Schema for Horse Net - Horse (Sep. 2007 (Broad/equCab2)) Alignment Net
Database: hg19    Primary Table: netEquCab2    Row Count: 4,108,574
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 11489int(10) unsigned Start on target
tEnd 37673int(10) unsigned End on target
strand -char(1) Orientation of query. + or -
qName chr6varchar(255) Query chromosome
qStart 30584688int(10) unsigned Start on query
qEnd 30613749int(10) unsigned End on query
chainId 1381int(10) unsigned Associated chain Id with alignment details
ali 19893int(10) unsigned Bases in gap-free alignments
score 848721double 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 25243int(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 731int(11) Unsequenced bases on query. -1 for undefined
tR 7061int(11) RepeatMasker bases on target. -1 for undefined
qR 8378int(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 270int(11) Bases of tandem repeats on target. -1 for undefined
qTrf 165int(11) Bases of tandem repeats on query. -1 for undefined
Connected Tables and Joining Fields
      hg19.chainEquCab2.id (via netEquCab2.chainId)
      hg19.chainEquCab2Link.chainId (via netEquCab2.chainId)
Sample Rows
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
5851chr11148937673-chr63058468830613749138119893848721-1-125243top073170618378-1-1-1-1270165
5852chr11213812176-chr63061130030613027000-1-1-1gap0000-1-1-1-100
5852chr11272212736-chr63061069330610693000-1-1-1gap0000-1-1-1-100
5852chr11356013570-chr63060979530609795000-1-1-1gap0000-1-1-1-100
5852chr11365813677-chr63060968230609682000-1-1-1gap0000-1-1-1-100
5852chr11548315494-chr63060765830607658000-1-1-1gap0000-1-1-1-100
5852chr11562515638-chr63060750530607505000-1-1-1gap0000-1-1-1-100
5852chr11655116562-chr63060654430606544000-1-1-1gap0000-1-1-1-100
5852chr11710317114-chr63060595530605955000-1-1-1gap0000-1-1-1-100
5852chr11811818130-chr63060489230604892000-1-1-1gap0000-1-1-1-100

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