Schema for xenoRefSeqAli
  Database: danRer3    Primary Table: xenoRefSeqAli    Row Count: 569,447   Data last updated: 2020-08-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 73smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 530int(10) unsigned Number of bases that match that aren't repeats
misMatches 193int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 0int(10) unsigned Number of 'N' bases
qNumInsert 1int(10) unsigned Number of inserts in query
qBaseInsert 9int(10) unsigned Number of bases inserted in query
tNumInsert 2int(10) unsigned Number of inserts in target
tBaseInsert 122544int(10) unsigned Number of bases inserted in target
strand +-char(2) + or - for strand. First character query, second target (optional)
qName NM_001079844varchar(255) Query sequence name
qSize 6780int(10) unsigned Query sequence size
qStart 798int(10) unsigned Alignment start position in query
qEnd 1530int(10) unsigned Alignment end position in query
tName chr1varchar(255) Target sequence name
tSize 55805710int(10) unsigned Target sequence size
tStart 9149int(10) unsigned Alignment start position in target
tEnd 132416int(10) unsigned Alignment end position in target
blockCount 3int(10) unsigned Number of blocks in alignment
blockSizes 158,397,168,longblob Size of each block
qStarts 798,956,1362,longblob Start of each block in query.
tStarts 55673294,55767540,55796393,longblob Start of each block in target.

Connected Tables and Joining Fields
        danRer3.all_est.qName (via xenoRefSeqAli.qName)
      danRer3.all_mrna.qName (via xenoRefSeqAli.qName)
      danRer3.refGene.name (via xenoRefSeqAli.qName)
      danRer3.refSeqAli.qName (via xenoRefSeqAli.qName)
      danRer3.xenoMrna.qName (via xenoRefSeqAli.qName)
      danRer3.xenoRefGene.name (via xenoRefSeqAli.qName)
      hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
7353019300192122544+-NM_00107984467807981530chr15580571091491324163158,397,168,798,956,1362,55673294,55767540,55796393,
7351221100192122544+-NM_00113144433557551487chr15580571091491324163160,395,168,755,915,1319,55673294,55767542,55796393,
74112264680088681712160+-NM_00134735847177523314chr15580571020541315205551691878,99,2,172,93,111,105,117,93,138,4,92,90,156,103,149,11,81,752,1205,1304,1306,1499,1814,1952,2057,2174,2267,2405,2409,2501,2600,2765,2868,3048,3233,35250541,35253508,35253644,35253731,35254065,35254993,35257772,35258066,35258292,35258889,35259115,35261426,35261656,35261864,35 ...
7353019300192122544+-NM_01182167507981530chr15580571091491324163158,397,168,798,956,1362,55673294,55767540,55796393,
732651190033213122856+-NM_00107884830756381343chr1558057109176132416448,138,90,108,638,860,1064,1235,55673294,55767604,55767808,55796426,
733521550021982122733+-NM_0013032271792185890chr1558057109176132416348,351,108,185,359,782,55673294,55767556,55796426,
733501570021982122733+-NM_0013050603953156861chr1558057109176132416348,351,108,156,330,753,55673294,55767556,55796426,
7869352920029397386++NM_0014041446461366chr1469208573264226142643122710177,60,144,144,141,21,80,173,124,163,46,223,283,427,571,793,826,906,1079,1203,26422614,26422877,26424884,26425117,26427005,26428682,26428709,26428869,26429214,26431064,
7896093270042251082962++NM_06374317201821343chr84383497826752805268367031192,134,116,105,114,93,3,49,74,60,96,182,274,408,569,728,953,1046,1049,1098,1187,1247,26752805,26762469,26762762,26765873,26791810,26795949,26796115,26800247,26800428,26813035,26836607,
7856834000000+-NM_0010291652087887989chr84383497826229993262300951102,887,17604883,

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