Schema for xenoRefSeqAli
  Database: galGal3    Primary Table: xenoRefSeqAli    Row Count: 262,009   Data last updated: 2020-08-21
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 163int(10) unsigned range Number of bases that match that aren't repeats
misMatches 38int(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 1int(10) unsigned range Number of inserts in query
qBaseInsert 21int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 1114int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001104700varchar(255) values Query sequence name
qSize 763int(10) unsigned range Query sequence size
qStart 421int(10) unsigned range Alignment start position in query
qEnd 643int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 200994015int(10) unsigned range Target sequence size
tStart 28075int(10) unsigned range Alignment start position in target
tEnd 29390int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 21,52,128,longblob   Size of each block
qStarts 421,463,515,longblob   Start of each block in query.
tStarts 200964625,200964664,200965812,longblob   Start of each block in target.

Connected Tables and Joining Fields
        galGal3.all_est.qName (via xenoRefSeqAli.qName)
      galGal3.all_mrna.qName (via xenoRefSeqAli.qName)
      galGal3.refGene.name (via xenoRefSeqAli.qName)
      galGal3.refSeqAli.qName (via xenoRefSeqAli.qName)
      galGal3.xenoMrna.qName (via xenoRefSeqAli.qName)
      galGal3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      galGal3.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
585163380012121114+-NM_001104700763421643chr12009940152807529390321,52,128,421,463,515,200964625,200964664,200965812,
5852182977002165612127788++NM_030035110251809900chr120099401535209661562257,120,144,63,78,147,102,99,84,87,276,264,279,330,408,159,63,33,87,36,105,138,180,957,1140,1365,1872,2850,3099,3654,4092,4578,4776,6630,7155,7494,8016,8553,8736,8805,9192,9435,9552,9762,35209,42356,45260,45482,50700,51678,51948,52470,52839,53304,53502,54117,55696,56035,56578,57160,57340,59370,61835,63389,64306,66 ...
5852041917001866091827989++NM_138885101702919858chr120099401535209661561957,117,78,147,102,207,93,93,288,264,279,330,408,144,63,33,87,30,138,291,939,1833,2811,3078,3636,4047,4527,4719,6585,7110,7449,7971,8508,8691,8760,9147,9396,9720,35209,42356,50700,51678,51948,52482,52839,53298,53490,54117,55696,56035,56578,57160,57340,59370,61835,63392,66018,
98856525400127316609++NM_001098927180187933chr56223893152847654528650824331,267,155,66,87,418,685,867,52847654,52856197,52864765,52865016,
585624169003643810306++NM_0010118981976291465chr12009940157145382552986,74,130,110,55,107,57,41,133,29,115,189,320,430,485,595,1291,1332,71453,74888,75090,76086,76779,78425,79070,82011,82419,
5856311520046811010314++NM_0082252031921556chr120099401571455825521184,74,130,110,55,107,4,56,15,13,135,92,176,250,381,491,546,653,657,782,1406,1421,71455,74888,75090,76086,76779,78425,78558,79071,79899,82035,82417,
58553926300618887720++NM_00108996418251211111chr12009940157149780019942,60,129,110,111,112,56,68,114,121,163,238,368,532,754,866,923,997,71497,74888,75091,76086,78424,78669,79071,79621,79905,
5856623120066341110078++NM_0010113141837891697chr120099401571497825491242,60,129,110,111,112,56,3,66,114,41,130,89,131,206,336,500,722,834,890,893,965,1526,1567,71497,74888,75091,76086,78424,78669,79071,79143,79623,79905,82011,82419,
5855612220046931010248++NM_00114181122931611637chr120099401571509825401127,2,73,120,3,108,55,107,57,111,120,161,188,190,275,395,398,506,561,782,911,1517,71509,71541,74887,75100,75234,76088,76779,78670,79070,79902,82420,
58541019500495557053++NM_00104500624951381698chr12009940157488882546671,133,110,57,111,123,138,209,343,951,1080,1575,74888,75087,76086,79070,79902,82423,

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