Schema for refSeqAli
  Database: equCab3    Primary Table: refSeqAli    Row Count: 1,948   Data last updated: 2019-07-17
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 586smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1714int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(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 8int(10) unsigned range Number of inserts in target
tBaseInsert 9865int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001111303varchar(255) values Query sequence name
qSize 1714int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1714int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 188260577int(10) unsigned range Target sequence size
tStart 131450int(10) unsigned range Alignment start position in target
tEnd 143029int(10) unsigned range Alignment end position in target
blockCount 9int(10) unsigned range Number of blocks in alignment
blockSizes 417,142,188,142,177,161,150...longblob   Size of each block
qStarts 0,417,559,747,889,1066,1227...longblob   Start of each block in query.
tStarts 131450,132685,133318,136079...longblob   Start of each block in target.

Connected Tables and Joining Fields
        equCab3.all_est.qName (via refSeqAli.qName)
      equCab3.all_mrna.qName (via refSeqAli.qName)
      equCab3.mrnaOrientInfo.name (via refSeqAli.qName)
      equCab3.refFlat.name (via refSeqAli.qName)
      equCab3.refGene.name (via refSeqAli.qName)
      equCab3.xenoRefGene.name (via refSeqAli.qName)
      equCab3.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
58617140000089865-NM_001111303171401714chr11882605771314501430299417,142,188,142,177,161,150,160,177,0,417,559,747,889,1066,1227,1377,1537,131450,132685,133318,136079,137329,137862,138357,141709,142852,
6411210000000+NR_1280601210121chr1188260577744899274491131121,0,7448992,
110913200000000+NM_001257161132001320chr985793548687311946873251411320,0,68731194,
5851030000000+NR_1279111030103chrUn_NW_019641870v117768734574481103,0,7345,
683710000000+NR_03277571071chr11882605771287732612877397171,0,12877326,
7041455000001115398-NM_001163949145501455chr1188260577156533771567023012121,165,109,130,119,120,120,112,135,123,155,46,0,121,286,395,525,644,764,884,996,1131,1254,1409,15653377,15658226,15658970,15660443,15662696,15663321,15663557,15664911,15666026,15668127,15668863,15670184,
7444184000003029230-NM_001308957418404184chr1188260577209105622094397631525,107,178,192,213,248,109,108,159,152,153,151,142,161,100,104,214,122,165,81,176,118,79,80,72,68,39,76,69,5,18,0,525,632,810,1002,1215,1463,1572,1680,1839,1991,2144,2295,2437,2598,2698,2802,3016,3138,3303,3384,3560,3678,3757,3837,3909,3977 ...20910562,20911989,20912751,20913080,20913622,20913920,20914710,20915307,20916031,20917519,20919089,20921140,20922853,20923347,20 ...
834154000001898434+NM_001163863415404154chr1188260577113238571142644519251,15,244,267,78,170,124,191,148,203,152,122,111,191,123,71,138,106,1449,0,251,266,510,777,855,1025,1149,1340,1488,1691,1843,1965,2076,2267,2390,2461,2599,2705,11323857,11327992,11328038,11349844,11350976,11361577,11372444,11387686,11389009,11392515,11401524,11404566,11406992,11408491,11 ...
7915920000003537983-NM_001309513592005920chr1188260577270562462710014936349,166,154,169,251,150,117,295,123,123,57,178,103,90,109,63,542,116,150,220,171,195,135,252,147,61,125,207,108,182,121,162,168, ...0,349,515,669,838,1089,1239,1356,1651,1774,1897,1954,2132,2235,2325,2434,2497,3039,3155,3305,3525,3696,3891,4026,4278,4425,4486, ...27056246,27057342,27057961,27058691,27059594,27060065,27060889,27061230,27061932,27063487,27064210,27066277,27066883,27067196,27 ...
7911250000000+NR_1280631250125chr118826057727102413271025381125,0,27102413,

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