Schema for refSeqAli
  Database: xenTro7    Primary Table: refSeqAli    Row Count: 8,995   Data last updated: 2020-09-02
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 2592int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1int(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 5int(10) unsigned range Number of inserts in target
tBaseInsert 22779int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001016845varchar(255) values Query sequence name
qSize 2612int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2593int(10) unsigned range Alignment end position in query
tName KB021649varchar(255) values Target sequence name
tSize 215906545int(10) unsigned range Target sequence size
tStart 35440int(10) unsigned range Alignment start position in target
tEnd 60812int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 1860,218,119,138,127,131,longblob   Size of each block
qStarts 19,1879,2097,2216,2354,2481,longblob   Start of each block in query.
tStarts 35440,39691,42987,46525,467...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)
      xenTro7.all_est.qName (via refSeqAli.qName)
      xenTro7.all_mrna.qName (via refSeqAli.qName)
      xenTro7.mrnaOrientInfo.name (via refSeqAli.qName)
      xenTro7.refFlat.name (via refSeqAli.qName)
      xenTro7.refGene.name (via refSeqAli.qName)
      xenTro7.xenoRefGene.name (via refSeqAli.qName)
      xenTro7.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585259210000522779-NM_001016845261202593KB021649215906545354406081261860,218,119,138,127,131,19,1879,2097,2216,2354,2481,35440,39691,42987,46525,46757,60681,
7335855201382630826-NM_001011358365803630KB0216492159065451164421508602747,264,102,201,90,125,98,153,164,155,118,138,76,149,123,178,78,102,59,121,164,129,169,180,117,222,70,28,75,339,441,642,732,857,955,1108,1272,1427,1545,1683,1759,1908,2031,2247,2325,2427,2486,2607,2771,2900,3069,3249,3366,3588,116442,116490,116993,117367,120070,123411,125436,125892,127032,128024,129305,129593,129821,130550,131112,131368,141195,141603,14 ...
586195861700315823448+NM_001079234215502149KB0216492159065451805112060931117,12,15,131,240,87,98,135,1093,159,147,0,17,29,51,189,429,516,614,749,1843,2002,180511,180529,180543,180951,181082,198873,200179,203020,204692,205785,205946,
73123141712877310967-NM_203667215802130KB0216492159065452543452665655103,406,320,255,169,28,145,551,1734,1989,254345,254448,254863,263572,266396,
58723582000056000+NM_00100580725041162476KB021649215906545302785311145641,125,894,189,102,1009,116,157,282,1176,1365,1467,302785,304033,305246,308050,309356,310136,
58719760350001700+NM_0010069172115612072KB0216492159065453385193412302147,1864,61,208,338519,339366,
58733511900011351-NM_00111298113300355KB0216492159065453765903782962237,118,975,1212,376590,378178,
589321050000198769-NM_001005677325803215KB0216492159065455360535480372071,15,494,207,155,156,309,213,123,165,113,136,134,103,132,131,143,173,112,130,43,114,129,623,830,985,1141,1450,1663,1786,1951,2064,2200,2334,2437,2569,2700,2843,3016,3128,536053,536125,536141,536636,537380,537686,538135,538530,538960,539165,539410,539618,539898,540393,540749,541390,542083,543197,54 ...
15627811000011163747+NM_001278413278202782KB02165810803804487633307877998361232,161,108,125,96,43,12,147,129,113,82,1734,0,32,193,301,426,522,565,577,724,853,966,1048,87633307,87723685,87725554,87752338,87754326,87757143,87763131,87765969,87776280,87794924,87797198,87798102,
1510245000005253992+NM_00127843510245010245KB02164921590654551329387513936245359,1353,64,87,311,282,186,141,79,38,96,58,179,178,137,170,172,137,187,167,167,165,165,153,89,290,203,170,197,112,138,159,84,132, ...0,59,1412,1476,1563,1874,2156,2342,2483,2562,2600,2696,2754,2933,3111,3248,3418,3590,3727,3914,4081,4248,4413,4578,4731,4820,511 ...51329387,51330748,51336498,51337537,51338568,51339520,51340791,51341316,51341666,51343523,51343659,51344566,51345473,51346498,51 ...

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