Schema for xenoRefSeqAli
  Database: priPac1    Primary Table: xenoRefSeqAli    Row Count: 238,292   Data last updated: 2020-08-22
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 103int(10) unsigned range Number of bases that match that aren't repeats
misMatches 13int(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 2int(10) unsigned range Number of inserts in query
qBaseInsert 255int(10) unsigned range Number of bases inserted in query
tNumInsert 5int(10) unsigned range Number of inserts in target
tBaseInsert 496095int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_007682varchar(255) values Query sequence name
qSize 2827int(10) unsigned range Query sequence size
qStart 1405int(10) unsigned range Alignment start position in query
qEnd 1776int(10) unsigned range Alignment end position in query
tName chrUnvarchar(255) values Target sequence name
tSize 174852139int(10) unsigned range Target sequence size
tStart 4542int(10) unsigned range Alignment start position in target
tEnd 500753int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 29,25,3,21,11,27,longblob   Size of each block
qStarts 1405,1448,1473,1476,1497,1749,longblob   Start of each block in query.
tStarts 174351386,174489844,1744901...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)
      priPac1.all_est.qName (via xenoRefSeqAli.qName)
      priPac1.all_mrna.qName (via xenoRefSeqAli.qName)
      priPac1.xenoMrna.qName (via xenoRefSeqAli.qName)
      priPac1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      priPac1.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
73103130022555496095+-NM_007682282714051776chrUn1748521394542500753629,25,3,21,11,27,1405,1448,1473,1476,1497,1749,174351386,174489844,174490101,174493330,174499627,174847570,
5853461750073977928++NM_00100383351193521270chrUn1748521391585617305854,45,11,105,108,69,72,57,352,475,529,589,721,865,964,1213,15856,16019,16121,16224,16399,16582,16723,17248,
585471261005153082190++NM_20093636682292491chrUn1748521391585618778981,64,143,66,75,78,60,57,108,229,505,569,742,841,916,1030,1090,2383,15856,16263,16370,16582,16723,16862,17143,17248,18670,
160511517000000++NM_001384164499118541986chrUn1748521391337467231337468551132,1854,133746723,
160515431001200+-NM_001286045361024852672chrUn1748521391337467231337469082121,64,2485,2608,41105231,41105352,
5852781440043735864++NM_00104809026102491044chrUn1748521391601917305645,11,103,134,72,57,249,303,363,466,738,987,16019,16121,16224,16370,16723,17248,
5852711510043735864++NM_00116184142489181713chrUn1748521391601917305645,11,103,134,72,57,918,972,1032,1135,1407,1656,16019,16121,16224,16370,16723,17248,
139236013200164885+-NM_0011606121263175673chrUn1748521391058717291058731065117,109,125,75,66,175,292,401,526,607,68979033,68979307,68979656,68979980,68980344,
5852711510043735864++NM_01883739095791374chrUn1748521391601917305645,11,103,134,72,57,579,633,693,796,1068,1317,16019,16121,16224,16370,16723,17248,
5852711510043735864++NM_19859642399181713chrUn1748521391601917305645,11,103,134,72,57,918,972,1032,1135,1407,1656,16019,16121,16224,16370,16723,17248,

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