Schema for all_mrna
  Database: rn4    Primary Table: all_mrna    Row Count: 84,977   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 594smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 589int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(10) unsigned range Number of bases that don't match
repMatches 402int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 1int(10) unsigned range Number of inserts in query
qBaseInsert 1int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 1int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName AY389467varchar(255) values Query sequence name
qSize 1192int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 992int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 267910886int(10) unsigned range Target sequence size
tStart 1306645int(10) unsigned range Alignment start position in target
tEnd 1307637int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 272,16,703,longblob   Size of each block
qStarts 0,273,289,longblob   Start of each block in query.
tStarts 1306645,1306917,1306934,longblob   Start of each block in target.

Connected Tables and Joining Fields
        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)
      rn4.all_est.qName (via all_mrna.qName)
      rn4.mgcFullMrna.qName (via all_mrna.qName)
      rn4.mgcGenes.name (via all_mrna.qName)
      rn4.mrnaOrientInfo.name (via all_mrna.qName)
      rn4.mrnaRefseq.mrna (via all_mrna.qName)
      rn4.refGene.name (via all_mrna.qName)
      rn4.refSeqAli.qName (via all_mrna.qName)
      rn4.xenoMrna.qName (via all_mrna.qName)
      rn4.xenoRefGene.name (via all_mrna.qName)
      rn4.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
594589040201111+AY38946711920992chr1267910886130664513076373272,16,703,0,273,289,1306645,1306917,1306934,
595588180000273377-DQ0835436060606chr126791088613453511419334329,261,316,0,29,290,1345351,1345642,1419018,
5951083211800053955-FJ971664120301203chr126791088614141761419334667,142,153,264,261,316,0,67,209,362,626,887,1414176,1414894,1415621,1416333,1416859,1419018,
599591150000217902-DQ0835436060606chr126791088619451531963661329,261,316,0,29,290,1945153,1961231,1963345,
6011074036000063541-BC079076145901434chr1267910886215061821555937345,142,144,264,261,134,144,25,370,512,656,920,1181,1315,2150618,2151622,2152351,2153061,2153587,2155023,2155449,
602224000000614418-BC08841724271612401chr12679108862287980230463871574,217,86,121,105,32,105,26,1600,1817,1903,2024,2129,2161,2287980,2293836,2295667,2296340,2300387,2303332,2304533,
602107220023814420-M2668616581151192chr12679108862289144230463811165,6,114,100,23,217,86,121,105,32,105,466,631,637,753,854,877,1094,1180,1301,1406,1438,2289144,2289310,2289317,2289431,2289531,2293836,2295667,2296340,2300387,2303332,2304533,
60294620011614418-D1147597021970chr1267910886228927223046388259,23,217,86,121,105,32,105,0,260,283,500,586,707,812,844,2289272,2289531,2293836,2295667,2296340,2300387,2303332,2304533,
603760112800000+FQ226937122101204chr12679108862378352237955611204,0,2378352,
6031833000001039793+BC097929188801833chr12679108862394946243657211183,175,158,181,122,106,159,127,135,127,360,0,183,358,516,697,819,925,1084,1211,1346,1473,2394946,2410228,2412554,2415185,2420857,2423588,2424823,2433080,2434115,2434623,2436212,

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