Schema for xenoRefSeqAli
  Database: bosTau7    Primary Table: xenoRefSeqAli    Row Count: 324,139   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 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 693int(10) unsigned range Number of bases that match that aren't repeats
misMatches 234int(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 3int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 13947int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_146848varchar(255) values Query sequence name
qSize 1012int(10) unsigned range Query sequence size
qStart 19int(10) unsigned range Alignment start position in query
qEnd 949int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 161428367int(10) unsigned range Target sequence size
tStart 27286int(10) unsigned range Alignment start position in target
tEnd 42160int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 666,77,184,longblob   Size of each block
qStarts 19,688,765,longblob   Start of each block in query.
tStarts 27286,27952,41976,longblob   Start of each block in target.

Connected Tables and Joining Fields
        bosTau7.all_est.qName (via xenoRefSeqAli.qName)
      bosTau7.all_mrna.qName (via xenoRefSeqAli.qName)
      bosTau7.refGene.name (via xenoRefSeqAli.qName)
      bosTau7.refSeqAli.qName (via xenoRefSeqAli.qName)
      bosTau7.xenoMrna.qName (via xenoRefSeqAli.qName)
      bosTau7.xenoRefFlat.name (via xenoRefSeqAli.qName)
      bosTau7.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
5856932340013113947++NM_146848101219949chr116142836727286421603666,77,184,19,688,765,27286,27952,41976,
5857101930013113947++NM_14664394539945chr116142836727325421753629,66,208,39,671,737,27325,27954,41967,
58518348004501414445++NM_001168808939168900chr11614283672745442130527,66,57,18,63,168,336,525,712,837,27454,27622,27811,41942,42067,
58513740002555214499++NM_207136954189921chr11614283672745442130327,72,78,189,690,843,27454,27952,42052,
58511034002603225721++NM_001001807933162909chr11614283672745453319333,27,84,162,709,825,27454,27995,53235,
58513335002402210339++NM_001031544939324894chr11614283672761638123372,30,66,324,510,828,27616,37740,38057,
5851494000238124387++NM_001031176939327897chr11614283673755742133369,30,90,327,510,807,37557,37740,42043,
5851484100238124387++NM_001031545957327897chr11614283673755742133369,30,90,327,510,807,37557,37740,42043,
58571913900330219++NM_00100549698748936chr116142836741289421664228,254,156,220,48,279,536,716,41289,41519,41773,41946,
125473729900132053770812+-NM_001366735525805241chr1285119472546299215470576942183,368,119,137,89,218,261,240,141,141,112,160,165,132,72,126,75,168,105,201,87,114,244,99,59,87,52,56,57,24,21,18,20,76,323,36, ...0,184,552,671,808,897,1115,1376,1616,1757,1898,2010,2170,2335,2467,2539,2665,2740,2908,3013,3214,3301,3415,3659,3760,3819,3906,3 ...30413703,30413886,30440778,30441509,30446225,30446993,30448933,30449949,30450846,30451333,30455312,30456531,30458842,30459704,30 ...

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