Schema for xenoRefSeqAli
  Database: caeJap1    Primary Table: xenoRefSeqAli    Row Count: 203,513   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 1297smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 112int(10) unsigned range Number of bases that match that aren't repeats
misMatches 38int(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 2int(10) unsigned range Number of inserts in query
qBaseInsert 1332int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 2054int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001322547varchar(255) values Query sequence name
qSize 1756int(10) unsigned range Query sequence size
qStart 174int(10) unsigned range Alignment start position in query
qEnd 1656int(10) unsigned range Alignment end position in query
tName chrUnvarchar(255) values Target sequence name
tSize 156378573int(10) unsigned range Target sequence size
tStart 93402952int(10) unsigned range Alignment start position in target
tEnd 93405156int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 60,45,45,longblob   Size of each block
qStarts 174,649,1611,longblob   Start of each block in query.
tStarts 93402952,93403627,93405111,longblob   Start of each block in target.

Connected Tables and Joining Fields
        caeJap1.all_est.qName (via xenoRefSeqAli.qName)
      caeJap1.all_mrna.qName (via xenoRefSeqAli.qName)
      caeJap1.xenoMrna.qName (via xenoRefSeqAli.qName)
      caeJap1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      caeJap1.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
129711238002133222054++NM_00132254717561741656chrUn1563785739340295293405156360,45,45,174,649,1611,93402952,93403627,93405111,
129711238002133222054++NM_0013225481644871569chrUn1563785739340295293405156360,45,45,87,562,1524,93402952,93403627,93405111,
129741311301727231273+-NM_07764210467622chrUn1563785739342920593431021445,114,165,219,7,109,238,403,62947552,62947966,62948142,62949149,
11017482340021723072++NM_0722481177731072chrUn1563785736771663667720690393,546,343,73,181,729,67716636,67716802,67720347,
1300539260020135200++NM_06507311552701092chrUn1563785739374686093747879646,175,181,3,285,129,270,316,491,672,675,963,93746860,93746951,93747170,93747383,93747411,93747750,
9546072520710051105+-NM_063298114825955chrUn15637857348390348483923836237,137,144,3,159,250,25,262,399,543,546,705,107986190,107986475,107986659,107986848,107987768,107987975,
7512351040022012262+-NM_001306614798147687chrUn15637857321883538218841393105,126,108,147,429,579,134494434,134494777,134494927,
736794000000+-NR_07029786386chrUn1563785731991658319916666183,3,136461907,
5857384520194607314+-NM_00100683123535871856chrUn15637857339720412438226,146,75,537,54,63,3,105,587,813,971,1052,1619,1685,1748,1751,156337330,156337606,156337764,156337897,156338521,156338635,156338728,156338748,
5857484420194607314+-NM_00109259525445801849chrUn15637857339720412438226,146,75,537,54,63,3,105,580,806,964,1045,1612,1678,1741,1744,156337330,156337606,156337764,156337897,156338521,156338635,156338728,156338748,

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