Schema for xenoRefSeqAli
  Database: allMis1    Primary Table: xenoRefSeqAli    Row Count: 425,570   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 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 101int(10) unsigned range Number of bases that match that aren't repeats
misMatches 45int(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 1int(10) unsigned range Number of inserts in query
qBaseInsert 39int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 39int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_021696varchar(255) values Query sequence name
qSize 1942int(10) unsigned range Query sequence size
qStart 1103int(10) unsigned range Alignment start position in query
qEnd 1289int(10) unsigned range Alignment end position in query
tName AKHW01000064varchar(255) values Target sequence name
tSize 1653int(10) unsigned range Target sequence size
tStart 990int(10) unsigned range Alignment start position in target
tEnd 1176int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 45,102,longblob   Size of each block
qStarts 1103,1187,longblob   Start of each block in query.
tStarts 477,561,longblob   Start of each block in target.

Connected Tables and Joining Fields
        allMis1.all_est.qName (via xenoRefSeqAli.qName)
      allMis1.all_mrna.qName (via xenoRefSeqAli.qName)
      allMis1.refGene.name (via xenoRefSeqAli.qName)
      allMis1.refSeqAli.qName (via xenoRefSeqAli.qName)
      allMis1.xenoMrna.qName (via xenoRefSeqAli.qName)
      allMis1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      allMis1.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
5851014501139139+-NM_021696194211031289AKHW0100006416539901176245,102,1103,1187,477,561,
5857220010000+-NM_001276386134711381231AKHW0100006416539991092193,1138,561,
5857124010000+-NM_205152187211351231AKHW0100006416539991095196,1135,558,
5851053201139139+-NM_001174115212811381315AKHW0100006416539991176245,93,1138,1222,477,561,
5851003200139139+-NM_001143818218014101581AKHW01000064165310051176245,87,1410,1494,477,561,
5851013100139139+-NM_001168916124810771248AKHW01000064165310051176245,87,1077,1161,477,561,
92391150038423172857+-NM_004297249711202316JH7318241407289100765311808644126,90,87,51,1120,1318,1489,2265,226425,229858,230567,399585,
5851406001127127+-NM_001105619168210141242AKHW010000641653100512332123,78,1014,1164,420,570,
5851507401115112+-NM_00116891411739331173AKHW010000641653100512422135,90,933,1083,411,558,
5851607001133139+-NM_199941143411121376AKHW010000641653100512752144,87,1112,1289,378,561,

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