Schema for all_mrna
  Database: galGal3    Primary Table: all_mrna    Row Count: 31,497   Data last updated: 2020-08-21
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 753int(10) unsigned range Number of bases that match that aren't repeats
misMatches 34int(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 9994int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName CR385728varchar(255) values Query sequence name
qSize 879int(10) unsigned range Query sequence size
qStart 2int(10) unsigned range Alignment start position in query
qEnd 789int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 200994015int(10) unsigned range Target sequence size
tStart 10132int(10) unsigned range Alignment start position in target
tEnd 20913int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 77,102,182,107,319,longblob   Size of each block
qStarts 2,79,181,363,470,longblob   Start of each block in query.
tStarts 10132,19704,20014,20398,20594,longblob   Start of each block in target.

Connected Tables and Joining Fields
        galGal3.all_est.qName (via all_mrna.qName)
      galGal3.mrnaOrientInfo.name (via all_mrna.qName)
      galGal3.refGene.name (via all_mrna.qName)
      galGal3.refSeqAli.qName (via all_mrna.qName)
      galGal3.xenoMrna.qName (via all_mrna.qName)
      galGal3.xenoRefGene.name (via all_mrna.qName)
      galGal3.xenoRefSeqAli.qName (via all_mrna.qName)
      hgFixed.gbCdnaInfo.acc (via all_mrna.qName)
      hgFixed.gbMiscDiff.acc (via all_mrna.qName)
      hgFixed.gbSeq.acc (via all_mrna.qName)
      hgFixed.gbWarn.acc (via all_mrna.qName)
      hgFixed.imageClone.acc (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58575334000049994+CR3857288792789chr12009940151013220913577,102,182,107,319,2,79,181,363,470,10132,19704,20014,20398,20594,
585866430052756198+DQ15649597135971chr120099401513751208581020,258,102,183,83,169,35,28,25,6,35,56,314,416,622,705,874,910,939,965,13751,13771,19704,20014,20422,20594,20764,20799,20827,20852,
5857131000044149+CR35248075942756chr120099401533903387665119,103,153,153,186,42,161,264,417,570,33903,35202,36124,36998,38580,
5852271122770001411835+AJ719284258602560chr120099401569103834981566,84,74,130,111,55,111,111,56,70,134,108,295,72,1083,0,66,150,224,354,465,520,631,742,798,868,1002,1110,1405,1477,69103,71455,74888,75090,76085,76779,78425,78670,79071,79620,79900,80553,81033,81976,82415,
5858300000041510+BX9297888311831chr120099401596610989505433,161,40,103,93,1,434,595,635,738,96610,97268,97813,98662,98857,
5858400000041510-CR7328728400840chr120099401596611989615432,161,40,103,104,0,432,593,633,736,96611,97268,97813,98662,98857,
58510036200072888+BX930967102091020chr1200994015990641029638121,30,80,80,112,98,84,406,9,130,160,240,320,432,530,614,99064,99261,99396,100433,101290,101859,102191,102557,
58510035200072888+BX933167101001010chr1200994015990651029638120,30,80,80,112,98,84,406,0,120,150,230,310,422,520,604,99065,99261,99396,100433,101290,101859,102191,102557,
5851083000003973+BX950545108301083chr12009940151009071029634495,98,84,406,0,495,593,677,100907,101859,102191,102557,
588926800287104791-BX931736102101021chr12009940154010484067731146,66,115,110,93,155,80,72,76,56,65,0,126,199,314,424,517,672,752,824,900,956,401048,401612,401685,401882,402229,402672,403200,403392,404382,406211,406708,

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