Schema for refSeqAli
  Database: fr3    Primary Table: refSeqAli    Row Count: 655   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 590smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 669int(10) unsigned range Number of bases that match that aren't repeats
misMatches 7int(10) unsigned range Number of bases that don't match
repMatches 35int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 2int(10) unsigned range Number of inserts in query
qBaseInsert 8int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 791int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001032632varchar(255) values Query sequence name
qSize 719int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 719int(10) unsigned range Alignment end position in query
tName HE591604varchar(255) values Target sequence name
tSize 765554int(10) unsigned range Target sequence size
tStart 660251int(10) unsigned range Alignment start position in target
tEnd 661753int(10) unsigned range Alignment end position in target
blockCount 7int(10) unsigned range Number of blocks in alignment
blockSizes 34,90,231,137,141,71,7,longblob   Size of each block
qStarts 0,36,132,363,500,641,712,longblob   Start of each block in query.
tStarts 660251,660285,660375,660779...longblob   Start of each block in target.

Connected Tables and Joining Fields
        fr3.all_est.qName (via refSeqAli.qName)
      fr3.all_mrna.qName (via refSeqAli.qName)
      fr3.mrnaOrientInfo.name (via refSeqAli.qName)
      fr3.refFlat.name (via refSeqAli.qName)
      fr3.refGene.name (via refSeqAli.qName)
      fr3.xenoMrna.qName (via refSeqAli.qName)
      hgFixed.gbCdnaInfo.acc (via refSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via refSeqAli.qName)
      hgFixed.gbSeq.acc (via refSeqAli.qName)
      hgFixed.gbWarn.acc (via refSeqAli.qName)
      hgFixed.imageClone.acc (via refSeqAli.qName)
      hgFixed.refLink.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName)
      knownGeneV39.kgXref.refseq (via refSeqAli.qName)
      knownGeneV39.knownToRefSeq.value (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5906697350284791-NM_0010326327190719HE591604765554660251661753734,90,231,137,141,71,7,0,36,132,363,500,641,712,660251,660285,660375,660779,661154,661674,661746,
58518924209011104081+NM_001032694238502106HE5916555508621042181104041210,477,239,132,74,134,78,103,111,455,67,225,0,11,488,727,859,933,1067,1145,1248,1359,1814,1881,104218,104228,106316,107933,108177,108580,108795,109015,109184,109370,109915,110179,
5881684010400073930+NM_001032704178801788HE591655550862469902475620846,369,297,258,261,306,100,151,0,46,415,712,970,1231,1537,1637,469902,470598,471462,472772,473648,474240,474799,475469,
5854623517101235415291-NM_001098644503718022705HE5916886580471297172565208,140,59,107,154,2332,2540,2680,2739,3081,1297,1599,1830,1972,17102,
58545227364011443210337-NM_001098644503705037HE59168865804711181264113468,67,60,42,1395,165,176,150,210,207,140,59,107,162,37,116,60,42,15,66,69,32,13,168,144,27,168,144,165,153,165,153,49,99,0,68,135,195,237,1632,1797,1973,2123,2333,2540,2680,2739,2846,3008,3189,3305,3365,3407,3422,3488,3557,3589,3602,3770,3914,3941,4 ...11181,11320,11542,11701,11825,13313,14023,14283,14524,14819,15171,15402,15544,16072,17101,17138,17347,17648,17691,17797,18153,18 ...
587149709900000+NM_001122862159601596HE59169344815530807830967411596,0,308078,
58624884379000153502+NM_001048037287102871HE59172239130413930814568116539,150,91,291,143,148,195,180,159,129,68,240,126,79,133,200,0,539,689,780,1071,1214,1362,1557,1737,1896,2025,2093,2333,2459,2538,2671,139308,140066,140625,141612,141993,142238,142483,142755,143210,143473,143930,144110,144822,145125,145273,145481,
5851187014800011-NM_001032664133501335HE5917243813438556686902211,1324,0,11,85566,85578,
58513771000011900-NM_001308665140701378HE591725411779827938607121292,86,29,1321,82793,85985,
5871308172290242510-NM_001032674157301558HE5917263693043373643394285261,914,217,17,145,15,279,1193,1410,1428,337364,337625,338632,339266,339283,

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