Schema for xenoRefSeqAli
  Database: mm39    Primary Table: xenoRefSeqAli    Row Count: 197,343   Data last updated: 2020-08-17
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 76smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 5144int(10) unsigned range Number of bases that match that aren't repeats
misMatches 671int(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 81int(10) unsigned range Number of inserts in query
qBaseInsert 14396int(10) unsigned range Number of bases inserted in query
tNumInsert 72int(10) unsigned range Number of inserts in target
tBaseInsert 466133int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_052898varchar(255) values Query sequence name
qSize 20241int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 20211int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 195154279int(10) unsigned range Target sequence size
tStart 3270069int(10) unsigned range Alignment start position in target
tEnd 3742017int(10) unsigned range Alignment end position in target
blockCount 88int(10) unsigned range Number of blocks in alignment
blockSizes 322,327,280,112,104,200,961...longblob   Size of each block
qStarts 0,347,722,1005,1163,1267,14...longblob   Start of each block in query.
tStarts 191412262,191412594,1914129...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)
      mm39.all_est.qName (via xenoRefSeqAli.qName)
      mm39.all_mrna.qName (via xenoRefSeqAli.qName)
      mm39.refGene.name (via xenoRefSeqAli.qName)
      mm39.refSeqAli.qName (via xenoRefSeqAli.qName)
      mm39.xenoMrna.qName (via xenoRefSeqAli.qName)
      mm39.xenoRefFlat.name (via xenoRefSeqAli.qName)
      mm39.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
76514467100811439672466133+-NM_05289820241020211chr11951542793270069374201788322,327,280,112,104,200,961,73,16,19,60,69,46,12,9,14,43,47,41,136,109,57,64,48,25,49,50,29,13,53,6,11,32,6,11,59,20,5,8,12,8,10 ...0,347,722,1005,1163,1267,1467,2437,2835,2852,3034,3102,3179,3351,3364,3544,3570,3697,3747,3789,3926,4036,4107,4171,4223,4249,445 ...191412262,191412594,191412963,191413243,191413401,191662155,191867088,191868049,191868603,191868619,191868761,191868830,19186890 ...
763073242001538215454619+-NM_0010119713727143711chr11951542793284702374263622186,17,54,129,58,76,266,104,200,1046,82,82,63,24,118,34,45,97,52,123,262,197,14,200,220,280,410,468,544,856,960,1160,2217,2316,2401,2479,2740,2871,2905,2951,3054,3108,3248,3514,191411643,191411830,191411847,191411908,191412037,191412100,191413089,191413401,191662155,191867088,191868134,191868218,19186830 ...
7618631780041064453471+-NM_001033036234322149chr1195154279328615737416697311,280,112,104,200,961,73,2,361,644,802,906,1106,2076,191412610,191412963,191413243,191413401,191662155,191867088,191868049,
7611793700053638453834+-NM_0010122582209581970chr119515427932861883741571939,69,259,27,88,195,569,282,21,58,97,226,571,661,749,944,1615,1949,191412708,191412750,191412975,191413323,191413422,191662160,191867088,191867753,191868070,
768593060043327454165+-NM_0010327141804381535chr119515427932862443741574842,69,274,27,77,202,213,261,38,80,215,566,656,733,935,1274,191412705,191412750,191412969,191413323,191413428,191662155,191867444,191867774,
7613853200031536453626+-NM_00103230729931111969chr119515427932862443741575742,85,280,51,100,200,947,111,153,319,640,722,822,1022,191412704,191412749,191412954,191413299,191413405,191662155,191867088,
6133651100032094320+-NM_00107775296684768chr119515427937407763741571539,69,259,27,81,84,123,252,597,687,191412708,191412750,191412975,191413323,191413422,
9320064800826530349421+-NM_00137565455921364249chr1195154279406979144230603253,364,179,176,161,84,3,133,152,79,76,73,27,130,95,152,216,178,56,174,87,135,150,155,59,45,164,189,157,79,16,51,136,192,583,762,938,1099,1183,1186,1319,1471,1550,1626,1708,1735,1865,1990,2142,2359,2537,2695,2869,2956,3091,3241,3396,3455,350 ...190731219,190731272,190731675,190731974,190772626,190791044,190791202,190799158,190816436,190822451,190838950,190840437,19084061 ...
6186019696009233159484+-NM_001195676699106948chr11951542794414416443061520145,46,636,172,11,214,123,813,1222,477,19,253,927,1067,211,87,158,28,64,42,0,145,191,827,999,1010,1224,1355,2168,3390,3886,4049,4305,5247,6314,6525,6613,6775,6836,6906,190723664,190723811,190731219,190731975,190733965,190733982,190734199,190734327,190735143,190736368,190736849,190736988,19073724 ...
618348790200252011253832+-NM_001280013646106400chr1195154279441482744230483043,370,179,186,249,105,99,36,66,192,10,29,9,102,4,10,35,108,314,28,599,51,118,78,57,97,315,738,36,126,0,46,429,608,850,1191,1329,1437,1476,1560,1882,1930,1960,2125,2228,2232,2254,2370,2527,2898,2998,3897,3955,4293,4371,4568,4665,5 ...190731231,190731274,190731675,190731974,190734028,190734360,190734492,190734591,190734627,190734702,190734941,190735057,19073516 ...

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