Schema for xenoRefSeqAli
  Database: droAna2    Primary Table: xenoRefSeqAli    Row Count: 265,089   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 677smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 96int(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 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_006177varchar(255) values Query sequence name
qSize 3731int(10) unsigned range Query sequence size
qStart 904int(10) unsigned range Alignment start position in query
qEnd 1045int(10) unsigned range Alignment end position in query
tName scaffold_12916varchar(255) values Target sequence name
tSize 16178318int(10) unsigned range Target sequence size
tStart 12111322int(10) unsigned range Alignment start position in target
tEnd 12111463int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 141,longblob   Size of each block
qStarts 904,longblob   Start of each block in query.
tStarts 4066855,longblob   Start of each block in target.

Connected Tables and Joining Fields
        droAna2.all_mrna.qName (via xenoRefSeqAli.qName)
      droAna2.xenoMrna.qName (via xenoRefSeqAli.qName)
      droAna2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      droAna2.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
6779645000000+-NM_00617737319041045scaffold_129161617831812111322121114631141,904,4066855,
66810455000000++NM_001314028198014881647scaffold_129161617831810934698109348571159,1488,10934698,
66810455000000++NM_001366537185413621521scaffold_129161617831810934698109348571159,1362,10934698,
69144721600672662800++NM_00110556758631871576scaffold_13266198915411394527913948742781,111,60,75,144,132,60,187,403,604,790,898,1072,1516,13945279,13945607,13946401,13946640,13946748,13947089,13948682,
6911316700255821431+-NM_00132232529316681424scaffold_132661989154113922012139236413129,42,27,668,1070,1397,5967900,5968293,5969502,
69144721600672662800++NM_00110556659021871576scaffold_13266198915411394527913948742781,111,60,75,144,132,60,187,403,604,790,898,1072,1516,13945279,13945607,13946401,13946640,13946748,13947089,13948682,
5857812000053227+-NM_0011405082411800890scaffold_1004644382809611413615,15,15,15,15,15,800,815,830,845,860,875,32969,33242,34066,35385,35744,36271,
5857812000052806+-NM_0011405082411800890scaffold_10046443821207014966615,15,15,16,14,15,800,815,830,845,861,875,29416,29864,30510,30688,32162,32297,
5857812000054335+-NM_0011405082411800890scaffold_10046443821220616631615,15,15,15,16,14,800,815,830,845,860,876,27751,29416,29864,30510,30688,32162,
58589130000612259+-NM_0011405082411791893scaffold_10046443821450026861714,10,15,15,15,15,18,791,805,815,830,845,860,875,17521,18015,27480,27612,27751,29416,29864,

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