Schema for xenoRefSeqAli
  Database: ponAbe2    Primary Table: xenoRefSeqAli    Row Count: 353,597   Data last updated: 2020-08-22
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 1133int(10) unsigned range Number of bases that match that aren't repeats
misMatches 60int(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 11int(10) unsigned range Number of inserts in query
qBaseInsert 3217int(10) unsigned range Number of bases inserted in query
tNumInsert 7int(10) unsigned range Number of inserts in target
tBaseInsert 16231int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NR_003572varchar(255) values Query sequence name
qSize 5811int(10) unsigned range Query sequence size
qStart 245int(10) unsigned range Alignment start position in query
qEnd 4655int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 229942017int(10) unsigned range Target sequence size
tStart 14706int(10) unsigned range Alignment start position in target
tEnd 32130int(10) unsigned range Alignment end position in target
blockCount 13int(10) unsigned range Number of blocks in alignment
blockSizes 15,51,44,26,206,20,30,147,1...longblob   Size of each block
qStarts 245,291,347,392,419,626,646...longblob   Start of each block in query.
tStarts 229909887,229911076,2299111...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)
      ponAbe2.all_est.qName (via xenoRefSeqAli.qName)
      ponAbe2.all_mrna.qName (via xenoRefSeqAli.qName)
      ponAbe2.refGene.name (via xenoRefSeqAli.qName)
      ponAbe2.refSeqAli.qName (via xenoRefSeqAli.qName)
      ponAbe2.xenoMrna.qName (via xenoRefSeqAli.qName)
      ponAbe2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      ponAbe2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58511336000113217716231+-NR_00357258112454655chr122994201714706321301315,51,44,26,206,20,30,147,147,39,82,165,221,245,291,347,392,419,626,646,677,826,3047,3198,3282,4434,229909887,229911076,229911127,229911171,229923261,229923467,229923490,229923522,229923669,229925756,229925907,229925989,22992709 ...
58517303400259415450+-NM_001017434203501823chr122994201749527667416100,64,1266,100,124,110,0,100,164,1487,1589,1713,229875276,229885699,229890829,229892152,229892252,229892380,
59055801640239772158373++NM_001317836605705844chr419833221869270775684730139,39,141,52,44,118,97,56,82,28,89,138,81,413,282,557,26,818,174,165,381,725,124,22,72,415,226,183,44,36,0,139,178,319,374,418,536,633,689,772,800,889,1027,1108,1523,1807,2367,2394,3212,3386,3551,3932,4657,4782,4805,4877,5292,5518,57 ...692707,717898,718238,719755,719807,720981,722244,724581,731390,731472,732536,747279,751027,752066,752479,752761,753318,753344,75 ...
58591414800213195523++NM_00102449618115941787chr12299420171172631238481024,47,219,78,79,115,100,193,120,87,594,663,710,929,1007,1086,1201,1301,1494,1700,117263,117341,117728,118036,118213,119646,123071,123335,123531,123761,
5856138000346975556++NM_00112627215631781340chr1229942017117342123591870,30,80,79,115,100,177,42,178,650,716,796,875,990,1090,1298,117342,117888,118034,118213,119646,123071,123335,123549,
58563010000324295617++NM_00104068618878131785chr12299420171173421236891046,21,80,79,115,100,178,6,66,39,813,1019,1076,1156,1235,1350,1450,1628,1634,1746,117342,117897,118034,118213,119646,123071,123335,123516,123525,123650,
58563010000324295617++NM_18299619498751847chr12299420171173421236891046,21,80,79,115,100,178,6,66,39,875,1081,1138,1218,1297,1412,1512,1690,1696,1808,117342,117897,118034,118213,119646,123071,123335,123516,123525,123650,
58520772001623480++NM_001123276176812641549chr12299420171196401233993120,95,64,1264,1390,1485,119640,123076,123335,
58591226400266260+-NM_00100766929475481790chr12299420171253021265383429,66,681,548,1013,1109,229815479,229815935,229816034,
58591524900278272+-NM_00125652028214751717chr12299420171253021265383417,66,681,475,940,1036,229815479,229815935,229816034,

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