Schema for xenoRefSeqAli
  Database: ornAna2    Primary Table: xenoRefSeqAli    Row Count: 710,922   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 385int(10) unsigned Number of bases that match that aren't repeats
misMatches 78int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 0int(10) unsigned Number of 'N' bases
qNumInsert 0int(10) unsigned Number of inserts in query
qBaseInsert 0int(10) unsigned Number of bases inserted in query
tNumInsert 3int(10) unsigned Number of inserts in target
tBaseInsert 45426int(10) unsigned Number of bases inserted in target
strand ++char(2) + or - for strand. First character query, second target (optional)
qName NM_001245255varchar(255) Query sequence name
qSize 669int(10) unsigned Query sequence size
qStart 112int(10) unsigned Alignment start position in query
qEnd 575int(10) unsigned Alignment end position in query
tName chr1varchar(255) Target sequence name
tSize 47594283int(10) unsigned Target sequence size
tStart 31286int(10) unsigned Alignment start position in target
tEnd 77175int(10) unsigned Alignment end position in target
blockCount 4int(10) unsigned Number of blocks in alignment
blockSizes 88,173,72,130,longblob Size of each block
qStarts 112,200,373,445,longblob Start of each block in query.
tStarts 31286,69584,73644,77045,longblob Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
      hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
      ornAna2.all_est.qName (via xenoRefSeqAli.qName)
      ornAna2.all_mrna.qName (via xenoRefSeqAli.qName)
      ornAna2.refGene.name (via xenoRefSeqAli.qName)
      ornAna2.refSeqAli.qName (via xenoRefSeqAli.qName)
      ornAna2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      ornAna2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585385780000345426++NM_001245255669112575chr1475942833128677175488,173,72,130,112,200,373,445,31286,69584,73644,77045,
585466840000345426++NM_175800678114664chr1475942833129277268482,174,73,221,114,196,370,443,31292,69584,73645,77047,
585359710200345426++NM_00107179452896528chr1475942833129377151481,174,73,104,96,177,351,424,31293,69584,73645,77047,
585361710000345426++NM_00127972252896528chr1475942833129377151481,174,73,104,96,177,351,424,31293,69584,73645,77047,
58526010900172245498++NM_001303711653106547chr1475942833129377160381,174,114,106,187,433,31293,69584,77046,
587398100000032413+-NM_0010870521380146644chrUn_DS181347v12520488288145291056495,100,183,120,146,241,341,524,2229432,2229778,2231186,2232223,
585458880000445428++NM_001131938781120666chr1475942833129377267581,174,73,121,97,120,201,375,448,569,31293,69584,73645,77047,77170,
5855922000000++NM_00445911024610691chrUn_DS184630v1283982013720218181,610,20137,
5851273600147013980++NM_024865518236004233chrUn_DS221553v1461004143265,98,3600,4135,0,4045,
58524696000000++NR_0456032695264606chrUn_DS207918v11072865910011342,264,659,

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