Schema for refSeqAli
  Database: allMis1    Primary Table: refSeqAli    Row Count: 54   Data last updated: 2019-09-19
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 2500int(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 13int(10) unsigned range Number of inserts in target
tBaseInsert 18799int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001287303varchar(255) values Query sequence name
qSize 2660int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2500int(10) unsigned range Alignment end position in query
tName JH731266varchar(255) values Target sequence name
tSize 785686int(10) unsigned range Target sequence size
tStart 398472int(10) unsigned range Alignment start position in target
tEnd 419771int(10) unsigned range Alignment end position in target
blockCount 14int(10) unsigned range Number of blocks in alignment
blockSizes 198,762,541,101,52,117,103,...longblob   Size of each block
qStarts 160,358,1120,1661,1762,1814...longblob   Start of each block in query.
tStarts 398472,398671,399434,402492...longblob   Start of each block in target.

Connected Tables and Joining Fields
        allMis1.all_est.qName (via refSeqAli.qName)
      allMis1.all_mrna.qName (via refSeqAli.qName)
      allMis1.mrnaOrientInfo.name (via refSeqAli.qName)
      allMis1.refFlat.name (via refSeqAli.qName)
      allMis1.refGene.name (via refSeqAli.qName)
      allMis1.xenoMrna.qName (via refSeqAli.qName)
      allMis1.xenoRefGene.name (via refSeqAli.qName)
      allMis1.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
5882500000001318799-NM_001287303266002500JH73126678568639847241977114198,762,541,101,52,117,103,111,85,67,71,70,58,164,160,358,1120,1661,1762,1814,1931,2034,2145,2230,2297,2368,2438,2496,398472,398671,399434,402492,402806,403534,406073,409311,411117,412994,413772,413971,416028,419607,
5854641711000000+NM_0012873071998412733JH73168117706192265925861321,412,92265,
58822319300000+NM_0012873071998390608JH7318327083725192525194701218,390,519252,
7329400180007180366+NM_001287313295802958JH7318515562588104026436481760,140,117,351,145,131,158,156,0,1760,1900,2017,2368,2513,2644,2802,81040,134856,186083,212939,214249,240470,245462,264208,
5867240000035579+NM_0012873097390724JH7318994499751605341668374413,64,89,158,0,413,477,566,160534,165659,166500,166679,
5853571143410045091-NM_001287272363903620JH731986150107162672497852632,233,99,614,42,19,2651,2884,2983,3597,16267,20067,20834,21501,24936,
5866092000021483+NM_0012873176110611JH7320524821002504602525543102,160,349,0,102,262,250460,251354,252205,
587211780011918002-NM_001287266214102126JH73217314254573379623580891190,74,570,242,163,115,115,177,155,151,273,15,106,180,750,992,1155,1270,1385,1562,1717,1868,337962,338052,338127,340689,344954,346253,348504,349578,350684,355934,357816,
58523190000047454+NM_001287280231902319JH7323621722311195461293195783,179,124,184,1049,0,783,962,1086,1270,119546,124543,127155,127562,128270,
5856110000016261+NM_00128726416470611JH7323685329042616494882434,177,0,434,42616,49311,

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