Schema for xenoRefSeqAli
  Database: rheMac10    Primary Table: xenoRefSeqAli    Row Count: 234,551   Data last updated: 2019-07-17
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 1681int(10) unsigned range Number of bases that match that aren't repeats
misMatches 79int(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 62int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 16483int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001017434varchar(255) values Query sequence name
qSize 2035int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1822int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 223616942int(10) unsigned range Target sequence size
tStart 8426int(10) unsigned range Alignment start position in target
tEnd 26669int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 100,64,1228,39,220,109,longblob   Size of each block
qStarts 0,100,164,1394,1493,1713,longblob   Start of each block in query.
tStarts 223590273,223603388,2236068...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)
      rheMac10.all_est.qName (via xenoRefSeqAli.qName)
      rheMac10.all_mrna.qName (via xenoRefSeqAli.qName)
      rheMac10.refGene.name (via xenoRefSeqAli.qName)
      rheMac10.refSeqAli.qName (via xenoRefSeqAli.qName)
      rheMac10.xenoRefFlat.name (via xenoRefSeqAli.qName)
      rheMac10.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58516817900262416483+-NM_001017434203501822chr12236169428426266696100,64,1228,39,220,109,0,100,164,1394,1493,1713,223590273,223603388,223606856,223608084,223608183,223608407,
58523519400262415806+-NM_170725271702507chr12236169428426266776108,64,1905,39,220,109,0,108,172,2079,2178,2398,223590265,223603388,223606179,223608084,223608183,223608407,
585999152006417117704++NM_0010406861887601628chr122361694271624804791233,172,32,256,51,34,21,80,79,115,100,178,60,204,376,409,675,825,1019,1076,1156,1235,1350,1450,71624,72386,72829,73189,74136,74374,74924,75061,75240,76825,80038,80301,
585999152006479117704++NM_1829961949601690chr122361694271624804791233,172,32,256,51,34,21,80,79,115,100,178,60,266,438,471,737,887,1081,1138,1218,1297,1412,1512,71624,72386,72829,73189,74136,74374,74924,75061,75240,76825,80038,80301,
5851188180004164126851++NM_0010244961811831615chr1223616942723998061813159,32,187,30,24,31,219,78,79,115,100,193,121,83,242,274,511,594,678,710,929,1007,1086,1201,1301,1494,72399,72829,73188,73425,74280,74376,74755,75063,75240,76825,80038,80301,80497,
5854589800173157394++NM_00109935616871541441chr122361694272415803656145,50,80,117,100,64,154,1030,1080,1160,1277,1377,72415,75088,75237,76823,80038,80301,
58535212800387347557++NM_00112327617682921645chr122361694272427804645126,120,95,64,75,292,1264,1390,1485,1570,72427,76819,80043,80301,80389,
5856058600254565654++NM_0011262721563281264chr12236169427413080475757,86,80,79,115,100,174,28,190,716,796,875,990,1090,74130,74374,75061,75240,76825,80038,80301,
58528851340071687418+-NM_024836304503035chr1223616942812689170515278,49,154,41,56,31,26,1561,141,78,110,154,105,199,36,0,279,328,482,523,579,610,637,2199,2341,2425,2535,2693,2800,2999,223525237,223525515,223530657,223531740,223531782,223533223,223533255,223533281,223534842,223534983,223535064,223535177,22353533 ...
58592325500270264+-NM_00125651629505981846chr122361694282224834663431,66,681,598,1069,1165,223533476,223533938,223534037,

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