Schema for refSeqAli
  Database: rn4    Primary Table: refSeqAli    Row Count: 18,448   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 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 2535int(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 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 6int(10) unsigned range Number of inserts in target
tBaseInsert 18589int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001099461varchar(255) values Query sequence name
qSize 2535int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2535int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 267910886int(10) unsigned range Target sequence size
tStart 245887int(10) unsigned range Alignment start position in target
tEnd 267011int(10) unsigned range Alignment end position in target
blockCount 7int(10) unsigned range Number of blocks in alignment
blockSizes 887,124,225,804,273,16,206,longblob   Size of each block
qStarts 0,887,1011,1236,2040,2313,2...longblob   Start of each block in query.
tStarts 245887,256156,257489,258566...longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via refSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via refSeqAli.qName)
      hgFixed.gbSeq.acc (via refSeqAli.qName)
      hgFixed.gbWarn.acc (via refSeqAli.qName)
      hgFixed.imageClone.acc (via refSeqAli.qName)
      hgFixed.refLink.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName)
      knownGeneV39.kgXref.refseq (via refSeqAli.qName)
      knownGeneV39.knownToRefSeq.value (via refSeqAli.qName)
      rn4.all_est.qName (via refSeqAli.qName)
      rn4.all_mrna.qName (via refSeqAli.qName)
      rn4.mrnaOrientInfo.name (via refSeqAli.qName)
      rn4.mrnaRefseq.refseq (via refSeqAli.qName)
      rn4.refFlat.name (via refSeqAli.qName)
      rn4.refGene.name (via refSeqAli.qName)
      rn4.rgdGene2ToRefSeq.value (via refSeqAli.qName)
      rn4.xenoMrna.qName (via refSeqAli.qName)
      rn4.xenoRefGene.name (via refSeqAli.qName)
      rn4.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
73253500000618589-NM_001099461253502535chr12679108862458872670117887,124,225,804,273,16,206,0,887,1011,1236,2040,2313,2329,245887,256156,257489,258566,259804,260546,266805,
59225260000059986+NM_001099460252602526chr1267910886100941110219236206,283,804,225,124,884,0,206,489,1293,1518,1642,1009411,1015935,1016643,1018297,1019750,1021039,
593252600000512542-NM_001099458252602526chr1267910886113479711498656884,124,225,804,283,206,0,884,1008,1233,2037,2320,1134797,1136833,1144442,1145623,1146814,1149659,
59425290000056125+NM_001099462252902529chr1267910886123490712435616206,283,804,225,124,887,0,206,489,1293,1518,1642,1234907,1237683,1238354,1240008,1241408,1242674,
59512012000053955-NM_001161691120301203chr126791088614141761419334667,142,153,264,261,316,0,67,209,362,626,887,1414176,1414894,1415621,1416333,1416859,1419018,
6011074036000063541-NM_001013063145901434chr1267910886215061821555937345,142,144,264,261,134,144,25,370,512,656,920,1181,1315,2150618,2151622,2152351,2153061,2153587,2155023,2155449,
602303707501143925325+NM_001106217325503255chr12679108862255891228432810203,45,96,301,161,142,126,177,93,1768,0,203,391,487,788,949,1091,1217,1394,1487,2255891,2256095,2256217,2256314,2262344,2265565,2270552,2273562,2276442,2282560,
602224000000614418-NM_01307324271612401chr12679108862287980230463871574,217,86,121,105,32,105,26,1600,1817,1903,2024,2129,2161,2287980,2293836,2295667,2296340,2300387,2303332,2304533,
6034427029700036167+NM_001134543708723637087chr1267910886237524523861364584,183,107,3850,2363,2947,3130,3237,2375245,2380511,2380895,2382286,
6031835000001039793+NM_001004217185201835chr12679108862394946243657411183,175,158,181,122,106,159,127,135,127,362,0,183,358,516,697,819,925,1084,1211,1346,1473,2394946,2410228,2412554,2415185,2420857,2423588,2424823,2433080,2434115,2434623,2436212,

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