Schema for xenoRefSeqAli
  Database: rheMac3    Primary Table: xenoRefSeqAli    Row Count: 338,858   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 145smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 5265int(10) unsigned range Number of bases that match that aren't repeats
misMatches 105int(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 6int(10) unsigned range Number of inserts in query
qBaseInsert 21int(10) unsigned range Number of bases inserted in query
tNumInsert 16int(10) unsigned range Number of inserts in target
tBaseInsert 135596int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_004272varchar(255) values Query sequence name
qSize 5798int(10) unsigned range Query sequence size
qStart 406int(10) unsigned range Alignment start position in query
qEnd 5797int(10) unsigned range Alignment end position in query
tName chr6varchar(255) values Target sequence name
tSize 180491593int(10) unsigned range Target sequence size
tStart 75998363int(10) unsigned range Alignment start position in target
tEnd 76139329int(10) unsigned range Alignment end position in target
blockCount 20int(10) unsigned range Number of blocks in alignment
blockSizes 333,291,335,157,132,93,140,...longblob   Size of each block
qStarts 406,739,1030,1365,1522,1654...longblob   Start of each block in query.
tStarts 104352264,104352598,1043528...longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
      hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
      rheMac3.all_est.qName (via xenoRefSeqAli.qName)
      rheMac3.all_mrna.qName (via xenoRefSeqAli.qName)
      rheMac3.refGene.name (via xenoRefSeqAli.qName)
      rheMac3.refSeqAli.qName (via xenoRefSeqAli.qName)
      rheMac3.xenoMrna.qName (via xenoRefSeqAli.qName)
      rheMac3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      rheMac3.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
14552651050062116135596+-NM_00427257984065797chr6180491593759983637613932920333,291,335,157,132,93,140,157,111,81,271,52,63,1062,410,502,507,545,77,51,406,739,1030,1365,1522,1654,1747,1887,2044,2155,2236,2511,2563,2626,3693,4110,4613,5123,5668,5746,104352264,104352598,104352890,104410031,104415976,104420013,104429208,104464525,104468627,104469348,104489651,104489942,10448999 ...
585786860014231367+-NM_13850617041741469chr122959036261568628072637,235,174,1234,229527555,229528559,
58584497005161741681+-NM_00741832141412699chr12295903626156864190615,23,15,16,637,235,141,162,351,367,1404,2464,229526172,229526198,229526417,229526432,229527555,229528559,
5855511820024312399+-NM_20763912991081272chr122959036261603627353411,123,199,108,549,1073,229527627,229528068,229528560,
5854951880024002410+-NM_19436512481381221chr122959036261606626993369,117,197,138,534,1024,229527663,229528074,229528559,
5855791740024382397+-NM_00112690321444381629chr122959036261606627563432,126,195,438,897,1434,229527606,229528065,229528561,
5855381440023832405+-NM_19436428043411406chr122959036261612626993369,122,191,341,732,1215,229527663,229528069,229528559,
1628387000167514129139+-NM_0011323813623403623chr717012464160712861608449081548,110,68,85,134,138,215,124,77,141,134,148,959,185,342,40,88,198,266,351,485,623,838,962,1039,1855,1989,2137,3096,3281,109279733,109280591,109281247,109287928,109299550,109300396,109302423,109310164,109312023,109313863,109377387,109383865,10938933 ...
585160116000000+-NM_0010982781640209485chr122959036262414626901276,209,229527672,
5868371020041663307++NR_03413610470955chr12295903621615941658409266,30,263,59,59,22,23,26,191,0,267,297,567,626,685,714,738,764,161594,161860,161892,162160,162220,162853,162879,162902,165649,

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