Schema for xenoRefSeqAli
  Database: panTro4    Primary Table: xenoRefSeqAli    Row Count: 343,020   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 712int(10) unsigned range Number of bases that match that aren't repeats
misMatches 11int(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 3int(10) unsigned range Number of inserts in target
tBaseInsert 14526int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NR_040415varchar(255) values Query sequence name
qSize 723int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 723int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 228333871int(10) unsigned range Target sequence size
tStart 257501int(10) unsigned range Alignment start position in target
tEnd 272750int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 350,169,58,146,longblob   Size of each block
qStarts 0,350,519,577,longblob   Start of each block in query.
tStarts 228061121,228065643,2280761...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)
      panTro4.all_est.qName (via xenoRefSeqAli.qName)
      panTro4.all_mrna.qName (via xenoRefSeqAli.qName)
      panTro4.refGene.name (via xenoRefSeqAli.qName)
      panTro4.refSeqAli.qName (via xenoRefSeqAli.qName)
      panTro4.xenoMrna.qName (via xenoRefSeqAli.qName)
      panTro4.xenoRefFlat.name (via xenoRefSeqAli.qName)
      panTro4.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
73712110000314526+-NR_0404157230723chr12283338712575012727504350,169,58,146,0,350,519,577,228061121,228065643,228076162,228076224,
73258300002443906+-NR_1307021370310571chr1228333871257551701718365,38,158,310,375,413,227632153,227632219,228076162,
12235231600712126168512++NM_024586366003660chr1228333871520089305218098132130,51,79,77,96,48,30,51,39,91,105,160,113,119,86,172,85,111,64,141,79,92,136,167,271,342,220,62,20,186,61,55,0,130,181,260,337,433,481,511,562,601,692,797,957,1070,1189,1275,1447,1532,1643,1707,1848,1927,2019,2155,2325,2649,2993,3219,333 ...52008930,52044171,52061645,52105736,52137303,52138473,52140130,52141903,52148067,52152451,52153634,52157616,52164078,52164613,52 ...
73260800001429119+-NR_1307001266305573chr1228333871268058697445298,170,305,403,227636426,228065643,
73358800003433294+-NR_1306991494310676chr1228333871268058701718465,38,93,170,310,375,413,506,227632153,227632219,227636431,228065643,
73407900004433244+-NR_1307011419310726chr1228333871268058701718565,38,50,93,170,310,375,413,463,556,227632153,227632219,227633700,227636431,228065643,
73146500002361918+-NR_109817442291442chr1228333871268112630181331,4,116,291,322,326,227703690,227735454,228065643,
73468215600929687355330+-NR_024368102633608166chr12283338712700136301811230,423,778,54,442,49,166,1069,1584,114,63,66,360,452,2040,2898,4285,4727,5083,5250,6319,7913,8036,8100,227703690,228058053,228058476,228059289,228059969,228060412,228060780,228060946,228062022,228063615,228063729,228063792,
73124810400430805355021+-NR_02449752708215253chr1228333871273808630181631,478,24,591,134,94,821,913,1571,1718,2309,5159,227703690,228058053,228058583,228058638,228059230,228059969,
7310917400913799390637+-NR_13211929474032947chr122833387127380866561013112,71,12,32,52,97,31,4,126,382,96,56,94,403,515,638,651,684,1072,1625,1656,1660,1920,2582,2679,2853,227668261,227673948,227677307,227677319,227677351,227677733,227703690,227735500,228057477,228058053,228058435,228058536,22805996 ...

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