Schema for refSeqAli
  Database: cavPor3    Primary Table: refSeqAli    Row Count: 491   Data last updated: 2018-03-31
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 696smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 2550int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1int(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 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 8604int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NM_001173111varchar(255) values Query sequence name
qSize 2570int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2551int(10) unsigned range Alignment end position in query
tName scaffold_0varchar(255) values Target sequence name
tSize 88675666int(10) unsigned range Target sequence size
tStart 14576619int(10) unsigned range Alignment start position in target
tEnd 14587774int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 275,103,204,150,1819,longblob   Size of each block
qStarts 0,275,378,582,732,longblob   Start of each block in query.
tStarts 14576619,14577021,14581983,...longblob   Start of each block in target.

Connected Tables and Joining Fields
        cavPor3.all_est.qName (via refSeqAli.qName)
      cavPor3.all_mrna.qName (via refSeqAli.qName)
      cavPor3.mrnaOrientInfo.name (via refSeqAli.qName)
      cavPor3.refFlat.name (via refSeqAli.qName)
      cavPor3.refGene.name (via refSeqAli.qName)
      cavPor3.xenoMrna.qName (via refSeqAli.qName)
      cavPor3.xenoRefGene.name (via refSeqAli.qName)
      cavPor3.xenoRefSeqAli.qName (via refSeqAli.qName)
      hgFixed.gbCdnaInfo.acc (via refSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via refSeqAli.qName)
      hgFixed.gbSeq.acc (via refSeqAli.qName)
      hgFixed.gbWarn.acc (via refSeqAli.qName)
      hgFixed.imageClone.acc (via refSeqAli.qName)
      hgFixed.refLink.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName)
      knownGeneV39.kgXref.refseq (via refSeqAli.qName)
      knownGeneV39.knownToRefSeq.value (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
69625501000048604+NM_001173111257002551scaffold_08867566614576619145877745275,103,204,150,1819,0,275,378,582,732,14576619,14577021,14581983,14583898,14585955,
80313820000067410-NM_001173075138201382scaffold_08867566628689230286980227681,156,63,93,119,198,72,0,681,837,900,993,1112,1310,28689230,28691253,28692304,28693383,28694835,28697058,28697950,
83365302700033399-NM_0011730926900680scaffold_08867566632608412326124914273,102,173,132,10,283,385,558,32608412,32609176,32609610,32612359,
111296000013762338377+NM_001198770333603336scaffold_088675666407345074077584424105,160,176,108,109,146,137,49,100,101,170,165,60,99,71,154,90,170,130,183,69,111,98,199,0,105,265,441,549,658,804,941,990,1090,1191,1361,1902,1962,2061,2132,2286,2376,2546,2676,2859,2928,3039,3137,40734507,40739735,40741713,40744532,40746303,40746591,40747437,40749805,40751312,40752053,40753131,40753384,40759071,40759634,40 ...
140167480012127158717-NM_001172731169401694scaffold_08867566671057244712176432031,39,55,159,205,177,161,142,149,401,6,15,4,2,6,20,6,3,11,90,0,32,72,127,286,491,668,829,971,1120,1522,1529,1545,1550,1553,1560,1581,1588,1592,1604,71057244,71057275,71057314,71059331,71060222,71072281,71081345,71148419,71190163,71217079,71217480,71217486,71217501,71217505,71 ...
18195710011429141+NM_001173087197001959scaffold_0886756668281748582848584658,133,171,167,1321,108,0,58,191,362,529,1851,82817485,82832982,82833897,82840515,82847155,82848476,
7931235918000051507+NM_001173399143301424scaffold_18113179027390978273939096117,136,84,465,343,279,0,117,253,337,802,1145,27390978,27391975,27392334,27392820,27393286,27393630,
7959842210003922+NM_001172938103501007scaffold_1811317902758517227587101491,124,84,708,0,91,215,299,27585172,27585390,27585617,27586393,
12116259003201215659-NM_0011730011702141668scaffold_1811317905123886151256154168,7,103,165,109,130,119,120,120,112,135,123,155,46,45,137,34,43,68,171,336,445,575,694,814,934,1046,1181,1304,1459,1505,1551,51238861,51238869,51238876,51242624,51243375,51245035,51247484,51248082,51248317,51250304,51251108,51253139,51254523,51255791,51 ...
100413410000000-NM_001173414134101341scaffold_181131790550100335501137411341,0,55010033,

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