610+chr12_random839115383913007176614710678-1-1147top00107106-1-1-1-100
5851chr11162540733+chr2b21132250211696571668287582279211-1-129168top0387963513467-1-1-1-1270159
5852chr11216712194+chr2b2113279121134626000-1-1-1gap01000-1-1-1-100
5852chr11934919419+chr2b2114185421141854000-1-1-1gap0000-1-1-1-1700
5852chr12012320141+chr2b2114256021142560000-1-1-1gap00180-1-1-1-100
5852chr12081820869+chr2b2114323621145314000-1-1-1gap000603-1-1-1-13547
5852chr12224422258+chr2b2114669821146698000-1-1-1gap0000-1-1-1-100
5852chr12508025090+chr2b2114953121149531000-1-1-1gap0000-1-1-1-100
5852chr13090730964+chr2b2115603621156813000-1-1-1gap0367571-1-1-1-1521
5851chr14073347723-chrUn44768614484030229245826472384-1-15876top0124543883637-1-1-1-14126

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