Schema for xenoRefSeqAli
  Database: cb3    Primary Table: xenoRefSeqAli    Row Count: 131,831   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 644smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 964int(10) unsigned range Number of bases that match that aren't repeats
misMatches 251int(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 3int(10) unsigned range Number of inserts in query
qBaseInsert 760int(10) unsigned range Number of bases inserted in query
tNumInsert 8int(10) unsigned range Number of inserts in target
tBaseInsert 1545int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001269304varchar(255) values Query sequence name
qSize 2295int(10) unsigned range Query sequence size
qStart 82int(10) unsigned range Alignment start position in query
qEnd 2057int(10) unsigned range Alignment end position in query
tName chrVvarchar(255) values Target sequence name
tSize 16004101int(10) unsigned range Target sequence size
tStart 7844850int(10) unsigned range Alignment start position in target
tEnd 7847610int(10) unsigned range Alignment end position in target
blockCount 9int(10) unsigned range Number of blocks in alignment
blockSizes 114,171,45,438,68,82,2,97,198,longblob   Size of each block
qStarts 82,196,370,415,868,936,1018...longblob   Start of each block in query.
tStarts 7844850,7845034,7845207,784...longblob   Start of each block in target.

Connected Tables and Joining Fields
        cb3.all_est.qName (via xenoRefSeqAli.qName)
      cb3.all_mrna.qName (via xenoRefSeqAli.qName)
      cb3.xenoMrna.qName (via xenoRefSeqAli.qName)
      cb3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      cb3.xenoRefGene.name (via xenoRefSeqAli.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
64496425100376081545++NM_0012693042295822057chrV16004101784485078476109114,171,45,438,68,82,2,97,198,82,196,370,415,868,936,1018,1020,1859,7844850,7845034,7845207,7845294,7845793,7845907,7846056,7846178,7847412,
64498025400491471526++NM_001269305237762154chrV16004101784485078476108114,171,45,438,68,85,115,198,6,120,294,339,792,860,1099,1956,7844850,7845034,7845207,7845294,7845793,7845907,7846160,7847412,
6151044186003149107474+-NM_05959215631031482chrUn7311690401747240261761130,20,70,163,186,158,86,250,166,80,21,103,133,269,339,502,688,846,932,1182,1349,1461,3285514,3285546,3285696,3288842,3289514,3289821,3290058,3290946,3291976,3294104,3294197,
7383900005225316+-NM_001081111678136053697chrI1127484317833243241615,9,19,15,4,30,3605,3620,3629,3648,3663,3667,11031602,11036438,11036625,11255971,11256037,11256980,
5858926001453358251+-NM_011448414626913259chrI112748431885677222433,53,14,15,2691,3177,3230,3244,11197621,11235970,11255722,11255972,
5856129000000++NM_053011147431145311543chrI112748431904119131190,11453,19041,
662894231000032315++NM_001277083337020853210chrX206080321013364210137082451,735,177,162,2085,2136,2871,3048,10133642,10135904,10136692,10136920,
67937418400124269+-NM_0013669771473294876chrIV1529027412360170123607973228,115,215,294,546,661,2929477,2929729,2929889,
5991513297006165123095+-NM_0013828882190302005chrI_random3509021185835918632641442,20,95,98,165,207,135,492,348,144,22,6,6,30,30,79,122,217,315,480,687,831,1323,1671,1932,1955,1961,1975,1645757,1645809,1646057,1646751,1648523,1649056,1649312,1649471,1650009,1650402,1650584,1650606,1650613,1650632,
62040022400446543030++NM_00136722422304971586chrII14512975469835647020105264,78,138,57,87,497,797,1019,1388,1499,4698356,4698656,4701422,4701809,4701923,

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