Schema for xenoRefSeqAli
  Database: melGal5    Primary Table: xenoRefSeqAli    Row Count: 231,886   Data last updated: 2017-01-18
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 1796int(10) unsigned range Number of bases that match that aren't repeats
misMatches 124int(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 22int(10) unsigned range Number of 'N' bases
qNumInsert 5int(10) unsigned range Number of inserts in query
qBaseInsert 447int(10) unsigned range Number of bases inserted in query
tNumInsert 17int(10) unsigned range Number of inserts in target
tBaseInsert 6303int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001031401varchar(255) values Query sequence name
qSize 2586int(10) unsigned range Query sequence size
qStart 170int(10) unsigned range Alignment start position in query
qEnd 2559int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 190651702int(10) unsigned range Target sequence size
tStart 18689int(10) unsigned range Alignment start position in target
tEnd 26934int(10) unsigned range Alignment end position in target
blockCount 18int(10) unsigned range Number of blocks in alignment
blockSizes 51,133,109,57,111,106,62,58...longblob   Size of each block
qStarts 170,221,354,463,520,631,737...longblob   Start of each block in query.
tStarts 18689,18861,19779,20344,219...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)
      melGal5.all_est.qName (via xenoRefSeqAli.qName)
      melGal5.all_mrna.qName (via xenoRefSeqAli.qName)
      melGal5.refGene.name (via xenoRefSeqAli.qName)
      melGal5.refSeqAli.qName (via xenoRefSeqAli.qName)
      melGal5.xenoRefFlat.name (via xenoRefSeqAli.qName)
      melGal5.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58517961240225447176303++NM_00103140125861702559chr119065170218689269341851,133,109,57,111,106,62,58,134,109,73,183,7,72,352,84,205,36,170,221,354,463,520,631,737,810,868,1002,1141,1215,1398,1405,1477,1829,2252,2523,18689,18861,19779,20344,21952,22218,22613,23158,23425,24003,24504,24581,24973,25389,25815,26176,26634,26898,
58543322700326764194++NM_00108996418251841111chr11906517021869023544739,129,99,112,111,56,114,184,238,367,532,644,755,997,18690,18865,19779,21951,22218,22618,23430,
58556722900462986454++NM_00114181122932121637chr11906517021869025940951,120,3,105,55,111,107,111,133,212,275,395,398,506,561,672,911,1504,18690,18874,19008,19782,20346,21952,22218,23427,25807,
585496217028479886515++NM_00104500624951591698chr11906517021869025946950,133,3,138,112,56,111,15,123,159,209,342,345,840,952,1080,1264,1575,18690,18861,19077,19782,21951,22618,23427,24046,25823,
58556227800470586419++NM_00101131418371521697chr11906517021869025949939,129,108,112,107,60,114,39,132,152,206,335,500,612,719,965,1526,1565,18690,18865,19779,21951,22218,22614,23430,25424,25817,
58550113800469096623++NM_00101189819761361465chr119065170218690259521051,129,3,105,55,107,15,36,3,135,136,190,319,322,430,485,721,1291,1327,1330,18690,18865,19156,19782,20346,21952,23424,25424,25463,25817,
58544814000476586674++NM_00103505731252241577chr11906517021869025952951,129,3,105,54,72,36,3,135,224,278,407,410,518,683,1403,1439,1442,18690,18865,19156,19782,20346,21951,25424,25463,25817,
58548613800369986638++NM_00125794719682171540chr11906517021869025952951,129,3,105,55,107,36,3,135,217,271,400,403,511,566,1366,1402,1405,18690,18865,19156,19782,20346,21952,25424,25463,25817,
58548713700369986638++NM_00128355220172121535chr11906517021869025952951,129,3,105,55,107,36,3,135,212,266,395,398,506,561,1361,1397,1400,18690,18865,19156,19782,20346,21952,25424,25463,25817,
58544913900365786674++NM_00129204119432341479chr11906517021869025952951,129,3,105,55,71,36,3,135,234,288,417,420,528,583,1305,1341,1344,18690,18865,19156,19782,20346,21952,25424,25463,25817,

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