Schema for refSeqAli
  Database: oryCun2    Primary Table: refSeqAli    Row Count: 1,750   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 587smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 808int(10) unsigned range Number of bases that match that aren't repeats
misMatches 5int(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 6int(10) unsigned range Number of inserts in query
qBaseInsert 10int(10) unsigned range Number of bases inserted in query
tNumInsert 9int(10) unsigned range Number of inserts in target
tBaseInsert 4397int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NM_001171048varchar(255) values Query sequence name
qSize 2484int(10) unsigned range Query sequence size
qStart 1660int(10) unsigned range Alignment start position in query
qEnd 2483int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 194850757int(10) unsigned range Target sequence size
tStart 367433int(10) unsigned range Alignment start position in target
tEnd 372643int(10) unsigned range Alignment end position in target
blockCount 14int(10) unsigned range Number of blocks in alignment
blockSizes 4,106,137,44,27,111,33,29,4...longblob   Size of each block
qStarts 1660,1665,1771,1908,1957,19...longblob   Start of each block in query.
tStarts 367433,367437,368521,369400...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)
      oryCun2.all_est.qName (via refSeqAli.qName)
      oryCun2.all_mrna.qName (via refSeqAli.qName)
      oryCun2.mrnaOrientInfo.name (via refSeqAli.qName)
      oryCun2.refFlat.name (via refSeqAli.qName)
      oryCun2.refGene.name (via refSeqAli.qName)
      oryCun2.xenoMrna.qName (via refSeqAli.qName)
      oryCun2.xenoRefGene.name (via refSeqAli.qName)
      oryCun2.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58780850061094397+NM_001171048248416602483chr1194850757367433372643144,106,137,44,27,111,33,29,40,22,21,48,64,127,1660,1665,1771,1908,1957,1984,2095,2129,2159,2199,2222,2243,2291,2356,367433,367437,368521,369400,369447,370145,370606,370639,370668,370883,370908,372403,372452,372516,
59813227169033918231+NM_001082702150101501chr11948507571704766172449513136,116,46,57,168,118,156,109,119,94,34,122,223,0,136,252,298,355,523,641,797,906,1025,1120,1155,1278,1704766,1705754,1709143,1709977,1714810,1716342,1717569,1720613,1722490,1724022,1724116,1724150,1724272,
7563900227000334793-NM_001204215661806617chr11948507573008830305024043950,179,2386,102,1,3951,4130,6516,3008830,3023315,3037571,3050138,
7686000960006166225-NM_001204216869608696chr11948507573200599337552078029,102,22,115,131,81,216,0,8029,8131,8153,8268,8399,8480,3200599,3220406,3224139,3225038,3282144,3294847,3375304,
617422913880003565295+NM_0010826554347174347chr11948507574234135430376036133,153,82,81,86,97,91,124,94,231,171,100,186,107,104,54,106,116,74,79,80,138,86,149,124,98,202,62,63,61,114,112,128,155,76,413,17,150,303,385,466,552,649,740,864,958,1189,1360,1460,1646,1753,1857,1911,2017,2133,2207,2286,2366,2504,2590,2739,2863,2961,3163 ...4234135,4234748,4237128,4237949,4242918,4246851,4247284,4249105,4249939,4252359,4253660,4257392,4259159,4263909,4264352,4265927, ...
673160400011811896+NM_001171114160501605chr119485075711570141115836411072,122,212,55,161,84,175,200,498,25,0,72,194,406,461,622,706,881,1081,1580,11570141,11574686,11575563,11576542,11577339,11578386,11579776,11580362,11583118,11583616,
74535591700002454752-NM_001082315357603576chr1194850757210285532108688125144,438,221,186,123,148,143,105,125,157,85,136,160,117,101,172,140,184,70,138,169,119,83,16,96,0,144,582,803,989,1112,1260,1403,1508,1633,1790,1875,2011,2171,2288,2389,2561,2701,2885,2955,3093,3262,3381,3464,3480,21028553,21028699,21029138,21030258,21033891,21035858,21036396,21037446,21038925,21040699,21042948,21044130,21045844,21047506,21 ...
9577906000011556+NM_0010823208040796chr119485075748871707488740592298,498,0,298,48871707,48873561,
9587897000011507+NM_0010823208040796chr119485075748907971489102742298,498,0,298,48907971,48909776,
96271180000420793+NM_0010821147250719chr119485075749501219495227315151,120,173,119,156,0,151,271,444,563,49501219,49514108,49518148,49518844,49522575,

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