Schema for refSeqAli
  Database: mm7    Primary Table: refSeqAli    Row Count: 47,406   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 76smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 3205int(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 429int(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 452079int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001011874varchar(255) values Query sequence name
qSize 3652int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 3634int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 194923535int(10) unsigned range Target sequence size
tStart 3211363int(10) unsigned range Alignment start position in target
tEnd 3667076int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 2487,200,947,longblob   Size of each block
qStarts 18,2505,2705,longblob   Start of each block in query.
tStarts 3211363,3417279,3666129,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via refSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via refSeqAli.qName)
      hgFixed.gbSeq.acc (via refSeqAli.qName)
      hgFixed.gbWarn.acc (via refSeqAli.qName)
      hgFixed.imageClone.acc (via refSeqAli.qName)
      hgFixed.refLink.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName)
      knownGeneV39.kgXref.refseq (via refSeqAli.qName)
      knownGeneV39.knownToRefSeq.value (via refSeqAli.qName)
      mm7.all_est.qName (via refSeqAli.qName)
      mm7.all_mrna.qName (via refSeqAli.qName)
      mm7.dupSpMrna.dupMrnaID (via refSeqAli.qName)
      mm7.dupSpMrna.mrnaID (via refSeqAli.qName)
      mm7.kgXref.refseq (via refSeqAli.qName)
      mm7.knownToRefSeq.value (via refSeqAli.qName)
      mm7.mrnaOrientInfo.name (via refSeqAli.qName)
      mm7.mrnaRefseq.mrna (via refSeqAli.qName)
      mm7.mrnaRefseq.refseq (via refSeqAli.qName)
      mm7.refFlat.name (via refSeqAli.qName)
      mm7.refGene.name (via refSeqAli.qName)
      mm7.xenoMrna.qName (via refSeqAli.qName)
      mm7.xenoRefGene.name (via refSeqAli.qName)
      mm7.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
76320504290002452079-NM_001011874365203634chr11949235353211363366707632487,200,947,18,2505,2705,3211363,3417279,3666129,
771723013240003115349-NM_001195662304703047chr11949235354286437440483342167,172,636,72,0,2167,2339,2975,4286437,4347501,4347793,4404761,
6187082042600039300-NM_011283750807508chr11949235354339098435590646585,172,636,115,0,6585,6757,7393,4339098,4347501,4347793,4355791,
61932880000033139-NM_001289464328803288chr11949235354486519449294641741,391,92,1064,0,1741,2132,2224,4486519,4488691,4489363,4491882,
61937040000032723-NM_001289465370403704chr11949235354486519449294641741,92,807,1064,0,1741,1833,2640,4486519,4489363,4490727,4491882,
61929600000033467-NM_001289466296002960chr11949235354486519449294641741,92,63,1064,0,1741,1833,1896,4486519,4489363,4490727,4491882,
61928970000023530-NM_001289467289702897chr11949235354486519449294631741,92,1064,0,1741,1833,4486519,4489363,4491882,
61940710000042356-NM_011441407104071chr11949235354486519449294651741,367,92,807,1064,0,1741,2108,2200,3007,4486519,4488691,4489363,4490727,4491882,
620145749192216638-NM_1338311572161559chr1194923535468347046850359432,31,105,32,259,469,55,26,118,13,445,476,587,619,878,1357,1412,1438,4683470,4683913,4683949,4684054,4684089,4684360,4684829,4684887,4684917,
6213331087000048326-NM_001177658421604201chr11949235354768791478131853602,124,166,155,154,15,3617,3741,3907,4062,4768791,4773116,4778159,4779542,4781164,

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