Schema for xenoRefSeqAli
  Database: petMar1    Primary Table: xenoRefSeqAli    Row Count: 390,110   Data last updated: 2020-08-22
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 814int(10) unsigned range Number of bases that match that aren't repeats
misMatches 391int(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 6int(10) unsigned range Number of inserts in query
qBaseInsert 1124int(10) unsigned range Number of bases inserted in query
tNumInsert 9int(10) unsigned range Number of inserts in target
tBaseInsert 23794int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001111149varchar(255) values Query sequence name
qSize 3400int(10) unsigned range Query sequence size
qStart 369int(10) unsigned range Alignment start position in query
qEnd 2698int(10) unsigned range Alignment end position in query
tName Contig1varchar(255) values Target sequence name
tSize 186824int(10) unsigned range Target sequence size
tStart 71187int(10) unsigned range Alignment start position in target
tEnd 96186int(10) unsigned range Alignment end position in target
blockCount 10int(10) unsigned range Number of blocks in alignment
blockSizes 144,134,4,102,180,160,72,15...longblob   Size of each block
qStarts 369,570,704,708,810,1157,16...longblob   Start of each block in query.
tStarts 71187,73943,74212,75024,774...longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
      hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
      petMar1.all_est.qName (via xenoRefSeqAli.qName)
      petMar1.all_mrna.qName (via xenoRefSeqAli.qName)
      petMar1.xenoMrna.qName (via xenoRefSeqAli.qName)
      petMar1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      petMar1.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5858143910061124923794++NM_00111114934003692698Contig1186824711879618610144,134,4,102,180,160,72,156,114,139,369,570,704,708,810,1157,1662,2016,2436,2559,71187,73943,74212,75024,77476,82246,87315,90772,95236,96047,
58549218300224862224+-NM_00114546328371201043Contig66722410057598658730,105,77,54,162,91,156,120,318,423,500,554,716,887,15442,16154,16381,16706,17394,17948,18185,
585118650012122648++NM_001277912748252456Contig1378323670067728983100,56,27,252,352,429,70067,71394,72871,
585103036400711711125728++NM_00104454930921622727Contig1186824711879830912187,136,2,102,181,131,165,84,34,87,162,123,162,363,499,501,603,784,951,1431,1898,2121,2373,2604,71187,73943,74214,75024,77476,81481,82247,87303,90834,92842,96047,98186,
5859274660071157925729++NM_00108883328321202670Contig1186824711879830910195,136,104,168,132,166,84,123,162,123,120,321,457,561,741,908,1389,2184,2319,2547,71187,73943,75022,77476,81480,82246,87303,95224,96047,98186,
585656273003196712439++NM_00108173326951901315Contig62833181618065314338132,94,95,132,90,93,162,131,190,436,530,625,757,856,949,1184,18065,19671,20811,22571,24305,25375,26181,31302,
58594146100611451025720++NM_00116189439934382985Contig1186824711879830911195,6,136,104,168,132,166,84,126,162,123,438,633,639,775,879,1059,1226,1707,2499,2634,2862,71187,71866,73943,75022,77476,81480,82246,87303,95224,96047,98186,
58597638300612061025763++NM_02220728381112676Contig1186824711879830911195,131,5,101,181,131,159,84,87,162,123,111,315,446,451,552,733,900,1380,2070,2322,2553,71187,73946,74212,75025,77476,81481,82247,87303,92842,96047,98186,
5853661230027543713++NM_0013592162650138702Contig10790240161772121923590,93,78,111,117,138,237,396,474,585,17721,18234,20536,21142,21806,
58518372001121766++NM_00332221208841151Contig2937811363789989202141,114,884,1037,7899,8806,

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