Schema for xenoRefSeqAli
  Database: felCat4    Primary Table: xenoRefSeqAli    Row Count: 527,169   Data last updated: 2020-08-21
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 563int(10) unsigned Number of bases that match that aren't repeats
misMatches 91int(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 3int(10) unsigned Number of inserts in query
qBaseInsert 350int(10) unsigned Number of bases inserted in query
tNumInsert 7int(10) unsigned Number of inserts in target
tBaseInsert 3555int(10) unsigned Number of bases inserted in target
strand ++char(2) + or - for strand. First character query, second target (optional)
qName NM_001009700varchar(255) Query sequence name
qSize 1795int(10) unsigned Query sequence size
qStart 207int(10) unsigned Alignment start position in query
qEnd 1211int(10) unsigned Alignment end position in query
tName chrA1varchar(255) Target sequence name
tSize 279330936int(10) unsigned Target sequence size
tStart 240int(10) unsigned Alignment start position in target
tEnd 4449int(10) unsigned Alignment end position in target
blockCount 8int(10) unsigned Number of blocks in alignment
blockSizes 33,90,85,110,54,92,74,116,longblob Size of each block
qStarts 207,335,443,528,875,929,102...longblob Start of each block in query.
tStarts 240,688,2793,3585,3821,3957...longblob Start of each block in target.

Connected Tables and Joining Fields
        felCat4.all_est.qName (via xenoRefSeqAli.qName)
      felCat4.all_mrna.qName (via xenoRefSeqAli.qName)
      felCat4.refGene.name (via xenoRefSeqAli.qName)
      felCat4.refSeqAli.qName (via xenoRefSeqAli.qName)
      felCat4.xenoMrna.qName (via xenoRefSeqAli.qName)
      felCat4.xenoRefFlat.name (via xenoRefSeqAli.qName)
      felCat4.xenoRefGene.name (via xenoRefSeqAli.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5855639100335073555++NM_00100970017952071211chrA12793309362404449833,90,85,110,54,92,74,116,207,335,443,528,875,929,1021,1095,240,688,2793,3585,3821,3957,4169,4333,
1691123300011661423++NM_001144982593827463065chrX145558876145000816145001392251,102,2746,2963,145000816,145001290,
1691123300011661423++NM_001144983593427423061chrX145558876145000816145001392251,102,2742,2959,145000816,145001290,
2037570026802335947++NR_1639841019453476109chrX145558876136641516136977545330,22,30,5347,5421,6079,136641516,136739508,136977515,
2037570026802335947++NR_1639851044055936355chrX145558876136641516136977545330,22,30,5593,5667,6325,136641516,136739508,136977515,
2037570026802335947++NR_1639821035255056267chrX145558876136641516136977545330,22,30,5505,5579,6237,136641516,136739508,136977515,
2037570026802335947++NR_1639831013552886050chrX145558876136641516136977545330,22,30,5288,5362,6020,136641516,136739508,136977515,
2037570026802335947++NM_1775381055257056467chrX145558876136641516136977545330,22,30,5705,5779,6437,136641516,136739508,136977515,
2037570026802335947++NR_1639811043155846346chrX145558876136641516136977545330,22,30,5584,5658,6316,136641516,136739508,136977515,
2037570026802335947++NM_0013717051102561786940chrX145558876136641516136977545330,22,30,6178,6252,6910,136641516,136739508,136977515,

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