Schema for xenoRefSeqAli
  Database: sorAra2    Primary Table: xenoRefSeqAli    Row Count: 469,604   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 404int(10) unsigned range Number of bases that match that aren't repeats
misMatches 54int(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 10int(10) unsigned range Number of inserts in query
qBaseInsert 326int(10) unsigned range Number of bases inserted in query
tNumInsert 11int(10) unsigned range Number of inserts in target
tBaseInsert 325int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001076066varchar(255) values Query sequence name
qSize 1989int(10) unsigned range Query sequence size
qStart 1039int(10) unsigned range Alignment start position in query
qEnd 1823int(10) unsigned range Alignment end position in query
tName AALT02185301varchar(255) values Target sequence name
tSize 23736int(10) unsigned range Target sequence size
tStart 22362int(10) unsigned range Alignment start position in target
tEnd 23145int(10) unsigned range Alignment end position in target
blockCount 13int(10) unsigned range Number of blocks in alignment
blockSizes 127,7,16,22,45,11,5,16,57,3...longblob   Size of each block
qStarts 1039,1189,1196,1274,1353,14...longblob   Start of each block in query.
tStarts 22362,22496,22517,22596,227...longblob   Start of each block in target.

Connected Tables and Joining Fields
        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)
      sorAra2.all_mrna.qName (via xenoRefSeqAli.qName)
      sorAra2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      sorAra2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58540454001032611325++NM_001076066198910391823AALT0218530123736223622314513127,7,16,22,45,11,5,16,57,37,16,9,90,1039,1189,1196,1274,1353,1407,1419,1424,1475,1623,1664,1702,1733,22362,22496,22517,22596,22702,22758,22771,22777,22827,22954,22991,23024,23055,
585137170015861629++NM_001243041183810671807AALT021853012373622362231452127,27,1067,1780,22362,23118,
585137170015861629++NM_134079179510241764AALT021853012373622362231452127,27,1024,1737,22362,23118,
585205370025152543++NM_00124485018279951752AALT021853012373622362231473127,57,58,995,1417,1694,22362,22827,23089,
6448592540012473488+-NM_00132130616981621299JH79818320915803779955478041558129,3,329,133,193,185,3,138,162,291,294,623,780,973,1158,1161,13111648,13111863,13112940,13113980,13114280,13115229,13115436,13116111,
5858442000000++NM_001141692216410721198AALT021853012373622363224891126,1072,22363,
5858343000000++NM_00125326014499891115AALT021853012373622363224891126,989,22363,
5857947000000++NM_00125576514429851111AALT021853012373622363224891126,985,22363,
5858145000000++NM_00128789512699301056AALT021853012373622363224891126,930,22363,
5858244000000++NM_202540167412281354AALT021853012373622363224891126,1228,22363,

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