Schema for xenoRefSeqAli
  Database: caeRem2    Primary Table: xenoRefSeqAli    Row Count: 271,110   Data last updated: 2020-08-20
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 870smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 66int(10) unsigned range Number of bases that match that aren't repeats
misMatches 24int(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 1int(10) unsigned range Number of inserts in query
qBaseInsert 21int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 273int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001374790varchar(255) values Query sequence name
qSize 6154int(10) unsigned range Query sequence size
qStart 2264int(10) unsigned range Alignment start position in query
qEnd 2375int(10) unsigned range Alignment end position in query
tName chrUnvarchar(255) values Target sequence name
tSize 161944676int(10) unsigned range Target sequence size
tStart 37455650int(10) unsigned range Alignment start position in target
tEnd 37456013int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 39,51,longblob   Size of each block
qStarts 2264,2324,longblob   Start of each block in query.
tStarts 37455650,37455962,longblob   Start of each block in target.

Connected Tables and Joining Fields
        caeRem2.all_est.qName (via xenoRefSeqAli.qName)
      caeRem2.all_mrna.qName (via xenoRefSeqAli.qName)
      caeRem2.xenoMrna.qName (via xenoRefSeqAli.qName)
      caeRem2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      caeRem2.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
8706624001211273++NM_001374790615422642375chrUn1619446763745565037456013239,51,2264,2324,37455650,37455962,
58514862002108921430++NM_00117251617671981497chrUn1619446761736619006339,45,126,198,1026,1371,17366,18487,18880,
585839000000+-NR_050163203092chrUn1619446761749717589192,0,161927087,
585878000000+-NR_052824100095chrUn1619446761749717592195,0,161927084,
585773000000+-NR_069188100080chrUn1619446761751017590180,0,161927086,
5852141100036873819++NM_00107999646764631474chrUn1619446761788119024484,75,84,81,463,610,970,1393,17881,18081,18472,18943,
585170820037623873++NM_00103437342597471761chrUn1619446761789019015475,36,69,72,747,903,1260,1689,17890,18099,18466,18943,
585179790037503867++NM_00113177339934381446chrUn1619446761789019015454,57,75,72,438,594,939,1374,17890,18099,18460,18943,
80934010100120148++NM_00353648623484chrUn16194467629400154294006432417,24,23,460,29400154,29400619,
1040165840027682888++NM_13396928986021619chrUn1619446765967328759674424393,42,114,602,1133,1505,59673287,59673840,59674310,

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