Schema for xenoRefSeqAli
  Database: macFas5    Primary Table: xenoRefSeqAli    Row Count: 338,383   Data last updated: 2020-08-19
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 142int(10) unsigned range Number of bases that match that aren't repeats
misMatches 41int(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 87int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 85int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_129504varchar(255) values Query sequence name
qSize 795int(10) unsigned range Query sequence size
qStart 321int(10) unsigned range Alignment start position in query
qEnd 591int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 227556264int(10) unsigned range Target sequence size
tStart 8956int(10) unsigned range Alignment start position in target
tEnd 9224int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 144,18,21,longblob   Size of each block
qStarts 321,551,570,longblob   Start of each block in query.
tStarts 227547040,227547269,227547287,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)
      macFas5.all_est.qName (via xenoRefSeqAli.qName)
      macFas5.all_mrna.qName (via xenoRefSeqAli.qName)
      macFas5.refGene.name (via xenoRefSeqAli.qName)
      macFas5.refSeqAli.qName (via xenoRefSeqAli.qName)
      macFas5.xenoRefFlat.name (via xenoRefSeqAli.qName)
      macFas5.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5851424100287185+-NM_129504795321591chr1227556264895692243144,18,21,321,551,570,227547040,227547269,227547287,
58556732002838+-NR_027055177910991706chr12275562643081831425639,31,166,56,100,207,1099,1138,1169,1339,1399,1499,227524839,227524879,227524911,227525077,227525133,227525239,
58528914003172113+-NR_024530786428748chr12275562643100931425542,89,51,105,16,428,479,572,627,732,227524839,227524988,227525077,227525128,227525239,
58516927700260416586+-NM_001017434203501829chr122755626443598619536100,64,1227,42,220,116,0,100,164,1393,1493,1713,227494311,227507529,227510998,227512225,227512326,227512550,
2320213512300196121932+-NM_19831725671942548chr122755626422746499622746918613283,122,222,117,214,145,168,89,74,182,343,34,265,194,477,599,821,938,1152,1297,1465,1554,1628,1810,2249,2283,87078,87437,87657,88176,88523,88928,89228,89813,90000,90242,90561,90968,91003,
5852439800146315892+-NM_001258110249302493chr12275562644360961948495,64,1947,341,0,95,159,2152,227494316,227507529,227510321,227512314,
585379180000316424+-NM_00130242918860397chr122755626445133619544101,64,99,133,0,101,165,264,227494310,227507529,227510321,227510998,
10334275128004102467662++NM_00133019946162034616chr14130733371587511915882325629124,126,135,126,117,90,117,123,117,123,117,105,156,207,171,168,162,198,153,80,762,21,311,324,52,81,79,37,21,203,327,453,588,714,831,921,1038,1161,1278,1401,1518,1623,1779,1986,2157,2325,2487,2685,2838,2918,3680,3701,4013,4342,4394,4476, ...58751191,58761403,58765832,58770585,58773235,58774063,58779406,58780506,58784014,58786118,58786662,58789119,58791732,58792265,58 ...
12842637200055887159292629+-NM_00131912613916013854chr3192294377579020285819964067149,57,132,95,375,225,485,271,90,123,159,28,36,72,139,15,20,30,102,61,20,16,114,42,23,55,97,13,13,17,4,40,44,42,62,25,55,112,72, ...0,162,238,370,482,857,1082,1567,1838,2219,2346,2537,2585,2622,2712,2991,3021,3041,3130,3244,3794,3816,4140,4324,4366,4389,4467,4 ...134094737,134096296,134121205,134121819,134135149,134137036,134261385,134368592,134368865,134369040,134369253,134369443,13436948 ...
5851174248006303157613++NM_0010406861887601785chr12275562641062401152751633,172,32,256,51,34,105,76,80,79,115,100,178,6,66,39,60,204,376,409,675,825,859,964,1076,1156,1235,1350,1450,1628,1634,1746,106240,107003,107446,107806,108753,108991,109369,109486,109678,109857,111448,114661,114924,115105,115114,115236,

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