Schema for refSeqAli
  Database: ci1    Primary Table: refSeqAli    Row Count: 1,035   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 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 2247int(10) unsigned range Number of bases that match that aren't repeats
misMatches 30int(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 3int(10) unsigned range Number of inserts in query
qBaseInsert 3int(10) unsigned range Number of bases inserted in query
tNumInsert 14int(10) unsigned range Number of inserts in target
tBaseInsert 2698int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001033828varchar(255) values Query sequence name
qSize 2280int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2280int(10) unsigned range Alignment end position in query
tName Scaffold_1varchar(255) values Target sequence name
tSize 972361int(10) unsigned range Target sequence size
tStart 26494int(10) unsigned range Alignment start position in target
tEnd 31469int(10) unsigned range Alignment end position in target
blockCount 18int(10) unsigned range Number of blocks in alignment
blockSizes 142,24,16,323,92,149,84,278...longblob   Size of each block
qStarts 0,143,167,184,507,599,748,8...longblob   Start of each block in query.
tStarts 26494,26636,26662,26678,272...longblob   Start of each block in target.

Connected Tables and Joining Fields
        ci1.all_est.qName (via refSeqAli.qName)
      ci1.all_mrna.qName (via refSeqAli.qName)
      ci1.mrnaOrientInfo.name (via refSeqAli.qName)
      ci1.refFlat.name (via refSeqAli.qName)
      ci1.refGene.name (via refSeqAli.qName)
      ci1.xenoMrna.qName (via refSeqAli.qName)
      ci1.xenoRefGene.name (via refSeqAli.qName)
      ci1.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
5852247300033142698-NM_001033828228002280Scaffold_1972361264943146918142,24,16,323,92,149,84,278,197,110,118,117,141,23,92,153,81,137,0,143,167,184,507,599,748,833,1111,1308,1418,1536,1653,1794,1817,1909,2062,2143,26494,26636,26662,26678,27286,27447,27733,27817,28345,28981,29158,29486,29828,30078,30264,30537,31177,31332,
58621211018400036819+NM_001032462233302315Scaffold_19723611495891587234661,127,132,1395,0,661,788,920,149589,154436,154617,157328,
58837034200001912278+NM_001078224376303745Scaffold_197236141393342995620139,98,133,170,243,182,191,96,269,156,166,140,136,150,74,251,172,132,152,695,0,139,237,370,540,783,965,1156,1252,1521,1677,1843,1983,2119,2269,2343,2594,2766,2898,3050,413933,415028,415499,415958,416466,417319,418784,419321,419847,421762,423282,424085,424966,425501,426275,426822,427653,428213,42 ...
58838462600424158107+NM_001032428392203896Scaffold_197236146107347305218456,114,138,135,69,187,124,57,1051,147,172,39,27,65,198,183,30,680,0,456,570,708,843,912,1099,1227,1284,2335,2482,2654,2694,2736,2801,2999,3186,3216,461073,462706,468006,468222,468429,468571,468876,469004,469543,470780,470999,471311,471350,471381,471595,472039,472222,472372,
588335200000165756+NM_001047999335203352Scaffold_19723614804434895511766,128,72,149,157,158,825,229,187,194,129,140,119,101,123,127,448,0,66,194,266,415,572,730,1555,1784,1971,2165,2294,2434,2553,2654,2777,2904,480443,480511,481061,481530,482491,483103,483630,484589,485375,485821,486407,487118,487576,487867,488075,488506,489103,
589256138330418104728+NM_001078301276502650Scaffold_19723615783645857241483,81,190,163,184,426,135,156,205,211,16,84,655,43,0,83,164,354,517,701,1127,1262,1418,1623,1835,1852,1951,2607,578364,579487,580038,580907,581762,582265,582908,583755,584160,584714,584925,584941,585026,585681,
589436650005232210036-NM_001047994445704439Scaffold_197236158575760020926205,190,47,91,1116,33,198,150,117,108,391,89,83,114,105,90,177,79,127,141,97,151,158,72,142,145,18,223,415,462,559,1687,1722,1920,2070,2187,2295,2687,2776,2859,2973,3078,3168,3345,3424,3551,3692,3789,3940,4098,4170,4312,585757,585963,586154,586207,586298,587414,587464,588517,589120,589483,590182,590573,591297,591448,592891,593252,593870,596393,59 ...
59015442627011328-NM_001032471162201598Scaffold_197236169631569794058,99,8,64,1418,24,33,132,140,204,696315,696323,696435,696451,696522,
5851867800004493-NM_001032580189301875Scaffold_65438391245392690751001,147,271,217,239,18,1019,1166,1437,1654,24539,25614,25839,26224,26668,
591346000000102872+NM_001048002346003460Scaffold_197236186740387373511190,611,170,183,143,209,588,176,283,66,841,0,190,801,971,1154,1297,1506,2094,2270,2553,2619,867403,867783,868638,869165,870381,870601,870882,871691,872056,872760,872894,

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