Schema for xenoRefSeqAli
  Database: eriEur2    Primary Table: xenoRefSeqAli    Row Count: 315,055   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 587smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1801int(10) unsigned range Number of bases that match that aren't repeats
misMatches 142int(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 5int(10) unsigned range Number of inserts in query
qBaseInsert 239int(10) unsigned range Number of bases inserted in query
tNumInsert 22int(10) unsigned range Number of inserts in target
tBaseInsert 16956int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001321359varchar(255) values Query sequence name
qSize 2200int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2182int(10) unsigned range Alignment end position in query
tName JH836434varchar(255) values Target sequence name
tSize 405474int(10) unsigned range Target sequence size
tStart 288939int(10) unsigned range Alignment start position in target
tEnd 307838int(10) unsigned range Alignment end position in target
blockCount 23int(10) unsigned range Number of blocks in alignment
blockSizes 88,243,123,102,90,41,95,24,...longblob   Size of each block
qStarts 0,88,331,454,556,646,687,78...longblob   Start of each block in query.
tStarts 97636,102325,102723,103022,...longblob   Start of each block in target.

Connected Tables and Joining Fields
        eriEur2.all_mrna.qName (via xenoRefSeqAli.qName)
      eriEur2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      eriEur2.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
58718011420052392216956+-NM_001321359220002182JH8364344054742889393078382388,243,123,102,90,41,95,24,84,59,99,132,106,48,131,62,64,56,114,33,88,22,39,0,88,331,454,556,646,687,782,806,890,949,1048,1181,1287,1335,1466,1528,1592,1648,1825,1914,2026,2143,97636,102325,102723,103022,104881,105926,106320,106862,107848,109034,109223,114547,114843,115085,115232,115456,115606,115894,116 ...
586136515000001649556+-NM_001197331165451520JH8364174835361790262300971775,100,76,78,94,75,84,57,49,73,173,88,55,62,78,109,189,5,80,180,256,334,428,503,587,644,693,766,939,1027,1082,1144,1222,1331,253439,257156,259405,272578,272793,275387,277213,278121,281153,283104,288011,299452,299664,301789,301937,302748,304321,
589918125001947846++NM_00101792329352921344JH83579416920586442766531655527,90,135,198,93,292,819,909,1044,1251,644276,648117,650181,652863,653072,
58534707740061933025301++NM_0010813921795948399276AMDU012189643608036923323731153,67,196,211,123,198,105,3,192,267,261,3,158,118,195,141,214,221,114,134,4,111,134,158,121,211,31,9,156,88,147,4839,4992,5059,5255,5466,5589,5787,5892,5895,6171,6438,6699,6702,6860,6978,7185,7333,7547,7768,7882,8016,8020,8131,8265,8423,854 ...3692,3848,4662,6766,7618,9195,12938,13057,13490,15920,16436,16714,17027,18390,19752,21366,22298,22757,23836,24560,26605,27369,28 ...
585755165000000+-NM_0010054879240920AMDU012199111566552914491920,0,14216,
585745173000000+-NM_0010005409240918AMDU012199111566553114491918,0,14216,
585744174000000+-NM_0010118669273921AMDU012199111566553114491918,3,14216,
58546720200151254+-NM_001000232918156876AMDU01219911156655731296383,160,426,156,239,450,14369,14455,14666,
5853521560022572257+-NM_147026930120885AMDU012199111566557313383130,123,255,120,273,630,14327,14480,14837,
5854692140021873193+-NM_0010002359120870AMDU01219911156655731449439,83,135,426,0,150,233,444,14216,14369,14455,14666,

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