Schema for xenoRefSeqAli
  Database: mm9    Primary Table: xenoRefSeqAli    Row Count: 193,733   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 1232smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1167int(10) unsigned range Number of bases that match that aren't repeats
misMatches 202int(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 1int(10) unsigned range Number of inserts in query
qBaseInsert 1int(10) unsigned range Number of bases inserted in query
tNumInsert 13int(10) unsigned range Number of inserts in target
tBaseInsert 10996int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_015604varchar(255) values Query sequence name
qSize 2474int(10) unsigned range Query sequence size
qStart 211int(10) unsigned range Alignment start position in query
qEnd 1581int(10) unsigned range Alignment end position in query
tName chr12varchar(255) values Target sequence name
tSize 121257530int(10) unsigned range Target sequence size
tStart 84870148int(10) unsigned range Alignment start position in target
tEnd 84882513int(10) unsigned range Alignment end position in target
blockCount 14int(10) unsigned range Number of blocks in alignment
blockSizes 70,158,79,100,2,145,50,77,1...longblob   Size of each block
qStarts 211,281,439,519,619,621,766...longblob   Start of each block in query.
tStarts 84870148,84870926,84871776,...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)
      mm9.all_est.qName (via xenoRefSeqAli.qName)
      mm9.all_mrna.qName (via xenoRefSeqAli.qName)
      mm9.refGene.name (via xenoRefSeqAli.qName)
      mm9.refSeqAli.qName (via xenoRefSeqAli.qName)
      mm9.xenoMrna.qName (via xenoRefSeqAli.qName)
      mm9.xenoRefFlat.name (via xenoRefSeqAli.qName)
      mm9.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
1232116720200111310996++NM_01560424742111581chr1212125753084870148848825131470,158,79,100,2,145,50,77,102,96,3,173,115,199,211,281,439,519,619,621,766,816,893,995,1091,1094,1267,1382,84870148,84870926,84871776,84873228,84873346,84874815,84875809,84876849,84878662,84878893,84879370,84880258,84880738,84882314,
763139240001431813454555+-NM_0010119713727143711chr11971954323204560366249422186,17,54,134,53,76,416,200,1046,82,81,64,24,119,34,45,95,56,106,32,262,197,14,200,220,280,415,468,544,960,1160,2217,2316,2400,2479,2740,2871,2905,2951,3050,3108,3214,3248,3514,193532938,193533125,193533142,193533203,193533337,193533395,193534384,193783450,193988383,193989429,193989513,193989596,19398967 ...
7617731730031473453512+-NM_0010330362343602153chr1197195432320601136614696179,267,262,200,961,77,60,374,644,906,1106,2076,193533963,193534271,193534538,193783450,193988383,193989344,
7611663640043097453797+-NM_0010122582209581897chr119719543232061023661429839,69,243,45,88,195,569,282,58,97,241,571,661,749,944,1615,193534003,193534045,193534285,193534618,193534717,193783455,193988383,193989048,
7613863240021476453620+-NM_00103230729931121969chr119719543232061023661432741,85,255,59,123,200,947,112,153,344,640,699,822,1022,193534000,193534044,193534274,193534594,193534677,193783450,193988383,
768692960053328454165+-NM_0010327141804381535chr119719543232061023661432942,69,258,34,9,77,202,213,261,38,80,231,572,614,656,733,935,1274,193534000,193534045,193534280,193534624,193534672,193534723,193783450,193988739,193989069,
6123711060032074318+-NM_00107775296684768chr119719543236606343661429539,69,243,45,81,84,123,267,597,687,193534003,193534045,193534285,193534618,193534717,
6185982704008293159552+-NM_001195676699106979chr11971954324334235435047318145,46,636,172,11,214,123,813,1222,477,108,257,927,1067,215,160,63,30,0,145,191,827,999,1010,1224,1355,2168,3390,3887,4045,4305,5247,6314,6613,6836,6949,192844959,192845106,192852514,192853270,192855260,192855277,192855494,192855622,192856438,192857663,192858145,192858279,19285853 ...
618270278400202832184740+-NM_173958631806318chr1197195432433468043429062333,384,178,173,308,99,23,4,57,120,73,5,163,33,246,348,78,54,261,84,623,36,103,0,48,432,610,853,1335,1443,1467,1482,1545,1936,2010,2018,2209,2971,3255,4215,4296,4476,4770,5197,6132,6215,192852526,192852571,192852970,192853268,192855323,192855787,192855886,192855909,192855922,192855979,192856355,192856435,19285644 ...
618335888100192114203938+-NM_0012800136461466399chr11971954324334686434286322363,179,186,249,105,99,23,66,192,123,96,314,599,69,108,78,57,93,315,738,66,121,46,429,608,850,1191,1329,1437,1476,1560,1923,2244,2527,2998,3943,4029,4293,4371,4568,4665,5148,6186,6278,192852569,192852970,192853269,192855323,192855655,192855787,192855886,192855922,192855997,192856345,192856660,192856943,19285742 ...

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