Schema for refSeqAli
  Database: oviAri4    Primary Table: refSeqAli    Row Count: 1,022   Data last updated: 2018-05-25
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 610smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 447int(10) unsigned range Number of bases that match that aren't repeats
misMatches 11int(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 1int(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 2322int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001009434varchar(255) values Query sequence name
qSize 477int(10) unsigned range Query sequence size
qStart 2int(10) unsigned range Alignment start position in query
qEnd 461int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 275406953int(10) unsigned range Target sequence size
tStart 3400706int(10) unsigned range Alignment start position in target
tEnd 3403487int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 277,142,40,longblob   Size of each block
qStarts 16,293,435,longblob   Start of each block in query.
tStarts 3400706,3401457,3403447,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)
      oviAri4.all_est.qName (via refSeqAli.qName)
      oviAri4.all_mrna.qName (via refSeqAli.qName)
      oviAri4.mrnaOrientInfo.name (via refSeqAli.qName)
      oviAri4.refFlat.name (via refSeqAli.qName)
      oviAri4.refGene.name (via refSeqAli.qName)
      oviAri4.xenoRefGene.name (via refSeqAli.qName)
      oviAri4.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
61044711010022322-NM_0010094344772461chr1275406953340070634034873277,142,40,16,293,435,3400706,3401457,3403447,
611194428036162139874-NM_001146271199101991chr12754069533410146345199527160,101,58,78,93,46,110,189,141,282,120,16,3,6,6,6,5,6,3,14,23,5,6,39,116,208,135,0,160,261,319,397,490,536,646,835,976,1258,1378,1394,1397,1403,1410,1417,1423,1429,1433,1447,1471,1476,1482,1521,1648,1856,3410146,3411707,3412522,3414343,3415139,3417480,3417550,3417887,3424888,3427142,3428282,3430458,3430476,3430480,3430487,3430493, ...
63356150011300+NM_0011625545790579chr1275406953636069863612642435,131,0,448,6360698,6361133,
63662510000618917-NM_0010094536330626chr127540695367545966774139793,51,55,108,123,125,71,7,100,151,206,314,437,562,6754596,6756949,6758197,6764710,6765899,6773846,6774068,
63813455000048609-NM_001205147230301350chr1275406953704029170502505233,88,132,878,19,953,1186,1274,1406,2284,7040291,7040813,7041756,7049344,7050231,
79133370000362724-NM_001205149229301340chr1275406953704029171043554233,88,132,887,953,1186,1274,1406,7040291,7040813,7041756,7103468,
791329150000388685-NM_001205148229701344chr1275406953704029171303204233,88,132,891,953,1186,1274,1406,7040291,7040813,7041756,7129429,
791351400003120167-NM_001205146230801355chr1275406953704029171618134233,88,132,902,953,1186,1274,1406,7040291,7040813,7041756,7160911,
7913941000003132200-NM_001009189233201404chr1275406953704029171738954233,88,132,951,928,1161,1249,1381,7040291,7040813,7041756,7172944,
68611817008121011778-NM_001161867120001200chr1275406953133356191334858517152,149,143,115,200,204,20,5,35,47,4,26,19,17,14,12,26,0,152,301,444,559,759,963,984,990,1026,1074,1079,1110,1130,1148,1162,1174,13335619,13339759,13341589,13342680,13345270,13346425,13348351,13348374,13348379,13348414,13348461,13348465,13348495,13348514,13 ...

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