Schema for refSeqAli
  Database: ponAbe2    Primary Table: refSeqAli    Row Count: 3,599   Data last updated: 2020-08-22
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 655smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 2851int(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 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 9659int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001134089varchar(255) values Query sequence name
qSize 2874int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2856int(10) unsigned range Alignment end position in query
tName chr20varchar(255) values Target sequence name
tSize 62736349int(10) unsigned range Target sequence size
tStart 9183416int(10) unsigned range Alignment start position in target
tEnd 9195931int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 2434,194,228,longblob   Size of each block
qStarts 18,2452,2646,longblob   Start of each block in query.
tStarts 9183416,9187420,9195703,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)
      ponAbe2.all_est.qName (via refSeqAli.qName)
      ponAbe2.all_mrna.qName (via refSeqAli.qName)
      ponAbe2.mrnaOrientInfo.name (via refSeqAli.qName)
      ponAbe2.refFlat.name (via refSeqAli.qName)
      ponAbe2.refGene.name (via refSeqAli.qName)
      ponAbe2.xenoMrna.qName (via refSeqAli.qName)
      ponAbe2.xenoRefGene.name (via refSeqAli.qName)
      ponAbe2.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
65528515000029659-NM_001134089287402856chr20627363499183416919593132434,194,228,18,2452,2646,9183416,9187420,9195703,
6021863300001148936-NM_0011333241899171883chr12299420172272846232364812646,82,112,57,120,118,131,50,130,81,113,226,16,662,744,856,913,1033,1151,1282,1332,1462,1543,1656,2272846,2274548,2276056,2285176,2285327,2286259,2286987,2304032,2307898,2312249,2320425,2323422,
762436821170007158977-NM_001131911457814562chr12299420174006050416958882337,1822,67,43,80,73,85,54,16,2353,4175,4242,4285,4365,4438,4523,4006050,4008388,4055561,4055764,4057057,4081386,4118271,4169534,
773702448025323502-NM_0011335553826503809chr12299420174437581446483761787,1256,401,142,94,74,17,1808,3065,3466,3608,3702,4437581,4439368,4440624,4459449,4462140,4464763,
6431654200001456626-NM_001132677167301656chr12299420177666499772478115335,59,102,83,58,148,122,72,166,88,49,90,98,70,116,17,352,411,513,596,654,802,924,996,1162,1250,1299,1389,1487,1557,7666499,7668292,7668441,7669726,7671820,7687882,7689916,7691484,7694171,7695751,7701142,7706133,7707393,7708171,7724665,
6441696291000920354+NM_001132068180201789chr12299420177737386775952910164,135,111,177,183,166,204,128,154,367,0,164,299,410,587,770,936,1140,1268,1422,7737386,7739881,7743477,7745139,7748408,7751017,7752925,7754600,7756569,7759162,
103438531011005534566-NM_001132433359213575chr1229942017942043299584726922,1995,130,53,109,265,17,939,2934,3164,3217,3326,9420432,9421355,9508647,9713508,9794977,9958207,
17341263001125116233-NM_001373942413004130chr913519152610575699610587735827616,779,136,146,129,147,62,91,161,157,57,75,187,177,135,173,64,89,88,121,53,45,79,43,108,155,56,0,617,1396,1532,1678,1807,1954,2016,2107,2268,2425,2482,2557,2744,2921,3056,3229,3293,3382,3470,3591,3644,3689,3768,3811,3919,40 ...105756996,105757612,105760916,105761557,105762663,105768461,105770217,105770550,105784058,105786073,105787942,105789557,10578978 ...
691119312475042316106498+NM_001135506191101911chr12299420171389447414002652881,112,109,1097,75,47,32,127,0,81,193,302,1400,1686,1744,1784,13894474,13949557,13966013,14000769,14001866,14002421,14002480,14002525,
69153413615016411+NM_00113550619117431911chr12299420171399605713997230520,32,4,33,1073,743,763,795,799,838,13996057,13996078,13996111,13996116,13996157,

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