Schema for xenoRefSeqAli
  Database: ce2    Primary Table: xenoRefSeqAli    Row Count: 33,808   Data last updated: 2020-08-21
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 317int(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 6int(10) unsigned range Number of inserts in query
qBaseInsert 409int(10) unsigned range Number of bases inserted in query
tNumInsert 6int(10) unsigned range Number of inserts in target
tBaseInsert 2695int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_205425varchar(255) values Query sequence name
qSize 1353int(10) unsigned range Query sequence size
qStart 279int(10) unsigned range Alignment start position in query
qEnd 1170int(10) unsigned range Alignment end position in query
tName chrIvarchar(255) values Target sequence name
tSize 15080483int(10) unsigned range Target sequence size
tStart 74622int(10) unsigned range Alignment start position in target
tEnd 77799int(10) unsigned range Alignment end position in target
blockCount 7int(10) unsigned range Number of blocks in alignment
blockSizes 114,39,14,54,135,42,84,longblob   Size of each block
qStarts 279,462,612,795,888,1035,1086,longblob   Start of each block in query.
tStarts 74622,75170,75374,76020,769...longblob   Start of each block in target.

Connected Tables and Joining Fields
        ce2.all_est.qName (via xenoRefSeqAli.qName)
      ce2.all_mrna.qName (via xenoRefSeqAli.qName)
      ce2.refGene.name (via xenoRefSeqAli.qName)
      ce2.refSeqAli.qName (via xenoRefSeqAli.qName)
      ce2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      ce2.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
58531716500640962695++NM_20542513532791170chrI1508048374622777997114,39,14,54,135,42,84,279,462,612,795,888,1035,1086,74622,75170,75374,76020,76949,77105,77715,
59351730500316898692+-NM_00727921465021492chrIII137833131063008107252210144,3,123,75,60,57,60,171,3,126,502,646,649,817,892,958,1015,1192,1363,1366,12710791,12711077,12712669,12712828,12715373,12715436,12718363,12718513,12718734,12720179,
656225990000145++NM_001360932979310634chrIII13783313933172093320892160,164,310,470,9331720,9331925,
7414112160011232405++NM_0013259749171751chrV2092223120477739204787713204,70,353,1,328,398,20477739,20478292,20478418,
59660233100558541129++NM_00132468220793701888chrX1771884914819781484040657,90,30,303,195,258,370,481,572,604,1282,1630,1481978,1482148,1482238,1482271,1482995,1483782,
585321168001152111+-NM_0010299711317170674chrI150804831093571099573114,279,96,170,299,578,14970526,14970706,14971030,
648467235002243159++NM_00132527415193021028chrIV1749379183618628362723460,234,294,114,302,377,611,914,8361862,8361934,8362253,8362609,
585326157001212117+-NM_0011466001368264768chrI150804831093571099573120,267,96,264,405,672,14970526,14970718,14971030,
61176431300326451922++NM_00679631607842125chrI1508048334695543472553639,342,81,132,372,111,784,1051,1393,1495,1642,2014,3469554,3470763,3471108,3471213,3471354,3472442,
67636117300219541330+-NM_000365135148777chrII152793081203716212039026539,139,2,96,258,48,219,358,360,519,3240282,3240453,3240781,3240817,3241888,

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