Schema for xenoRefSeqAli
  Database: ponAbe3    Primary Table: xenoRefSeqAli    Row Count: 228,415   Data last updated: 2018-10-26
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 1738int(10) unsigned range Number of bases that match that aren't repeats
misMatches 36int(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 1int(10) unsigned range Number of inserts in query
qBaseInsert 52int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 13958int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001017434varchar(255) values Query sequence name
qSize 2035int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1826int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 227913704int(10) unsigned range Target sequence size
tStart 2141int(10) unsigned range Alignment start position in target
tEnd 17873int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 100,64,1266,231,113,longblob   Size of each block
qStarts 0,100,164,1482,1713,longblob   Start of each block in query.
tStarts 227895831,227906237,2279098...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)
      ponAbe3.all_est.qName (via xenoRefSeqAli.qName)
      ponAbe3.all_mrna.qName (via xenoRefSeqAli.qName)
      ponAbe3.refGene.name (via xenoRefSeqAli.qName)
      ponAbe3.refSeqAli.qName (via xenoRefSeqAli.qName)
      ponAbe3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      ponAbe3.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58517383600152413958+-NM_001017434203501826chr12279137042141178735100,64,1266,231,113,0,100,164,1482,1713,227895831,227906237,227909897,227911215,227911450,
58524074400152413281+-NM_170725271202503chr12279137042141178735100,64,1943,231,113,0,100,164,2159,2390,227895831,227906237,227909220,227911215,227911450,
58523428500164413290+-NM_001258110249302491chr1227913704215117868595,64,1903,38,327,0,95,159,2062,2164,227895836,227906237,227909220,227911125,227911226,
5851711190000107407++NM_001193328176001730chr1227913704655757471211102,191,32,264,49,222,78,79,115,100,498,0,102,293,325,589,638,860,938,1017,1132,1232,65575,66369,66831,67190,68138,68747,69058,69235,70668,73950,74214,
58518832400152127230++NM_001350072198901959chr1227913704655757471213199,191,32,264,49,36,47,219,78,79,115,100,498,0,199,390,422,686,735,823,870,1089,1167,1246,1361,1461,65575,66369,66831,67190,68138,68278,68363,68750,69058,69235,70668,73950,74214,
58521492500152126963++NM_001350073225602226chr1227913704655757471213199,191,296,264,49,36,47,222,78,79,115,100,498,0,199,390,686,950,999,1087,1134,1356,1434,1513,1628,1728,65575,66369,66656,67190,68138,68278,68363,68747,69058,69235,70668,73950,74214,
58518862400152127227++NM_017865199201962chr1227913704655757471213199,191,32,264,49,36,47,222,78,79,115,100,498,0,199,390,422,686,735,823,870,1092,1170,1249,1364,1464,65575,66369,66831,67190,68138,68278,68363,68747,69058,69235,70668,73950,74214,
5851148217007332157534++NM_0010406861887881785chr122791370465669745681622,172,31,256,51,46,103,21,80,79,115,100,178,6,66,39,88,204,376,409,675,813,859,1019,1076,1156,1235,1350,1450,1628,1634,1746,65669,66388,66831,67191,68141,68364,68747,68919,69056,69235,70668,73950,74214,74395,74404,74529,
5851148217007394157534++NM_1829961949881847chr122791370465669745681622,172,31,256,51,46,103,21,80,79,115,100,178,6,66,39,88,266,438,471,737,875,921,1081,1138,1218,1297,1412,1512,1690,1696,1808,65669,66388,66831,67191,68141,68364,68747,68919,69056,69235,70668,73950,74214,74395,74404,74529,
58521012400253126822++NM_001136036220802178chr1227913704657657471214279,135,191,32,264,49,36,47,222,78,79,115,100,498,0,280,415,606,638,902,951,1039,1086,1308,1386,1465,1580,1680,65765,66044,66369,66831,67190,68138,68278,68363,68747,69058,69235,70668,73950,74214,

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