Schema for xenoRefSeqAli
  Database: xenLae2    Primary Table: xenoRefSeqAli    Row Count: 196,785   Data last updated: 2020-08-20
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 589smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1021int(10) unsigned range Number of bases that match that aren't repeats
misMatches 96int(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 2int(10) unsigned range Number of inserts in query
qBaseInsert 139int(10) unsigned range Number of bases inserted in query
tNumInsert 9int(10) unsigned range Number of inserts in target
tBaseInsert 38836int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001030418varchar(255) values Query sequence name
qSize 1281int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1256int(10) unsigned range Alignment end position in query
tName chr1Lvarchar(255) values Target sequence name
tSize 219802468int(10) unsigned range Target sequence size
tStart 532171int(10) unsigned range Alignment start position in target
tEnd 572124int(10) unsigned range Alignment end position in target
blockCount 10int(10) unsigned range Number of blocks in alignment
blockSizes 101,104,117,213,84,152,192,...longblob   Size of each block
qStarts 0,101,205,322,593,677,829,1...longblob   Start of each block in query.
tStarts 532171,542406,547429,549061...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)
      xenLae2.all_est.qName (via xenoRefSeqAli.qName)
      xenLae2.all_mrna.qName (via xenoRefSeqAli.qName)
      xenLae2.refGene.name (via xenoRefSeqAli.qName)
      xenLae2.refSeqAli.qName (via xenoRefSeqAli.qName)
      xenLae2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      xenLae2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
589102196002139938836++NM_001030418128101256chr1L21980246853217157212410101,104,117,213,84,152,192,45,63,46,0,101,205,322,593,677,829,1021,1066,1210,532171,542406,547429,549061,564260,566076,568062,571877,571924,572078,
58966021000272628623++NM_01987914072511193chr1L2198024685424085719017102,117,213,82,152,180,24,251,353,470,743,825,977,1169,542408,547429,549061,564262,566076,568062,571877,
58967520700160728611++NM_05375212731111053chr1L2198024685424085719018102,117,213,82,152,189,3,24,111,213,330,603,685,837,1026,1029,542408,547429,549061,564262,566076,568062,568355,571877,
589682193025293628593++NM_2144091318951088chr1L2198024685424085719017102,117,213,112,152,180,24,95,197,314,608,720,872,1064,542408,547429,549061,564232,566076,568062,571877,
58967918800272628623++NM_00113335314001361075chr1L219802468542411571901799,117,213,82,152,180,24,136,235,352,625,707,859,1051,542411,547429,549061,564262,566076,568062,571877,
58968218500272628623++NM_00128337214803091248chr1L219802468542411571901799,117,213,82,152,180,24,309,408,525,798,880,1032,1224,542411,547429,549061,564262,566076,568062,571877,
114287782609042872334001+-NM_01460250165554635chr6S128359586435054714354326524270,391,60,136,579,135,222,174,146,189,202,2,57,148,167,3,161,215,106,23,101,84,51,171,555,842,1233,1293,1429,2008,2143,2365,2539,2700,2889,3091,3093,3342,3490,3657,3660,3821,4036,4142,4165,4266,4413,4464,84816321,84816602,84816996,84821892,84822519,84825732,84826338,84828824,84830986,84832753,84842963,84843506,84843695,84845837,84 ...
58961020000160524988++NM_0010025771364103973chr1L219802468542444568242666,117,213,82,152,180,103,169,286,559,641,793,542444,547429,549061,564262,566076,568062,
589304140002414325342++NM_14255211881981056chr1L219802468542456568242454,82,137,171,198,642,724,885,542456,564262,566076,568071,
589327171002156523247++NM_001183561990102756chr1L219802468542468566213639,114,126,74,7,138,102,141,273,537,611,618,542468,547426,549073,564262,564448,566075,

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