Schema for xenoRefSeqAli
  Database: equCab3    Primary Table: xenoRefSeqAli    Row Count: 301,814   Data last updated: 2019-07-17
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 398int(10) unsigned range Number of bases that match that aren't repeats
misMatches 66int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 4int(10) unsigned range Number of inserts in query
qBaseInsert 328int(10) unsigned range Number of bases inserted in query
tNumInsert 7int(10) unsigned range Number of inserts in target
tBaseInsert 4252int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001143765varchar(255) values Query sequence name
qSize 1462int(10) unsigned range Query sequence size
qStart 118int(10) unsigned range Alignment start position in query
qEnd 910int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 188260577int(10) unsigned range Target sequence size
tStart 10433int(10) unsigned range Alignment start position in target
tEnd 15149int(10) unsigned range Alignment end position in target
blockCount 8int(10) unsigned range Number of blocks in alignment
blockSizes 64,60,73,56,93,64,18,36,longblob   Size of each block
qStarts 118,182,242,364,420,577,657...longblob   Start of each block in query.
tStarts 10433,11144,11567,12534,133...longblob   Start of each block in target.

Connected Tables and Joining Fields
        equCab3.all_est.qName (via xenoRefSeqAli.qName)
      equCab3.all_mrna.qName (via xenoRefSeqAli.qName)
      equCab3.refGene.name (via xenoRefSeqAli.qName)
      equCab3.refSeqAli.qName (via xenoRefSeqAli.qName)
      equCab3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      equCab3.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
5853986600432874252++NM_0011437651462118910chr11882605771043315149864,60,73,56,93,64,18,36,118,182,242,364,420,577,657,874,10433,11144,11567,12534,13318,14536,14698,15113,
58581110300459144218++NM_00103814911081021075chr118826057710433155651564,60,75,48,55,90,64,3,64,75,39,60,90,73,54,102,166,226,301,349,404,494,558,561,625,704,747,855,945,1021,10433,11144,11567,12236,12535,13318,13656,14095,14536,14682,14764,14877,15113,15433,15511,
585694117005118125089++NM_00114376314521771106chr118826057710433163331364,60,74,36,53,93,64,65,125,3,61,86,27,177,241,301,380,423,476,569,635,700,825,828,933,1079,10433,11144,11567,12240,12534,13315,13656,14535,14682,14873,14880,15113,16306,
5854198400431074234++NM_0010250581471116929chr11882605771044515182852,60,75,56,93,64,34,69,116,168,228,350,406,563,639,860,10445,11144,11567,12534,13318,14536,14694,15113,
58567811700356124210++NM_00128013413921901041chr118826057710445154501352,60,74,36,53,93,64,67,125,3,61,89,18,190,242,302,381,424,477,570,634,701,826,829,934,1023,10445,11144,11567,12240,12534,13315,13656,14533,14682,14873,14880,15113,15432,
585685114005118125089++NM_1307841362991016chr118826057710445163331352,60,74,36,53,93,64,65,125,3,61,86,27,99,151,211,290,333,386,479,545,610,735,738,843,989,10445,11144,11567,12240,12534,13315,13656,14535,14682,14873,14880,15113,16306,
58562012200312193628++NM_00128383313171961059chr118826057711164155341040,73,36,56,90,64,67,125,89,102,196,236,315,358,414,504,568,635,868,957,11164,11567,12240,12534,13318,13656,14533,14682,15113,15432,
585446202002199336838+-NM_001078916261711391986chr118826057728744662304437,127,60,24,1139,1576,1811,1962,188194347,188231066,188231298,188231809,
58537622200183336951+-NM_00110092515076381319chr11882605772874466293564,193,34,289,18,638,702,895,929,1301,188194284,188194684,188231324,188231526,188231815,
585398206006597536966+-NM_00117152923878042005chr11882605772874466314760,133,45,111,111,114,30,804,899,1065,1248,1482,1842,1975,188194263,188194526,188194692,188231076,188231475,188231586,188231803,

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