Schema for xenoRefSeqAli
  Database: xenTro9    Primary Table: xenoRefSeqAli    Row Count: 164,095   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 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 479int(10) unsigned range Number of bases that match that aren't repeats
misMatches 232int(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 1548int(10) unsigned range Number of bases inserted in query
tNumInsert 3int(10) unsigned range Number of inserts in target
tBaseInsert 202639int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001205282varchar(255) values Query sequence name
qSize 2550int(10) unsigned range Query sequence size
qStart 246int(10) unsigned range Alignment start position in query
qEnd 2505int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 194866763int(10) unsigned range Target sequence size
tStart 4212int(10) unsigned range Alignment start position in target
tEnd 207562int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 54,252,346,59,longblob   Size of each block
qStarts 246,1797,2100,2446,longblob   Start of each block in query.
tStarts 194659201,194707544,1947767...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)
      xenTro9.all_est.qName (via xenoRefSeqAli.qName)
      xenTro9.all_mrna.qName (via xenoRefSeqAli.qName)
      xenTro9.refGene.name (via xenoRefSeqAli.qName)
      xenTro9.refSeqAli.qName (via xenoRefSeqAli.qName)
      xenTro9.xenoRefFlat.name (via xenoRefSeqAli.qName)
      xenTro9.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
7347923200215483202639+-NM_00120528225502462505chr11948667634212207562454,252,346,59,246,1797,2100,2446,194659201,194707544,194776751,194862492,
73297141001291169256+-NM_00112824716429041633chr119486676364325134019293,345,904,1288,194732744,194802093,
7360729300213684746666+-NM_0010995332409482316chr119486676364343811909545,117,18,381,339,48,1320,1578,1596,1977,194054854,194401751,194403122,194707544,194802081,
7345725100215783142508+-NM_00110515225682462532chr119486676364346207562445,252,121,290,246,1815,2121,2242,194659201,194707544,194707850,194802127,
7345625200215783142508+-NM_00110517925592372523chr119486676364346207562445,252,121,290,237,1806,2112,2233,194659201,194707544,194707850,194802127,
7343420500316413142586+-NM_00110243525201892469chr119486676364361207586484,168,81,306,189,1767,1962,2163,194659177,194707544,194707739,194802096,
919902520062861566577+-NM_00138442134251391667chr4133473341194830251955084416121,170,114,3,126,72,22,169,93,56,100,43,89,24,17,23,139,260,436,550,553,679,886,934,1111,1213,1269,1369,1412,1501,1627,1644,113922497,113928336,113932149,113932265,113932396,113934022,113934310,113935632,113936215,113936320,113939360,113939463,11393951 ...
7982356780001016031414524++NM_17828067084795218chr613513483228020903280385631654,125,73,93,117,21,696,800,230,344,432,5,42,36,30,38,479,629,754,980,1094,1365,1514,2429,3229,3459,3803,4916,4922,4980,5150,5180,28020903,28030443,28030571,28030815,28030929,28031215,28031373,28032285,28033088,28033534,28037227,28038264,28038269,28038315,28 ...
64414184750065281739047++NM_03203430892372658chr1194866763779197378329131881,219,83,1,123,147,64,126,110,3,134,64,71,103,86,109,195,174,237,387,618,701,702,825,1074,1138,1264,1374,1377,1511,1767,1838,2028,2114,2289,2484,7791973,7806225,7809632,7809741,7813042,7813823,7817470,7818061,7821394,7821524,7823459,7825326,7826486,7829023,7830128,7831043, ...
5864482450021593273555+-NM_00110506825592372523chr1194866763133314207562345,237,411,237,1821,2112,194659201,194732747,194733038,

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