Schema for refSeqAli
  Database: xenTro3    Primary Table: refSeqAli    Row Count: 9,395   Data last updated: 2020-09-02
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 870int(10) unsigned range Number of bases that match that aren't repeats
misMatches 2int(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 1int(10) unsigned range Number of inserts in target
tBaseInsert 4341int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NM_001113850varchar(255) values Query sequence name
qSize 1122int(10) unsigned range Query sequence size
qStart 236int(10) unsigned range Alignment start position in query
qEnd 1108int(10) unsigned range Alignment end position in query
tName GL172637varchar(255) values Target sequence name
tSize 7817814int(10) unsigned range Target sequence size
tStart 20066int(10) unsigned range Alignment start position in target
tEnd 25279int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 106,766,longblob   Size of each block
qStarts 236,342,longblob   Start of each block in query.
tStarts 20066,24513,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)
      xenTro3.all_est.qName (via refSeqAli.qName)
      xenTro3.all_mrna.qName (via refSeqAli.qName)
      xenTro3.mrnaOrientInfo.name (via refSeqAli.qName)
      xenTro3.refFlat.name (via refSeqAli.qName)
      xenTro3.refGene.name (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5858702000014341+NM_00111385011222361108GL172637781781420066252792106,766,236,342,20066,24513,
58529726330121031143-NM_001016196303223015GL1726377817814574419159512811,1256,75,109,79,56,87,97,130,122,43,146,17,830,2086,2161,2270,2349,2405,2492,2589,2719,2841,2884,57441,58252,63050,64382,74344,75918,76176,76539,86918,87798,91226,91449,
731150323000397592-NM_001113927119101176GL17263778178141165612153294242,130,736,68,15,257,387,1123,116561,122799,206780,215261,
5881885000001030520-NM_001005440193101885GL172637781781446300749541211509,287,73,72,186,168,159,196,92,110,33,46,555,842,915,987,1173,1341,1500,1696,1788,1898,463007,472734,474142,482057,484803,486452,487908,491398,492665,493967,495379,
589200405300021004-NM_001045768207402057GL17263778178145571705602313904,1006,147,17,921,1927,557170,558603,560084,
591278400000216089+NM_001045708280872791GL17263778178148558088746813724,130,1930,7,731,861,855808,871387,872751,
592145110011713391-NM_001017064147001453GL17263778178149700129848559674,174,191,52,70,78,84,49,80,17,692,866,1057,1109,1179,1257,1341,1390,970012,970686,971957,974972,977060,977894,978308,980869,984775,
59288400000521633-NM_0011138969010884GL1726377817814102287410453916171,231,109,129,100,144,17,188,419,528,657,757,1022874,1026466,1037585,1038459,1043003,1045247,
74616011000028124361+NM_001128649618606171GL17263778178141057947118847929267,148,146,32,92,76,79,155,76,210,102,133,68,92,209,139,133,166,102,123,110,152,323,207,227,123,137,188,2156,0,267,415,561,593,685,761,840,995,1071,1281,1383,1516,1584,1676,1885,2024,2157,2323,2425,2548,2658,2810,3133,3340,3567,3690,3827 ...1057947,1069778,1072900,1109324,1134813,1146236,1150148,1151403,1155511,1156716,1165644,1169486,1171685,1172507,1172691,1173850, ...
594235202000910907-NM_001017229237302354GL17263778178141255300126856110929,171,75,177,143,126,181,99,109,344,19,948,1119,1194,1371,1514,1640,1821,1920,2029,1255300,1256614,1257037,1257682,1259498,1260661,1261499,1262019,1263251,1268217,

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