Schema for xenoRefSeqAli
  Database: galGal5    Primary Table: xenoRefSeqAli    Row Count: 260,635   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 401int(10) unsigned range Number of bases that match that aren't repeats
misMatches 91int(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 72int(10) unsigned range Number of bases inserted in query
tNumInsert 3int(10) unsigned range Number of inserts in target
tBaseInsert 4290int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001032618varchar(255) values Query sequence name
qSize 1196int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 564int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 196202544int(10) unsigned range Target sequence size
tStart 9917int(10) unsigned range Alignment start position in target
tEnd 14699int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 198,150,21,123,longblob   Size of each block
qStarts 0,198,348,441,longblob   Start of each block in query.
tStarts 196187845,196189283,1961913...longblob   Start of each block in target.

Connected Tables and Joining Fields
        galGal5.all_est.qName (via xenoRefSeqAli.qName)
      galGal5.all_mrna.qName (via xenoRefSeqAli.qName)
      galGal5.refGene.name (via xenoRefSeqAli.qName)
      galGal5.refSeqAli.qName (via xenoRefSeqAli.qName)
      galGal5.xenoMrna.qName (via xenoRefSeqAli.qName)
      galGal5.xenoRefFlat.name (via xenoRefSeqAli.qName)
      galGal5.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
585401910017234290+-NM_00103261811960564chr11962025449917146994198,150,21,123,0,198,348,441,196187845,196189283,196191321,196192504,
5854431000012144239+-NM_00110470076373637chr11962025449917146995198,150,21,52,122,73,271,421,463,515,196187845,196189283,196191321,196191360,196192505,
5854341180011244230+-NM_131870157574638chr11962025449917146995198,150,21,61,122,74,272,422,455,516,196187845,196189283,196191321,196191351,196192505,
585442122000034221+-NM_00107903933444791043chr11962025449917147024201,150,91,122,479,680,830,921,196187842,196189283,196191321,196192505,
585323940012454242+-NM_174546918258699chr11962025449995146546153,146,4,18,52,44,258,411,557,561,603,655,196187890,196189283,196189666,196191321,196191360,196192505,
585427910024844302+-NM_00110470076373639chr119620254420938257585198,150,27,19,124,73,271,463,496,515,196176786,196178224,196180336,196180370,196181482,
5854011080025734311+-NM_131870157574640chr119620254420938257584198,150,36,125,74,272,455,515,196176786,196178224,196180327,196181481,
585383880019324347+-NM_00103261811960564chr119620254420940257583198,150,123,0,198,441,196176786,196178224,196181481,
585443121000044257+-NM_00107903933444791043chr119620254420940257615201,150,66,25,122,479,680,830,896,921,196176783,196178224,196180297,196180364,196181482,
1731304299038611716117652+-NM_00137471064803072065chr31113021221050905901052098831779,2,210,81,135,100,167,125,78,82,84,4,59,113,121,114,87,307,386,388,604,706,847,947,1114,1239,1317,1408,1492,1496,1579,1692,1813,1978,6092239,6092335,6094024,6098738,6107446,6111850,6121031,6127305,6143428,6157373,6162417,6168366,6171931,6173182,6177316,6207057, ...

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