Schema for refSeqAli
  Database: ci3    Primary Table: refSeqAli    Row Count: 1,304   Data last updated: 2017-04-10
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 1581int(10) unsigned range Number of bases that match that aren't repeats
misMatches 49int(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 33int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 9int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001128115varchar(255) values Query sequence name
qSize 1692int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1663int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 10041005int(10) unsigned range Target sequence size
tStart 343978int(10) unsigned range Alignment start position in target
tEnd 345617int(10) unsigned range Alignment end position in target
blockCount 9int(10) unsigned range Number of blocks in alignment
blockSizes 216,72,5,25,60,133,15,149,955,longblob   Size of each block
qStarts 29,265,337,343,369,429,563,...longblob   Start of each block in query.
tStarts 343978,344197,344270,344275...longblob   Start of each block in target.

Connected Tables and Joining Fields
        ci3.all_est.qName (via refSeqAli.qName)
      ci3.all_mrna.qName (via refSeqAli.qName)
      ci3.mrnaOrientInfo.name (via refSeqAli.qName)
      ci3.refFlat.name (via refSeqAli.qName)
      ci3.refGene.name (via refSeqAli.qName)
      ci3.xenoRefGene.name (via refSeqAli.qName)
      ci3.xenoRefSeqAli.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
5871581490063349-NM_001128115169201663chr1100410053439783456179216,72,5,25,60,133,15,149,955,29,265,337,343,369,429,563,582,737,343978,344197,344270,344275,344300,344364,344497,344513,344662,
589353820000073927-NM_001245043356403558chr11004100554018254766781554,228,232,976,203,143,144,78,6,1560,1788,2020,2996,3199,3342,3486,540182,542094,542594,543125,544450,545757,546322,547589,
59011391100123679-NM_001078521118301152chr1100410056824126842415279,612,91,96,72,31,312,924,1015,1111,682412,682691,683591,683784,684169,
591217311000037825+NM_001078308220002184chr1100410058240448340534590,204,167,1223,0,590,794,961,824044,831619,832492,832830,
59170920000105791-NM_0010338387110711chr11004100583836784486911168,42,135,41,40,21,42,47,37,95,43,0,168,210,345,386,426,447,489,536,573,668,838367,838707,839045,839542,840036,840252,840821,841208,842017,843027,844826,
591213923001144-NM_0011289012175112174chr110041005891041893207650,27,1146,25,49,865,1,52,79,1225,1250,1299,891041,891091,891119,892266,892292,892342,
73199700000174363-NM_001128903199801997chr1100410059164009227601862,166,49,71,110,146,201,111,112,176,145,80,118,73,37,92,67,181,1,63,229,278,349,459,605,806,917,1029,1205,1350,1430,1548,1621,1658,1750,1817,916400,916672,917057,917165,917335,917689,918084,918499,918877,919389,919915,920405,920802,921253,921381,921591,921990,922579,
592530000000+NR_03456153053chr110041005919766919819153,0,919766,
59236683800002115217+NM_001128105372503706chr11004100598013599905822211,62,158,121,114,175,105,156,109,145,82,206,331,126,233,219,150,188,153,344,95,223,0,211,273,431,552,666,841,946,1102,1211,1356,1438,1644,1975,2101,2334,2553,2703,2891,3044,3388,3483,980135,980451,982044,982490,983001,983601,984487,989959,991941,992429,992870,993637,994326,995039,995520,996051,996805,997261,99 ...
592530000000+NR_03453653053chr11004100510095031009556153,0,1009503,

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