Schema for xenoRefSeqAli
  Database: dp3    Primary Table: xenoRefSeqAli    Row Count: 122,793   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 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 925int(10) unsigned range Number of bases that match that aren't repeats
misMatches 304int(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 2int(10) unsigned range Number of inserts in query
qBaseInsert 63int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 54int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_142637varchar(255) values Query sequence name
qSize 1582int(10) unsigned range Query sequence size
qStart 135int(10) unsigned range Alignment start position in query
qEnd 1427int(10) unsigned range Alignment end position in query
tName chr2varchar(255) values Target sequence name
tSize 30711475int(10) unsigned range Target sequence size
tStart 4682int(10) unsigned range Alignment start position in target
tEnd 5965int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 15,23,1191,longblob   Size of each block
qStarts 135,157,236,longblob   Start of each block in query.
tStarts 4682,4701,4774,longblob   Start of each block in target.

Connected Tables and Joining Fields
        dp3.all_est.qName (via xenoRefSeqAli.qName)
      dp3.all_mrna.qName (via xenoRefSeqAli.qName)
      dp3.xenoMrna.qName (via xenoRefSeqAli.qName)
      dp3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      dp3.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
58592530400263254++NM_14263715821351427chr23071147546825965315,23,1191,135,157,236,4682,4701,4774,
585153770024692469++NM_00103372613783111010chr230711475477754763150,11,69,311,491,941,4777,4963,5407,
5852992200022372237++NM_0011050361969133889chr230711475477755333147,246,126,133,484,763,4777,5128,5407,
6313762090023512516++NM_00137578628075741510chr4_group46604331611431561154163408,33,144,574,1306,1366,6114315,6115212,6115272,
6313762090023512516++NM_00137578527855521488chr4_group46604331611431561154163408,33,144,552,1284,1344,6114315,6115212,6115272,
61798663200113104126339+-NM_001112887848423487070chr4_group153025874271508427946513144,48,126,180,24,186,447,25,114,66,105,81,72,2348,2510,2876,3002,3221,4022,5522,6242,6350,6605,6692,6833,6998,1023122,1023284,1023662,1023856,1024072,1025130,1026763,1027498,1027677,1030474,1030634,1030772,1031007,
5851711020014831483++NM_1386541727144900chr230711475477755332147,126,144,774,4777,5407,
5852041090024552455++NM_0010141461734116884chr230711475477755453147,28,138,116,375,746,4777,5036,5407,
5854583070022642258++NM_00104671915383091338chr23071147548915914333,510,222,309,447,1116,4891,5023,5692,
585246186000000++NM_0012426831316461893chr230711475511355451432,461,5113,

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