Schema for Lamprey Net - Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) Alignment Net
Database: hg19    Primary Table: netPetMar1    Row Count: 150,080
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 17242int(10) unsigned range Start on target
tEnd 17767int(10) unsigned range End on target
strand +char(1) values Orientation of query. + or -
qName Contig25515varchar(255) values Query chromosome
qStart 3357int(10) unsigned range Start on query
qEnd 7045int(10) unsigned range End on query
chainId 294790int(10) unsigned range Associated chain Id with alignment details
ali 318int(10) unsigned range Bases in gap-free alignments
score 10494double 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 328int(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 0int(11) range RepeatMasker bases on target. -1 for undefined
qR 1869int(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 0int(11) range Bases of tandem repeats on target. -1 for undefined
qTrf 84int(11) range Bases of tandem repeats on query. -1 for undefined
Connected Tables and Joining Fields
      hg19.chainPetMar1.id (via netPetMar1.chainId)
      hg19.chainPetMar1Link.chainId (via netPetMar1.chainId)
Sample Rows
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
5851chr11724217767+Contig255153357704529479031810494-1-1328top0001869-1-1-1-1084
5852chr11738817595+Contig2551535046864000-1-1-1gap0001864-1-1-1-1084
5851chr11790118073+Contig417312994745343071726935-1-1175top0000-1-1-1-100
5851chr16896569964+Contig154624150251633511799749455-1-11013top00026-1-1-1-100
5861chr1131161131849-Contig23930257908019437051012895-1-1520top0131003456-1-1-1-1052
5862chr1131355131368-Contig2393088928892000-1-1-1gap0000-1-1-1-100
5862chr1131493131640-Contig239304638766000-1-1-1gap0131003450-1-1-1-1052
5861chr1138819139522-Contig766456866630926455310217-1-1598top00021-1-1-1-180563
5862chr1138948139074-Contig76645548548000-1-1-1gap0000-1-1-1-100
5861chr1139526139715+Contig1987314156143364291421643327-1-1180top0080-1-1-1-10180

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