Schema for refSeqAli
  Database: ci2    Primary Table: refSeqAli    Row Count: 1,263   Data last updated: 2019-07-17
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 592smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1632int(10) unsigned range Number of bases that match that aren't repeats
misMatches 4int(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 1int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 1int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001128115varchar(255) values Query sequence name
qSize 1639int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1637int(10) unsigned range Alignment end position in query
tName chr01pvarchar(255) values Target sequence name
tSize 6220112int(10) unsigned range Target sequence size
tStart 923780int(10) unsigned range Alignment start position in target
tEnd 925417int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 32,483,1121,longblob   Size of each block
qStarts 2,35,518,longblob   Start of each block in query.
tStarts 923780,923812,924296,longblob   Start of each block in target.

Connected Tables and Joining Fields
        ci2.all_est.qName (via refSeqAli.qName)
      ci2.all_mrna.qName (via refSeqAli.qName)
      ci2.mrnaOrientInfo.name (via refSeqAli.qName)
      ci2.refFlat.name (via refSeqAli.qName)
      ci2.refGene.name (via refSeqAli.qName)
      ci2.xenoMrna.qName (via refSeqAli.qName)
      ci2.xenoRefGene.name (via refSeqAli.qName)
      ci2.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
59216324001111-NM_001128115163901637chr01p6220112923780925417332,483,1121,2,35,518,923780,923812,924296,
58542721000031044-NM_00136901023387481196scaffold_6917159111493489,161,73,125,1142,1231,1392,1465,1,400,931,1368,
59411401100113679-NM_001078521118301152chr01p6220112127917412810045279,613,91,96,72,31,311,924,1015,1111,1279174,1279453,1280354,1280547,1280932,
5951956160027111558+NM_001078213200201979chr01p6220112138412913876591463,229,58,143,185,57,166,141,69,149,167,46,417,82,0,69,298,356,499,684,741,907,1048,1117,1266,1433,1479,1897,1384129,1384192,1384683,1384794,1385101,1385445,1385557,1385813,1386022,1386290,1386761,1387051,1387160,1387577,
59610135240003481+NM_001032561105801042chr01p6220112145604614575694165,215,199,463,0,165,380,579,1456046,1456578,1456842,1457106,
59736693700002115159+NM_001128105372503706chr01p62201121627050164591522211,62,158,121,114,175,105,156,109,145,82,206,331,126,233,219,150,188,153,344,95,223,0,211,273,431,552,666,841,946,1102,1211,1356,1438,1644,1975,2101,2334,2553,2703,2891,3044,3388,3483,1627050,1627366,1628958,1629404,1629915,1630513,1631399,1636846,1638811,1639299,1639740,1640507,1641196,1641899,1642377,1642908, ...
601255212010011264+NM_001128858258402565chr01p6220112217306021768892462,2103,0,462,2173060,2174786,
751983140000534375-NM_001078227203001997chr01p6220112221860722549796120,1049,174,108,284,262,33,153,1202,1376,1484,1768,2218607,2218728,2220921,2231815,2242589,2254717,
602347000003286-NM_00112622935912359chr01p622011222950762295709456,93,44,154,0,56,149,193,2295076,2295184,2295412,2295555,
603209380011382262-NM_001032433213002114chr01p6220112243516424395271054,375,156,120,145,255,85,114,53,744,16,83,458,614,734,879,1134,1219,1333,1386,2435164,2435218,2435959,2436521,2436924,2437292,2437635,2437950,2438393,2438783,

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