Schema for Stickleback Net - Stickleback (Feb. 2006 (Broad/gasAcu1)) Alignment Net
Database: hg19    Primary Table: netGasAcu1    Row Count: 279,763
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 25018int(10) unsigned range End on target
strand +char(1) values Orientation of query. + or -
qName chrXIXvarchar(255) values Query chromosome
qStart 16729201int(10) unsigned range Start on query
qEnd 16735795int(10) unsigned range End on query
chainId 7283int(10) unsigned range Associated chain Id with alignment details
ali 2584int(10) unsigned range Bases in gap-free alignments
score 79706double 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 2873int(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 35int(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 0int(11) range Bases of tandem repeats on query. -1 for undefined
Connected Tables and Joining Fields
      hg19.chainGasAcu1.id (via netGasAcu1.chainId)
      hg19.chainGasAcu1Link.chainId (via netGasAcu1.chainId)
Sample Rows
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
5851chr11217825018+chrXIX16729201167357957283258479706-1-12873top00184835-1-1-1-11730
5852chr11224912594+chrXIX1672927216729329000-1-1-1gap0000-1-1-1-100
5852chr11271812974+chrXIX1672945316729524000-1-1-1gap0000-1-1-1-100
5852chr11306113078+chrXIX1672960816729608000-1-1-1gap0000-1-1-1-100
5852chr11309213167+chrXIX1672962216729622000-1-1-1gap0000-1-1-1-100
5852chr11337714696+chrXIX1672983316730887000-1-1-1gap0000-1-1-1-100
5852chr11485914879+chrXIX1673106916731069000-1-1-1gap0000-1-1-1-100
5852chr11491314962+chrXIX1673109916731099000-1-1-1gap0000-1-1-1-100
5852chr11506215779+chrXIX1673119916731611000-1-1-1gap00910-1-1-1-100
5852chr11598116534+chrXIX1673181516731895000-1-1-1gap0000-1-1-1-100

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