Schema for xenoRefSeqAli
  Database: ci3    Primary Table: xenoRefSeqAli    Row Count: 84,144   Data last updated: 2017-04-25
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 1781int(10) unsigned range Number of bases that match that aren't repeats
misMatches 832int(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 17int(10) unsigned range Number of 'N' bases
qNumInsert 15int(10) unsigned range Number of inserts in query
qBaseInsert 2113int(10) unsigned range Number of bases inserted in query
tNumInsert 24int(10) unsigned range Number of inserts in target
tBaseInsert 15887int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001102430varchar(255) values Query sequence name
qSize 7042int(10) unsigned range Query sequence size
qStart 632int(10) unsigned range Alignment start position in query
qEnd 5375int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 10041005int(10) unsigned range Target sequence size
tStart 38483int(10) unsigned range Alignment start position in target
tEnd 57000int(10) unsigned range Alignment end position in target
blockCount 25int(10) unsigned range Number of blocks in alignment
blockSizes 117,66,36,61,98,132,3,192,1...longblob   Size of each block
qStarts 632,749,1409,1445,1506,1613...longblob   Start of each block in query.
tStarts 9984005,9984612,9988213,998...longblob   Start of each block in target.

Connected Tables and Joining Fields
        ci3.all_est.qName (via xenoRefSeqAli.qName)
      ci3.all_mrna.qName (via xenoRefSeqAli.qName)
      ci3.refGene.name (via xenoRefSeqAli.qName)
      ci3.refSeqAli.qName (via xenoRefSeqAli.qName)
      ci3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      ci3.xenoRefGene.name (via xenoRefSeqAli.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58517818320171521132415887+-NM_00110243070426325375chr110041005384835700025117,66,36,61,98,132,3,192,162,74,142,108,169,56,99,141,219,111,11,60,171,165,81,76,80,632,749,1409,1445,1506,1613,1745,1748,2441,2612,2686,2906,3134,3303,3485,3590,3740,3959,4124,4169,4292,4469,4646,5219,5295,9984005,9984612,9988213,9988478,9989003,9989652,9989785,9990128,9992668,9993295,9994038,9994703,9996021,9996642,9996963,9997330, ...
58517568430171421272315901+-NM_00127705669456125355chr110041005384835700024117,66,36,61,98,132,3,192,162,74,142,108,169,56,99,141,219,108,60,171,165,81,76,80,612,729,1389,1425,1486,1593,1725,1728,2421,2592,2666,2886,3114,3283,3465,3570,3720,3939,4149,4272,4449,4626,5199,5275,9984005,9984612,9988213,9988478,9989003,9989652,9989785,9990128,9992668,9993295,9994038,9994703,9996021,9996642,9996963,9997330, ...
58516387600171523281916986+-NM_00108549587774165159chr110041005384835788420141,112,65,42,132,192,168,75,141,108,160,56,90,141,228,60,177,165,81,81,416,557,669,1250,1454,1589,2258,2435,2510,2729,2966,3126,3323,3419,3569,3998,4115,4298,4475,5078,9983121,9984008,9984610,9988213,9989652,9990128,9992662,9993295,9994039,9994703,9996030,9996642,9996972,9997330,9997762,9998993, ...
615202860011711904+-NM_00119318415647071166chr96586237398074739819392102,186,707,980,2604298,2605304,
5851589101821112562++NM_001320383875227605chrUn_NW_004190345v1979753889339722354,78,135,227,284,470,38893,39113,39587,
58516747640171622672116946+-NM_00642090044345156chr110041005384835788422141,112,65,42,12,132,192,168,74,142,108,160,56,90,141,219,37,60,177,165,81,81,434,575,687,1247,1342,1451,1586,2255,2432,2506,2726,2963,3123,3320,3416,3566,3785,3995,4112,4295,4472,5075,9983121,9984008,9984610,9988213,9989001,9989652,9990128,9992662,9993295,9994038,9994703,9996030,9996642,9996972,9997330,9997762, ...
58518588940171521212516632+-NM_17399770164755365chr110041005384835788426141,114,66,36,61,98,132,3,192,163,74,142,108,169,56,99,141,219,111,11,60,171,165,81,76,80,475,616,730,1399,1435,1496,1603,1735,1738,2431,2602,2676,2896,3124,3293,3475,3580,3730,3949,4114,4159,4282,4459,4636,5209,5285,9983121,9984008,9984612,9988213,9988478,9989003,9989652,9989785,9990128,9992668,9993295,9994038,9994703,9996021,9996642,9996963, ...
58516267720171523281916986+-NM_18108357842825025chr110041005384835788420141,112,65,42,132,192,168,75,141,108,160,56,90,141,228,60,177,165,81,81,282,423,535,1116,1320,1455,2124,2301,2376,2595,2832,2992,3189,3285,3435,3864,3981,4164,4341,4944,9983121,9984008,9984610,9988213,9989652,9990128,9992662,9993295,9994039,9994703,9996030,9996642,9996972,9997330,9997762,9998993, ...
58519329300171623172618320+-NM_00126104670943245520chr110041005384835968227111,141,114,66,36,61,98,132,3,192,162,74,142,108,169,56,99,141,219,111,11,60,171,165,81,76,80,324,630,771,885,1554,1590,1651,1758,1890,1893,2586,2757,2831,3051,3279,3448,3630,3735,3885,4104,4269,4314,4437,4614,4791,5364,54 ...9981323,9983121,9984008,9984612,9988213,9988478,9989003,9989652,9989785,9990128,9992668,9993295,9994038,9994703,9996021,9996642, ...
58519349280171623172618320+-NM_00642172394025598chr110041005384835968227111,141,114,66,36,61,98,132,3,192,162,74,142,108,169,56,99,141,219,111,11,60,171,165,81,76,80,402,708,849,963,1632,1668,1729,1836,1968,1971,2664,2835,2909,3129,3357,3526,3708,3813,3963,4182,4347,4392,4515,4692,4869,5442,55 ...9981323,9983121,9984008,9984612,9988213,9988478,9989003,9989652,9989785,9990128,9992668,9993295,9994038,9994703,9996021,9996642, ...

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