Schema for refSeqAli
  Database: xenTro10    Primary Table: refSeqAli    Row Count: 8,952   Data last updated: 2021-03-24
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 586smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 719int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(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 4int(10) unsigned range Number of inserts in target
tBaseInsert 6167int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001102819varchar(255) values Query sequence name
qSize 842int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 719int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 217471166int(10) unsigned range Target sequence size
tStart 200865int(10) unsigned range Alignment start position in target
tEnd 207751int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 200,124,147,231,17,longblob   Size of each block
qStarts 123,323,447,594,825,longblob   Start of each block in query.
tStarts 200865,201382,203466,205059...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)
      xenTro10.all_est.qName (via refSeqAli.qName)
      xenTro10.all_mrna.qName (via refSeqAli.qName)
      xenTro10.mrnaOrientInfo.name (via refSeqAli.qName)
      xenTro10.refFlat.name (via refSeqAli.qName)
      xenTro10.refGene.name (via refSeqAli.qName)
      xenTro10.xenoRefGene.name (via refSeqAli.qName)
      xenTro10.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5867190000046167-NM_0011028198420719chr12174711662008652077515200,124,147,231,17,123,323,447,594,825,200865,201382,203466,205059,207734,
5862834130021041021999-NM_0011303772978102961chr121747116621943924428512888,155,370,165,207,142,139,144,169,186,250,32,17,954,1164,1534,1699,1906,2048,2187,2331,2500,2686,2936,219439,220331,220486,221263,225223,226029,228360,230401,232272,237228,243195,244253,
587177290011108465-NM_001113903179901782chr121747116635062436087012206,89,128,199,67,74,73,188,151,138,130,338,17,223,312,440,639,706,780,853,1041,1192,1330,1461,350624,350913,351179,351651,352900,354154,354375,354553,355235,356047,360402,360532,
7342261100001438208+NM_001079275426304237chr121747116636296640541115135,92,230,194,379,243,97,159,192,123,185,182,505,1264,257,0,135,227,457,651,1030,1273,1370,1529,1721,1844,2029,2211,2716,3980,362966,370054,370147,378332,381305,381813,387737,387911,388511,390831,395391,398219,402823,403877,405154,
590193180000127072+NM_001197203195301939chr121747116672679073580113139,90,115,162,199,188,152,101,149,122,156,281,85,0,139,229,344,506,705,893,1045,1146,1295,1417,1573,1854,726790,728775,731247,731477,731723,732498,732842,733602,734043,734447,735163,735433,735716,
5921401100001115055-NM_001126521141601402chr121747116692497094142712332,61,95,147,103,134,133,61,121,99,60,56,14,346,407,502,649,752,886,1019,1080,1201,1300,1360,924970,929307,930044,931124,932176,932401,932712,933330,933494,933798,934333,941371,
593137900000730116-NM_001004786141501379chr1217471166106627710977728492,90,114,167,88,129,235,64,36,528,618,732,899,987,1116,1351,1066277,1067263,1079482,1080890,1082167,1082598,1083016,1097708,
63615999000048074-NM_001142230171701608chr12174711666694707670438951086,161,119,184,58,109,1195,1356,1475,1659,6694707,6697054,6699213,6699591,6704331,
636144300000313612+NM_001015807148601443chr1217471166670471067197654101,106,162,1074,0,101,207,369,6704710,6715934,6718293,6718691,
636146400000942482-NM_00100681416591731637chr12174711666737885678183110171,140,111,108,115,98,222,114,98,287,22,193,333,444,552,667,765,987,1101,1199,6737885,6744476,6744895,6769503,6770163,6771267,6771473,6776179,6776471,6781544,

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