Schema for xenoRefSeqAli
  Database: aquChr2    Primary Table: xenoRefSeqAli    Row Count: 381,519   Data last updated: 2020-08-18
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 258int(10) unsigned range Number of bases that match that aren't repeats
misMatches 136int(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 24int(10) unsigned range Number of 'N' bases
qNumInsert 4int(10) unsigned range Number of inserts in query
qBaseInsert 704int(10) unsigned range Number of bases inserted in query
tNumInsert 3int(10) unsigned range Number of inserts in target
tBaseInsert 26755int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001089982varchar(255) values Query sequence name
qSize 2459int(10) unsigned range Query sequence size
qStart 196int(10) unsigned range Alignment start position in query
qEnd 1318int(10) unsigned range Alignment end position in query
tName JRUM01015595v1varchar(255) values Target sequence name
tSize 35866int(10) unsigned range Target sequence size
tStart 5563int(10) unsigned range Alignment start position in target
tEnd 32736int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 153,6,13,138,108,longblob   Size of each block
qStarts 196,446,454,1024,1210,longblob   Start of each block in query.
tStarts 5563,14376,14382,32358,32628,longblob   Start of each block in target.

Connected Tables and Joining Fields
        aquChr2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      aquChr2.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
5852581360244704326755++NM_00108998224591961318JRUM01015595v1358665563327365153,6,13,138,108,196,446,454,1024,1210,5563,14376,14382,32358,32628,
5857532570443461727962++NM_00103754421382071722JRUM01015595v1358665590346069124,134,126,37,190,125,111,100,107,207,331,465,1041,1080,1270,1404,1515,1615,5590,7515,7993,32309,32346,32620,32845,34161,34499,
5855512190464612528200++NM_00132645023831411569JRUM01015595v1358665590346067126,132,114,39,192,105,108,141,267,399,886,927,1332,1461,5590,7517,7993,32307,32346,34131,34498,
5857662710443428727935++NM_02004934333381847JRUM01015595v1358665590346069124,134,153,37,190,125,111,100,107,338,462,596,1166,1205,1395,1529,1640,1740,5590,7515,7993,32309,32346,32620,32845,34161,34499,
5858152850444534829071++NM_00109846132481531831JRUM01015595v13586655903580510124,134,120,37,192,123,111,100,110,93,153,277,411,987,1026,1218,1350,1461,1561,1738,5590,7515,7993,32309,32346,32622,32845,34161,34499,35712,
5858723150445441828986++NM_00109118526541641836JRUM01015595v13586655903580711124,43,91,153,37,190,119,111,102,111,150,164,288,332,423,990,1029,1219,1353,1464,1566,1686,5590,7515,7558,7993,32309,32346,32620,32845,34161,34501,35657,
5852371020242798326774++NM_13799263614351596JRUM01015595v1358665602327394114,111,27,111,435,549,1323,1485,5602,7517,32382,32628,
58513272000021801++NM_1352912069215419JRUM01015595v135866560576103109,2,93,215,324,326,5605,5776,7517,
585301128003522426402++NM_00130531638452311182JRUM01015595v135866563532466579,134,69,39,108,231,310,486,1023,1074,5635,7515,8035,32309,32358,
585166830241753226816++NM_00111046140264431469JRUM01015595v135866565032739364,98,111,443,507,1358,5650,7515,32628,

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