Schema for xenoRefSeqAli
  Database: gorGor4    Primary Table: xenoRefSeqAli    Row Count: 242,648   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 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 738int(10) unsigned range Number of bases that match that aren't repeats
misMatches 165int(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 NM_146400varchar(255) values Query sequence name
qSize 939int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 903int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 228908639int(10) unsigned range Target sequence size
tStart 18798int(10) unsigned range Alignment start position in target
tEnd 19701int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 903,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 18798,longblob   Start of each block in target.

Connected Tables and Joining Fields
        gorGor4.all_mrna.qName (via xenoRefSeqAli.qName)
      gorGor4.refGene.name (via xenoRefSeqAli.qName)
      gorGor4.refSeqAli.qName (via xenoRefSeqAli.qName)
      gorGor4.xenoRefFlat.name (via xenoRefSeqAli.qName)
      gorGor4.xenoRefGene.name (via xenoRefSeqAli.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585738165000000++NM_1464009390903chr122890863918798197011903,0,18798,
585769170000000++NM_0010003699390939chr122890863918798197371939,0,18798,
585769170000000+-NM_0010003699390939chr122890863924522254611939,0,228883178,
585738165000000+-NM_1464009390903chr122890863924558254611903,0,228883178,
58654015025545741538++NR_130735103901037chr1228908639180197182315771,45,20,228,83,107,26,0,102,150,170,703,860,1011,180197,180299,180344,181498,182031,182182,182289,
5881472380043313862++NR_103536194401841chr12289086394153144176865794,34,292,306,84,0,800,883,1413,1757,415314,416108,416729,417258,417602,
7362400141369051++NR_1303261228115chr1228908639456847525964424,5,16,21,8,32,37,94,456847,457094,458519,525943,
588127839000011+-NR_024321131701317chr12289086394588324601502945,372,0,945,228448489,228449435,
588223932003396641869++NR_0475262712252692chr12289086394603145044547120,38,317,20,1094,63,619,25,145,280,730,916,2010,2073,460314,460437,473830,502488,502674,503770,503835,
58828857600634901260157++NR_0475196776256476chr122890863946031452343214120,38,109,12,172,97,1245,37,85,143,530,20,250,103,25,145,284,440,452,624,961,5237,5278,5363,5506,6036,6056,6373,460314,460437,480337,484620,484637,485368,486137,519168,519205,519292,519437,519983,523012,523329,

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