Schema for ncbiRefSeqPsl
  Database: hg38    Primary Table: ncbiRefSeqPsl    Row Count: 196,387   Data last updated: 2024-09-11
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 1652int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(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 2int(10) unsigned range Number of inserts in target
tBaseInsert 884int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NR_046018.2varchar(255) values Query sequence name
qSize 1652int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1652int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 248956422int(10) unsigned range Target sequence size
tStart 11873int(10) unsigned range Alignment start position in target
tEnd 14409int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 354,109,1189,longblob   Size of each block
qStarts 0,354,463,longblob   Start of each block in query.
tStarts 11873,12612,13220,longblob   Start of each block in target.

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Connected Tables and Joining Fields
        hg38.ncbiRefSeq.name (via ncbiRefSeqPsl.qName)
      hg38.ncbiRefSeqCds.id (via ncbiRefSeqPsl.qName)
      hg38.ncbiRefSeqCurated.name (via ncbiRefSeqPsl.qName)
      hg38.ncbiRefSeqHgmd.name (via ncbiRefSeqPsl.qName)
      hg38.ncbiRefSeqLink.id (via ncbiRefSeqPsl.qName)
      hg38.ncbiRefSeqPredicted.name (via ncbiRefSeqPsl.qName)
      hg38.ncbiRefSeqSelect.name (via ncbiRefSeqPsl.qName)
      hg38.seqNcbiRefSeq.acc (via ncbiRefSeqPsl.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5851652000002884+NR_046018.2165201652chr124895642211873144093354,109,1189,0,354,463,11873,12612,13220,
58516850840001013240-NR_024540.1178601769chr1248956422143612937011468,69,152,159,198,136,137,147,99,154,50,17,485,554,706,865,1063,1199,1336,1483,1582,1736,14361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320,
585680000000-NR_106918.168068chr12489564221736817436168,0,17368,
5859700129300023382+XR_007065314.1226302263chr124895642229773354183894,118,1251,0,894,1012,29773,30975,34167,
5850013800000+NR_036051.11380138chr124895642230365305031138,0,30365,
58561405160002341-NR_026818.1113001130chr124895642234610360813564,205,361,0,564,769,34610,35276,35720,
5851959065900023549+NM_001005484.2261802618chr12489564226541871585315,54,2549,0,15,69,65418,65519,69036,
58543730100600027127+XR_007065338.1537905379chr12489564229522110772734498,107,774,0,4498,4605,95221,106635,106953,
58545610102900016916+XR_007065337.1559005590chr12489564229522110772724498,1092,0,4498,95221,106635,
7311640887000552347-XR_001737579.3205102051chr1248956422120848175246684,59,66,216,132,1494,0,84,143,209,425,557,120848,165883,168099,169048,172556,173752,

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