Schema for xenoRefSeqAli
  Database: oviAri3    Primary Table: xenoRefSeqAli    Row Count: 226,920   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 450int(10) unsigned range Number of bases that match that aren't repeats
misMatches 96int(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 18int(10) unsigned range Number of 'N' bases
qNumInsert 3int(10) unsigned range Number of inserts in query
qBaseInsert 248int(10) unsigned range Number of bases inserted in query
tNumInsert 3int(10) unsigned range Number of inserts in target
tBaseInsert 7163int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001314097varchar(255) values Query sequence name
qSize 942int(10) unsigned range Query sequence size
qStart 17int(10) unsigned range Alignment start position in query
qEnd 829int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 275612895int(10) unsigned range Target sequence size
tStart 79896int(10) unsigned range Alignment start position in target
tEnd 87623int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 106,250,157,51,longblob   Size of each block
qStarts 17,231,489,778,longblob   Start of each block in query.
tStarts 79896,86211,86787,87572,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)
      oviAri3.all_est.qName (via xenoRefSeqAli.qName)
      oviAri3.all_mrna.qName (via xenoRefSeqAli.qName)
      oviAri3.refGene.name (via xenoRefSeqAli.qName)
      oviAri3.refSeqAli.qName (via xenoRefSeqAli.qName)
      oviAri3.xenoMrna.qName (via xenoRefSeqAli.qName)
      oviAri3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      oviAri3.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58545096018324837163++NM_00131409794217829chr127561289579896876234106,250,157,51,17,231,489,778,79896,86211,86787,87572,
5851410116018513187377++NM_001083506170301675chr127561289579903888241198,107,253,164,262,212,16,161,92,132,47,0,98,205,458,736,998,1222,1241,1402,1495,1628,79903,86099,86209,86780,87554,88151,88373,88390,88553,88645,88777,
585714148018872587894++NM_0012043791821331638chr127561289579906886801096,102,253,165,47,143,8,9,22,35,33,130,235,488,766,831,1080,1094,1106,1603,79906,86101,86209,86780,87554,87601,87871,87886,87899,88645,
58566849018111447029++NM_0012909228490849chr12756128957992587689576,107,253,164,135,0,76,183,436,714,79925,86099,86209,86780,87554,
585543120018516457091++NM_00114551014620845chr12756128957992587697677,84,252,166,42,60,0,79,180,434,732,785,79925,86102,86206,86778,87572,87637,
5854219300328231081++NM_001284136972106902chr12756128958610987704597,254,13,50,100,106,203,573,728,802,86109,86209,86903,87554,87604,
5854219200328231081++NM_0011143581023166961chr12756128958611087704596,254,13,50,100,166,262,632,787,861,86110,86209,86903,87554,87604,
7492777342002123313521554+-NM_0027165553135463chr1580923592214991492152382239129,91,101,235,144,156,115,71,135,174,61,155,141,94,31,47,72,61,72,57,21,23,36,199,41,35,11,30,15,54,63,96,63,42,17,18,78,63,72,13,142,233,334,571,715,871,986,1057,1192,1366,1427,1582,1723,1817,1851,1898,1970,2075,2181,2243,2264,2294,2362,2773,2818,2862,28 ...59399770,59400982,59401477,59404740,59405263,59409795,59410613,59411148,59411570,59412428,59415575,59419620,59420136,59420666,59 ...
585587205001723766+-NM_19936628465801444chr1275612895105664107222442,431,133,186,580,622,1053,1258,275505673,275506370,275506897,275507045,
58578912600225431963+-NM_2137781197281197chr1275612895105667108545524,129,427,140,195,28,249,378,805,1002,275504350,275505586,275506370,275506893,275507033,

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