Schema for netCalJac4
  Database: mm10    Primary Table: netCalJac4    Row Count: 2,772,680   Data last updated: 2020-09-03
Format description: Database representation of a net of alignments.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 607smallint(5) unsigned Indexing field to speed chromosome range queries.
level 1int(10) unsigned Level of alignment
tName chr1varchar(255) Target chromosome
tStart 3007027int(10) unsigned Start on target
tEnd 3007923int(10) unsigned End on target
strand +char(1) Orientation of query. + or -
qName chr13varchar(255) Query chromosome
qStart 12881728int(10) unsigned Start on query
qEnd 12882743int(10) unsigned End on query
chainId 978147int(10) unsigned Associated chain Id with alignment details
ali 836int(10) unsigned Bases in gap-free alignments
score 15185double 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 1015int(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 241int(11) RepeatMasker bases on target. -1 for undefined
qR 618int(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
        mm10.chainCalJac4.id (via netCalJac4.chainId)
      mm10.chainCalJac4Link.chainId (via netCalJac4.chainId)

Sample Rows
 
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
6071chr130070273007923+chr13128817281288274397814783615185-1-11015top00241618-1-1-1-100
6072chr130076213007647+chr131288246012882460000-1-1-1gap0000-1-1-1-100
6081chr130271223028229-chr161055255610553412109473767914076-1-10top00368721-1-1-1-100
6082chr130275033027513-chr161055302210553022000-1-1-1gap0000-1-1-1-100
6082chr130276113027879-chr161055276610552924000-1-1-1gap000158-1-1-1-100
6082chr130279193027936-chr161055273710552737000-1-1-1gap0000-1-1-1-100
6082chr130279573027976-chr161055271810552718000-1-1-1gap0000-1-1-1-100
6082chr130279893028001-chr161055270510552705000-1-1-1gap0000-1-1-1-100
6082chr130280143028087-chr161055269210552692000-1-1-1gap0000-1-1-1-100
6081chr130441413049463-chr161053885510541732878361100816280-1-10top0032051420-1-1-1-13050

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