Schema for refSeqAli
  Database: macFas5    Primary Table: refSeqAli    Row Count: 2,163   Data last updated: 2019-12-05
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 74smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1807int(10) unsigned range Number of bases that match that aren't repeats
misMatches 5int(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 1int(10) unsigned range Number of inserts in query
qBaseInsert 9int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 50291int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001283475varchar(255) values Query sequence name
qSize 1924int(10) unsigned range Query sequence size
qStart 3int(10) unsigned range Alignment start position in query
qEnd 1824int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 227556264int(10) unsigned range Target sequence size
tStart 1699586int(10) unsigned range Alignment start position in target
tEnd 1751689int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 557,939,29,50,60,177,longblob   Size of each block
qStarts 100,666,1605,1634,1684,1744,longblob   Start of each block in query.
tStarts 1699586,1700143,1710585,171...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)
      macFas5.all_est.qName (via refSeqAli.qName)
      macFas5.all_mrna.qName (via refSeqAli.qName)
      macFas5.mrnaOrientInfo.name (via refSeqAli.qName)
      macFas5.refFlat.name (via refSeqAli.qName)
      macFas5.refGene.name (via refSeqAli.qName)
      macFas5.xenoRefGene.name (via refSeqAli.qName)
      macFas5.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
74180750019450291-NM_001283475192431824chr1227556264169958617516896557,939,29,50,60,177,100,666,1605,1634,1684,1744,1699586,1700143,1710585,1712907,1720103,1751512,
604172270021041051719-NM_001283331185201833chr12275562642533456258690412198,414,82,112,57,120,118,131,50,132,113,202,19,242,656,738,850,907,1027,1145,1276,1326,1537,1650,2533456,2533654,2535100,2536550,2541801,2541964,2542904,2543622,2561797,2565509,2584375,2586702,
645159770000920823+NM_001285175161901604chr12275562647937257795968410160,135,111,177,183,166,204,128,154,186,0,160,295,406,583,766,932,1136,1264,1418,7937257,7939725,7943345,7945093,7948338,7950958,7952857,7954523,7956896,7959498,
673178760000126309+NM_001285045181001793chr1227556264115832991159140113133,200,122,103,153,188,98,131,190,151,79,102,143,0,133,333,455,558,711,899,997,1128,1318,1469,1548,1650,11583299,11583433,11583893,11584100,11585546,11586495,11587188,11588170,11588477,11588738,11589202,11590968,11591258,
85293319031007178237-NM_001283135298302983chr1227556264129989001318012082471,46,59,40,59,92,71,145,0,2471,2517,2576,2616,2675,2767,2838,12998900,13015501,13053806,13067307,13072789,13144875,13177810,13179975,
722185720000537732-NM_001284818216101859chr1227556264179844661802405761209,128,131,115,105,171,302,1511,1639,1770,1885,1990,17984466,17988841,18010481,18015735,18023349,18023886,
11182112001159928+NM_001283634183401834chr12275562641886313418874895736,859,268,145,263,111,151,0,36,895,1163,1308,1572,1683,18863134,18866358,18871017,18872883,18874365,18874628,18874744,
93207050000654160-NM_001283325209102075chr122755626421209160212653957349,1266,167,62,111,110,10,16,365,1631,1798,1860,1971,2081,21209160,21209515,21215793,21223306,21229670,21265274,21265385,
766128420000639255-NM_001284144130801286chr122755626423800085238406267680,145,68,47,60,78,208,22,702,847,915,962,1022,1100,23800085,23813872,23824538,23826309,23831501,23839926,23840418,
9749530000787676-NM_0012838314980498chr12275562642539720925485383866,42,57,33,81,57,104,58,0,66,108,165,198,279,336,440,25397209,25398531,25399489,25400472,25403607,25404381,25405701,25485325,

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