Schema for xenoRefSeqAli
  Database: rn4    Primary Table: xenoRefSeqAli    Row Count: 316,767   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 1998int(10) unsigned range Number of bases that match that aren't repeats
misMatches 293int(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 3int(10) unsigned range Number of inserts in query
qBaseInsert 71int(10) unsigned range Number of bases inserted in query
tNumInsert 7int(10) unsigned range Number of inserts in target
tBaseInsert 309605int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001104625varchar(255) values Query sequence name
qSize 2547int(10) unsigned range Query sequence size
qStart 185int(10) unsigned range Alignment start position in query
qEnd 2547int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 267910886int(10) unsigned range Target sequence size
tStart 8266int(10) unsigned range Alignment start position in target
tEnd 320162int(10) unsigned range Alignment end position in target
blockCount 9int(10) unsigned range Number of blocks in alignment
blockSizes 171,62,596,209,2,219,124,51...longblob   Size of each block
qStarts 185,423,485,1084,1293,1295,...longblob   Start of each block in query.
tStarts 8266,8507,8993,9589,9803,10...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)
      rn4.all_est.qName (via xenoRefSeqAli.qName)
      rn4.all_mrna.qName (via xenoRefSeqAli.qName)
      rn4.refGene.name (via xenoRefSeqAli.qName)
      rn4.refSeqAli.qName (via xenoRefSeqAli.qName)
      rn4.xenoMrna.qName (via xenoRefSeqAli.qName)
      rn4.xenoRefFlat.name (via xenoRefSeqAli.qName)
      rn4.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
731998293003717309605++NM_00110462525471852547chr126791088682663201629171,62,596,209,2,219,124,510,398,185,423,485,1084,1293,1295,1515,1639,2149,8266,8507,8993,9589,9803,10773,14683,15965,319764,
7358323300210682669882++NM_00109956423674052289chr12679108869108679806381,357,378,405,1503,1911,9108,319319,679428,
96923178000000+-NM_06880137263372chr179729636350386809503871181309,63,46909245,
96923376000000+-NM_07279637263372chr179729636350386809503871181309,63,46909245,
7320483080051527210568++NM_0011033652547392547chr126791088610723832016210148,97,62,211,588,227,121,428,76,398,39,195,429,491,705,1294,1521,1642,2070,2149,107238,109958,110190,110621,110832,112274,317975,319257,319688,319764,
736392790039673568153++NM_00109955723674042289chr1267910886110735679806487,99,354,378,404,924,1503,1911,110735,315504,319319,679428,
735932400034984653756++NM_00109955123439672298chr1267910886111301765890550,276,105,90,312,967,1446,1749,1896,1986,111301,319268,319571,679419,765578,
5862324800434731304+-NM_153780177611041731chr1267910886172519174103519,78,17,64,102,1104,1124,1208,1406,1629,267736783,267736802,267736885,267737079,267738265,
7371029500412667450659++NM_00109955525682522523chr1267910886314226765890878,72,55,5,279,102,102,312,252,1185,1611,1666,1671,1977,2109,2211,314226,315531,318044,318546,319268,319574,679407,765578,
587664244006109964332++NM_00109954123492972304chr12679108863148773201177195,39,54,150,105,53,312,297,984,1392,1578,1755,1900,1992,314877,315564,318044,319394,319571,319716,319805,

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