Schema for refSeqAli
  Database: oryLat2    Primary Table: refSeqAli    Row Count: 903   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 601smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 561int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1int(10) unsigned range Number of bases that don't match
repMatches 20int(10) unsigned range Number of bases that match but are part of repeats
nCount 3int(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 33155int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NM_001104768varchar(255) values Query sequence name
qSize 585int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 585int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 39973033int(10) unsigned range Target sequence size
tStart 2127568int(10) unsigned range Alignment start position in target
tEnd 2161308int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 188,232,165,longblob   Size of each block
qStarts 0,188,420,longblob   Start of each block in query.
tStarts 2127568,2140494,2161143,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)
      oryLat2.all_est.qName (via refSeqAli.qName)
      oryLat2.all_mrna.qName (via refSeqAli.qName)
      oryLat2.mrnaOrientInfo.name (via refSeqAli.qName)
      oryLat2.refFlat.name (via refSeqAli.qName)
      oryLat2.refGene.name (via refSeqAli.qName)
      oryLat2.xenoMrna.qName (via refSeqAli.qName)
      oryLat2.xenoRefGene.name (via refSeqAli.qName)
      oryLat2.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
601561120300233155+NM_0011047685850585chr139973033212756821613083188,232,165,0,188,420,2127568,2140494,2161143,
6028412201121394+NM_0011048328460846chr13997303322600942262333435,172,155,483,0,36,208,363,2260094,2260129,2260411,2261850,
63111400270133675466-NM_001278873120001200chr139973033605152861281617109,326,94,140,194,201,103,0,109,435,529,669,863,1097,6051528,6056494,6061064,6072534,6081809,6083343,6128058,
666111231000085038+NM_001163134112501125chr1399730331064514510651308971,99,97,176,123,177,114,90,178,0,71,170,267,443,566,743,857,947,10645145,10645962,10647322,10648102,10649751,10650190,10650451,10650668,10651130,
6713321200033415+NM_0011720463350335chr1399730331128728111291031443,132,72,88,0,43,175,247,11287281,11288096,11290042,11290943,
675980000000+NR_10707798098chr1399730331180571511805813198,0,11805715,
69871421920003286+NM_0012015109080908chr13997303314895309148965034129,381,106,292,0,129,510,616,14895309,14895526,14895999,14896211,
7151050000000-NR_1070781050105chr13997303317054064170541691105,0,17054064,
71727625010477845236+NM_001291290355703555chr13997303317407688174157018160,309,319,106,287,139,14,1443,0,160,469,792,898,1195,2097,2112,17407688,17410610,17411000,17411319,17411426,17411713,17414244,17414258,
91123702000435221-NM_001278910123901239chr13997303319124261191607215334,197,151,189,368,0,334,531,682,871,19124261,19127171,19154584,19158267,19160353,

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