Schema for refSeqAli
  Database: dm3    Primary Table: refSeqAli    Row Count: 37,634   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 629smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 3133int(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 7int(10) unsigned range Number of inserts in target
tBaseInsert 10365int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001382028varchar(255) values Query sequence name
qSize 3133int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 3133int(10) unsigned range Alignment end position in query
tName chr2Rvarchar(255) values Target sequence name
tSize 21146708int(10) unsigned range Target sequence size
tStart 5803622int(10) unsigned range Alignment start position in target
tEnd 5817120int(10) unsigned range Alignment end position in target
blockCount 8int(10) unsigned range Number of blocks in alignment
blockSizes 774,416,173,137,319,204,394...longblob   Size of each block
qStarts 0,774,1190,1363,1500,1819,2...longblob   Start of each block in query.
tStarts 5803622,5805442,5805973,580...longblob   Start of each block in target.

Connected Tables and Joining Fields
        dm3.all_est.qName (via refSeqAli.qName)
      dm3.all_mrna.qName (via refSeqAli.qName)
      dm3.flyBaseToRefSeq.value (via refSeqAli.qName)
      dm3.mrnaOrientInfo.name (via refSeqAli.qName)
      dm3.refFlat.name (via refSeqAli.qName)
      dm3.refGene.name (via refSeqAli.qName)
      dm3.xenoMrna.qName (via refSeqAli.qName)
      dm3.xenoRefGene.name (via refSeqAli.qName)
      dm3.xenoRefSeqAli.qName (via refSeqAli.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
629313300000710365-NM_001382028313303133chr2R21146708580362258171208774,416,173,137,319,204,394,716,0,774,1190,1363,1500,1819,2023,2417,5803622,5805442,5805973,5806216,5806933,5808023,5809114,5816404,
7582947003003200-NR_167782295202950chr2L2301154422733250227364004597,2209,37,107,2,599,2808,2845,22733250,22733921,22736195,22736293,
6271200000000+NR_0480711200120chr2R21146708550873855088581120,0,5508738,
627880000000-NR_04807288088chr2R2114670855087555508843188,0,5508755,
6491379000003174+NM_141961137901379chr3R2790505384642028465755484,60,696,539,0,84,144,840,8464202,8464341,8464457,8465216,
6491330000002107+NM_141960133001330chr3R27905053846226184636983142,696,492,0,142,838,8462261,8462457,8463206,
681741400000257084-NM_001259444741407414chr2R211467081263900712653505262035,102,137,190,112,393,190,363,297,91,178,410,191,167,783,117,42,140,164,256,185,240,83,143,237,168,0,2035,2137,2274,2464,2576,2969,3159,3522,3819,3910,4088,4498,4689,4856,5639,5756,5798,5938,6102,6358,6543,6783,6866,7009,7246,12639007,12641103,12641270,12641467,12643391,12643562,12644060,12644305,12644737,12645101,12645252,12645497,12646756,12647014,12 ...
626562100000126159-NM_001103776562105621chr2R211467085475457548723713378,415,180,773,182,383,1090,735,66,167,175,854,223,0,378,793,973,1746,1928,2311,3401,4136,4202,4369,4544,5398,5475457,5475895,5480251,5480494,5481893,5482134,5482572,5483718,5484506,5484629,5484849,5485076,5487014,
63444540271000727838+NM_165791472504725chr2R21146708647119065037538438,966,139,540,639,103,184,1716,0,438,1404,1543,2083,2722,2825,3009,6471190,6498054,6499184,6499419,6500241,6501272,6501447,6502037,
64827210000052289-NM_001259736272102721chr3L24543557830359283086026734,69,300,467,720,431,0,734,803,1103,1570,2290,8303592,8304746,8304873,8305383,8307056,8308171,

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