Schema for all_mrna
  Database: rn5    Primary Table: all_mrna    Row Count: 137,958   Data last updated: 2020-08-20
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 63int(10) unsigned range Number of bases that match that aren't repeats
misMatches 33int(10) unsigned range Number of bases that don't match
repMatches 1783int(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 35int(10) unsigned range Number of bases inserted in query
tNumInsert 5int(10) unsigned range Number of inserts in target
tBaseInsert 373473int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName AY539927varchar(255) values Query sequence name
qSize 1914int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1914int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 290094216int(10) unsigned range Target sequence size
tStart 297885int(10) unsigned range Alignment start position in target
tEnd 673237int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 64,802,208,318,295,192,longblob   Size of each block
qStarts 0,64,901,1109,1427,1722,longblob   Start of each block in query.
tStarts 297885,582420,583239,583652...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)
      rn5.all_est.qName (via all_mrna.qName)
      rn5.mgcFullMrna.qName (via all_mrna.qName)
      rn5.mgcGenes.name (via all_mrna.qName)
      rn5.mrnaOrientInfo.name (via all_mrna.qName)
      rn5.refGene.name (via all_mrna.qName)
      rn5.refSeqAli.qName (via all_mrna.qName)
      rn5.xenoMrna.qName (via all_mrna.qName)
      rn5.xenoRefGene.name (via all_mrna.qName)
      rn5.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
736333178301355373473-AY539927191401914chr1290094216297885673237664,802,208,318,295,192,0,64,901,1109,1427,1722,297885,582420,583239,583652,605671,673045,
7510674330901156331742-BC079076145901434chr1290094216281060431437658345,142,144,123,126,261,137,141,25,370,512,656,794,920,1181,1318,2810604,2811613,3140491,3141198,3141321,3141708,3143196,3143624,
606108130670425613826-FJ971664120301203chr1290094216281088228258861067,142,62,10,79,120,129,55,198,316,0,67,209,272,283,362,497,626,689,887,2810882,2811613,2812346,2812408,2812418,2813044,2813164,2813555,2813618,2825570,
606587190000212016-DQ0835436060606chr129009421628132642825886329,261,316,0,29,290,2813264,2813555,2825570,
609660037501111+AY389467119201036chr1290094216324360232446383272,16,747,0,273,289,3243602,3243874,3243891,
6112365000118830038-BC0884172427182401chr12900942163432542346494591388,168,217,86,121,105,32,105,143,26,1432,1600,1817,1903,2024,2129,2161,2266,3432542,3433955,3438406,3440237,3440910,3443978,3447045,3448470,3464802,
61111623003211130041-M26686165861192chr12900942163433706346491214165,6,51,45,100,23,217,86,121,105,32,105,69,40,466,631,637,706,753,854,877,1094,1180,1301,1406,1438,1543,1612,3433706,3433872,3433879,3433955,3434000,3434100,3438406,3440237,3440910,3443978,3447045,3448470,3464802,3464872,
611949200219830038-D114759700970chr1290094216343383434648231096,145,23,217,86,121,105,32,105,21,0,114,260,283,500,586,707,812,844,949,3433834,3433955,3434100,3438406,3440237,3440910,3443978,3447045,3448470,3464802,
61112850000078538+BC158756131201285chr1290094216346847434782978165,123,78,181,136,152,123,327,0,165,288,366,547,683,835,958,3468474,3468945,3470028,3470912,3473100,3474541,3475788,3477970,
611760112800000+FQ226937122101204chr12900942163506276350748011204,0,3506276,

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