Schema for xenoRefSeqAli
  Database: dm3    Primary Table: xenoRefSeqAli    Row Count: 56,731   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 1092int(10) unsigned range Number of bases that match that aren't repeats
misMatches 387int(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 1779int(10) unsigned range Number of bases inserted in query
tNumInsert 7int(10) unsigned range Number of inserts in target
tBaseInsert 11739int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001110269varchar(255) values Query sequence name
qSize 3674int(10) unsigned range Query sequence size
qStart 277int(10) unsigned range Alignment start position in query
qEnd 3535int(10) unsigned range Alignment end position in query
tName chr2Lvarchar(255) values Target sequence name
tSize 23011544int(10) unsigned range Target sequence size
tStart 26544int(10) unsigned range Alignment start position in target
tEnd 39762int(10) unsigned range Alignment end position in target
blockCount 8int(10) unsigned range Number of blocks in alignment
blockSizes 159,120,193,227,437,198,2,143,longblob   Size of each block
qStarts 277,637,2335,2528,2755,3192...longblob   Start of each block in query.
tStarts 22971782,22972813,22982619,...longblob   Start of each block in target.

Connected Tables and Joining Fields
        dm3.all_est.qName (via xenoRefSeqAli.qName)
      dm3.all_mrna.qName (via xenoRefSeqAli.qName)
      dm3.refGene.name (via xenoRefSeqAli.qName)
      dm3.refSeqAli.qName (via xenoRefSeqAli.qName)
      dm3.xenoMrna.qName (via xenoRefSeqAli.qName)
      dm3.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
58510923870021779711739+-NM_00111026936742773535chr2L2301154426544397628159,120,193,227,437,198,2,143,277,637,2335,2528,2755,3192,3390,3392,22971782,22972813,22982619,22983304,22984055,22984580,22984801,22984857,
58510923870021779711739+-NM_00111432736742773535chr2L2301154426544397628159,120,193,227,437,198,2,143,277,637,2335,2528,2755,3192,3390,3392,22971782,22972813,22982619,22983304,22984055,22984580,22984801,22984857,
73414265000000++NM_00116068842579286chrX2242282719537919195381261207,79,19537919,
58515499020083084103359++NM_00119157467597266261chr2L230115449577410158411213,108,90,297,255,711,123,174,177,144,159,726,969,1155,1701,4443,4698,5442,5571,5751,5928,6102,95774,96017,96182,96824,99468,99784,100577,100764,101017,101248,101425,
58515818760083069103353++NM_00119290667497026228chr2L230115449577410158411213,108,90,297,255,711,129,174,177,144,159,702,945,1131,1677,4416,4671,5403,5538,5718,5895,6069,95774,96017,96182,96824,99468,99784,100571,100764,101017,101248,101425,
5941908798003333910280++NM_13914454153013340chr2R211467081203772121675810209,187,69,197,196,705,489,243,167,244,301,510,697,766,963,1159,1894,2650,2929,3096,1203772,1207509,1207752,1207923,1213308,1213567,1214299,1215031,1215366,1216514,
63085739700002175+-NM_00127194825788682122chr3R2790505359538745955303384,805,365,868,952,1757,21949750,21949895,21950814,
87613116001123286+-NR_1206081916155885chr2R211467081533497915338994357,222,450,155,212,435,5807714,5810457,5811279,
5851327863009319293554++NM_00110899767977796161chr2L230115449583410157810168,90,351,12,252,711,123,168,162,153,779,980,1607,2212,4358,4613,5347,5477,5672,6008,95834,96035,96764,98124,99468,99784,100577,100764,101032,101425,
5851346925007302783473++NM_00119216663457506048chr2L23011544958341015789291,351,57,255,711,123,168,162,153,750,1578,4143,4236,4491,5235,5364,5559,5895,95834,96764,99381,99468,99784,100577,100764,101032,101425,

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