Schema for refSeqAli
  Database: canFam5    Primary Table: refSeqAli    Row Count: 2,322   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 619smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 123int(10) unsigned range Number of bases that match that aren't repeats
misMatches 6int(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 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NR_128902varchar(255) values Query sequence name
qSize 129int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 129int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 122894117int(10) unsigned range Target sequence size
tStart 4518940int(10) unsigned range Alignment start position in target
tEnd 4519069int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 129,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 4518940,longblob   Start of each block in target.

Connected Tables and Joining Fields
        canFam5.all_est.qName (via refSeqAli.qName)
      canFam5.all_mrna.qName (via refSeqAli.qName)
      canFam5.mrnaOrientInfo.name (via refSeqAli.qName)
      canFam5.refFlat.name (via refSeqAli.qName)
      canFam5.refGene.name (via refSeqAli.qName)
      canFam5.xenoMrna.qName (via refSeqAli.qName)
      canFam5.xenoRefGene.name (via refSeqAli.qName)
      canFam5.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
6191236000000-NR_1289021290129chr1122894117451894045190691129,0,4518940,
62246000000435246+NM_0011932984600460chr1122894117492023549559415161,129,30,35,105,0,161,290,320,355,4920235,4948066,4950045,4954097,4955836,
8613368003112165146+NM_001002949137401355chr11228941171363348213799972688,60,209,284,365,338,0,89,149,359,652,1017,13633482,13633570,13633856,13634065,13634349,13799634,
6967240040000-NR_0366697370728chr112289411714563520145642481728,9,14563520,
70038077005101147666-NM_001286988382403824chr1122894117150796841513116417583,116,360,45,537,40,170,40,118,122,137,254,188,168,120,295,521,0,588,706,1067,1112,1649,1690,1861,1901,2019,2141,2278,2532,2720,2888,3008,3303,15079684,15080267,15080383,15080743,15080789,15085526,15085566,15085736,15090112,15095454,15098298,15104655,15114148,15118612,15 ...
7079990000000+NM_0010807249990999chr112289411716032382160333811999,0,16032382,
7091680000013182-NM_0011957711680168chr112289411716376896163802462108,60,0,108,16376896,16380186,
71468200000514861-NM_001003312820138820chr11228941171693284416948387687,58,120,150,110,157,0,87,145,265,415,525,16932844,16933543,16935648,16937892,16941802,16948230,
718580000000-NR_04924658058chr11228941171753243217532490158,0,17532432,
9226450003318354176+NM_001003268264802648chr1122894117200000572035687822168,63,40,255,73,62,97,65,127,50,106,134,133,68,79,77,204,136,151,230,141,186,0,169,233,274,529,602,664,761,826,953,1003,1109,1243,1376,1444,1523,1600,1804,1940,2091,2321,2462,20000057,20000225,20000288,20000328,20004799,20121535,20124646,20180497,20231728,20232335,20305214,20308900,20314897,20322841,20 ...

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