Schema for refSeqAli
  Database: rn6    Primary Table: refSeqAli    Row Count: 19,160   Data last updated: 2020-08-20
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 588smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 2507int(10) unsigned range Number of bases that match that aren't repeats
misMatches 19int(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 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 5int(10) unsigned range Number of inserts in target
tBaseInsert 10451int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NM_001099460varchar(255) values Query sequence name
qSize 2526int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2526int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 282763074int(10) unsigned range Target sequence size
tStart 396699int(10) unsigned range Alignment start position in target
tEnd 409676int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 206,283,804,225,124,884,longblob   Size of each block
qStarts 0,206,489,1293,1518,1642,longblob   Start of each block in query.
tStarts 396699,399544,400255,401911...longblob   Start of each block in target.

Connected Tables and Joining Fields
        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)
      rn6.all_est.qName (via refSeqAli.qName)
      rn6.all_mrna.qName (via refSeqAli.qName)
      rn6.mrnaOrientInfo.name (via refSeqAli.qName)
      rn6.refFlat.name (via refSeqAli.qName)
      rn6.refGene.name (via refSeqAli.qName)
      rn6.xenoMrna.qName (via refSeqAli.qName)
      rn6.xenoRefGene.name (via refSeqAli.qName)
      rn6.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5882507190000510451+NM_001099460252602526chr12827630743966994096766206,283,804,225,124,884,0,206,489,1293,1518,1642,396699,399544,400255,401911,407503,408792,
59025281000056124+NM_001099462252902529chr12827630746994127080656206,283,804,225,124,887,0,206,489,1293,1518,1642,699412,702188,702859,704512,705912,707178,
59125290000056127-NM_001099462252902529chr12827630748048618135176887,124,225,804,283,206,0,887,1011,1236,2040,2323,804861,806890,808191,809266,810458,813311,
74137643001156339334-NM_001013063145901434chr1282763074110168614424398345,142,144,123,126,261,137,141,25,370,512,656,794,920,1181,1318,1101686,1102695,1439165,1439872,1439995,1440382,1441870,1442298,
59311483000425613784-NM_001161691120301203chr1282763074110196411169261067,142,62,10,79,120,129,55,198,316,0,67,209,272,283,362,497,626,689,887,1101964,1102695,1103428,1103490,1103500,1104126,1104246,1104637,1104700,1116610,
743214100140825300+NM_001106217325503255chr1282763074170269517312109284,51,413,161,142,126,177,93,1768,0,284,375,788,949,1091,1217,1394,1487,1702695,1702980,1703084,1709226,1712447,1717434,1720444,1723324,1729442,
5982383000118930514-NM_013073242702401chr128276307417348621767759101388,168,217,86,121,105,32,105,138,23,26,1432,1600,1817,1903,2024,2129,2161,2266,2404,1734862,1736275,1740726,1742557,1743230,1746298,1749365,1750790,1767597,1767736,
59812180000068616+NM_001128191121801218chr1282763074177172017815547169,123,181,136,152,123,334,0,169,292,473,609,761,884,1771720,1772195,1774162,1776350,1777791,1779038,1781220,
598708700000726146+NM_001134543708707087chr1282763074178407718173108228,474,148,1514,583,183,107,3850,0,228,702,850,2364,2947,3130,3237,1784077,1795667,1800333,1802692,1806420,1811685,1812069,1813460,
741835000001039782+NM_001004217185201835chr12827630741826169186778611183,175,158,181,122,106,159,127,135,127,362,0,183,358,516,697,819,925,1084,1211,1346,1473,1826169,1841451,1843777,1846408,1852080,1854811,1856046,1864292,1865327,1865835,1867424,

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